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datalad__datalad-next-495
diff --git a/.github/workflows/mypy.yml b/.github/workflows/mypy.yml new file mode 100644 index 0000000..e1e2d36 --- /dev/null +++ b/.github/workflows/mypy.yml @@ -0,0 +1,26 @@ +name: Type annotation + +on: + push: + paths: + - '*.py' + +jobs: + mypy: + runs-on: ubuntu-latest + steps: + - name: Setup Python + uses: actions/setup-python@v4 + with: + python-version: 3.8 + architecture: x64 + - name: Checkout + uses: actions/checkout@v3 + - name: Install mypy + run: pip install mypy + - name: Run mypy + uses: sasanquaneuf/mypy-github-action@releases/v1 + with: + checkName: 'mypy' # NOTE: this needs to be the same as the job name + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/changelog.d/20231023_064405_michael.hanke_www_auth.md b/changelog.d/20231023_064405_michael.hanke_www_auth.md new file mode 100644 index 0000000..f4752d5 --- /dev/null +++ b/changelog.d/20231023_064405_michael.hanke_www_auth.md @@ -0,0 +1,8 @@ +### 🏠 Internal + +- The `www-authenticate` dependencies is dropped. The functionality is + replaced by a `requests`-based implementation of an alternative parser. + This trims the dependency footprint and facilitates Debian-packaging. + The previous test cases are kept and further extended. + Fixes https://github.com/datalad/datalad-next/issues/493 via + https://github.com/datalad/datalad-next/pull/495 (by @mih) diff --git a/datalad_next/url_operations/http.py b/datalad_next/url_operations/http.py index 854677c..5d660e0 100644 --- a/datalad_next/url_operations/http.py +++ b/datalad_next/url_operations/http.py @@ -9,11 +9,13 @@ import sys from typing import Dict import requests from requests_toolbelt import user_agent -import www_authenticate import datalad -from datalad_next.utils.requests_auth import DataladAuth +from datalad_next.utils.requests_auth import ( + DataladAuth, + parse_www_authenticate, +) from . import ( UrlOperations, UrlOperationsRemoteError, @@ -233,7 +235,7 @@ class HttpUrlOperations(UrlOperations): headers=headers, ) if 'www-authenticate' in req.headers: - props['auth'] = www_authenticate.parse( + props['auth'] = parse_www_authenticate( req.headers['www-authenticate']) props['is_redirect'] = True if req.history else False props['status_code'] = req.status_code diff --git a/datalad_next/utils/requests_auth.py b/datalad_next/utils/requests_auth.py index 62cb5a4..fb4f3ce 100644 --- a/datalad_next/utils/requests_auth.py +++ b/datalad_next/utils/requests_auth.py @@ -7,7 +7,6 @@ import logging from typing import Dict from urllib.parse import urlparse import requests -import www_authenticate from datalad_next.config import ConfigManager from datalad_next.utils import CredentialManager @@ -16,7 +15,77 @@ from datalad_next.utils.http_helpers import get_auth_realm lgr = logging.getLogger('datalad.ext.next.utils.requests_auth') -__all__ = ['DataladAuth', 'HTTPBearerTokenAuth'] +__all__ = ['DataladAuth', 'HTTPBearerTokenAuth', 'parse_www_authenticate'] + + +def parse_www_authenticate(hdr: str) -> dict: + """Parse HTTP www-authenticate header + + This helper uses ``requests`` utilities to parse the ``www-authenticate`` + header as represented in a ``requests.Response`` instance. The header may + contain any number of challenge specifications. + + The implementation follows RFC7235, where a challenge parameters set is + specified as: either a comma-separated list of parameters, or a single + sequence of characters capable of holding base64-encoded information, + and parameters are name=value pairs, where the name token is matched + case-insensitively, and each parameter name MUST only occur once + per challenge. + + Returns + ------- + dict + Keys are casefolded challenge labels (e.g., 'basic', 'digest'). + Values are: ``None`` (no parameter), ``str`` (a token68), or + ``dict`` (name/value mapping of challenge parameters) + """ + plh = requests.utils.parse_list_header + pdh = requests.utils.parse_dict_header + challenges = {} + challenge = None + # challenges as well as their properties are in a single + # comma-separated list + for item in plh(hdr): + # parse the item into a key/value set + # the value will be `None` if this item was no mapping + k, v = pdh(item).popitem() + # split the key to check for a challenge spec start + key_split = k.split(' ', maxsplit=1) + if len(key_split) > 1 or v is None: + item_suffix = item[len(key_split[0]) + 1:] + challenge = [item[len(key_split[0]) + 1:]] if item_suffix else None + challenges[key_split[0].casefold()] = challenge + else: + # implementation logic assumes that the above conditional + # was triggered before we ever get here + assert challenge + challenge.append(item) + + return { + challenge: _convert_www_authenticate_items(items) + for challenge, items in challenges.items() + } + + +def _convert_www_authenticate_items(items: list) -> None | str | dict: + pdh = requests.utils.parse_dict_header + # according to RFC7235, items can be: + # either a comma-separated list of parameters + # or a single sequence of characters capable of holding base64-encoded + # information. + # parameters are name=value pairs, where the name token is matched + # case-insensitively, and each parameter name MUST only occur once + # per challenge. + if items is None: + return None + elif len(items) == 1 and pdh(items[0].rstrip('=')).popitem()[1] is None: + # this items matches the token68 appearance (no name value + # pair after potential base64 padding its removed + return items[0] + else: + return { + k.casefold(): v for i in items for k, v in pdh(i).items() + } class DataladAuth(requests.auth.AuthBase): @@ -201,7 +270,7 @@ class DataladAuth(requests.auth.AuthBase): # www-authenticate with e.g. 403s return r # which auth schemes does the server support? - auth_schemes = www_authenticate.parse(r.headers['www-authenticate']) + auth_schemes = parse_www_authenticate(r.headers['www-authenticate']) ascheme, credname, cred = self._get_credential(r.url, auth_schemes) if cred is None or 'secret' not in cred: diff --git a/setup.cfg b/setup.cfg index 8e31daa..3f6897a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -16,7 +16,6 @@ python_requires = >= 3.8 install_requires = annexremote datalad >= 0.18.4 - www-authenticate humanize packages = find_namespace: include_package_data = True
datalad/datalad-next
6a2d65eaec84a7e380a7077c4642c938f590ce88
diff --git a/datalad_next/utils/tests/test_parse_www_authenticate.py b/datalad_next/utils/tests/test_parse_www_authenticate.py new file mode 100644 index 0000000..d69fcd6 --- /dev/null +++ b/datalad_next/utils/tests/test_parse_www_authenticate.py @@ -0,0 +1,45 @@ + +from ..requests_auth import parse_www_authenticate + + +challenges = ( + # just challenge type + ('Negotiate', + [('negotiate', None)]), + # challenge and just a token, tolerate any base64 padding + ('Negotiate abcdef', + [('negotiate', 'abcdef')]), + ('Negotiate abcdef=', + [('negotiate', 'abcdef=')]), + ('Negotiate abcdef==', + [('negotiate', 'abcdef==')]), + # standard bearer + ('Bearer realm=example.com', + [('bearer', {'realm': 'example.com'})]), + # standard digest + ('Digest realm="example.com", qop="auth,auth-int", nonce="abcdef", ' + 'opaque="ghijkl"', + [('digest', {'realm': 'example.com', 'qop': 'auth,auth-int', + 'nonce': 'abcdef', 'opaque': 'ghijkl'})]), + # multi challenge + ('Basic speCial="paf ram", realm="basIC", ' + 'Bearer, ' + 'Digest realm="[email protected]", qop="auth, auth-int", ' + 'algorithm=MD5', + [('basic', {'special': 'paf ram', 'realm': 'basIC'}), + ('bearer', None), + ('digest', {'realm': "[email protected]", 'qop': "auth, auth-int", + 'algorithm': 'MD5'})]), + # same challenge, multiple times, last one wins + ('Basic realm="basIC", ' + 'Basic realm="complex"', + [('basic', {'realm': 'complex'})]), +) + + +def test_parse_www_authenticate(): + for hdr, targets in challenges: + res = parse_www_authenticate(hdr) + for ctype, props in targets: + assert ctype in res + assert res[ctype] == props
Replace `www-authenticate` We need this as a dependency for #490. However, packaging it for Debian seems like overkill. The whole thing is ~80 lines of code in a single file. The last update was 8 years ago. I would consider adopting a copy, unless @basilgello has other preferences.
0.0
6a2d65eaec84a7e380a7077c4642c938f590ce88
[ "datalad_next/utils/tests/test_parse_www_authenticate.py::test_parse_www_authenticate" ]
[]
{ "failed_lite_validators": [ "has_issue_reference", "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-10-22 20:17:25+00:00
mit
1,834
datalad__datalad-next-518
diff --git a/changelog.d/20231026_185357_michael.hanke_archivist_tgz.md b/changelog.d/20231026_185357_michael.hanke_archivist_tgz.md new file mode 100644 index 0000000..f41dadc --- /dev/null +++ b/changelog.d/20231026_185357_michael.hanke_archivist_tgz.md @@ -0,0 +1,6 @@ +### 💫 Enhancements and new features + +- The `archivist` remote now supports archive type detection + from `*E`-type annex keys for `.tgz` archives too. + Fixes https://github.com/datalad/datalad-next/issues/517 via + https://github.com/datalad/datalad-next/pull/518 (by @mih) diff --git a/datalad_next/types/archivist.py b/datalad_next/types/archivist.py index 12e9b2b..17c538d 100644 --- a/datalad_next/types/archivist.py +++ b/datalad_next/types/archivist.py @@ -74,7 +74,7 @@ class ArchivistLocator: """ akey: AnnexKey member: PurePosixPath - size: int + size: int | None = None # datalad-archives did not have the type info, we want to be # able to handle those too, make optional atype: ArchiveType | None = None @@ -91,21 +91,21 @@ class ArchivistLocator: @classmethod def from_str(cls, url: str): """Return ``ArchivistLocator`` from ``str`` form""" - url_matched = _recognized_urls.match(url) - if not url_matched: + url_match = _recognized_urls.match(url) + if not url_match: raise ValueError('Unrecognized dl+archives locator syntax') - url_matched = url_matched.groupdict() + url_matched = url_match.groupdict() # convert to desired type akey = AnnexKey.from_str(url_matched['key']) # archive member properties - props_matched = _archive_member_props.match(url_matched['props']) - if not props_matched: + props_match = _archive_member_props.match(url_matched['props']) + if not props_match: # without at least a 'path' there is nothing we can do here raise ValueError( 'dl+archives locator contains invalid archive member ' f'specification: {url_matched["props"]!r}') - props_matched = props_matched.groupdict() + props_matched = props_match.groupdict() amember_path = PurePosixPath(props_matched['path']) if amember_path.is_absolute(): raise ValueError( @@ -116,6 +116,8 @@ class ArchivistLocator: # size is optional, regex ensure that it is an int size = props_matched.get('size') + if size is not None: + size = int(size) # archive type, could be None atype = props_matched.get('atype') @@ -134,6 +136,8 @@ class ArchivistLocator: atype = ArchiveType.zip elif '.tar' in suf: atype = ArchiveType.tar + elif '.tgz' in suf: + atype = ArchiveType.tar return cls( akey=akey,
datalad/datalad-next
1f7d9f5fc2874078600fc64009428550c720823f
diff --git a/datalad_next/types/tests/test_archivist.py b/datalad_next/types/tests/test_archivist.py index 8f78163..b3d03ac 100644 --- a/datalad_next/types/tests/test_archivist.py +++ b/datalad_next/types/tests/test_archivist.py @@ -23,6 +23,12 @@ def test_archivistlocator(): assert ArchivistLocator.from_str( 'dl+archive:MD5E-s1--e9f624eb778e6f945771c543b6e9c7b2.tar#path=f.txt' ).atype == ArchiveType.tar + assert ArchivistLocator.from_str( + 'dl+archive:MD5E-s1--e9f624eb778e6f945771c543b6e9c7b2.tgz#path=f.txt' + ).atype == ArchiveType.tar + assert ArchivistLocator.from_str( + 'dl+archive:MD5E-s1--e9f624eb778e6f945771c543b6e9c7b2.tar.gz#path=f.txt' + ).atype == ArchiveType.tar assert ArchivistLocator.from_str( 'dl+archive:MD5E-s1--e9f624eb778e6f945771c543b6e9c7b2.zip#path=f.txt' ).atype == ArchiveType.zip
archivist special remote: add support for tar archives with `.tgz` extension I'm working on building a dataset from `.tgz` archives using the replacement for `add-archive-content` demonstrated [here](https://github.com/datalad/datalad-next/issues/183#issuecomment-1539943754) in combination with the archivist special remote. The demo below works if the archive is a `.tar.gz` extension but not with `.tgz`. With `.tgz`, I need to configure the `archivist.legacy-mode` for a successful `datalad get`. Here's a quick demo: ```shell % mkdir project % touch project/file1.txt project/file2.txt project/file3.txt % tar -czvf project.tgz project ``` ```shell % datalad create tmp && cd tmp % cp ../project.tgz ./ % datalad save -m "add archive" project.tgz % git annex initremote archivist type=external externaltype=archivist encryption=none autoenable=true % archivekey=$(git annex lookupkey project.tgz) % datalad -f json ls-file-collection tarfile project.tgz --hash md5 | jq '. | select(.type == "file")' | jq --slurp . | datalad addurls --key 'et:MD5-s{size}--{hash-md5}' - "dl+archive:${archivekey}#path={item}&size={size}" '{item}' % filekey=$(git annex lookupkey project/file1.txt) % archivist_uuid=$(git annex info archivist | grep 'uuid' | cut -d ' ' -f 2) % git annex setpresentkey $filekey $archivist_uuid 1 % datalad get project/file1.txt get(error): project/file1.txt (file) [Could not obtain 'MD5E-s0--d41d8cd98f00b204e9800998ecf8427e.txt' -caused by- NotImplementedError] ``` ```shell % datalad configuration --scope local set datalad.archivist.legacy-mode=yes 1 ! set_configuration(ok): . [datalad.archivist.legacy-mode=yes] % datalad get project/file1.txt [INFO ] datalad-archives special remote is using an extraction cache under /playground/loj/abcd/tmp3/.git/datalad/tmp/archives/8bc4249de3. Remove it with DataLad's 'clean' command to save disk space. get(ok): project/file1.txt (file) [from archivist...] ``` <details><summary>datalad wtf</summary> ``` # WTF ## configuration <SENSITIVE, report disabled by configuration> ## credentials - keyring: - active_backends: - PlaintextKeyring with no encyption v.1.0 at /home/loj/.local/share/python_keyring/keyring_pass.cfg - config_file: /home/loj/.config/python_keyring/keyringrc.cfg - data_root: /home/loj/.local/share/python_keyring ## datalad - version: 0.19.3 ## dependencies - annexremote: 1.6.0 - boto: 2.49.0 - cmd:7z: 16.02 - cmd:annex: 10.20221003 - cmd:bundled-git: UNKNOWN - cmd:git: 2.39.2 - cmd:ssh: 8.4p1 - cmd:system-git: 2.39.2 - cmd:system-ssh: 8.4p1 - humanize: 4.8.0 - iso8601: 2.1.0 - keyring: 24.2.0 - keyrings.alt: 5.0.0 - msgpack: 1.0.7 - platformdirs: 3.11.0 - requests: 2.31.0 ## environment - LANG: en_US.UTF-8 - LANGUAGE: en_US.UTF-8 - LC_ALL: en_US.UTF-8 - LC_CTYPE: en_US.UTF-8 - PATH: /home/loj/.venvs/abcd-long/bin:/home/loj/.dotfiles/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/local/games:/usr/games ## extensions - container: - description: Containerized environments - entrypoints: - datalad_container.containers_add.ContainersAdd: - class: ContainersAdd - module: datalad_container.containers_add - names: - containers-add - containers_add - datalad_container.containers_list.ContainersList: - class: ContainersList - module: datalad_container.containers_list - names: - containers-list - containers_list - datalad_container.containers_remove.ContainersRemove: - class: ContainersRemove - module: datalad_container.containers_remove - names: - containers-remove - containers_remove - datalad_container.containers_run.ContainersRun: - class: ContainersRun - module: datalad_container.containers_run - names: - containers-run - containers_run - module: datalad_container - version: 1.2.3 - next: - description: What is next in DataLad - entrypoints: - datalad_next.commands.create_sibling_webdav.CreateSiblingWebDAV: - class: CreateSiblingWebDAV - module: datalad_next.commands.create_sibling_webdav - names: - create-sibling-webdav - datalad_next.commands.credentials.Credentials: - class: Credentials - module: datalad_next.commands.credentials - names: - datalad_next.commands.download.Download: - class: Download - module: datalad_next.commands.download - names: - download - datalad_next.commands.ls_file_collection.LsFileCollection: - class: LsFileCollection - module: datalad_next.commands.ls_file_collection - names: - ls-file-collection - datalad_next.commands.tree.TreeCommand: - class: TreeCommand - module: datalad_next.commands.tree - names: - tree - module: datalad_next - version: 1.0.1 ## git-annex - build flags: - Assistant - Webapp - Pairing - Inotify - DBus - DesktopNotify - TorrentParser - MagicMime - Benchmark - Feeds - Testsuite - S3 - WebDAV - dependency versions: - aws-0.22 - bloomfilter-2.0.1.0 - cryptonite-0.26 - DAV-1.3.4 - feed-1.3.0.1 - ghc-8.8.4 - http-client-0.6.4.1 - persistent-sqlite-2.10.6.2 - torrent-10000.1.1 - uuid-1.3.13 - yesod-1.6.1.0 - key/value backends: - SHA256E - SHA256 - SHA512E - SHA512 - SHA224E - SHA224 - SHA384E - SHA384 - SHA3_256E - SHA3_256 - SHA3_512E - SHA3_512 - SHA3_224E - SHA3_224 - SHA3_384E - SHA3_384 - SKEIN256E - SKEIN256 - SKEIN512E - SKEIN512 - BLAKE2B256E - BLAKE2B256 - BLAKE2B512E - BLAKE2B512 - BLAKE2B160E - BLAKE2B160 - BLAKE2B224E - BLAKE2B224 - BLAKE2B384E - BLAKE2B384 - BLAKE2BP512E - BLAKE2BP512 - BLAKE2S256E - BLAKE2S256 - BLAKE2S160E - BLAKE2S160 - BLAKE2S224E - BLAKE2S224 - BLAKE2SP256E - BLAKE2SP256 - BLAKE2SP224E - BLAKE2SP224 - SHA1E - SHA1 - MD5E - MD5 - WORM - URL - X* - operating system: linux x86_64 - remote types: - git - gcrypt - p2p - S3 - bup - directory - rsync - web - bittorrent - webdav - adb - tahoe - glacier - ddar - git-lfs - httpalso - borg - hook - external - supported repository versions: - 8 - 9 - 10 - upgrade supported from repository versions: - 0 - 1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9 - 10 - version: 10.20221003 ## location - path: /playground/loj/abcd - type: directory ## metadata.extractors - container_inspect: - distribution: datalad-container 1.2.3 - load_error: ModuleNotFoundError(No module named 'datalad_metalad') - module: datalad_container.extractors.metalad_container ## metadata.filters ## metadata.indexers ## python - implementation: CPython - version: 3.9.2 ## system - distribution: debian/11/bullseye - encoding: - default: utf-8 - filesystem: utf-8 - locale.prefered: UTF-8 - filesystem: - CWD: - path: /playground/loj/abcd - HOME: - path: /home/loj - TMP: - path: /tmp - max_path_length: 276 - name: Linux - release: 5.10.0-23-amd64 - type: posix - version: #1 SMP Debian 5.10.179-1 (2023-05-12) ``` </details>
0.0
1f7d9f5fc2874078600fc64009428550c720823f
[ "datalad_next/types/tests/test_archivist.py::test_archivistlocator" ]
[ "datalad_next/types/tests/test_archivist.py::test_archivistlocatori_errors" ]
{ "failed_lite_validators": [ "has_added_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-10-26 16:56:54+00:00
mit
1,835
datalad__datalad-next-577
diff --git a/datalad_next/commands/create_sibling_webdav.py b/datalad_next/commands/create_sibling_webdav.py index 1b286ed..ba808a9 100644 --- a/datalad_next/commands/create_sibling_webdav.py +++ b/datalad_next/commands/create_sibling_webdav.py @@ -9,9 +9,6 @@ """High-level interface for creating a combi-target on a WebDAV capable server """ import logging -from typing import ( - Dict, -) from unittest.mock import patch from urllib.parse import ( quote as urlquote, @@ -38,12 +35,19 @@ from datalad_next.constraints import ( EnsureInt, EnsureParsedURL, EnsureRange, + EnsureRemoteName, EnsureStr, ) -from datalad_next.constraints.dataset import EnsureDataset +from datalad_next.constraints.dataset import ( + DatasetParameter, + EnsureDataset, +) +from datalad_next.constraints.exceptions import ( + ConstraintError, + ParameterConstraintContext, +) from datalad_next.utils import CredentialManager from datalad_next.utils import ( - ParamDictator, get_specialremote_credential_properties, update_specialremote_credential, _yield_ds_w_matching_siblings, @@ -56,37 +60,119 @@ lgr = logging.getLogger('datalad.distributed.create_sibling_webdav') class CreateSiblingWebDAVParamValidator(EnsureCommandParameterization): - def joint_validation(self, params: Dict, on_error: str) -> Dict: - p = ParamDictator(params) - if p.url.scheme == "http": + def __init__(self): + super().__init__( + param_constraints=dict( + url=EnsureParsedURL( + required=['scheme', 'netloc'], + forbidden=['query', 'fragment'], + match='^(http|https)://', + ), + dataset=EnsureDataset( + installed=True, purpose='create WebDAV sibling(s)'), + name=EnsureRemoteName(), + storage_name=EnsureRemoteName(), + mode=EnsureChoice( + 'annex', 'filetree', 'annex-only', 'filetree-only', + 'git-only', + ), + # TODO https://github.com/datalad/datalad-next/issues/131 + credential=EnsureStr(), + existing=EnsureChoice('skip', 'error', 'reconfigure'), + recursive=EnsureBool(), + recursion_limit=EnsureInt() & EnsureRange(min=0), + ), + validate_defaults=('dataset',), + joint_constraints={ + ParameterConstraintContext(('url',), 'url'): + self._validate_param_url, + ParameterConstraintContext( + ('url', 'name'), 'default name'): + self._validate_default_name, + ParameterConstraintContext( + ('mode', 'name', 'storage_name'), 'default storage name'): + self._validate_default_storage_name, + ParameterConstraintContext( + ('mode', 'name', 'storage_name'), 'default storage name'): + self._validate_default_storage_name, + ParameterConstraintContext( + ('existing', 'recursive', 'name', 'storage_name', + 'dataset', 'mode')): + self._validate_existing_names, + }, + ) + + def _validate_param_url(self, url): + if url.scheme == "http": lgr.warning( - f"Using 'http:' ({p.url.geturl()!r}) means that WebDAV " + f"Using 'http:' ({url.geturl()!r}) means that WebDAV " "credentials are sent unencrypted over network links. " "Consider using 'https:'.") - if not params['name']: + def _validate_default_name(self, url, name): + if not name: # not using .netloc to avoid ports to show up in the name - params['name'] = p.url.hostname + return {'name': url.hostname} - if p.mode in ('annex-only', 'filetree-only') and p.storage_name: + def _validate_default_storage_name(self, mode, name, storage_name): + if mode in ('annex-only', 'filetree-only') and storage_name: lgr.warning( "Sibling name will be used for storage sibling in " "storage-sibling-only mode, but a storage sibling name " "was provided" ) - if p.mode == 'git-only' and p.storage_name: + if mode == 'git-only' and storage_name: lgr.warning( "Storage sibling setup disabled, but a storage sibling name " "was provided" ) - if p.mode != 'git-only' and not p.storage_name: - p.storage_name = f"{p.name}-storage" + if mode != 'git-only' and not storage_name: + storage_name = f"{name}-storage" - if p.mode != 'git-only' and p.name == p.storage_name: + if mode != 'git-only' and name == storage_name: # leads to unresolvable, circular dependency with publish-depends - raise ValueError("sibling names must not be equal") + self.raise_for( + dict(mode=mode, name=name, storage_name=storage_name), + "sibling names must not be equal", + ) + return dict(mode=mode, name=name, storage_name=storage_name) + + def _validate_existing_names( + self, existing, recursive, name, storage_name, dataset, + mode): + if recursive: + # we don't do additional validation for recursive processing, + # this has to be done when things are running, because an + # upfront validation would require an expensive traversal + return - return params + if existing != 'error': + # nothing to check here + return + + if not isinstance(dataset, DatasetParameter): + # we did not get a proper dataset parameter, + # hence cannot tailor to a dataset to check a remote + # name against + return + + validator = EnsureRemoteName(known=False, dsarg=dataset) + try: + if mode != 'annex-only': + validator(name) + if mode != 'git-only': + validator(storage_name) + except ConstraintError as e: + self.raise_for( + dict(existing=existing, + recursive=recursive, + name=name, + storage_name=storage_name, + dataset=dataset, + mode=mode), + e.msg, + ) + return @build_doc @@ -251,29 +337,7 @@ class CreateSiblingWebDAV(ValidatedInterface): """), ) - _validators = dict( - url=EnsureParsedURL( - required=['scheme', 'netloc'], - forbidden=['query', 'fragment'], - match='^(http|https)://', - ), - dataset=EnsureDataset( - installed=True, purpose='create WebDAV sibling(s)'), - name=EnsureStr(), - storage_name=EnsureStr(), - mode=EnsureChoice( - 'annex', 'filetree', 'annex-only', 'filetree-only', 'git-only' - ), - # TODO https://github.com/datalad/datalad-next/issues/131 - credential=EnsureStr(), - existing=EnsureChoice('skip', 'error', 'reconfigure'), - recursive=EnsureBool(), - recursion_limit=EnsureInt() & EnsureRange(min=0), - ) - _validator_ = CreateSiblingWebDAVParamValidator( - _validators, - validate_defaults=('dataset',), - ) + _validator_ = CreateSiblingWebDAVParamValidator() @staticmethod @datasetmethod(name='create_sibling_webdav') diff --git a/datalad_next/constraints/__init__.py b/datalad_next/constraints/__init__.py index e6f0139..42fea3f 100644 --- a/datalad_next/constraints/__init__.py +++ b/datalad_next/constraints/__init__.py @@ -85,3 +85,8 @@ from .formats import ( EnsureURL, EnsureParsedURL, ) + +from .git import ( + EnsureGitRefName, + EnsureRemoteName +) \ No newline at end of file diff --git a/datalad_next/constraints/git.py b/datalad_next/constraints/git.py index 25f8363..073c131 100644 --- a/datalad_next/constraints/git.py +++ b/datalad_next/constraints/git.py @@ -1,8 +1,12 @@ """Constraints for Git-related concepts and parameters""" +from __future__ import annotations import subprocess -from .base import Constraint +from .base import ( + Constraint, + DatasetParameter, +) class EnsureGitRefName(Constraint): @@ -74,3 +78,101 @@ class EnsureGitRefName(Constraint): '(single-level) ' if self._allow_onelevel else '', ' or refspec pattern' if self._refspec_pattern else '', ) + + +class EnsureRemoteName(Constraint): + """Ensures a valid remote name, and optionally if such a remote is known + """ + _label = 'remote' + + def __init__(self, + known: bool | None = None, + dsarg: DatasetParameter | None = None): + """ + Parameters + ---------- + known: bool, optional + By default, a given value is only checked if it is a syntactically + correct remote name. + If ``True``, also checks that the given name corresponds to a + known remote in the dataset given by ``dsarg``. If ``False``, + checks that the given remote does not match any known remote + in that dataset. + dsarg: DatasetParameter, optional + Identifies a dataset for testing remote existence, if requested. + """ + self._label = 'remote' + self._known = known + self._dsarg = dsarg + + def __call__(self, value: str) -> str: + if not value: + # simple, do here + self.raise_for( + value, + f'missing {self._label} name', + ) + + if self._known is not None: + assert self._dsarg, \ + f"Existence check for {self._label} requires dataset " \ + "specification" + + if self._known: + # we don't need to check much, only if a remote of this name + # already exists -- no need to check for syntax compliance + # again + if not any( + k.startswith(f"remote.{value}.") + for k in self._dsarg.ds.config.keys() + ): + self.raise_for( + value, + f'is not a known {self._label}', + ) + else: + # whether or not the remote must not exist, or we would not care, + # in all cases we need to check for syntax compliance + EnsureGitRefName( + allow_onelevel=True, + refspec_pattern=False, + )(value) + + if self._known is None: + # we only need to know that something was provided, + # no further check + return value + + if self._known is False and any( + k.startswith(f"remote.{value}.") + for k in self._dsarg.ds.config.keys() + ): + self.raise_for( + value, + f'name conflicts with a known {self._label}', + ) + + return value + + def short_description(self): + return f"Name of a{{desc}} {self._label}".format( + desc=' known' if self._known + else ' not-yet-known' if self._known is False else '' + ) + + def for_dataset(self, dataset: DatasetParameter) -> Constraint: + """Return an similarly parametrized variant that checks remote names + against a given dataset (argument)""" + return self.__class__( + known=self._known, + dsarg=dataset, + ) + + +class EnsureSiblingName(EnsureRemoteName): + """Identical to ``EnsureRemoteName``, but used the term "sibling" + + Only error messages and documentation differ, with "remote" being + replaced with "sibling". + """ + _label = 'sibling'
datalad/datalad-next
2138efef0cf69a9b6a57505c5a48b9b13ad27088
diff --git a/datalad_next/commands/tests/test_create_sibling_webdav.py b/datalad_next/commands/tests/test_create_sibling_webdav.py index 5fda1fd..cd22232 100644 --- a/datalad_next/commands/tests/test_create_sibling_webdav.py +++ b/datalad_next/commands/tests/test_create_sibling_webdav.py @@ -74,6 +74,26 @@ def check_common_workflow( if declare_credential else None, mode=mode, ) + # Ensure that remote name constraint check works + # second time should raise because the sibling exists already + with pytest.raises(ValueError) as e: + create_sibling_webdav( + url, + credential=webdav_credential['name'] + if declare_credential else None, + mode=mode, + name='127.0.0.1', + ) + with pytest.raises(ValueError) as e: + create_sibling_webdav( + url, + credential=webdav_credential['name'] + if declare_credential else None, + mode=mode, + name='other', + storage_name='127.0.0.1-storage', + ) + assert_in_results( res, action='create_sibling_webdav.storage', diff --git a/datalad_next/constraints/tests/test_special_purpose.py b/datalad_next/constraints/tests/test_special_purpose.py index fb3d508..c69b3be 100644 --- a/datalad_next/constraints/tests/test_special_purpose.py +++ b/datalad_next/constraints/tests/test_special_purpose.py @@ -4,6 +4,7 @@ import pytest from datalad_next.commands import Parameter from datalad_next.utils import chpwd +from ..base import DatasetParameter from ..basic import ( EnsureInt, EnsureStr, @@ -22,6 +23,7 @@ from ..formats import ( ) from ..git import ( EnsureGitRefName, + EnsureRemoteName ) from ..parameter_legacy import EnsureParameterConstraint @@ -52,6 +54,36 @@ def test_EnsureGitRefName(): 'refs/heads/*') == 'refs/heads/*' +def test_EnsureRemoteName(existing_dataset): + # empty sibling name must raise + with pytest.raises(ValueError): + EnsureRemoteName()('') + assert EnsureRemoteName().short_description() == 'Name of a remote' + assert EnsureRemoteName( + known=True).short_description() == 'Name of a known remote' + assert EnsureRemoteName( + known=False).short_description() == 'Name of a not-yet-known remote' + ds = existing_dataset + c = EnsureRemoteName(known=False) + tc = c.for_dataset(DatasetParameter(None, ds)) + assert tc('newremotename') == 'newremotename' + # add a remote + ds._repo.add_remote('my-remote', 'here') + # check should fail when it shouldn't exist + with pytest.raises(ValueError): + tc('my-remote') + # should work when it should exist + c = EnsureRemoteName(known=True) + tc = c.for_dataset(DatasetParameter(None, ds)) + assert tc('my-remote') == 'my-remote' + # but fail with non-existing remote + with pytest.raises(ValueError) as e: + tc('not-my-remote') + assert str(e.value) == "is not a known remote" + # return sibling name with no existence checks + assert EnsureRemoteName()('anything') == 'anything' + + def test_EnsureParameterConstraint(): # most basic case, no value constraint c = EnsureParameterConstraint(NoConstraint())
Provide `EnsureRemoteName` Many commands needs sibling names, existing or prospective. Checking for syntax compliance is essentially `EnsureGitRefName(allow_onelevel=True, refspec_pattern=False)` for any given dataset, it can be turned into a `EnsureChoice()`, but it would also need some kind of `EnsureNotIn()` (for setting a non-existing remote name). So likely the best is to implement dataset interaction directly in `EnsureRemoteName`, and make it a subclass of `EnsureGitRefName`
0.0
2138efef0cf69a9b6a57505c5a48b9b13ad27088
[ "datalad_next/constraints/tests/test_special_purpose.py::test_EnsureGitRefName", "datalad_next/constraints/tests/test_special_purpose.py::test_EnsureParameterConstraint", "datalad_next/constraints/tests/test_special_purpose.py::test_EnsureParameterConstraint_passthrough", "datalad_next/constraints/tests/test_special_purpose.py::test_EnsureJSONLines", "datalad_next/constraints/tests/test_special_purpose.py::test_EnsureURL", "datalad_next/constraints/tests/test_special_purpose.py::test_EnsureURL_match" ]
[]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-12-17 19:39:48+00:00
mit
1,836
datalad__datalad-next-632
diff --git a/datalad_next/gitremotes/datalad_annex.py b/datalad_next/gitremotes/datalad_annex.py index a39fa8d..561d4c4 100755 --- a/datalad_next/gitremotes/datalad_annex.py +++ b/datalad_next/gitremotes/datalad_annex.py @@ -210,8 +210,9 @@ from datalad_next.datasets import ( from datalad_next.exceptions import CapturedException from datalad_next.runners import ( CommandError, - NoCapture, - StdOutCapture, + call_git, + call_git_oneline, + call_git_success, ) from datalad_next.uis import ui_switcher as ui from datalad_next.utils import ( @@ -224,6 +225,7 @@ from datalad_next.utils import ( get_specialremote_credential_envpatch, get_specialremote_credential_properties, needs_specialremote_credential_envpatch, + patched_env, specialremote_credential_envmap, update_specialremote_credential, ) @@ -494,8 +496,9 @@ class RepoAnnexGitRemote(object): try: # send annex into private mode, if supported # this repo will never ever be shared - ra.call_git(['config', 'annex.private', 'true']) - ra.call_git(['annex', 'init']) + call_git_success(['config', 'annex.private', 'true'], + cwd=ra.pathobj, capture_output=True) + call_git_success(['annex', 'init'], capture_output=True) ra = AnnexRepo(self._repoannexdir) if 'type=web' in self.initremote_params: self._init_repoannex_type_web(ra) @@ -620,8 +623,15 @@ class RepoAnnexGitRemote(object): # otherwise we can end up in a conflict situation where the mirror # points to 'master' (or something else) and the source actually # has 'main' (or something different) - src_head_ref = self.repo.call_git(['symbolic-ref', 'HEAD']).strip() - mr.call_git(['symbolic-ref', 'HEAD', src_head_ref]) + src_head_ref = call_git_oneline( + ['symbolic-ref', 'HEAD'], + cwd=self.repo.pathobj, + ).strip() + call_git_success( + ['symbolic-ref', 'HEAD', src_head_ref], + cwd=mr.pathobj, + capture_output=True, + ) self.log('Established mirror') self._mirrorrepo = mr @@ -669,9 +679,9 @@ class RepoAnnexGitRemote(object): pre_refs = sorted(self.mirrorrepo.for_each_ref_(), key=lambda x: x['refname']) # must not capture -- git is talking to it directly from here - self.mirrorrepo._git_runner.run( - ['git', 'receive-pack', self.mirrorrepo.path], - protocol=NoCapture, + call_git( + ['receive-pack', self.mirrorrepo.path], + cwd=self.mirrorrepo.pathobj, ) post_refs = sorted(self.mirrorrepo.for_each_ref_(), key=lambda x: x['refname']) @@ -698,12 +708,15 @@ class RepoAnnexGitRemote(object): for ref in post_refs: # best MIH can think of is to leave behind another # ref to indicate the unsuccessful upload - self.repo.call_git([ + call_git_success([ 'update-ref', # strip 'refs/heads/' from refname f'refs/dlra-upload-failed/{self.remote_name}/' f'{ref["refname"][11:]}', - ref['objectname']]) + ref['objectname']], + cwd=self.repo.pathobj, + capture_output=True, + ) raise # clean-up potential upload failure markers for this particular @@ -712,7 +725,11 @@ class RepoAnnexGitRemote(object): for ref in self.repo.for_each_ref_( fields=('refname',), pattern=f'refs/dlra-upload-failed/{self.remote_name}'): - self.repo.call_git(['update-ref', '-d', ref['refname']]) + call_git_success( + ['update-ref', '-d', ref['refname']], + cwd=self.repo.pathobj, + capture_output=True, + ) # we do not need to update `self._cached_remote_refs`, # because we end the remote-helper process here # everything has worked, if we used a credential, update it @@ -724,9 +741,9 @@ class RepoAnnexGitRemote(object): # must not capture -- git is talking to it directly from here. # the `self.mirrorrepo` access will ensure that the mirror # is up-to-date - self.mirrorrepo._git_runner.run( - ['git', 'upload-pack', self.mirrorrepo.path], - protocol=NoCapture, + call_git( + ['upload-pack', self.mirrorrepo.path], + cwd=self.mirrorrepo.pathobj, ) # everything has worked, if we used a credential, update it self._store_credential() @@ -766,7 +783,7 @@ class RepoAnnexGitRemote(object): repoannex = self.repoannex # trim it down, as much as possible - mirrorrepo.call_git(['gc']) + call_git(['gc'], cwd=mirrorrepo.pathobj) # update the repo state keys # it is critical to drop the local keys first, otherwise @@ -1047,7 +1064,10 @@ def _format_refs(repo, refs=None): if refstr: refstr += '\n' refstr += '@{} HEAD\n'.format( - repo.call_git(['symbolic-ref', 'HEAD']).strip() + call_git_oneline( + ['symbolic-ref', 'HEAD'], + cwd=repo.pathobj, + ).strip() ) return refstr @@ -1156,69 +1176,67 @@ def make_export_tree(repo): # we need to force Git to use a throwaway index file to maintain # the bare nature of the repoannex, git-annex would stop functioning # properly otherwise - env = os.environ.copy() index_file = repo.pathobj / 'datalad_tmp_index' - env['GIT_INDEX_FILE'] = str(index_file) - try: - for key, kinfo in RepoAnnexGitRemote.xdlra_key_locations.items(): - # create a blob for the annex link - out = repo._git_runner.run( - ['git', 'hash-object', '-w', '--stdin'], - stdin=bytes( - f'../../.git/annex/objects/{kinfo["prefix"]}/{key}/{key}', - 'utf-8'), - protocol=StdOutCapture) - linkhash = out['stdout'].strip() - # place link into a tree - out = repo._git_runner.run( - ['git', 'update-index', '--add', '--cacheinfo', '120000', - linkhash, kinfo["loc"]], - protocol=StdOutCapture, - env=env) - # write the complete tree, and return ID - out = repo._git_runner.run( - ['git', 'write-tree'], - protocol=StdOutCapture, - env=env) - exporttree = out['stdout'].strip() - # this should always come out identically - # unless we made changes in the composition of the export tree - assert exporttree == '7f0e7953e93b4c9920c2bff9534773394f3a5762' - - # clean slate - if index_file.exists(): - index_file.unlink() - # fake export.log record - # <unixepoch>s <here>:<origin> <exporttree> - now_ts = datetime.datetime.now().timestamp() - out = repo._git_runner.run( - ['git', 'hash-object', '-w', '--stdin'], - stdin=bytes( - f'{now_ts}s {here}:{origin} {exporttree}\n', 'utf-8'), - protocol=StdOutCapture) - exportlog = out['stdout'].strip() - repo._git_runner.run( - ['git', 'read-tree', 'git-annex'], - env=env) - out = repo._git_runner.run( - ['git', 'update-index', '--add', '--cacheinfo', '100644', - exportlog, 'export.log'], - protocol=StdOutCapture, - env=env) - out = repo._git_runner.run( - ['git', 'write-tree'], - protocol=StdOutCapture, - env=env) - gaupdate = out['stdout'].strip() - out = repo._git_runner.run( - ['git', 'commit-tree', '-m', 'Fake export', '-p', 'git-annex', - gaupdate], - protocol=StdOutCapture, - env=env) - gacommit = out['stdout'].strip() - repo.call_git(['update-ref', 'refs/heads/git-annex', gacommit]) - finally: - index_file.unlink() + with patched_env(GIT_INDEX_FILE=index_file): + try: + for key, kinfo in RepoAnnexGitRemote.xdlra_key_locations.items(): + # create a blob for the annex link + linkhash = call_git_oneline( + ['hash-object', '-w', '--stdin'], + cwd=repo.pathobj, + input=f'../../.git/annex/objects/{kinfo["prefix"]}/{key}/{key}', + ).strip() + # place link into a tree + call_git_success( + ['update-index', '--add', '--cacheinfo', '120000', + linkhash, kinfo["loc"]], + cwd=repo.pathobj, + capture_output=True, + ) + # write the complete tree, and return ID + exporttree = call_git_oneline( + ['write-tree'], cwd=repo.pathobj + ).strip() + # this should always come out identically + # unless we made changes in the composition of the export tree + assert exporttree == '7f0e7953e93b4c9920c2bff9534773394f3a5762' + + # clean slate + if index_file.exists(): + index_file.unlink() + # fake export.log record + # <unixepoch>s <here>:<origin> <exporttree> + now_ts = datetime.datetime.now().timestamp() + exportlog = call_git_oneline( + ['hash-object', '-w', '--stdin'], + input=f'{now_ts}s {here}:{origin} {exporttree}\n', + cwd=repo.pathobj, + ).strip() + call_git_success( + ['read-tree', 'git-annex'], + cwd=repo.pathobj, + ) + call_git_success( + ['update-index', '--add', '--cacheinfo', '100644', + exportlog, 'export.log'], + cwd=repo.pathobj, + capture_output=True, + ) + gaupdate = call_git_oneline( + ['write-tree'], cwd=repo.pathobj, + ).strip() + gacommit = call_git_oneline( + ['commit-tree', '-m', 'Fake export', '-p', 'git-annex', + gaupdate], + cwd=repo.pathobj, + ).strip() + call_git_success( + ['update-ref', 'refs/heads/git-annex', gacommit], + cwd=repo.pathobj, + ) + finally: + if index_file.exists(): + index_file.unlink() return exporttree diff --git a/datalad_next/runners/git.py b/datalad_next/runners/git.py index ec158f2..bc6b74b 100644 --- a/datalad_next/runners/git.py +++ b/datalad_next/runners/git.py @@ -18,6 +18,7 @@ def _call_git( cwd: Path | None = None, check: bool = False, text: bool | None = None, + input: str | bytes | None = None, # TODO #patch_env: dict[str, str] | None = None, ) -> subprocess.CompletedProcess: @@ -39,6 +40,7 @@ def _call_git( cwd=cwd, check=check, text=text, + input=input, ) except subprocess.CalledProcessError as e: # TODO we could support post-error forensics, but some client @@ -77,6 +79,7 @@ def call_git_success( args: list[str], *, cwd: Path | None = None, + capture_output: bool = False, ) -> bool: """Call Git for a single line of output. @@ -86,11 +89,14 @@ def call_git_success( If ``cwd`` is not None, the function changes the working directory to ``cwd`` before executing the command. + + If ``capture_output`` is ``True``, process output is captured, but not + returned. By default process output is not captured. """ try: _call_git( args, - capture_output=False, + capture_output=capture_output, cwd=cwd, check=True, ) @@ -104,7 +110,8 @@ def call_git_lines( args: list[str], *, cwd: Path | None = None, -) -> bool: + input: str | None = None, +) -> list[str]: """Call Git for any (small) number of lines of output. ``args`` is a list of arguments for the Git command. This list must not @@ -114,6 +121,10 @@ def call_git_lines( If ``cwd`` is not None, the function changes the working directory to ``cwd`` before executing the command. + If ``input`` is not None, the argument becomes the subprocess’s stdin. + This is intended for small-scale inputs. For call that require processing + large inputs, ``iter_git_subproc()`` is to be preferred. + Raises ------ CommandError if the call exits with a non-zero status. @@ -124,6 +135,7 @@ def call_git_lines( cwd=cwd, check=True, text=True, + input=input, ) return res.stdout.splitlines() @@ -132,6 +144,7 @@ def call_git_oneline( args: list[str], *, cwd: Path | None = None, + input: str | None = None, ) -> str: """Call git for a single line of output. @@ -143,7 +156,7 @@ def call_git_oneline( CommandError if the call exits with a non-zero status. AssertionError if there is more than one line of output. """ - lines = call_git_lines(args, cwd=cwd) + lines = call_git_lines(args, cwd=cwd, input=input) if len(lines) > 1: raise AssertionError( f"Expected Git {args} to return a single line, but got {lines}" diff --git a/datalad_next/utils/__init__.py b/datalad_next/utils/__init__.py index 6729d0c..faed7c2 100644 --- a/datalad_next/utils/__init__.py +++ b/datalad_next/utils/__init__.py @@ -12,6 +12,7 @@ external_versions log_progress parse_www_authenticate + patched_env rmtree get_specialremote_param_dict get_specialremote_credential_properties @@ -72,7 +73,7 @@ from .specialremote import ( needs_specialremote_credential_envpatch, get_specialremote_credential_envpatch, ) - +from .patch import patched_env # TODO REMOVE EVERYTHING BELOW FOR V2.0 # https://github.com/datalad/datalad-next/issues/611 diff --git a/datalad_next/utils/patch.py b/datalad_next/utils/patch.py index 299b321..3ea1cdb 100644 --- a/datalad_next/utils/patch.py +++ b/datalad_next/utils/patch.py @@ -1,2 +1,31 @@ +import contextlib +from os import environ + # legacy import from datalad_next.patches import apply_patch + + [email protected] +def patched_env(**env): + """Context manager for patching the process environment + + Any number of kwargs can be given. Keys represent environment variable + names, and values their values. A value of ``None`` indicates that + the respective variable should be unset, i.e., removed from the + environment. + """ + preserve = {} + for name, val in env.items(): + preserve[name] = environ.get(name, None) + if val is None: + del environ[name] + else: + environ[name] = str(val) + try: + yield + finally: + for name, val in preserve.items(): + if val is None: + del environ[name] + else: + environ[name] = val
datalad/datalad-next
7a08a58eb3110b491640c6628f74baf7ecc4faea
diff --git a/datalad_next/utils/tests/test_patch.py b/datalad_next/utils/tests/test_patch.py new file mode 100644 index 0000000..c281cce --- /dev/null +++ b/datalad_next/utils/tests/test_patch.py @@ -0,0 +1,15 @@ +from ..patch import patched_env +from os import environ + + +def test_patched_env(): + if 'HOME' in environ: + home = environ['HOME'] + with patched_env(HOME=None): + assert 'HOME' not in environ + assert environ['HOME'] == home + unusual_name = 'DATALADPATCHENVTESTVAR' + if unusual_name not in environ: + with patched_env(**{unusual_name: 'dummy'}): + assert environ[unusual_name] == 'dummy' + assert unusual_name not in environ
Discontinue (direct) usage of any runner implementations With #538 we made the start of a new paradigm: iterator-based interaction with (concurrent) subprocesses. It is our (@mih and @christian-monch) understanding that this basic approach would work for most (if not all) use cases that involve the execution of subprocesses. Respective experiments have been made and the results look promising. The "ultimate" challenge will be the implementation of a queue-based remote shell. In order to bring down the complexity of implementations after the introduction of this new paradigm, all subprocess execution in datalad-next should be switch to it. Afterwards all runner-related imports from datalad-core should be discontinued (which involves updating any extensions that make use of it). This plan answers the questions of #519. `GitRunner` has no future.
0.0
7a08a58eb3110b491640c6628f74baf7ecc4faea
[ "datalad_next/utils/tests/test_patch.py::test_patched_env" ]
[]
{ "failed_lite_validators": [ "has_issue_reference", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2024-02-07 11:52:00+00:00
mit
1,837
datalad__datalad-next-93
diff --git a/changelog.d/20220812_190404_benjaminpoldrack_fix_push_patch.md b/changelog.d/20220812_190404_benjaminpoldrack_fix_push_patch.md new file mode 100644 index 0000000..b092504 --- /dev/null +++ b/changelog.d/20220812_190404_benjaminpoldrack_fix_push_patch.md @@ -0,0 +1,7 @@ +### 🐛 Bug Fixes + +- Fixed datalad-push always reporting success when pushing to + an export remote. + Fixes https://github.com/datalad/datalad-next/issues/88 via + https://github.com/datalad/datalad-next/pull/93 (by @bpoldrack) + diff --git a/datalad_next/patches/push_to_export_remote.py b/datalad_next/patches/push_to_export_remote.py index d6b82ed..432f209 100644 --- a/datalad_next/patches/push_to_export_remote.py +++ b/datalad_next/patches/push_to_export_remote.py @@ -167,6 +167,8 @@ def _transfer_data(repo: AnnexRepo, ) return + from datalad.interface.results import annexjson2result + # TODO: # - check for configuration entries, e.g. what to export @@ -221,12 +223,13 @@ def _transfer_data(repo: AnnexRepo, ], progress=True ): - yield { - **res_kwargs, - "action": "copy", - "status": "ok", - "path": str(Path(res_kwargs["path"]) / result["file"]) - } + result_adjusted = \ + annexjson2result(result, ds, **res_kwargs) + # annexjson2result overwrites 'action' with annex' 'command', + # even if we provided our 'action' within res_kwargs. Therefore, + # change afterwards instead: + result_adjusted['action'] = "copy" + yield result_adjusted except CommandError as cmd_error: ce = CapturedException(cmd_error) diff --git a/docs/policy/release-management.md b/docs/policy/release-management.md new file mode 100644 index 0000000..fdf9313 --- /dev/null +++ b/docs/policy/release-management.md @@ -0,0 +1,15 @@ +# Release team + +The release team (RT) is an charge reviewing merge requests, and issuing new releases. + +The members of the RT are defined in `docs/CODEOWNERS` in the `main` branch of the repository. + +The RT itself adds or removes RT members. + +It is the RT's duty to act on any merge request in a timely manner. + +A code review of at least one RT member is required for any changeset to be merged into the `main` branch. + +When all technical checks pass (e.g., CI success, resolved pull-request conversations), any RT member approval is a sufficient condition for an (automatic) merge of a changeset into the `main` branch. + +RT members are not expected to be an expert in all techniques, features, and parts of the code base. Consequently, a team member should seek feedback prior to approving merge requests whenever necessary.
datalad/datalad-next
35af20542c46c523f4d635ffc187fcc3d50ade6a
diff --git a/datalad_next/conftest.py b/datalad_next/conftest.py index 7c727c3..1b42ad0 100644 --- a/datalad_next/conftest.py +++ b/datalad_next/conftest.py @@ -1,16 +1,1 @@ -try: - from datalad.conftest import setup_package -except ImportError: - # assume old datalad without pytest support introduced in - # https://github.com/datalad/datalad/pull/6273 - import pytest - from datalad import setup_package as _setup_package - from datalad import teardown_package as _teardown_package - - - @pytest.fixture(autouse=True, scope="session") - def setup_package(): - _setup_package() - yield - _teardown_package() - +from datalad.conftest import setup_package diff --git a/datalad_next/patches/tests/test_push_to_export_remote.py b/datalad_next/patches/tests/test_push_to_export_remote.py index 3b0ef55..bb51c0d 100644 --- a/datalad_next/patches/tests/test_push_to_export_remote.py +++ b/datalad_next/patches/tests/test_push_to_export_remote.py @@ -11,6 +11,7 @@ from datalad.tests.utils_pytest import ( SkipTest, assert_false, assert_in, + assert_in_results, assert_true, eq_, ) @@ -55,11 +56,19 @@ class MockRepo: def _call_annex_records_items_(self, *args, **kwargs): yield { - 'target': args[0][3], - 'action': 'copy', - 'status': 'ok', + "command": f"export {args[0][3]}", "file": "file.txt", + "success": True, + "input": [], + "error-messages": [] } + yield { + "command": f"export {args[0][3]}", + "success": False, + "input": [], + "error-messages": + ["external special remote error: WHATEVER WENT WRONG"], + "file": "somefile"} def _call_transfer(target: str, @@ -67,6 +76,7 @@ def _call_transfer(target: str, return_special_remotes: bool = True) -> Generator: ds_mock = MagicMock() ds_mock.config.getbool.return_value = config_result + ds_mock.pathobj = Path("/root") return _transfer_data( repo=MockRepo(return_special_remotes), ds=ds_mock, @@ -107,14 +117,16 @@ def test_patch_execute_export(): gele_mock.return_value = None results = tuple(_call_transfer("yes-target", False)) eq_(pd_mock.call_count, 0) - assert_in( - { - "path": str(Path("/root/file.txt")), - "target": "yes-target", - "action": "copy", - "status": "ok", - }, - results) + assert_in_results(results, + path=str(Path("/root/file.txt")), + target="yes-target", + action="copy", + status="ok") + assert_in_results(results, + path=str(Path("/root/somefile")), + target="yes-target", + action="copy", + status="error") def test_patch_skip_ignore_targets_export(): @@ -144,14 +156,16 @@ def test_patch_check_envpatch(): gc_mock.return_value = {"secret": "abc", "user": "hans"} results = tuple(_call_transfer("yes-target", False)) eq_(pd_mock.call_count, 0) - assert_in( - { - "path": str(Path("/root/file.txt")), - "target": "yes-target", - "action": "copy", - "status": "ok", - }, - results) + assert_in_results(results, + path=str(Path("/root/file.txt")), + target="yes-target", + action="copy", + status="ok") + assert_in_results(results, + path=str(Path("/root/somefile")), + target="yes-target", + action="copy", + status="error") def test_no_special_remotes():
push to export remote patch swallows errors This `try ... except`: https://github.com/datalad/datalad-next/blob/864896e26af7361b739b05df4fcd302b0b407db3/datalad_next/patches/push_to_export_remote.py#L216 is wrong. If `annex export` fails we get an error result from `_call_annex_records_items_` rather than an exception. And this error result is unconditionally turned into an `status='ok'` record here.
0.0
35af20542c46c523f4d635ffc187fcc3d50ade6a
[ "datalad_next/patches/tests/test_push_to_export_remote.py::test_patch_execute_export", "datalad_next/patches/tests/test_push_to_export_remote.py::test_patch_check_envpatch" ]
[ "datalad_next/patches/tests/test_push_to_export_remote.py::test_is_export_remote", "datalad_next/patches/tests/test_push_to_export_remote.py::test_patch_pass_through", "datalad_next/patches/tests/test_push_to_export_remote.py::test_patch_skip_ignore_targets_export", "datalad_next/patches/tests/test_push_to_export_remote.py::test_no_special_remotes", "datalad_next/patches/tests/test_push_to_export_remote.py::test_get_export_records_no_exports", "datalad_next/patches/tests/test_push_to_export_remote.py::test_get_export_records", "datalad_next/patches/tests/test_push_to_export_remote.py::test_get_export_log_entry" ]
{ "failed_lite_validators": [ "has_added_files" ], "has_test_patch": true, "is_lite": false }
2022-08-12 16:59:17+00:00
mit
1,838
datapythonista__mnist-12
diff --git a/README.md b/README.md index b164037..80a9d4e 100644 --- a/README.md +++ b/README.md @@ -63,4 +63,18 @@ train_images = mnist.train_images() x = images.reshape((images.shape[0], images.shape[1] * images.shape[2])) ``` +Both the url where the files can be found, and the temporary directory where +they will be cached locally can be modified in the next way: +``` +import mnist + +mnist.datasets_url = 'http://url-to-the/datasets' + +# temporary_dir is a function, so it can be dinamically created +# like Python stdlib `tempfile.gettempdir` (which is the default) +mnist.temporary_dir = lambda: '/tmp/mnist' + +train_images = mnist.train_images() +``` + It supports Python 2.7 and Python >= 3.5. diff --git a/mnist/__init__.py b/mnist/__init__.py index 2a41398..a567875 100644 --- a/mnist/__init__.py +++ b/mnist/__init__.py @@ -16,8 +16,11 @@ except ImportError: import numpy -# the url can be changed by the users of the library (not a constant) +# `datasets_url` and `temporary_dir` can be set by the user using: +# >>> mnist.datasets_url = 'http://my.mnist.url' +# >>> mnist.temporary_dir = lambda: '/tmp/mnist' datasets_url = 'http://yann.lecun.com/exdb/mnist/' +temporary_dir = tempfile.gettempdir class IdxDecodeError(ValueError): @@ -45,8 +48,7 @@ def download_file(fname, target_dir=None, force=False): fname : str Full path of the downloaded file """ - if not target_dir: - target_dir = tempfile.gettempdir() + target_dir = target_dir or temporary_dir() target_fname = os.path.join(target_dir, fname) if force or not os.path.isfile(target_fname):
datapythonista/mnist
aeae1406afea11c1c23788f23856053edcfc536b
diff --git a/tests/test_download_mnist.py b/tests/test_download_mnist.py index 631104d..e71aabe 100644 --- a/tests/test_download_mnist.py +++ b/tests/test_download_mnist.py @@ -97,8 +97,20 @@ class TestDownloadMNIST(unittest.TestCase): @mock.patch('mnist.urlretrieve') def test_datasets_url_is_used(self, urlretrieve): + original_url = mnist.datasets_url mnist.datasets_url = 'http://aaa.com/' mnist.download_file('mnist_datasets_url.gz') fname = os.path.join(tempfile.gettempdir(), 'mnist_datasets_url.gz') urlretrieve.assert_called_once_with( 'http://aaa.com/mnist_datasets_url.gz', fname) + mnist.datasets_url = original_url + + @mock.patch('mnist.urlretrieve') + def test_temporary_dir_is_used(self, urlretrieve): + original_temp_dir = mnist.temporary_dir + mnist.temporary_dir = lambda: '/another/tmp/dir/' + fname = mnist.download_file('test') + urlretrieve.assert_called_once_with(mnist.datasets_url + 'test', + '/another/tmp/dir/test') + self.assertEqual(fname, '/another/tmp/dir/test') + mnist.temporary_dir = original_temp_dir
Allowing specification of the download directory Right now the functions listed on the README.md doesn't allow specifying the target directory. This functionality should be possible just by propagating extra parameters to the download function.
0.0
aeae1406afea11c1c23788f23856053edcfc536b
[ "tests/test_download_mnist.py::TestDownloadMNIST::test_temporary_dir_is_used" ]
[ "tests/test_download_mnist.py::TestDownloadMNIST::test_datasets_url_is_used", "tests/test_download_mnist.py::TestDownloadMNIST::test_file_is_downloaded_to_target_dir", "tests/test_download_mnist.py::TestDownloadMNIST::test_file_is_downloaded_when_exists_and_force_is_true", "tests/test_download_mnist.py::TestDownloadMNIST::test_file_is_not_downloaded_when_force_is_false" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2018-09-24 13:52:46+00:00
bsd-3-clause
1,839
datosgobar__pydatajson-125
diff --git a/docs/MANUAL.md b/docs/MANUAL.md index 2191b01..39d9678 100644 --- a/docs/MANUAL.md +++ b/docs/MANUAL.md @@ -94,8 +94,11 @@ Toma los siguientes parámetros: - **portal_url**: URL del portal de CKAN de destino. - **apikey**: La apikey de un usuario del portal de destino con los permisos para crear el dataset bajo la organización pasada como parámetro. + - **demote_superThemes** (opcional, default: True):Si está en true, los ids de los themes del dataset, se escriben + como groups de CKAN. - **demote_themes** (opcional, default: True): Si está en true, los labels de los themes del dataset, se escriben como tags de CKAN; sino,se pasan como grupo. + Retorna el id en el nodo de destino del dataset federado. diff --git a/pydatajson/ckan_utils.py b/pydatajson/ckan_utils.py index 31f6737..b915bde 100644 --- a/pydatajson/ckan_utils.py +++ b/pydatajson/ckan_utils.py @@ -14,7 +14,8 @@ def append_attribute_to_extra(package, dataset, attribute, serialize=False): package['extras'].append({'key': attribute, 'value': value}) -def map_dataset_to_package(dataset, catalog_id, owner_org, theme_taxonomy, demote_themes=True): +def map_dataset_to_package(dataset, catalog_id, owner_org, theme_taxonomy, + demote_superThemes=True, demote_themes=True): package = dict() package['extras'] = [] # Obligatorios @@ -33,8 +34,10 @@ def map_dataset_to_package(dataset, catalog_id, owner_org, theme_taxonomy, demot package['resources'] = map_distributions_to_resources(distributions, catalog_id) super_themes = dataset['superTheme'] - package['groups'] = [{'name': title_to_name(super_theme, decode=False)} for super_theme in super_themes] append_attribute_to_extra(package, dataset, 'superTheme', serialize=True) + if demote_superThemes: + package['groups'] = [{'name': title_to_name(super_theme, decode=False)} for super_theme in super_themes] + # Recomendados y opcionales package['url'] = dataset.get('landingPage') @@ -66,7 +69,8 @@ def map_dataset_to_package(dataset, catalog_id, owner_org, theme_taxonomy, demot label = next(x['label'] for x in theme_taxonomy if x['id'] == theme) package['tags'].append({'name': label}) else: - package['groups'] += [{'name': title_to_name(theme, decode=False)} for theme in themes] + package['groups'] = package.get('groups', []) + [{'name': title_to_name(theme, decode=False)} + for theme in themes] return package diff --git a/pydatajson/federation.py b/pydatajson/federation.py index f9a4f6b..7807dfe 100644 --- a/pydatajson/federation.py +++ b/pydatajson/federation.py @@ -10,7 +10,7 @@ from .search import get_datasets def push_dataset_to_ckan(catalog, catalog_id, owner_org, dataset_origin_identifier, portal_url, apikey, - demote_themes=True): + demote_superThemes=True, demote_themes=True): """Escribe la metadata de un dataset en el portal pasado por parámetro. Args: @@ -20,6 +20,7 @@ def push_dataset_to_ckan(catalog, catalog_id, owner_org, dataset_origin_identifi dataset_origin_identifier (str): El id del dataset que se va a federar. portal_url (str): La URL del portal CKAN de destino. apikey (str): La apikey de un usuario con los permisos que le permitan crear o actualizar el dataset. + demote_superThemes(bool): Si está en true, los ids de los super themes del dataset, se propagan como grupo. demote_themes(bool): Si está en true, los labels de los themes del dataset, pasan a ser tags. Sino, se pasan como grupo. @@ -30,7 +31,8 @@ def push_dataset_to_ckan(catalog, catalog_id, owner_org, dataset_origin_identifi ckan_portal = RemoteCKAN(portal_url, apikey=apikey) theme_taxonomy = catalog.themes - package = map_dataset_to_package(dataset, catalog_id, owner_org, theme_taxonomy, demote_themes=demote_themes) + package = map_dataset_to_package(dataset, catalog_id, owner_org, theme_taxonomy, + demote_superThemes, demote_themes) # Get license id if dataset.get('license'):
datosgobar/pydatajson
3c428354f3f1b48b9b70815ba370e8cd1b11b07b
diff --git a/tests/test_ckan_utils.py b/tests/test_ckan_utils.py index 3884251..dca112c 100644 --- a/tests/test_ckan_utils.py +++ b/tests/test_ckan_utils.py @@ -67,8 +67,8 @@ class DatasetConversionTestCase(unittest.TestCase): self.assertCountEqual(keywords + theme_labels, tags) def test_themes_are_preserved_if_not_demoted(self): - package = map_dataset_to_package(self.dataset, self.catalog_id, 'owner', self.catalog.themes, - demote_themes=False) + package = map_dataset_to_package(self.dataset, self.catalog_id, 'owner', + self.catalog.themes, demote_themes=False) groups = [group['name'] for group in package.get('groups', [])] super_themes = [title_to_name(s_theme.lower()) for s_theme in self.dataset.get('superTheme')] themes = self.dataset.get('theme', []) @@ -84,15 +84,48 @@ class DatasetConversionTestCase(unittest.TestCase): except AttributeError: self.assertCountEqual(keywords, tags) + def test_superThemes_dont_impact_groups_if_not_demoted(self): + package = map_dataset_to_package(self.dataset, self.catalog_id, 'owner', + self.catalog.themes, demote_superThemes=False) + groups = [group['name'] for group in package.get('groups', [])] + tags = [tag['name'] for tag in package['tags']] + keywords = self.dataset.get('keyword', []) + themes = self.dataset.get('theme', []) + theme_labels = [] + for theme in themes: + label = next(x['label'] for x in self.catalog.themes if x['id'] == theme) + theme_labels.append(label) + try: + self.assertItemsEqual([], groups) + except AttributeError: + self.assertCountEqual([], groups) + try: + self.assertItemsEqual(keywords + theme_labels, tags) + except AttributeError: + self.assertCountEqual(keywords + theme_labels, tags) + + def test_preserve_themes_and_superThemes(self): + package = map_dataset_to_package(self.dataset, self.catalog_id, 'owner', + self.catalog.themes, False, False) + groups = [group['name'] for group in package.get('groups', [])] + tags = [tag['name'] for tag in package['tags']] + keywords = self.dataset.get('keyword', []) + themes = self.dataset.get('theme', []) + try: + self.assertItemsEqual(themes, groups) + except AttributeError: + self.assertCountEqual(themes, groups) + try: + self.assertItemsEqual(keywords, tags) + except AttributeError: + self.assertCountEqual(keywords, tags) + def test_dataset_extra_attributes_are_correct(self): package = map_dataset_to_package(self.dataset, self.catalog_id, 'owner', self.catalog.themes) # extras are included in dataset if package['extras']: for extra in package['extras']: - if extra['key'] == 'super_theme': - dataset_value = self.dataset['superTheme'] - else: - dataset_value = self.dataset[extra['key']] + dataset_value = self.dataset[extra['key']] if type(dataset_value) is list: extra_value = json.loads(extra['value']) try: @@ -106,7 +139,7 @@ class DatasetConversionTestCase(unittest.TestCase): def test_dataset_extra_attributes_are_complete(self): package = map_dataset_to_package(self.dataset, self.catalog_id, 'owner', self.catalog.themes) # dataset attributes are included in extras - extra_attrs = ['issued', 'modified', 'accrualPeriodicity', 'temporal', 'language', 'spatial'] + extra_attrs = ['issued', 'modified', 'accrualPeriodicity', 'temporal', 'language', 'spatial', 'superTheme'] for key in extra_attrs: value = self.dataset.get(key) if value: @@ -115,8 +148,6 @@ class DatasetConversionTestCase(unittest.TestCase): resulting_dict = {'key': key, 'value': value} self.assertTrue(resulting_dict in package['extras']) - self.assertTrue({'key': 'super_theme', 'value': json.dumps(self.dataset['superTheme'])}) - def test_resources_replicated_attributes_stay_the_same(self): resources = map_distributions_to_resources(self.distributions, self.catalog_id+'_'+self.dataset_id) for resource in resources:
Agregar opción para copiar `superTheme` a `theme` en `push_dataset_to_ckan` **Contexto** Los temas globales (`superTheme`) son temas transversales bajo los cuales los nodos originales clasifican a sus datasets para indexarlos en un nodo integrador. El `superTheme` de un dataset en su nodo original, es el `theme` de ese dataset en el nodo integrador (son los temas que usa CKAN para visualizar en la landing del Portal). **Implementar** Agregar a la función `push_dataset_to_ckan` un argumento opcional `superTheme_to_theme` con default `True`. Este _flag_ copia todos los elementos del array `superTheme` en la metadata original de un dataset y los agrega al array `theme` del dataset que va a ser empujado a un CKAN. **Notas** Esto es una operación de transformación de los metadatos originales cuyo sentido es federar correctamente los metadatos de un dataset en un contexto de portal diferente (con un público y alcance temático _transversal_, mientras que el nodo original tiene un público y alcance temático _específico_). **Entregable** La nueva opción en `push_dataset_to_ckan`, junto con sus tests asociados y las modificaciones correspondientes a la documentación en los docs de RTD.
0.0
3c428354f3f1b48b9b70815ba370e8cd1b11b07b
[ "tests/test_ckan_utils.py::DatasetConversionTestCase::test_preserve_themes_and_superThemes", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_superThemes_dont_impact_groups_if_not_demoted" ]
[ "tests/test_ckan_utils.py::DatasetConversionTestCase::test_dataset_array_attributes_are_correct", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_dataset_extra_attributes_are_complete", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_dataset_extra_attributes_are_correct", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_dataset_nested_replicated_attributes_stay_the_same", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_replicated_plain_attributes_are_corrext", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_resources_extra_attributes_are_created_correctly", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_resources_replicated_attributes_stay_the_same", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_resources_transformed_attributes_are_correct", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_themes_are_preserved_if_not_demoted", "tests/test_ckan_utils.py::DatetimeConversionTests::test_dates_change_correctly", "tests/test_ckan_utils.py::DatetimeConversionTests::test_dates_stay_the_same", "tests/test_ckan_utils.py::DatetimeConversionTests::test_datetimes_without_microseconds_are_handled_correctly", "tests/test_ckan_utils.py::DatetimeConversionTests::test_datetimes_without_seconds_are_handled_correctly", "tests/test_ckan_utils.py::DatetimeConversionTests::test_datetimes_without_timezones_stay_the_same", "tests/test_ckan_utils.py::DatetimeConversionTests::test_timezones_are_handled_correctly" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2018-03-12 20:48:48+00:00
mit
1,840
datosgobar__pydatajson-137
diff --git a/docs/MANUAL.md b/docs/MANUAL.md index cd72809..914f87c 100644 --- a/docs/MANUAL.md +++ b/docs/MANUAL.md @@ -107,7 +107,7 @@ Toma los siguientes parámetros: mantener una consistencia más estricta dentro del catálogo a federar, es necesario validar los datos antes de pasarlos a la función. -- **pydatajson.DataJson.remove_dataset_from_ckan()**: Hace un borrado físico de un dataset en un portal de CKAN. +- **pydatajson.federation.remove_dataset_from_ckan()**: Hace un borrado físico de un dataset en un portal de CKAN. Toma los siguientes parámetros: - **portal_url**: La URL del portal CKAN. Debe implementar la funcionalidad de `/data.json`. - **apikey**: La apikey de un usuario con los permisos que le permitan borrar el dataset. @@ -121,6 +121,16 @@ Toma los siguientes parámetros: En caso de pasar más de un parámetro opcional, la función `remove_dataset_from_ckan()` borra aquellos datasets que cumplan con todas las condiciones. +- **pydatajson.DataJson.push_theme_to_ckan()**: Crea un tema en el portal de destino +Toma los siguientes parámetros: + - **portal_url**: La URL del portal CKAN. Debe implementar la funcionalidad de `/data.json`. + - **apikey**: La apikey de un usuario con los permisos que le permitan borrar el dataset. + - **identifier** (opcional, default: None): Id del `theme` que se quiere federar, en el catálogo de origen. + - **label** (opcional, default: None): label del `theme` que se quiere federar, en el catálogo de origen. + + Debe pasarse por lo menos uno de los 2 parámetros opcionales. En caso de que se provean los 2, se prioriza el + identifier sobre el label. + ## Uso ### Setup diff --git a/pydatajson/ckan_utils.py b/pydatajson/ckan_utils.py index 9724f44..9f68692 100644 --- a/pydatajson/ckan_utils.py +++ b/pydatajson/ckan_utils.py @@ -2,7 +2,6 @@ # -*- coding: utf-8 -*- import json import re -import sys from datetime import time from dateutil import parser, tz from .helpers import title_to_name @@ -109,10 +108,21 @@ def map_distributions_to_resources(distributions, catalog_id=None): resource['mimetype'] = distribution.get('mediaType') resource['size'] = distribution.get('byteSize') resource['accessURL'] = distribution.get('accessURL') - resource['fileName'] = distribution.get('fileName') + fileName = distribution.get('fileName') + if fileName: + resource['fileName'] = fileName dist_fields = distribution.get('field') if dist_fields: resource['attributesDescription'] = json.dumps(dist_fields) resources.append(resource) return resources + + +def map_theme_to_group(theme): + + return { + "name": title_to_name(theme.get('id') or theme['label']), + "title": theme.get('label'), + "description": theme.get('description'), + } diff --git a/pydatajson/federation.py b/pydatajson/federation.py index 9573040..9f132cd 100644 --- a/pydatajson/federation.py +++ b/pydatajson/federation.py @@ -5,7 +5,7 @@ from __future__ import print_function from ckanapi import RemoteCKAN from ckanapi.errors import NotFound -from .ckan_utils import map_dataset_to_package +from .ckan_utils import map_dataset_to_package, map_theme_to_group from .search import get_datasets @@ -23,7 +23,6 @@ def push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, portal_u demote_superThemes(bool): Si está en true, los ids de los super themes del dataset, se propagan como grupo. demote_themes(bool): Si está en true, los labels de los themes del dataset, pasan a ser tags. Sino, se pasan como grupo. - Returns: str: El id del dataset en el catálogo de destino. """ @@ -103,3 +102,22 @@ def remove_datasets_from_ckan(portal_url, apikey, filter_in=None, filter_out=Non for identifier in identifiers: ckan_portal.call_action('dataset_purge', data_dict={'id': identifier}) + + +def push_theme_to_ckan(catalog, portal_url, apikey, identifier=None, label=None): + """Escribe la metadata de un theme en el portal pasado por parámetro. + + Args: + catalog (DataJson): El catálogo de origen que contiene el theme. + portal_url (str): La URL del portal CKAN de destino. + apikey (str): La apikey de un usuario con los permisos que le permitan crear o actualizar el dataset. + identifier (str): El identificador para buscar el theme en la taxonomia. + label (str): El label para buscar el theme en la taxonomia. + Returns: + str: El name del theme en el catálogo de destino. + """ + ckan_portal = RemoteCKAN(portal_url, apikey=apikey) + theme = catalog.get_theme(identifier=identifier, label=label) + group = map_theme_to_group(theme) + pushed_group = ckan_portal.call_action('group_create', data_dict=group) + return pushed_group['name']
datosgobar/pydatajson
afc2856312e6ebea0e76396c2b1f663193b962e0
diff --git a/tests/test_ckan_utils.py b/tests/test_ckan_utils.py index f90406e..83a7697 100644 --- a/tests/test_ckan_utils.py +++ b/tests/test_ckan_utils.py @@ -2,12 +2,8 @@ import unittest import os -import json -import re -import sys -from dateutil import parser, tz from .context import pydatajson -from pydatajson.ckan_utils import map_dataset_to_package, map_distributions_to_resources, convert_iso_string_to_utc +from pydatajson.ckan_utils import * from pydatajson.helpers import title_to_name SAMPLES_DIR = os.path.join("tests", "samples") @@ -216,6 +212,57 @@ class DatasetConversionTestCase(unittest.TestCase): self.assertIsNone(resource.get('attributesDescription')) +class ThemeConversionTests(unittest.TestCase): + + @classmethod + def get_sample(cls, sample_filename): + return os.path.join(SAMPLES_DIR, sample_filename) + + @classmethod + def setUpClass(cls): + catalog = pydatajson.DataJson(cls.get_sample('full_data.json')) + cls.theme = catalog.get_theme(identifier='adjudicaciones') + + def test_all_attributes_are_replicated_if_present(self): + group = map_theme_to_group(self.theme) + self.assertEqual('adjudicaciones', group['name']) + self.assertEqual('Adjudicaciones', group['title']) + self.assertEqual('Datasets sobre licitaciones adjudicadas.', group['description']) + + def test_label_is_used_as_name_if_id_not_present(self): + missing_id = dict(self.theme) + missing_id['label'] = u'#Will be used as name#' + missing_id.pop('id') + group = map_theme_to_group(missing_id) + self.assertEqual('will-be-used-as-name', group['name']) + self.assertEqual('#Will be used as name#', group['title']) + self.assertEqual('Datasets sobre licitaciones adjudicadas.', group['description']) + + def test_theme_missing_label(self): + missing_label = dict(self.theme) + missing_label.pop('label') + group = map_theme_to_group(missing_label) + self.assertEqual('adjudicaciones', group['name']) + self.assertIsNone(group.get('title')) + self.assertEqual('Datasets sobre licitaciones adjudicadas.', group['description']) + + def test_theme_missing_description(self): + missing_description = dict(self.theme) + missing_description.pop('description') + group = map_theme_to_group(missing_description) + self.assertEqual('adjudicaciones', group['name']) + self.assertEqual('Adjudicaciones', group['title']) + self.assertIsNone(group['description']) + + def test_id_special_characters_are_removed(self): + special_char_id = dict(self.theme) + special_char_id['id'] = u'#Théme& $id?' + group = map_theme_to_group(special_char_id) + self.assertEqual('theme-id', group['name']) + self.assertEqual('Adjudicaciones', group['title']) + self.assertEqual('Datasets sobre licitaciones adjudicadas.', group['description']) + + class DatetimeConversionTests(unittest.TestCase): def test_timezones_are_handled_correctly(self): diff --git a/tests/test_federation.py b/tests/test_federation.py index e6804b9..fd8284e 100644 --- a/tests/test_federation.py +++ b/tests/test_federation.py @@ -3,14 +3,14 @@ import unittest import os import re -import sys + try: from mock import patch, MagicMock except ImportError: from unittest.mock import patch, MagicMock from .context import pydatajson -from pydatajson.federation import push_dataset_to_ckan, remove_datasets_from_ckan +from pydatajson.federation import push_dataset_to_ckan, remove_datasets_from_ckan, push_theme_to_ckan from ckanapi.errors import NotFound SAMPLES_DIR = os.path.join("tests", "samples") @@ -215,3 +215,40 @@ class RemoveDatasetTestCase(unittest.TestCase): 'portal', 'key', only_time_series=True, organization='some_org') mock_portal.return_value.call_action.assert_called_with( 'dataset_purge', data_dict={'id': 'id_2'}) + + +class PushThemeTestCase(unittest.TestCase): + + @classmethod + def get_sample(cls, sample_filename): + return os.path.join(SAMPLES_DIR, sample_filename) + + @classmethod + def setUpClass(cls): + cls.catalog = pydatajson.DataJson(cls.get_sample('full_data.json')) + + @patch('pydatajson.federation.RemoteCKAN', autospec=True) + def test_empty_theme_search_raises_exception(self, mock_portal): + with self.assertRaises(AssertionError): + push_theme_to_ckan(self.catalog, 'portal_url', 'apikey') + + @patch('pydatajson.federation.RemoteCKAN', autospec=True) + def test_function_pushes_theme_by_identifier(self, mock_portal): + mock_portal.return_value.call_action = MagicMock(return_value={'name': 'group_name'}) + result = push_theme_to_ckan(self.catalog, 'portal_url', 'apikey', identifier='compras') + self.assertEqual('group_name', result) + + @patch('pydatajson.federation.RemoteCKAN', autospec=True) + def test_function_pushes_theme_by_label(self, mock_portal): + mock_portal.return_value.call_action = MagicMock(return_value={'name': 'other_name'}) + result = push_theme_to_ckan(self.catalog, 'portal_url', 'apikey', label='Adjudicaciones') + self.assertEqual('other_name', result) + + @patch('pydatajson.federation.RemoteCKAN', autospec=True) + def test_ckan_portal_is_called_with_correct_parametres(self, mock_portal): + mock_portal.return_value.call_action = MagicMock(return_value={'name': u'contrataciones'}) + group = {'name': u'contrataciones', + 'title': u'Contrataciones', + 'description': u'Datasets sobre contrataciones.'} + push_theme_to_ckan(self.catalog, 'portal_url', 'apikey', identifier='contrataciones') + mock_portal.return_value.call_action.assert_called_once_with('group_create', data_dict=group)
Función push theme_to_ckan() **Contexto** Por el momento, la función `push_dataset_to_ckan()` federa los datasets sin tener en cuenta los `themes` presentes en el catálogo de destino. La operación se concreta, pero cualquier `theme` del dataset que no esté presente en el catálogo es ignorado. El objetivo es implementar una función `push_theme_to_ckan()`, que mediante la API, cree los grupos de CKAN indicados. Esta función será luego utilizada por si sola o en conjunto con los wrappers para generar los temas pertinentes de un catalogo.
0.0
afc2856312e6ebea0e76396c2b1f663193b962e0
[ "tests/test_ckan_utils.py::DatasetConversionTestCase::test_catalog_id_is_prefixed_in_resource_id_if_passed", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_catalog_id_is_prepended_to_dataset_id_if_passed", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_dataset_array_attributes_are_correct", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_dataset_extra_attributes_are_complete", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_dataset_extra_attributes_are_correct", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_dataset_id_is_preserved_if_catlog_id_is_not_passed", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_dataset_nested_replicated_attributes_stay_the_same", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_preserve_themes_and_superThemes", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_replicated_plain_attributes_are_corrext", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_resource_id_is_preserved_if_catalog_id_is_not_passed", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_resources_extra_attributes_are_created_correctly", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_resources_replicated_attributes_stay_the_same", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_resources_transformed_attributes_are_correct", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_superThemes_dont_impact_groups_if_not_demoted", "tests/test_ckan_utils.py::DatasetConversionTestCase::test_themes_are_preserved_if_not_demoted", "tests/test_ckan_utils.py::ThemeConversionTests::test_all_attributes_are_replicated_if_present", "tests/test_ckan_utils.py::ThemeConversionTests::test_id_special_characters_are_removed", "tests/test_ckan_utils.py::ThemeConversionTests::test_label_is_used_as_name_if_id_not_present", "tests/test_ckan_utils.py::ThemeConversionTests::test_theme_missing_description", "tests/test_ckan_utils.py::ThemeConversionTests::test_theme_missing_label", "tests/test_ckan_utils.py::DatetimeConversionTests::test_dates_change_correctly", "tests/test_ckan_utils.py::DatetimeConversionTests::test_dates_stay_the_same", "tests/test_ckan_utils.py::DatetimeConversionTests::test_datetimes_without_microseconds_are_handled_correctly", "tests/test_ckan_utils.py::DatetimeConversionTests::test_datetimes_without_seconds_are_handled_correctly", "tests/test_ckan_utils.py::DatetimeConversionTests::test_datetimes_without_timezones_stay_the_same", "tests/test_ckan_utils.py::DatetimeConversionTests::test_timezones_are_handled_correctly", "tests/test_federation.py::PushDatasetTestCase::test_dataset_id_is_preserved_if_catalog_id_is_not_passed", "tests/test_federation.py::PushDatasetTestCase::test_dataset_without_license_sets_notspecified", "tests/test_federation.py::PushDatasetTestCase::test_id_is_created_correctly", "tests/test_federation.py::PushDatasetTestCase::test_id_is_updated_correctly", "tests/test_federation.py::PushDatasetTestCase::test_licenses_are_interpreted_correctly", "tests/test_federation.py::PushDatasetTestCase::test_tags_are_passed_correctly", "tests/test_federation.py::RemoveDatasetTestCase::test_empty_search_doesnt_call_purge", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_out_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_query_one_dataset", "tests/test_federation.py::RemoveDatasetTestCase::test_query_over_500_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_remove_through_filters_and_organization", "tests/test_federation.py::PushThemeTestCase::test_ckan_portal_is_called_with_correct_parametres", "tests/test_federation.py::PushThemeTestCase::test_empty_theme_search_raises_exception", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_identifier", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_label" ]
[]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }
2018-04-06 14:20:19+00:00
mit
1,841
datosgobar__pydatajson-153
diff --git a/pydatajson/ckan_utils.py b/pydatajson/ckan_utils.py index 6df8eaa..c67d3dc 100644 --- a/pydatajson/ckan_utils.py +++ b/pydatajson/ckan_utils.py @@ -1,5 +1,7 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- +from __future__ import print_function + import json import re from datetime import time @@ -76,12 +78,13 @@ def map_dataset_to_package(catalog, dataset, owner_org, catalog_id=None, if themes and demote_themes: package['tags'] = package.get('tags', []) for theme in themes: + # si falla continúa sin agregar ese theme a los tags del dataset try: - label = catalog.get_theme(identifier=theme)['label'] - except: - label = catalog.get_theme(label=theme)['label'] - label = re.sub(r'[^\wá-úÁ-ÚñÑ .-]+', '', label, flags=re.UNICODE) - package['tags'].append({'name': label}) + label = _get_theme_label(catalog, theme) + package['tags'].append({'name': label}) + except Exception as e: + print(e) + continue else: package['groups'] = package.get('groups', []) + [ {'name': title_to_name(theme, decode=False)} @@ -91,6 +94,18 @@ def map_dataset_to_package(catalog, dataset, owner_org, catalog_id=None, return package +def _get_theme_label(catalog, theme): + """Intenta conseguir el theme por id o por label.""" + try: + label = catalog.get_theme(identifier=theme)['label'] + except: + label = catalog.get_theme(label=theme)['label'] + + label = re.sub(r'[^\wá-úÁ-ÚñÑ .-]+', '', + label, flags=re.UNICODE) + return label + + def convert_iso_string_to_utc(date_string): date_time = parser.parse(date_string) if date_time.time() == time(0): diff --git a/pydatajson/federation.py b/pydatajson/federation.py index 43e932e..b503d95 100644 --- a/pydatajson/federation.py +++ b/pydatajson/federation.py @@ -5,11 +5,13 @@ de la API de CKAN. """ from __future__ import print_function +import logging from ckanapi import RemoteCKAN -from ckanapi.errors import NotFound +from ckanapi.errors import NotFound, NotAuthorized from .ckan_utils import map_dataset_to_package, map_theme_to_group from .search import get_datasets +logger = logging.getLogger(__name__) def push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, portal_url, apikey, catalog_id=None, @@ -250,14 +252,20 @@ def harvest_catalog_to_ckan(catalog, portal_url, apikey, catalog_id, Returns: str: El id del dataset en el catálogo de destino. """ - dataset_list = dataset_list or [ds['identifier'] - for ds in catalog.datasets] + # Evitar entrar con valor falsy + if dataset_list is None: + dataset_list = [ds['identifier'] for ds in catalog.datasets] owner_org = owner_org or catalog_id harvested = [] for dataset_id in dataset_list: - harvested_id = harvest_dataset_to_ckan( - catalog, owner_org, dataset_id, portal_url, apikey, catalog_id) - harvested.append(harvested_id) + try: + harvested_id = harvest_dataset_to_ckan( + catalog, owner_org, dataset_id, portal_url, apikey, catalog_id) + harvested.append(harvested_id) + except (NotAuthorized, NotFound, KeyError, TypeError) as e: + logger.error("Error federando catalogo:"+catalog_id+", dataset:"+dataset_id + "al portal: "+portal_url) + logger.error(str(e)) + return harvested
datosgobar/pydatajson
dae546a739eb2aab1c34b3d8bbb5896fe804e0aa
diff --git a/tests/test_federation.py b/tests/test_federation.py index fe95079..9d0515f 100644 --- a/tests/test_federation.py +++ b/tests/test_federation.py @@ -223,6 +223,13 @@ class PushDatasetTestCase(unittest.TestCase): self.assertCountEqual([self.catalog_id+'_'+ds['identifier'] for ds in self.catalog.datasets], harvested_ids) + @patch('pydatajson.federation.RemoteCKAN', autospec=True) + def test_harvest_catalog_with_empty_list(self, mock_portal): + harvested_ids = harvest_catalog_to_ckan(self.catalog, 'portal', 'key', self.catalog_id, + owner_org='owner', dataset_list=[]) + mock_portal.assert_not_called() + self.assertEqual([], harvested_ids) + class RemoveDatasetTestCase(unittest.TestCase):
Robustecer el manejo de harvest_catalog_to_ckan() Hay que corregir 2 problemas: - En caso de pasar una lista vacía en el dataset list, no se debe federar ningún dataset. Actualmente se federan todos. -En caso de que alguno de las llamadas a `harvest_dataset_to_ckan()` falle, loggear y continuar con el resto. Actualmente la federación entera del catálogo levanta la excepción.
0.0
dae546a739eb2aab1c34b3d8bbb5896fe804e0aa
[ "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_empty_list" ]
[ "tests/test_federation.py::PushDatasetTestCase::test_dataset_id_is_preserved_if_catalog_id_is_not_passed", "tests/test_federation.py::PushDatasetTestCase::test_dataset_level_wrappers", "tests/test_federation.py::PushDatasetTestCase::test_dataset_without_license_sets_notspecified", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_dataset_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_no_optional_parametres", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_owner_org", "tests/test_federation.py::PushDatasetTestCase::test_id_is_created_correctly", "tests/test_federation.py::PushDatasetTestCase::test_id_is_updated_correctly", "tests/test_federation.py::PushDatasetTestCase::test_licenses_are_interpreted_correctly", "tests/test_federation.py::PushDatasetTestCase::test_tags_are_passed_correctly", "tests/test_federation.py::RemoveDatasetTestCase::test_empty_search_doesnt_call_purge", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_out_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_query_one_dataset", "tests/test_federation.py::RemoveDatasetTestCase::test_query_over_500_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_remove_through_filters_and_organization", "tests/test_federation.py::PushThemeTestCase::test_ckan_portal_is_called_with_correct_parametres", "tests/test_federation.py::PushThemeTestCase::test_empty_theme_search_raises_exception", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_identifier", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_label", "tests/test_federation.py::PushCatalogThemesTestCase::test_empty_portal_pushes_every_theme", "tests/test_federation.py::PushCatalogThemesTestCase::test_full_portal_pushes_nothing", "tests/test_federation.py::PushCatalogThemesTestCase::test_non_empty_intersection_pushes_missing_themes" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2018-04-24 17:27:32+00:00
mit
1,842
datosgobar__pydatajson-181
diff --git a/pydatajson/time_series.py b/pydatajson/time_series.py index 683020d..182986c 100644 --- a/pydatajson/time_series.py +++ b/pydatajson/time_series.py @@ -10,7 +10,8 @@ definidas según la extensión del perfil de metadatos para series de tiempo. from __future__ import unicode_literals from __future__ import print_function from __future__ import with_statement -import os + +from . import custom_exceptions as ce def field_is_time_series(field, distribution=None): @@ -42,10 +43,10 @@ def get_distribution_time_index(distribution): def distribution_has_time_index(distribution): - for field in distribution.get('field', []): - if field.get('specialType') == 'time_index': - return True - return False + try: + return any([field.get('specialType') == 'time_index' for field in distribution.get('field', [])]) + except AttributeError: + return False def dataset_has_time_series(dataset):
datosgobar/pydatajson
0a8a32e5c1def9f73f2f98b03c8c7d72d4c0ad54
diff --git a/tests/test_time_series.py b/tests/test_time_series.py new file mode 100644 index 0000000..716314c --- /dev/null +++ b/tests/test_time_series.py @@ -0,0 +1,41 @@ +from __future__ import unicode_literals +from __future__ import print_function +from __future__ import with_statement + +import os.path +import unittest +from pydatajson.core import DataJson +from pydatajson.time_series import get_distribution_time_index, distribution_has_time_index, dataset_has_time_series +from pydatajson.custom_exceptions import DistributionTimeIndexNonExistentError + +SAMPLES_DIR = os.path.join("tests", "samples") + + +class TimeSeriesTestCase(unittest.TestCase): + + @classmethod + def get_sample(cls, sample_filename): + return os.path.join(SAMPLES_DIR, sample_filename) + + def setUp(self): + ts_catalog = DataJson(self.get_sample('time_series_data.json')) + full_catalog = DataJson(self.get_sample('full_data.json')) + self.ts_dataset = ts_catalog.datasets[0] + self.non_ts_datasets = full_catalog.datasets[0] + self.ts_distribution = ts_catalog.distributions[1] + self.non_ts_distribution = full_catalog.distributions[0] + + def test_get_distribution_time_index(self): + self.assertEqual('indice_tiempo', get_distribution_time_index(self.ts_distribution)) + with self.assertRaises(DistributionTimeIndexNonExistentError): + get_distribution_time_index(self.non_ts_distribution) + + def test_distribution_has_time_index(self): + self.assertTrue(distribution_has_time_index(self.ts_distribution)) + self.assertFalse(distribution_has_time_index(self.non_ts_distribution)) + self.ts_distribution['field'] = ['p', 'r', 'o', 'b', 'l', 'e', 'm'] + self.assertFalse(distribution_has_time_index(self.ts_distribution)) + + def test_dataset_has_time_series(self): + self.assertTrue(dataset_has_time_series(self.ts_dataset)) + self.assertFalse(dataset_has_time_series(self.non_ts_datasets))
Robustecer la función `distribution_has_time_index` para que no se rompa **Contexto** Actualmente si el campo `field` de una distribución no tiene la estructura esperada, la función presume que puede realizar acciones contra ella para validar si tiene o no un índice de tiempo que pueden fallar (como presumir que hay un `dict` contra el que hacer un `get`). **Propuesta** Re-factorizar la función con un `try` `except` (o con cualquier otra estrategia) para que si falla por cualquier motivo interprete que la distribución *no tiene un índice de tiempo*. La justificación detrás es que la función *sólo devuelve True cuando consigue encontrar una distribución que cumple con la especificación de series de tiempo para tener un índice de tiempo, si esto no es así - por el motivo que sea - se considera que la distribución _no tiene un índice de tiempo_*, pero no rompe.
0.0
0a8a32e5c1def9f73f2f98b03c8c7d72d4c0ad54
[ "tests/test_time_series.py::TimeSeriesTestCase::test_distribution_has_time_index", "tests/test_time_series.py::TimeSeriesTestCase::test_get_distribution_time_index" ]
[ "tests/test_time_series.py::TimeSeriesTestCase::test_dataset_has_time_series" ]
{ "failed_lite_validators": [ "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }
2018-07-27 19:24:18+00:00
mit
1,843
datosgobar__pydatajson-210
diff --git a/docs/MANUAL.md b/docs/MANUAL.md index 207d9fe..e03b74f 100644 --- a/docs/MANUAL.md +++ b/docs/MANUAL.md @@ -428,6 +428,15 @@ Toma los siguientes parámetros: portal de destino. Si no se pasa, se toma como organización el catalog_id Retorna el id en el nodo de destino de los datasets federados. + +### Métodos para manejo de organizaciones + +- **pydatajson.federation.get_organizations_from_ckan()**: Devuelve el árbol de organizaciones del portal pasado por parámetro. +Toma los siguientes parámetros: + - **portal_url**: URL del portal de CKAN. Debe implementar el endpoint `/group_tree`. + + Retorna una lista de diccionarios con la información de las organizaciones. Recursivamente, dentro del campo `children`, + se encuentran las organizaciones dependientes en la jerarquía. ## Anexo I: Estructura de respuestas diff --git a/pydatajson/federation.py b/pydatajson/federation.py index 6e57ec1..1138121 100644 --- a/pydatajson/federation.py +++ b/pydatajson/federation.py @@ -300,3 +300,17 @@ def push_new_themes(catalog, portal_url, apikey): catalog, portal_url, apikey, identifier=new_theme) pushed_names.append(name) return pushed_names + + +def get_organizations_from_ckan(portal_url): + """Toma la url de un portal y devuelve su árbol de organizaciones. + + Args: + portal_url (str): La URL del portal CKAN de origen. + Returns: + dict: Diccionarios anidados con la información de + las organizaciones. + """ + ckan_portal = RemoteCKAN(portal_url) + return ckan_portal.call_action('group_tree', + data_dict={'type': 'organization'})
datosgobar/pydatajson
3b9447bbe8f4250cc1b3def1e014f67c4fca0eb0
diff --git a/tests/test_federation.py b/tests/test_federation.py index 746ae23..58449e4 100644 --- a/tests/test_federation.py +++ b/tests/test_federation.py @@ -18,12 +18,15 @@ from ckanapi.errors import NotFound SAMPLES_DIR = os.path.join("tests", "samples") -class PushDatasetTestCase(unittest.TestCase): - +class FederationSuite(unittest.TestCase): @classmethod def get_sample(cls, sample_filename): return os.path.join(SAMPLES_DIR, sample_filename) + +@patch('pydatajson.federation.RemoteCKAN', autospec=True) +class PushDatasetTestCase(FederationSuite): + @classmethod def setUpClass(cls): cls.catalog = pydatajson.DataJson(cls.get_sample('full_data.json')) @@ -43,7 +46,6 @@ class PushDatasetTestCase(unittest.TestCase): cls.minimum_dataset['distribution'][0][ 'identifier'] = cls.dataset['distribution'][0]['identifier'] - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_id_is_created_correctly(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'package_update': @@ -62,7 +64,6 @@ class PushDatasetTestCase(unittest.TestCase): catalog_id=self.catalog_id) self.assertEqual(self.catalog_id + '_' + self.dataset_id, res_id) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_id_is_updated_correctly(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'package_update': @@ -81,7 +82,6 @@ class PushDatasetTestCase(unittest.TestCase): catalog_id=self.catalog_id) self.assertEqual(self.catalog_id + '_' + self.dataset_id, res_id) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_dataset_id_is_preserved_if_catalog_id_is_not_passed( self, mock_portal): def mock_call_action(action, data_dict=None): @@ -97,7 +97,6 @@ class PushDatasetTestCase(unittest.TestCase): 'portal', 'key') self.assertEqual(self.dataset_id, res_id) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_tags_are_passed_correctly(self, mock_portal): themes = self.dataset['theme'] keywords = [kw for kw in self.dataset['keyword']] @@ -132,7 +131,6 @@ class PushDatasetTestCase(unittest.TestCase): catalog_id=self.catalog_id) self.assertEqual(self.catalog_id + '_' + self.dataset_id, res_id) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_licenses_are_interpreted_correctly(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'license_list': @@ -149,7 +147,6 @@ class PushDatasetTestCase(unittest.TestCase): push_dataset_to_ckan(self.catalog, 'owner', self.dataset_id, 'portal', 'key', catalog_id=self.catalog_id) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_dataset_without_license_sets_notspecified(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'license_list': @@ -172,7 +169,6 @@ class PushDatasetTestCase(unittest.TestCase): 'key', catalog_id=self.minimum_catalog_id) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_dataset_level_wrappers(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'package_update': @@ -192,7 +188,6 @@ class PushDatasetTestCase(unittest.TestCase): self.assertEqual(self.dataset_id, restored_id) self.assertEqual(self.catalog_id + '_' + self.dataset_id, harvested_id) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_harvest_catalog_with_no_optional_parametres(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'package_update': @@ -218,7 +213,6 @@ class PushDatasetTestCase(unittest.TestCase): for ds in self.catalog.datasets], harvested_ids) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_harvest_catalog_with_dataset_list(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'package_update': @@ -254,7 +248,6 @@ class PushDatasetTestCase(unittest.TestCase): [self.catalog_id + '_' + ds_id for ds_id in dataset_list], harvested_ids) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_harvest_catalog_with_owner_org(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'package_update': @@ -275,7 +268,6 @@ class PushDatasetTestCase(unittest.TestCase): for ds in self.catalog.datasets], harvested_ids) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_harvest_catalog_with_errors(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'package_update': @@ -292,7 +284,6 @@ class PushDatasetTestCase(unittest.TestCase): self.assertDictEqual( {self.catalog.datasets[1]['identifier']: "some message"}, errors) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_harvest_catalog_with_empty_list(self, mock_portal): harvested_ids, _ = harvest_catalog_to_ckan( self.catalog, 'portal', 'key', self.catalog_id, @@ -301,7 +292,7 @@ class PushDatasetTestCase(unittest.TestCase): self.assertEqual([], harvested_ids) -class RemoveDatasetTestCase(unittest.TestCase): +class RemoveDatasetTestCase(FederationSuite): @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_empty_search_doesnt_call_purge(self, mock_portal): @@ -378,22 +369,17 @@ class RemoveDatasetTestCase(unittest.TestCase): 'dataset_purge', data_dict={'id': 'id_2'}) -class PushThemeTestCase(unittest.TestCase): - - @classmethod - def get_sample(cls, sample_filename): - return os.path.join(SAMPLES_DIR, sample_filename) +@patch('pydatajson.federation.RemoteCKAN', autospec=True) +class PushThemeTestCase(FederationSuite): @classmethod def setUpClass(cls): cls.catalog = pydatajson.DataJson(cls.get_sample('full_data.json')) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_empty_theme_search_raises_exception(self, mock_portal): with self.assertRaises(AssertionError): push_theme_to_ckan(self.catalog, 'portal_url', 'apikey') - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_function_pushes_theme_by_identifier(self, mock_portal): mock_portal.return_value.call_action = MagicMock( return_value={'name': 'group_name'}) @@ -404,7 +390,6 @@ class PushThemeTestCase(unittest.TestCase): identifier='compras') self.assertEqual('group_name', result) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_function_pushes_theme_by_label(self, mock_portal): mock_portal.return_value.call_action = MagicMock( return_value={'name': 'other_name'}) @@ -415,7 +400,6 @@ class PushThemeTestCase(unittest.TestCase): label='Adjudicaciones') self.assertEqual('other_name', result) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_ckan_portal_is_called_with_correct_parametres(self, mock_portal): mock_portal.return_value.call_action = MagicMock( return_value={'name': u'contrataciones'}) @@ -431,16 +415,13 @@ class PushThemeTestCase(unittest.TestCase): 'group_create', data_dict=group) -class PushCatalogThemesTestCase(unittest.TestCase): - @classmethod - def get_sample(cls, sample_filename): - return os.path.join(SAMPLES_DIR, sample_filename) +@patch('pydatajson.federation.RemoteCKAN', autospec=True) +class PushCatalogThemesTestCase(FederationSuite): @classmethod def setUpClass(cls): cls.catalog = pydatajson.DataJson(cls.get_sample('full_data.json')) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_empty_portal_pushes_every_theme(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'group_list': @@ -461,7 +442,6 @@ class PushCatalogThemesTestCase(unittest.TestCase): [theme['id'] for theme in self.catalog['themeTaxonomy']], res_names) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_full_portal_pushes_nothing(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'group_list': @@ -476,7 +456,6 @@ class PushCatalogThemesTestCase(unittest.TestCase): except AttributeError: self.assertCountEqual([], res_names) - @patch('pydatajson.federation.RemoteCKAN', autospec=True) def test_non_empty_intersection_pushes_missing_themes(self, mock_portal): def mock_call_action(action, data_dict=None): if action == 'group_list': @@ -497,3 +476,12 @@ class PushCatalogThemesTestCase(unittest.TestCase): self.assertCountEqual( [theme['id'] for theme in self.catalog['themeTaxonomy']][2:], res_names) + + +@patch('pydatajson.federation.RemoteCKAN', autospec=True) +class OrganizationsTestCase(FederationSuite): + + def test_get_organization_calls_api_correctly(self, mock_portal): + get_organizations_from_ckan('portal_url') + mock_portal.return_value.call_action.assert_called_with( + 'group_tree', data_dict={'type': 'organization'})
Get organizations from ckan El objetivo es implementar un método que pasada la url de un portal, devuelva las organizaciones presentes completas con su jerarquía.
0.0
3b9447bbe8f4250cc1b3def1e014f67c4fca0eb0
[ "tests/test_federation.py::OrganizationsTestCase::test_get_organization_calls_api_correctly" ]
[ "tests/test_federation.py::PushDatasetTestCase::test_dataset_id_is_preserved_if_catalog_id_is_not_passed", "tests/test_federation.py::PushDatasetTestCase::test_dataset_level_wrappers", "tests/test_federation.py::PushDatasetTestCase::test_dataset_without_license_sets_notspecified", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_dataset_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_empty_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_errors", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_no_optional_parametres", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_owner_org", "tests/test_federation.py::PushDatasetTestCase::test_id_is_created_correctly", "tests/test_federation.py::PushDatasetTestCase::test_id_is_updated_correctly", "tests/test_federation.py::PushDatasetTestCase::test_licenses_are_interpreted_correctly", "tests/test_federation.py::PushDatasetTestCase::test_tags_are_passed_correctly", "tests/test_federation.py::RemoveDatasetTestCase::test_empty_search_doesnt_call_purge", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_out_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_query_one_dataset", "tests/test_federation.py::RemoveDatasetTestCase::test_query_over_500_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_remove_through_filters_and_organization", "tests/test_federation.py::PushThemeTestCase::test_ckan_portal_is_called_with_correct_parametres", "tests/test_federation.py::PushThemeTestCase::test_empty_theme_search_raises_exception", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_identifier", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_label", "tests/test_federation.py::PushCatalogThemesTestCase::test_empty_portal_pushes_every_theme", "tests/test_federation.py::PushCatalogThemesTestCase::test_full_portal_pushes_nothing", "tests/test_federation.py::PushCatalogThemesTestCase::test_non_empty_intersection_pushes_missing_themes" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }
2018-10-19 14:09:54+00:00
mit
1,844
datosgobar__pydatajson-211
diff --git a/docs/MANUAL.md b/docs/MANUAL.md index e03b74f..8a0c2f6 100644 --- a/docs/MANUAL.md +++ b/docs/MANUAL.md @@ -438,6 +438,19 @@ Toma los siguientes parámetros: Retorna una lista de diccionarios con la información de las organizaciones. Recursivamente, dentro del campo `children`, se encuentran las organizaciones dependientes en la jerarquía. +- **pydatajson.federation.push_organization_tree_to_ckan()**: Tomando un árbol de organizaciones como el creado por +`get_organizations_from_ckan()` crea en el portal de destino las organizaciones dentro de su jerarquía. Toma los siguientes +parámetros: + - **portal_url**: La URL del portal CKAN de destino. + - **apikey**: La apikey de un usuario con los permisos que le permitan crear las organizaciones. + - **org_tree**: lista de diccionarios con la data de organizaciones a crear. + - **parent** (opcional, default: None): Si se pasa, el árbol de organizaciones pasado en `org_tree` se + crea bajo la organización con `name` pasado en `parent`. Si no se pasa un parámetro, las organizaciones son creadas + como primer nivel. + + Retorna el árbol de organizaciones creadas. Cada nodo tiene un campo `success` que indica si fue creado exitosamente o + no. En caso de que `success` sea False, los hijos de esa organización no son creados. + ## Anexo I: Estructura de respuestas ### validate_catalog() diff --git a/pydatajson/documentation.py b/pydatajson/documentation.py index 48d8b99..51745d1 100644 --- a/pydatajson/documentation.py +++ b/pydatajson/documentation.py @@ -47,10 +47,12 @@ def dataset_to_markdown(dataset): def distribution_to_markdown(distribution): - """Genera texto en markdown a partir de los metadatos de una `distribution`. + """Genera texto en markdown a partir de los metadatos de una + `distribution`. Args: - distribution (dict): Diccionario con metadatos de una `distribution`. + distribution (dict): Diccionario con metadatos de una + `distribution`. Returns: str: Texto que describe una `distribution`. diff --git a/pydatajson/federation.py b/pydatajson/federation.py index 1138121..fa0b31b 100644 --- a/pydatajson/federation.py +++ b/pydatajson/federation.py @@ -286,7 +286,7 @@ def push_new_themes(catalog, portal_url, apikey): taxonomía. portal_url (str): La URL del portal CKAN de destino. apikey (str): La apikey de un usuario con los permisos que le - permitan crear o actualizar el dataset. + permitan crear o actualizar los temas. Returns: str: Los ids de los temas creados. """ @@ -314,3 +314,42 @@ def get_organizations_from_ckan(portal_url): ckan_portal = RemoteCKAN(portal_url) return ckan_portal.call_action('group_tree', data_dict={'type': 'organization'}) + + +def push_organization_tree_to_ckan(portal_url, apikey, org_tree, parent=None): + """Toma un árbol de organizaciones y lo replica en el portal de + destino. + + Args: + portal_url (str): La URL del portal CKAN de destino. + apikey (str): La apikey de un usuario con los permisos que le + permitan crear las organizaciones. + org_tree(list): lista de diccionarios con la data de las + organizaciones a crear. + parent(str): campo name de la organizacion padre. + Returns: + (list): Devuelve el arbol de organizaciones recorridas, + junto con el status detallando si la creación fue + exitosa o no. + + """ + portal = RemoteCKAN(portal_url, apikey=apikey) + created = [] + for node in org_tree: + if parent: + node['groups'] = [{'name': parent}] + try: + pushed_org = portal.call_action('organization_create', + data_dict=node) + pushed_org['success'] = True + except Exception as e: + logger.exception('Ocurrió un error creando la organización {}: {}' + .format(node['title'], str(e))) + pushed_org = {'name': node, 'success': False} + + if pushed_org['success']: + pushed_org['children'] = push_organization_tree_to_ckan( + portal_url, apikey, node['children'], parent=node['name']) + + created.append(pushed_org) + return created
datosgobar/pydatajson
185d79d95555dd3041404b208a09583cb95a9a19
diff --git a/tests/samples/organization_tree.json b/tests/samples/organization_tree.json new file mode 100644 index 0000000..0e0ff6d --- /dev/null +++ b/tests/samples/organization_tree.json @@ -0,0 +1,235 @@ +[ + { + "highlighted": false, + "title": " Jefatura de Gabinete de Ministros", + "children": [ + { + "highlighted": false, + "title": "Agencia de Acceso a la Informaci\u00f3n P\u00fablica", + "children": [], + "name": "aaip", + "id": "daa8b40c-fa37-478c-a7ef-081305aeadd8" + }, + { + "highlighted": false, + "title": "Secretar\u00eda de Gobierno de Ambiente y Desarrollo Sustentable", + "children": [ + { + "highlighted": false, + "title": "Autoridad de Cuenca Matanza Riachuelo", + "children": [], + "name": "acumar", + "id": "1b6b28cd-098f-41d7-b43f-d5a01ffa8759" + } + ], + "name": "ambiente", + "id": "0e5aa328-825e-4509-851d-5421e866635e" + }, + { + "highlighted": false, + "title": "Secretar\u00eda de Gobierno de Modernizaci\u00f3n", + "children": [ + { + "highlighted": false, + "title": "Empresa Argentina de Soluciones Satelitales", + "children": [], + "name": "arsat", + "id": "b2509ac0-3af6-4f66-9ffa-8c6fb4206791" + }, + { + "highlighted": false, + "title": "Ente Nacional de Comunicaciones", + "children": [], + "name": "enacom", + "id": "6eb7d19b-2d42-494f-8e57-d67c501d23eb" + } + ], + "name": "modernizacion", + "id": "4c7a6f6b-5caf-42a1-aae5-0a07e609a235" + }, + { + "highlighted": false, + "title": "Secretar\u00eda de Gobierno de Turismo", + "children": [], + "name": "turismo", + "id": "3a751de6-128e-4f9a-a479-4672ef79a0e8" + } + ], + "name": "jgm", + "id": "f917ad65-28ea-42a9-81ae-61a2bb8f58d0" + }, + { + "highlighted": false, + "title": " Ministerio de Defensa", + "children": [ + { + "highlighted": false, + "title": "Instituto Geogr\u00e1fico Nacional", + "children": [], + "name": "ign", + "id": "9b47c8eb-bb5c-40df-bbaa-589374d14da8" + }, + { + "highlighted": false, + "title": "Servicio Meteorol\u00f3gico Nacional", + "children": [], + "name": "smn", + "id": "dba2a17e-e2ea-4e0b-b0ef-bf4ffe9f9ad9" + } + ], + "name": "defensa", + "id": "5e80ed4f-8bfb-4451-8240-e8f39e695ee1" + }, + { + "highlighted": false, + "title": "Ministerio de Educaci\u00f3n, Cultura, Ciencia y Tecnolog\u00eda", + "children": [ + { + "highlighted": false, + "title": "Secretar\u00eda de Gobierno de Ciencia y Tecnolog\u00eda", + "children": [], + "name": "mincyt", + "id": "772ab9b7-056d-4ae4-b7a2-a1329e979690" + }, + { + "highlighted": false, + "title": "Secretar\u00eda de Gobierno de Cultura", + "children": [], + "name": "cultura", + "id": "9fcc8ffc-3dcc-4437-acc8-72c5b08d8d51" + } + ], + "name": "educacion", + "id": "27d39ff7-7110-4c6d-b7e8-1b8eba392d7e" + }, + { + "highlighted": false, + "title": " Ministerio de Hacienda", + "children": [ + { + "highlighted": false, + "title": "Secretar\u00eda de Gobierno de Energ\u00eda", + "children": [ + { + "highlighted": false, + "title": "Ente Nacional Regulador del Gas", + "children": [], + "name": "enargas", + "id": "dddda9d3-644d-4e3d-974b-302fd8945a86" + } + ], + "name": "energia", + "id": "cd1b32a2-2d3a-44ac-8c98-a425a7b62d42" + }, + { + "highlighted": false, + "title": "Subsecretar\u00eda de Presupuesto", + "children": [], + "name": "sspre", + "id": "a753aeb8-52eb-4cfc-a6ee-6d930094b0f2" + }, + { + "highlighted": false, + "title": "Subsecretar\u00eda de Programaci\u00f3n Macroecon\u00f3mica", + "children": [], + "name": "sspm", + "id": "68f9ee22-5ec3-44cf-a32b-b87d9db46b93" + }, + { + "highlighted": false, + "title": "Subsecretar\u00eda de Programaci\u00f3n Microecon\u00f3mica", + "children": [], + "name": "sspmi", + "id": "b4baa84a-16a7-4db0-af9c-bd925971d26a" + } + ], + "name": "hacienda", + "id": "b2a6e77e-a3c8-4e1a-bcba-7134a9436051" + }, + { + "highlighted": false, + "title": " Ministerio de Justicia y Derechos Humanos", + "children": [], + "name": "justicia", + "id": "06b380f8-888f-43c0-8367-16a7ddf47d4f" + }, + { + "highlighted": false, + "title": " Ministerio del Interior, Obras P\u00fablicas y Vivienda ", + "children": [], + "name": "interior", + "id": "c88b1ad1-f78d-4cf9-848d-d73ccae6cd8e" + }, + { + "highlighted": false, + "title": "Ministerio de Producci\u00f3n y Trabajo", + "children": [ + { + "highlighted": false, + "title": "Secretar\u00eda de Gobierno de Agroindustria", + "children": [], + "name": "agroindustria", + "id": "b10c94e2-ade1-4a97-8c4c-b1ada7878d60" + }, + { + "highlighted": false, + "title": "Secretar\u00eda de Gobierno de Trabajo y Empleo", + "children": [], + "name": "trabajo", + "id": "f31cb5dc-79ab-442b-ac7f-87ef6ad7749d" + }, + { + "highlighted": false, + "title": "Secretar\u00eda de Transformaci\u00f3n Productiva", + "children": [], + "name": "siep", + "id": "83a04686-747a-4ba3-a0b1-2f05c3196bc4" + } + ], + "name": "produccion", + "id": "1ca8d15b-31fc-4f09-ba09-53edd3d4cce6" + }, + { + "highlighted": false, + "title": "Ministerio de Relaciones Exteriores y Culto", + "children": [], + "name": "exterior", + "id": "89cd05f2-11c1-4f1a-875f-b4faf97eb4d4" + }, + { + "highlighted": false, + "title": "Ministerio de Salud y Desarrollo Social", + "children": [ + { + "highlighted": false, + "title": "Secretar\u00eda de Gobierno de Salud", + "children": [], + "name": "salud", + "id": "dd1f2018-587f-43af-9b07-fc32f5ab588b" + } + ], + "name": "desarrollo-social", + "id": "ef25c735-2abb-4165-94a6-a6798a103603" + }, + { + "highlighted": false, + "title": " Ministerio de Seguridad", + "children": [], + "name": "seguridad", + "id": "908fd413-5a22-40e7-9204-38ef380ae232" + }, + { + "highlighted": false, + "title": " Ministerio de Transporte", + "children": [], + "name": "transporte", + "id": "71418928-10c4-4625-aeaf-69a4d73d00ed" + }, + { + "highlighted": false, + "title": "Sin organizaci\u00f3n asignada", + "children": [], + "name": "otros", + "id": "109d53ef-3ed3-498e-97d0-a456698969f7" + } +] \ No newline at end of file diff --git a/tests/test_federation.py b/tests/test_federation.py index 58449e4..d2a0af6 100644 --- a/tests/test_federation.py +++ b/tests/test_federation.py @@ -5,6 +5,7 @@ from __future__ import unicode_literals import unittest import os import re +import json try: from mock import patch, MagicMock @@ -481,7 +482,49 @@ class PushCatalogThemesTestCase(FederationSuite): @patch('pydatajson.federation.RemoteCKAN', autospec=True) class OrganizationsTestCase(FederationSuite): + def setUp(self): + self.portal_url = 'portal_url' + self.apikey = 'apikey' + self.org_tree = json.load(open( + self.get_sample('organization_tree.json'))) + + def check_hierarchy(self, node, parent=None): + if not node['success']: + self.assertTrue('children' not in node) + return + if parent is None: + self.assertTrue('groups' not in node) + else: + self.assertDictEqual(node['groups'][0], + {'name': parent}) + + for child in node['children']: + self.check_hierarchy(child, parent=node['name']) + def test_get_organization_calls_api_correctly(self, mock_portal): - get_organizations_from_ckan('portal_url') + get_organizations_from_ckan(self.portal_url) mock_portal.return_value.call_action.assert_called_with( 'group_tree', data_dict={'type': 'organization'}) + + def test_push_organizations_sends_correct_hierarchy(self, mock_portal): + mock_portal.return_value.call_action = (lambda _, data_dict: data_dict) + pushed_tree = push_organization_tree_to_ckan(self.portal_url, + self.apikey, + self.org_tree) + for node in pushed_tree: + self.check_hierarchy(node) + + def test_push_organizations_cuts_trees_on_failures(self, mock_portal): + def mock_org_create(_action, data_dict): + broken_orgs = ('acumar', 'modernizacion', 'hacienda') + if data_dict['name'] in broken_orgs: + raise Exception('broken org on each level') + else: + return data_dict + + mock_portal.return_value.call_action = mock_org_create + pushed_tree = push_organization_tree_to_ckan(self.portal_url, + self.apikey, + self.org_tree) + for node in pushed_tree: + self.check_hierarchy(node)
Push organizations to ckan Dado un árbol jerárquico de organizaciones, el objetivo es crear las organizaciones allí descriptas, manteniendo la jerarquía original
0.0
185d79d95555dd3041404b208a09583cb95a9a19
[ "tests/test_federation.py::OrganizationsTestCase::test_push_organizations_cuts_trees_on_failures", "tests/test_federation.py::OrganizationsTestCase::test_push_organizations_sends_correct_hierarchy" ]
[ "tests/test_federation.py::PushDatasetTestCase::test_dataset_id_is_preserved_if_catalog_id_is_not_passed", "tests/test_federation.py::PushDatasetTestCase::test_dataset_level_wrappers", "tests/test_federation.py::PushDatasetTestCase::test_dataset_without_license_sets_notspecified", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_dataset_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_empty_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_errors", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_no_optional_parametres", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_owner_org", "tests/test_federation.py::PushDatasetTestCase::test_id_is_created_correctly", "tests/test_federation.py::PushDatasetTestCase::test_id_is_updated_correctly", "tests/test_federation.py::PushDatasetTestCase::test_licenses_are_interpreted_correctly", "tests/test_federation.py::PushDatasetTestCase::test_tags_are_passed_correctly", "tests/test_federation.py::RemoveDatasetTestCase::test_empty_search_doesnt_call_purge", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_out_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_query_one_dataset", "tests/test_federation.py::RemoveDatasetTestCase::test_query_over_500_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_remove_through_filters_and_organization", "tests/test_federation.py::PushThemeTestCase::test_ckan_portal_is_called_with_correct_parametres", "tests/test_federation.py::PushThemeTestCase::test_empty_theme_search_raises_exception", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_identifier", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_label", "tests/test_federation.py::PushCatalogThemesTestCase::test_empty_portal_pushes_every_theme", "tests/test_federation.py::PushCatalogThemesTestCase::test_full_portal_pushes_nothing", "tests/test_federation.py::PushCatalogThemesTestCase::test_non_empty_intersection_pushes_missing_themes", "tests/test_federation.py::OrganizationsTestCase::test_get_organization_calls_api_correctly" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2018-10-23 12:34:37+00:00
mit
1,845
datosgobar__pydatajson-212
diff --git a/docs/MANUAL.md b/docs/MANUAL.md index 8a0c2f6..a84878b 100644 --- a/docs/MANUAL.md +++ b/docs/MANUAL.md @@ -438,6 +438,16 @@ Toma los siguientes parámetros: Retorna una lista de diccionarios con la información de las organizaciones. Recursivamente, dentro del campo `children`, se encuentran las organizaciones dependientes en la jerarquía. +- **pydatajson.federation.get_organization_from_ckan()**: Devuelve un diccionario con la información de una +organización en base a un id y un portal pasados por parámetro. +Toma los siguientes parámetros: + - **portal_url**: URL del portal de CKAN. Debe implementar el endpoint `/organization_show`. + - **org_id**: Identificador o name de la organización a buscar. + + Retorna un diccionario con la información de la organización correspondiente al identificador obtenido. + _No_ incluye su jerarquía, por lo cual ésta deberá ser conseguida mediante el uso de la función + `get_organizations_from_ckan`. + - **pydatajson.federation.push_organization_tree_to_ckan()**: Tomando un árbol de organizaciones como el creado por `get_organizations_from_ckan()` crea en el portal de destino las organizaciones dentro de su jerarquía. Toma los siguientes parámetros: diff --git a/pydatajson/federation.py b/pydatajson/federation.py index fa0b31b..eb5564b 100644 --- a/pydatajson/federation.py +++ b/pydatajson/federation.py @@ -308,7 +308,7 @@ def get_organizations_from_ckan(portal_url): Args: portal_url (str): La URL del portal CKAN de origen. Returns: - dict: Diccionarios anidados con la información de + list: Lista de diccionarios anidados con la información de las organizaciones. """ ckan_portal = RemoteCKAN(portal_url) @@ -316,6 +316,20 @@ def get_organizations_from_ckan(portal_url): data_dict={'type': 'organization'}) +def get_organization_from_ckan(portal_url, org_id): + """Toma la url de un portal y un id, y devuelve la organización a buscar. + + Args: + portal_url (str): La URL del portal CKAN de origen. + org_id (str): El id de la organización a buscar. + Returns: + dict: Diccionario con la información de la organización. + """ + ckan_portal = RemoteCKAN(portal_url) + return ckan_portal.call_action('organization_show', + data_dict={'id': org_id}) + + def push_organization_tree_to_ckan(portal_url, apikey, org_tree, parent=None): """Toma un árbol de organizaciones y lo replica en el portal de destino.
datosgobar/pydatajson
bcc401111ada65362839f1f92490198ddc5d94ea
diff --git a/tests/test_federation.py b/tests/test_federation.py index d2a0af6..daf9df4 100644 --- a/tests/test_federation.py +++ b/tests/test_federation.py @@ -501,11 +501,16 @@ class OrganizationsTestCase(FederationSuite): for child in node['children']: self.check_hierarchy(child, parent=node['name']) - def test_get_organization_calls_api_correctly(self, mock_portal): + def test_get_organizations_calls_api_correctly(self, mock_portal): get_organizations_from_ckan(self.portal_url) mock_portal.return_value.call_action.assert_called_with( 'group_tree', data_dict={'type': 'organization'}) + def test_get_organization_calls_api_correctly(self, mock_portal): + get_organization_from_ckan(self.portal_url, 'test_id') + mock_portal.return_value.call_action.assert_called_with( + 'organization_show', data_dict={'id': 'test_id'}) + def test_push_organizations_sends_correct_hierarchy(self, mock_portal): mock_portal.return_value.call_action = (lambda _, data_dict: data_dict) pushed_tree = push_organization_tree_to_ckan(self.portal_url,
Get organization from ckan El objetivo es implementar un método que devuelva la información de una organizacion a partir de su nombre o id y la url del portal pasado por parametro.
0.0
bcc401111ada65362839f1f92490198ddc5d94ea
[ "tests/test_federation.py::OrganizationsTestCase::test_get_organization_calls_api_correctly" ]
[ "tests/test_federation.py::PushDatasetTestCase::test_dataset_id_is_preserved_if_catalog_id_is_not_passed", "tests/test_federation.py::PushDatasetTestCase::test_dataset_level_wrappers", "tests/test_federation.py::PushDatasetTestCase::test_dataset_without_license_sets_notspecified", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_dataset_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_empty_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_errors", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_no_optional_parametres", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_owner_org", "tests/test_federation.py::PushDatasetTestCase::test_id_is_created_correctly", "tests/test_federation.py::PushDatasetTestCase::test_id_is_updated_correctly", "tests/test_federation.py::PushDatasetTestCase::test_licenses_are_interpreted_correctly", "tests/test_federation.py::PushDatasetTestCase::test_tags_are_passed_correctly", "tests/test_federation.py::RemoveDatasetTestCase::test_empty_search_doesnt_call_purge", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_out_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_query_one_dataset", "tests/test_federation.py::RemoveDatasetTestCase::test_query_over_500_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_remove_through_filters_and_organization", "tests/test_federation.py::PushThemeTestCase::test_ckan_portal_is_called_with_correct_parametres", "tests/test_federation.py::PushThemeTestCase::test_empty_theme_search_raises_exception", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_identifier", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_label", "tests/test_federation.py::PushCatalogThemesTestCase::test_empty_portal_pushes_every_theme", "tests/test_federation.py::PushCatalogThemesTestCase::test_full_portal_pushes_nothing", "tests/test_federation.py::PushCatalogThemesTestCase::test_non_empty_intersection_pushes_missing_themes", "tests/test_federation.py::OrganizationsTestCase::test_get_organizations_calls_api_correctly", "tests/test_federation.py::OrganizationsTestCase::test_push_organizations_cuts_trees_on_failures", "tests/test_federation.py::OrganizationsTestCase::test_push_organizations_sends_correct_hierarchy" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2018-10-24 13:57:03+00:00
mit
1,846
datosgobar__pydatajson-219
diff --git a/docs/MANUAL.md b/docs/MANUAL.md index 6ab393f..d68ab0a 100644 --- a/docs/MANUAL.md +++ b/docs/MANUAL.md @@ -350,6 +350,10 @@ Toma los siguientes parámetros: como groups de CKAN. - **demote_themes** (opcional, default: True): Si está en true, los labels de los themes del dataset, se escriben como tags de CKAN; sino,se pasan como grupo. + - **download_strategy** (opcional, default None): La referencia a una función que toma (catalog, distribution) de + entrada y devuelve un booleano. Esta función se aplica sobre todas las distribuciones del dataset. Si devuelve `True`, + se descarga el archivo indicado en el `downloadURL` de la distribución y se lo sube al portal de destino. Si es None, + se omite esta operación. Retorna el id en el nodo de destino del dataset federado. @@ -400,6 +404,10 @@ Toma los siguientes parámetros: organización pasada como parámetro. - **catalog_id**: El prefijo que va a preceder el id y name del dataset en el portal destino, separado por un guión. + - **download_strategy** (opcional, default None): La referencia a una función que toma (catalog, distribution) de + entrada y devuelve un booleano. Esta función se aplica sobre todas las distribuciones del dataset. Si devuelve `True`, + se descarga el archivo indicado en el `downloadURL` de la distribución y se lo sube al portal de destino. Si es None, + se omite esta operación. Retorna el id en el nodo de destino del dataset federado. @@ -411,6 +419,10 @@ Toma los siguientes parámetros: - **portal_url**: URL del portal de CKAN de destino. - **apikey**: La apikey de un usuario del portal de destino con los permisos para crear el dataset bajo la organización pasada como parámetro. + - **download_strategy** (opcional, default None): La referencia a una función que toma (catalog, distribution) de + entrada y devuelve un booleano. Esta función se aplica sobre todas las distribuciones del dataset. Si devuelve `True`, + se descarga el archivo indicado en el `downloadURL` de la distribución y se lo sube al portal de destino. Si es None, + se omite esta operación. Retorna el id del dataset restaurado. @@ -424,7 +436,11 @@ Toma los siguientes parámetros: - **dataset_list** (opcional, default: None): Lista de ids de los datasets a federar. Si no se pasa, se federan todos los datasets del catálogo. - **owner_org** (opcional, default: None): La organización a la que pertence el dataset. Debe encontrarse en el - portal de destino. Si no se pasa, se toma como organización el catalog_id + portal de destino. Si no se pasa, se toma como organización el catalog_id. + - **download_strategy** (opcional, default None): La referencia a una función que toma (catalog, distribution) de + entrada y devuelve un booleano. Esta función se aplica sobre todas las distribuciones del catálogo. Si devuelve + `True`, se descarga el archivo indicado en el `downloadURL` de la distribución y se lo sube al portal de destino. Si + es None, se omite esta operación. Retorna el id en el nodo de destino de los datasets federados. diff --git a/pydatajson/federation.py b/pydatajson/federation.py index 0cd1e5e..646f470 100644 --- a/pydatajson/federation.py +++ b/pydatajson/federation.py @@ -10,13 +10,15 @@ from ckanapi import RemoteCKAN from ckanapi.errors import NotFound from .ckan_utils import map_dataset_to_package, map_theme_to_group from .search import get_datasets +from .helpers import resource_files_download logger = logging.getLogger('pydatajson.federation') def push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, portal_url, apikey, catalog_id=None, - demote_superThemes=True, demote_themes=True): + demote_superThemes=True, demote_themes=True, + download_strategy=None): """Escribe la metadata de un dataset en el portal pasado por parámetro. Args: @@ -33,6 +35,10 @@ def push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, themes del dataset, se propagan como grupo. demote_themes(bool): Si está en true, los labels de los themes del dataset, pasan a ser tags. Sino, se pasan como grupo. + download_strategy(callable): Una función (catálogo, distribución)-> + bool. Sobre las distribuciones que evalúa True, descarga el + recurso en el downloadURL y lo sube al portal de destino. + Por default no sube ninguna distribución. Returns: str: El id del dataset en el catálogo de destino. """ @@ -64,11 +70,17 @@ def push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, pushed_package = ckan_portal.call_action( 'package_create', data_dict=package) + if download_strategy: + with resource_files_download(catalog, dataset.get('distribution', []), + download_strategy) as resource_files: + resources_upload(portal_url, apikey, resource_files, + catalog_id=catalog_id) + ckan_portal.close() return pushed_package['id'] -def resources_upload(portal_url, apikey, resource_files): +def resources_upload(portal_url, apikey, resource_files, catalog_id=None): """Sube archivos locales a sus distribuciones correspondientes en el portal pasado por parámetro. @@ -78,15 +90,18 @@ def resources_upload(portal_url, apikey, resource_files): permitan crear o actualizar el dataset. resource_files(dict): Diccionario con entradas id_de_distribucion:path_al_recurso a subir + catalog_id(str): prependea el id al id del recurso para + encontrarlo antes de subirlo Returns: list: los ids de los recursos modificados """ ckan_portal = RemoteCKAN(portal_url, apikey=apikey) res = [] for resource in resource_files: + resource_id = catalog_id + '_' + resource if catalog_id else resource try: pushed = ckan_portal.action.resource_patch( - id=resource, + id=resource_id, resource_type='file.upload', upload=open(resource_files[resource], 'rb')) res.append(pushed['id']) @@ -199,7 +214,7 @@ def push_theme_to_ckan(catalog, portal_url, apikey, def restore_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, - portal_url, apikey): + portal_url, apikey, download_strategy=None): """Restaura la metadata de un dataset en el portal pasado por parámetro. Args: @@ -210,15 +225,22 @@ def restore_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, portal_url (str): La URL del portal CKAN de destino. apikey (str): La apikey de un usuario con los permisos que le permitan crear o actualizar el dataset. + download_strategy(callable): Una función (catálogo, distribución)-> + bool. Sobre las distribuciones que evalúa True, descarga el + recurso en el downloadURL y lo sube al portal de destino. + Por default no sube ninguna distribución. Returns: str: El id del dataset restaurado. """ - return push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, - portal_url, apikey, None, False, False) + + return push_dataset_to_ckan(catalog, owner_org, + dataset_origin_identifier, portal_url, + apikey, None, False, False, download_strategy) def harvest_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, - portal_url, apikey, catalog_id): + portal_url, apikey, catalog_id, + download_strategy=None): """Federa la metadata de un dataset en el portal pasado por parámetro. Args: @@ -229,17 +251,22 @@ def harvest_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, portal_url (str): La URL del portal CKAN de destino. apikey (str): La apikey de un usuario con los permisos que le permitan crear o actualizar el dataset. - catalog_id(str): El id que prep + catalog_id(str): El id que prependea al dataset y recursos + download_strategy(callable): Una función (catálogo, distribución)-> + bool. Sobre las distribuciones que evalúa True, descarga el + recurso en el downloadURL y lo sube al portal de destino. + Por default no sube ninguna distribución. Returns: str: El id del dataset restaurado. """ return push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, - portal_url, apikey, catalog_id=catalog_id) + portal_url, apikey, catalog_id=catalog_id, + download_strategy=download_strategy) def restore_catalog_to_ckan(catalog, owner_org, portal_url, apikey, - dataset_list=None): + dataset_list=None, download_strategy=None): """Restaura los datasets de un catálogo al portal pasado por parámetro. Si hay temas presentes en el DataJson que no están en el portal de CKAN, los genera. @@ -253,6 +280,10 @@ def restore_catalog_to_ckan(catalog, owner_org, portal_url, apikey, se pasa una lista, todos los datasests se restauran. owner_org (str): La organización a la cual pertencen los datasets. Si no se pasa, se utiliza el catalog_id. + download_strategy(callable): Una función (catálogo, distribución)-> + bool. Sobre las distribuciones que evalúa True, descarga el + recurso en el downloadURL y lo sube al portal de destino. + Por default no sube ninguna distribución. Returns: str: El id del dataset en el catálogo de destino. """ @@ -261,14 +292,16 @@ def restore_catalog_to_ckan(catalog, owner_org, portal_url, apikey, for ds in catalog.datasets] restored = [] for dataset_id in dataset_list: - restored_id = restore_dataset_to_ckan( - catalog, owner_org, dataset_id, portal_url, apikey) + restored_id = restore_dataset_to_ckan(catalog, owner_org, dataset_id, + portal_url, apikey, + download_strategy) restored.append(restored_id) return restored def harvest_catalog_to_ckan(catalog, portal_url, apikey, catalog_id, - dataset_list=None, owner_org=None): + dataset_list=None, owner_org=None, + download_strategy=None): """Federa los datasets de un catálogo al portal pasado por parámetro. Args: @@ -282,6 +315,10 @@ def harvest_catalog_to_ckan(catalog, portal_url, apikey, catalog_id, se pasa una lista, todos los datasests se federan. owner_org (str): La organización a la cual pertencen los datasets. Si no se pasa, se utiliza el catalog_id. + download_strategy(callable): Una función (catálogo, distribución)-> + bool. Sobre las distribuciones que evalúa True, descarga el + recurso en el downloadURL y lo sube al portal de destino. + Por default no sube ninguna distribución. Returns: str: El id del dataset en el catálogo de destino. """ @@ -293,8 +330,10 @@ def harvest_catalog_to_ckan(catalog, portal_url, apikey, catalog_id, errors = {} for dataset_id in dataset_list: try: - harvested_id = harvest_dataset_to_ckan( - catalog, owner_org, dataset_id, portal_url, apikey, catalog_id) + harvested_id = harvest_dataset_to_ckan(catalog, owner_org, + dataset_id, portal_url, + apikey, catalog_id, + download_strategy) harvested.append(harvested_id) except Exception as e: msg = "Error federando catalogo: %s, dataset: %s al portal: %s\n"\ diff --git a/pydatajson/helpers.py b/pydatajson/helpers.py index 1e0b48c..8331c83 100644 --- a/pydatajson/helpers.py +++ b/pydatajson/helpers.py @@ -11,13 +11,20 @@ from datetime import datetime import os import json import re +import logging +import tempfile +from contextlib import contextmanager from openpyxl import load_workbook from six.moves.urllib_parse import urlparse from six import string_types, iteritems from unidecode import unidecode +from pydatajson.download import download_to_file + +logger = logging.getLogger('pydatajson.helpers') + ABSOLUTE_PROJECT_DIR = os.path.dirname(os.path.abspath(__file__)) ABSOLUTE_SCHEMA_DIR = os.path.join(ABSOLUTE_PROJECT_DIR, "schemas") STOP_WORDS = [ @@ -392,3 +399,39 @@ def pprint(result): result, indent=4, separators=(",", ": "), ensure_ascii=False ))) + + +@contextmanager +def resource_files_download(catalog, distributions, download_strategy): + resource_files = {} + distributions = [dist for dist in distributions if + download_strategy(catalog, dist)] + for dist in distributions: + try: + tmpfile = tempfile.NamedTemporaryFile(delete=False) + tmpfile.close() + download_to_file(dist['downloadURL'], tmpfile.name) + resource_files[dist['identifier']] = tmpfile.name + except Exception as e: + logger.exception( + "Error descargando el recurso {} de la distribución {}: {}" + .format(dist.get('downloadURL'), + dist.get('identifier'), str(e)) + ) + continue + try: + yield resource_files + + finally: + for resource in resource_files: + os.remove(resource_files[resource]) + + +def is_local_andino_resource(catalog, distribution): + dist_type = distribution.get('type') + if dist_type is not None: + return dist_type == 'file.upload' + homepage = catalog.get('homepage') + if homepage is not None: + return distribution.get('downloadURL', '').startswith(homepage) + return False
datosgobar/pydatajson
bdc7e8f4d6e1128c657ffa5b8e66215311da9e9c
diff --git a/tests/test_federation.py b/tests/test_federation.py index 21c1c5e..900cf42 100644 --- a/tests/test_federation.py +++ b/tests/test_federation.py @@ -14,6 +14,7 @@ except ImportError: from .context import pydatajson from pydatajson.federation import * +from pydatajson.helpers import is_local_andino_resource from ckanapi.errors import NotFound SAMPLES_DIR = os.path.join("tests", "samples") @@ -317,6 +318,43 @@ class PushDatasetTestCase(FederationSuite): ) self.assertEqual([], res) + @patch('pydatajson.helpers.download_to_file') + def test_push_dataset_upload_strategy(self, mock_download, mock_portal): + def mock_call_action(action, data_dict=None): + if action == 'package_update': + return data_dict + else: + return [] + mock_portal.return_value.call_action = mock_call_action + push_dataset_to_ckan( + self.catalog, + 'owner', + self.dataset_id, + 'portal', + 'key', + download_strategy=(lambda _, x: x['identifier'] == '1.1')) + mock_portal.return_value.action.resource_patch.assert_called_with( + id='1.1', + resource_type='file.upload', + upload=ANY + ) + + def test_push_dataset_upload_empty_strategy(self, mock_portal): + def mock_call_action(action, data_dict=None): + if action == 'package_update': + return data_dict + else: + return [] + mock_portal.return_value.call_action = mock_call_action + push_dataset_to_ckan( + self.minimum_catalog, + 'owner', + self.dataset_id, + 'portal', + 'key', + download_strategy=is_local_andino_resource) + mock_portal.return_value.action.resource_patch.not_called() + class RemoveDatasetTestCase(FederationSuite):
Agregar la posibilidad de carga/descarga de distribuciones en el método `restore_catalog_to_ckan()` El método tendría 2 flags que permitirían discriminar estas situaciones: + Quiero restaurar un catálogo solamente transfiriendo los metadatos (sin descargar ni volver a cargar distribuciones). + Quiero restaurar un catálogo descargando todas las distribuciones y cargándolas por API al CKAN de destino. + Quiero restaurar un catálogo descargando solamente las distribuciones que cumplen un determinado patrón (aka. el "pattern" de URL de descarga que tiene un CKAN) y cargándolas en el CKAN de destino, el resto de las distribuciones sólo se transfiere la metadata de downloadURL como está. Nota: implementar el patrón regular de identificación de "qué me tengo que descargar" como una variable con el default hecho para las URLs de CKAN.
0.0
bdc7e8f4d6e1128c657ffa5b8e66215311da9e9c
[ "tests/test_federation.py::PushDatasetTestCase::test_dataset_id_is_preserved_if_catalog_id_is_not_passed", "tests/test_federation.py::PushDatasetTestCase::test_dataset_level_wrappers", "tests/test_federation.py::PushDatasetTestCase::test_dataset_without_license_sets_notspecified", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_dataset_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_empty_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_errors", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_no_optional_parametres", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_owner_org", "tests/test_federation.py::PushDatasetTestCase::test_id_is_created_correctly", "tests/test_federation.py::PushDatasetTestCase::test_id_is_updated_correctly", "tests/test_federation.py::PushDatasetTestCase::test_licenses_are_interpreted_correctly", "tests/test_federation.py::PushDatasetTestCase::test_push_dataset_upload_empty_strategy", "tests/test_federation.py::PushDatasetTestCase::test_push_dataset_upload_strategy", "tests/test_federation.py::PushDatasetTestCase::test_resource_upload_error", "tests/test_federation.py::PushDatasetTestCase::test_resource_upload_succesfully", "tests/test_federation.py::PushDatasetTestCase::test_tags_are_passed_correctly", "tests/test_federation.py::RemoveDatasetTestCase::test_empty_search_doesnt_call_purge", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_out_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_query_one_dataset", "tests/test_federation.py::RemoveDatasetTestCase::test_query_over_500_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_remove_through_filters_and_organization", "tests/test_federation.py::PushThemeTestCase::test_ckan_portal_is_called_with_correct_parametres", "tests/test_federation.py::PushThemeTestCase::test_empty_theme_search_raises_exception", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_identifier", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_label", "tests/test_federation.py::PushCatalogThemesTestCase::test_empty_portal_pushes_every_theme", "tests/test_federation.py::PushCatalogThemesTestCase::test_full_portal_pushes_nothing", "tests/test_federation.py::PushCatalogThemesTestCase::test_non_empty_intersection_pushes_missing_themes", "tests/test_federation.py::OrganizationsTestCase::test_get_organization_calls_api_correctly", "tests/test_federation.py::OrganizationsTestCase::test_get_organizations_calls_api_correctly", "tests/test_federation.py::OrganizationsTestCase::test_push_organization_assigns_parent_correctly", "tests/test_federation.py::OrganizationsTestCase::test_push_organization_sets_correct_attributes_on_failures", "tests/test_federation.py::OrganizationsTestCase::test_push_organization_sets_correct_attributes_on_success", "tests/test_federation.py::OrganizationsTestCase::test_push_organizations_cuts_trees_on_failures", "tests/test_federation.py::OrganizationsTestCase::test_push_organizations_sends_correct_hierarchy" ]
[]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2018-11-06 18:10:59+00:00
mit
1,847
datosgobar__pydatajson-220
diff --git a/docs/MANUAL.md b/docs/MANUAL.md index 6ab393f..0e27a6b 100644 --- a/docs/MANUAL.md +++ b/docs/MANUAL.md @@ -350,6 +350,10 @@ Toma los siguientes parámetros: como groups de CKAN. - **demote_themes** (opcional, default: True): Si está en true, los labels de los themes del dataset, se escriben como tags de CKAN; sino,se pasan como grupo. + - **download_strategy** (opcional, default None): La referencia a una función que toma (catalog, distribution) de + entrada y devuelve un booleano. Esta función se aplica sobre todas las distribuciones del dataset. Si devuelve `True`, + se descarga el archivo indicado en el `downloadURL` de la distribución y se lo sube al portal de destino. Si es None, + se omite esta operación. Retorna el id en el nodo de destino del dataset federado. @@ -400,6 +404,10 @@ Toma los siguientes parámetros: organización pasada como parámetro. - **catalog_id**: El prefijo que va a preceder el id y name del dataset en el portal destino, separado por un guión. + - **download_strategy** (opcional, default None): La referencia a una función que toma (catalog, distribution) de + entrada y devuelve un booleano. Esta función se aplica sobre todas las distribuciones del dataset. Si devuelve `True`, + se descarga el archivo indicado en el `downloadURL` de la distribución y se lo sube al portal de destino. Si es None, + se omite esta operación. Retorna el id en el nodo de destino del dataset federado. @@ -411,6 +419,10 @@ Toma los siguientes parámetros: - **portal_url**: URL del portal de CKAN de destino. - **apikey**: La apikey de un usuario del portal de destino con los permisos para crear el dataset bajo la organización pasada como parámetro. + - **download_strategy** (opcional, default None): La referencia a una función que toma (catalog, distribution) de + entrada y devuelve un booleano. Esta función se aplica sobre todas las distribuciones del dataset. Si devuelve `True`, + se descarga el archivo indicado en el `downloadURL` de la distribución y se lo sube al portal de destino. Si es None, + se omite esta operación. Retorna el id del dataset restaurado. @@ -424,7 +436,11 @@ Toma los siguientes parámetros: - **dataset_list** (opcional, default: None): Lista de ids de los datasets a federar. Si no se pasa, se federan todos los datasets del catálogo. - **owner_org** (opcional, default: None): La organización a la que pertence el dataset. Debe encontrarse en el - portal de destino. Si no se pasa, se toma como organización el catalog_id + portal de destino. Si no se pasa, se toma como organización el catalog_id. + - **download_strategy** (opcional, default None): La referencia a una función que toma (catalog, distribution) de + entrada y devuelve un booleano. Esta función se aplica sobre todas las distribuciones del catálogo. Si devuelve + `True`, se descarga el archivo indicado en el `downloadURL` de la distribución y se lo sube al portal de destino. Si + es None, se omite esta operación. Retorna el id en el nodo de destino de los datasets federados. @@ -483,6 +499,16 @@ en el portal de destino. Toma los siguientes parámetros: Retorna el diccionario de la organización creada. El resultado tiene un campo `success` que indica si fue creado exitosamente o no. +- **pydatajson.federation.remove_organization_from_ckan()**: Tomando el id o name de una organización; la borra en el +portal de destino. Toma los siguientes parámetros: + - **portal_url**: La URL del portal CKAN de destino. + - **apikey**: La apikey de un usuario con los permisos que le permitan borrar la organización. + - **organization_id**: Id o name de la organización a borrar. + + Retorna None. + + **Advertencia**: En caso de que la organización tenga hijos en la jerarquía, estos pasan a ser de primer nivel. + ## Anexo I: Estructura de respuestas diff --git a/pydatajson/federation.py b/pydatajson/federation.py index 0cd1e5e..1b4465c 100644 --- a/pydatajson/federation.py +++ b/pydatajson/federation.py @@ -10,13 +10,15 @@ from ckanapi import RemoteCKAN from ckanapi.errors import NotFound from .ckan_utils import map_dataset_to_package, map_theme_to_group from .search import get_datasets +from .helpers import resource_files_download logger = logging.getLogger('pydatajson.federation') def push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, portal_url, apikey, catalog_id=None, - demote_superThemes=True, demote_themes=True): + demote_superThemes=True, demote_themes=True, + download_strategy=None): """Escribe la metadata de un dataset en el portal pasado por parámetro. Args: @@ -33,6 +35,10 @@ def push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, themes del dataset, se propagan como grupo. demote_themes(bool): Si está en true, los labels de los themes del dataset, pasan a ser tags. Sino, se pasan como grupo. + download_strategy(callable): Una función (catálogo, distribución)-> + bool. Sobre las distribuciones que evalúa True, descarga el + recurso en el downloadURL y lo sube al portal de destino. + Por default no sube ninguna distribución. Returns: str: El id del dataset en el catálogo de destino. """ @@ -64,11 +70,17 @@ def push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, pushed_package = ckan_portal.call_action( 'package_create', data_dict=package) + if download_strategy: + with resource_files_download(catalog, dataset.get('distribution', []), + download_strategy) as resource_files: + resources_upload(portal_url, apikey, resource_files, + catalog_id=catalog_id) + ckan_portal.close() return pushed_package['id'] -def resources_upload(portal_url, apikey, resource_files): +def resources_upload(portal_url, apikey, resource_files, catalog_id=None): """Sube archivos locales a sus distribuciones correspondientes en el portal pasado por parámetro. @@ -78,15 +90,18 @@ def resources_upload(portal_url, apikey, resource_files): permitan crear o actualizar el dataset. resource_files(dict): Diccionario con entradas id_de_distribucion:path_al_recurso a subir + catalog_id(str): prependea el id al id del recurso para + encontrarlo antes de subirlo Returns: list: los ids de los recursos modificados """ ckan_portal = RemoteCKAN(portal_url, apikey=apikey) res = [] for resource in resource_files: + resource_id = catalog_id + '_' + resource if catalog_id else resource try: pushed = ckan_portal.action.resource_patch( - id=resource, + id=resource_id, resource_type='file.upload', upload=open(resource_files[resource], 'rb')) res.append(pushed['id']) @@ -199,7 +214,7 @@ def push_theme_to_ckan(catalog, portal_url, apikey, def restore_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, - portal_url, apikey): + portal_url, apikey, download_strategy=None): """Restaura la metadata de un dataset en el portal pasado por parámetro. Args: @@ -210,15 +225,22 @@ def restore_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, portal_url (str): La URL del portal CKAN de destino. apikey (str): La apikey de un usuario con los permisos que le permitan crear o actualizar el dataset. + download_strategy(callable): Una función (catálogo, distribución)-> + bool. Sobre las distribuciones que evalúa True, descarga el + recurso en el downloadURL y lo sube al portal de destino. + Por default no sube ninguna distribución. Returns: str: El id del dataset restaurado. """ - return push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, - portal_url, apikey, None, False, False) + + return push_dataset_to_ckan(catalog, owner_org, + dataset_origin_identifier, portal_url, + apikey, None, False, False, download_strategy) def harvest_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, - portal_url, apikey, catalog_id): + portal_url, apikey, catalog_id, + download_strategy=None): """Federa la metadata de un dataset en el portal pasado por parámetro. Args: @@ -229,17 +251,22 @@ def harvest_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, portal_url (str): La URL del portal CKAN de destino. apikey (str): La apikey de un usuario con los permisos que le permitan crear o actualizar el dataset. - catalog_id(str): El id que prep + catalog_id(str): El id que prependea al dataset y recursos + download_strategy(callable): Una función (catálogo, distribución)-> + bool. Sobre las distribuciones que evalúa True, descarga el + recurso en el downloadURL y lo sube al portal de destino. + Por default no sube ninguna distribución. Returns: str: El id del dataset restaurado. """ return push_dataset_to_ckan(catalog, owner_org, dataset_origin_identifier, - portal_url, apikey, catalog_id=catalog_id) + portal_url, apikey, catalog_id=catalog_id, + download_strategy=download_strategy) def restore_catalog_to_ckan(catalog, owner_org, portal_url, apikey, - dataset_list=None): + dataset_list=None, download_strategy=None): """Restaura los datasets de un catálogo al portal pasado por parámetro. Si hay temas presentes en el DataJson que no están en el portal de CKAN, los genera. @@ -253,6 +280,10 @@ def restore_catalog_to_ckan(catalog, owner_org, portal_url, apikey, se pasa una lista, todos los datasests se restauran. owner_org (str): La organización a la cual pertencen los datasets. Si no se pasa, se utiliza el catalog_id. + download_strategy(callable): Una función (catálogo, distribución)-> + bool. Sobre las distribuciones que evalúa True, descarga el + recurso en el downloadURL y lo sube al portal de destino. + Por default no sube ninguna distribución. Returns: str: El id del dataset en el catálogo de destino. """ @@ -261,14 +292,16 @@ def restore_catalog_to_ckan(catalog, owner_org, portal_url, apikey, for ds in catalog.datasets] restored = [] for dataset_id in dataset_list: - restored_id = restore_dataset_to_ckan( - catalog, owner_org, dataset_id, portal_url, apikey) + restored_id = restore_dataset_to_ckan(catalog, owner_org, dataset_id, + portal_url, apikey, + download_strategy) restored.append(restored_id) return restored def harvest_catalog_to_ckan(catalog, portal_url, apikey, catalog_id, - dataset_list=None, owner_org=None): + dataset_list=None, owner_org=None, + download_strategy=None): """Federa los datasets de un catálogo al portal pasado por parámetro. Args: @@ -282,6 +315,10 @@ def harvest_catalog_to_ckan(catalog, portal_url, apikey, catalog_id, se pasa una lista, todos los datasests se federan. owner_org (str): La organización a la cual pertencen los datasets. Si no se pasa, se utiliza el catalog_id. + download_strategy(callable): Una función (catálogo, distribución)-> + bool. Sobre las distribuciones que evalúa True, descarga el + recurso en el downloadURL y lo sube al portal de destino. + Por default no sube ninguna distribución. Returns: str: El id del dataset en el catálogo de destino. """ @@ -293,8 +330,10 @@ def harvest_catalog_to_ckan(catalog, portal_url, apikey, catalog_id, errors = {} for dataset_id in dataset_list: try: - harvested_id = harvest_dataset_to_ckan( - catalog, owner_org, dataset_id, portal_url, apikey, catalog_id) + harvested_id = harvest_dataset_to_ckan(catalog, owner_org, + dataset_id, portal_url, + apikey, catalog_id, + download_strategy) harvested.append(harvested_id) except Exception as e: msg = "Error federando catalogo: %s, dataset: %s al portal: %s\n"\ @@ -417,3 +456,24 @@ def push_organization_to_ckan(portal_url, apikey, organization, parent=None): pushed_org = {'name': organization, 'success': False} return pushed_org + + +def remove_organization_from_ckan(portal_url, apikey, organization_id): + """Toma un id de organización y la purga del portal de destino. + Args: + portal_url (str): La URL del portal CKAN de destino. + apikey (str): La apikey de un usuario con los permisos que le + permitan borrar la organización. + organization_id(str): Id o name de la organización a borrar. + Returns: + None. + + """ + portal = RemoteCKAN(portal_url, apikey=apikey) + try: + portal.call_action('organization_purge', + data_dict={'id': organization_id}) + + except Exception as e: + logger.exception('Ocurrió un error borrando la organización {}: {}' + .format(organization_id, str(e))) diff --git a/pydatajson/helpers.py b/pydatajson/helpers.py index 1e0b48c..8331c83 100644 --- a/pydatajson/helpers.py +++ b/pydatajson/helpers.py @@ -11,13 +11,20 @@ from datetime import datetime import os import json import re +import logging +import tempfile +from contextlib import contextmanager from openpyxl import load_workbook from six.moves.urllib_parse import urlparse from six import string_types, iteritems from unidecode import unidecode +from pydatajson.download import download_to_file + +logger = logging.getLogger('pydatajson.helpers') + ABSOLUTE_PROJECT_DIR = os.path.dirname(os.path.abspath(__file__)) ABSOLUTE_SCHEMA_DIR = os.path.join(ABSOLUTE_PROJECT_DIR, "schemas") STOP_WORDS = [ @@ -392,3 +399,39 @@ def pprint(result): result, indent=4, separators=(",", ": "), ensure_ascii=False ))) + + +@contextmanager +def resource_files_download(catalog, distributions, download_strategy): + resource_files = {} + distributions = [dist for dist in distributions if + download_strategy(catalog, dist)] + for dist in distributions: + try: + tmpfile = tempfile.NamedTemporaryFile(delete=False) + tmpfile.close() + download_to_file(dist['downloadURL'], tmpfile.name) + resource_files[dist['identifier']] = tmpfile.name + except Exception as e: + logger.exception( + "Error descargando el recurso {} de la distribución {}: {}" + .format(dist.get('downloadURL'), + dist.get('identifier'), str(e)) + ) + continue + try: + yield resource_files + + finally: + for resource in resource_files: + os.remove(resource_files[resource]) + + +def is_local_andino_resource(catalog, distribution): + dist_type = distribution.get('type') + if dist_type is not None: + return dist_type == 'file.upload' + homepage = catalog.get('homepage') + if homepage is not None: + return distribution.get('downloadURL', '').startswith(homepage) + return False
datosgobar/pydatajson
bdc7e8f4d6e1128c657ffa5b8e66215311da9e9c
diff --git a/tests/test_federation.py b/tests/test_federation.py index 21c1c5e..14fac16 100644 --- a/tests/test_federation.py +++ b/tests/test_federation.py @@ -14,6 +14,7 @@ except ImportError: from .context import pydatajson from pydatajson.federation import * +from pydatajson.helpers import is_local_andino_resource from ckanapi.errors import NotFound SAMPLES_DIR = os.path.join("tests", "samples") @@ -317,6 +318,43 @@ class PushDatasetTestCase(FederationSuite): ) self.assertEqual([], res) + @patch('pydatajson.helpers.download_to_file') + def test_push_dataset_upload_strategy(self, mock_download, mock_portal): + def mock_call_action(action, data_dict=None): + if action == 'package_update': + return data_dict + else: + return [] + mock_portal.return_value.call_action = mock_call_action + push_dataset_to_ckan( + self.catalog, + 'owner', + self.dataset_id, + 'portal', + 'key', + download_strategy=(lambda _, x: x['identifier'] == '1.1')) + mock_portal.return_value.action.resource_patch.assert_called_with( + id='1.1', + resource_type='file.upload', + upload=ANY + ) + + def test_push_dataset_upload_empty_strategy(self, mock_portal): + def mock_call_action(action, data_dict=None): + if action == 'package_update': + return data_dict + else: + return [] + mock_portal.return_value.call_action = mock_call_action + push_dataset_to_ckan( + self.minimum_catalog, + 'owner', + self.dataset_id, + 'portal', + 'key', + download_strategy=is_local_andino_resource) + mock_portal.return_value.action.resource_patch.not_called() + class RemoveDatasetTestCase(FederationSuite): @@ -586,3 +624,17 @@ class OrganizationsTestCase(FederationSuite): self.org_tree) for node in pushed_tree: self.check_hierarchy(node) + + def test_remove_organization_sends_correct_parameters(self, mock_portal): + remove_organization_from_ckan(self.portal_url, self.apikey, 'test_id') + mock_portal.return_value.call_action.assert_called_with( + 'organization_purge', data_dict={'id': 'test_id'}) + + @patch('logging.Logger.exception') + def test_remove_organization_logs_failures(self, mock_logger, mock_portal): + mock_portal.return_value.call_action.side_effect = Exception('test') + remove_organization_from_ckan(self.portal_url, self.apikey, 'test_id') + mock_portal.return_value.call_action.assert_called_with( + 'organization_purge', data_dict={'id': 'test_id'}) + mock_logger.assert_called_with( + 'Ocurrió un error borrando la organización test_id: test')
remove_organization_from_ckan() Implementar el método `remove_organization_from_ckan()`, el cual borra una organización de acuerdo a un id.
0.0
bdc7e8f4d6e1128c657ffa5b8e66215311da9e9c
[ "tests/test_federation.py::PushDatasetTestCase::test_dataset_id_is_preserved_if_catalog_id_is_not_passed", "tests/test_federation.py::PushDatasetTestCase::test_dataset_level_wrappers", "tests/test_federation.py::PushDatasetTestCase::test_dataset_without_license_sets_notspecified", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_dataset_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_empty_list", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_errors", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_no_optional_parametres", "tests/test_federation.py::PushDatasetTestCase::test_harvest_catalog_with_owner_org", "tests/test_federation.py::PushDatasetTestCase::test_id_is_created_correctly", "tests/test_federation.py::PushDatasetTestCase::test_id_is_updated_correctly", "tests/test_federation.py::PushDatasetTestCase::test_licenses_are_interpreted_correctly", "tests/test_federation.py::PushDatasetTestCase::test_push_dataset_upload_empty_strategy", "tests/test_federation.py::PushDatasetTestCase::test_push_dataset_upload_strategy", "tests/test_federation.py::PushDatasetTestCase::test_resource_upload_error", "tests/test_federation.py::PushDatasetTestCase::test_resource_upload_succesfully", "tests/test_federation.py::PushDatasetTestCase::test_tags_are_passed_correctly", "tests/test_federation.py::RemoveDatasetTestCase::test_empty_search_doesnt_call_purge", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_filter_in_out_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_query_one_dataset", "tests/test_federation.py::RemoveDatasetTestCase::test_query_over_500_datasets", "tests/test_federation.py::RemoveDatasetTestCase::test_remove_through_filters_and_organization", "tests/test_federation.py::PushThemeTestCase::test_ckan_portal_is_called_with_correct_parametres", "tests/test_federation.py::PushThemeTestCase::test_empty_theme_search_raises_exception", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_identifier", "tests/test_federation.py::PushThemeTestCase::test_function_pushes_theme_by_label", "tests/test_federation.py::PushCatalogThemesTestCase::test_empty_portal_pushes_every_theme", "tests/test_federation.py::PushCatalogThemesTestCase::test_full_portal_pushes_nothing", "tests/test_federation.py::PushCatalogThemesTestCase::test_non_empty_intersection_pushes_missing_themes", "tests/test_federation.py::OrganizationsTestCase::test_get_organization_calls_api_correctly", "tests/test_federation.py::OrganizationsTestCase::test_get_organizations_calls_api_correctly", "tests/test_federation.py::OrganizationsTestCase::test_push_organization_assigns_parent_correctly", "tests/test_federation.py::OrganizationsTestCase::test_push_organization_sets_correct_attributes_on_failures", "tests/test_federation.py::OrganizationsTestCase::test_push_organization_sets_correct_attributes_on_success", "tests/test_federation.py::OrganizationsTestCase::test_push_organizations_cuts_trees_on_failures", "tests/test_federation.py::OrganizationsTestCase::test_push_organizations_sends_correct_hierarchy", "tests/test_federation.py::OrganizationsTestCase::test_remove_organization_logs_failures", "tests/test_federation.py::OrganizationsTestCase::test_remove_organization_sends_correct_parameters" ]
[]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2018-11-06 20:01:09+00:00
mit
1,848
dave-shawley__setupext-janitor-14
diff --git a/README.rst b/README.rst index 6a767de..3b7d103 100644 --- a/README.rst +++ b/README.rst @@ -38,7 +38,7 @@ imported into *setup.py* so that it can be passed as a keyword parameter import setuptools try: - from setupext import janitor + from setupext_janitor import janitor CleanCommand = janitor.CleanCommand except ImportError: CleanCommand = None @@ -49,8 +49,13 @@ imported into *setup.py* so that it can be passed as a keyword parameter setup( # normal parameters - setup_requires=['setupext.janitor'], + setup_requires=['setupext_janitor'], cmdclass=cmd_classes, + entry_points={ + # normal parameters, ie. console_scripts[] + 'distutils.commands': [ + ' clean = setupext_janitor.janitor:CleanCommand'] + } ) You can use a different approach if you are simply a developer that wants @@ -67,7 +72,7 @@ few new command line parameters. ``setup.py clean --dist`` Removes directories that the various *dist* commands produce. -``setup.py clean --egg`` +``setup.py clean --eggs`` Removes *.egg* and *.egg-info* directories. ``setup.py clean --environment`` diff --git a/docs/conf.py b/docs/conf.py index 718339e..f1efef7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,7 +3,7 @@ import sphinx_rtd_theme -from setupext import janitor +from setupext_janitor import janitor project = 'Setupext: janitor' diff --git a/setup.py b/setup.py index d564df8..a267c85 100755 --- a/setup.py +++ b/setup.py @@ -3,7 +3,7 @@ import codecs import setuptools import sys -from setupext import janitor +from setupext_janitor import janitor with codecs.open('README.rst', 'rb', encoding='utf-8') as file_obj: @@ -26,7 +26,6 @@ setuptools.setup( description='Making setup.py clean more useful.', long_description=long_description, packages=setuptools.find_packages(exclude=['tests', 'tests.*']), - namespace_packages=['setupext'], zip_safe=True, platforms='any', install_requires=install_requirements, @@ -41,7 +40,7 @@ setuptools.setup( ], entry_points={ 'distutils.commands': [ - 'clean = setupext.janitor:CleanCommand', + 'clean = setupext_janitor.janitor:CleanCommand', ], }, cmdclass={ diff --git a/setupext/__init__.py b/setupext/__init__.py deleted file mode 100644 index de40ea7..0000000 --- a/setupext/__init__.py +++ /dev/null @@ -1,1 +0,0 @@ -__import__('pkg_resources').declare_namespace(__name__) diff --git a/setupext_janitor/__init__.py b/setupext_janitor/__init__.py new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/setupext_janitor/__init__.py @@ -0,0 +1,1 @@ + diff --git a/setupext/janitor.py b/setupext_janitor/janitor.py similarity index 83% rename from setupext/janitor.py rename to setupext_janitor/janitor.py index 1a014e0..13b08c1 100644 --- a/setupext/janitor.py +++ b/setupext_janitor/janitor.py @@ -1,11 +1,11 @@ from distutils import dir_util, errors from distutils.command.clean import clean as _CleanCommand import os.path +import traceback - -version_info = (1, 0, 0) +version_info = (1, 0, 1) __version__ = '.'.join(str(v) for v in version_info) - +debug = False class CleanCommand(_CleanCommand): """ @@ -71,17 +71,32 @@ class CleanCommand(_CleanCommand): for cmd_name, _ in self.distribution.get_command_list(): if 'dist' in cmd_name: command = self.distribution.get_command_obj(cmd_name) - command.ensure_finalized() + #command.ensure_finalized() + # Stop premature exit for RPM-on-NT err + # https://github.com/dave-shawley/setupext-janitor/issues/12 + try: + command.ensure_finalized() + except Exception as err: + skip = "don't know how to create RPM distributions on platform nt" + if skip in err.args: + print('-'*50,'\nException encountered and ignored:') + print('{} {}'.format(err.__class__.__name__, err.args[0])) + if debug: traceback.print_exc() + print('-'*50) + else: + raise err + if getattr(command, 'dist_dir', None): dir_names.add(command.dist_dir) - + if self.eggs: for name in os.listdir(self.egg_base): if name.endswith('.egg-info'): dir_names.add(os.path.join(self.egg_base, name)) for name in os.listdir(os.curdir): - if name.endswith('.egg'): - dir_names.add(name) + for e in ['.egg', '.eggs']: + if name.endswith(e): + dir_names.add(name) if self.environment and self.virtualenv_dir: dir_names.add(self.virtualenv_dir)
dave-shawley/setupext-janitor
801d4e51b10c8880be16c99fd6316051808141fa
diff --git a/tests.py b/tests.py index 39af958..53f0d20 100644 --- a/tests.py +++ b/tests.py @@ -12,7 +12,7 @@ if sys.version_info >= (2, 7): else: # noinspection PyPackageRequirements,PyUnresolvedReferences import unittest2 as unittest -from setupext import janitor +from setupext_janitor import janitor def run_setup(*command_line): @@ -171,6 +171,16 @@ class EggDirectoryCleanupTests(DirectoryCleanupMixin, unittest.TestCase): os.rmdir(dir_name) raise + def test_that_eggs_directories_are_removed(self): + dir_name = uuid.uuid4().hex + '.eggs' + os.mkdir(dir_name) + try: + run_setup('clean', '--eggs') + self.assert_path_does_not_exist(dir_name) + except: + os.rmdir(dir_name) + raise + def test_that_directories_are_not_removed_in_dry_run_mode(self): egg_root = self.create_directory('egg-info-root') os.mkdir(os.path.join(egg_root, 'package.egg-info'))
clean --egg misses .eggs (plural) Eggs downloaded via `setup_requires=...` are put in `.eggs` not `.egg` and `python setup.py clean --eggs` misses them. (sidebar: setup_requires isn't necessary post PEP-518 and pip >v10)
0.0
801d4e51b10c8880be16c99fd6316051808141fa
[ "tests.py::CommandOptionTests::test_that_distutils_options_are_present", "tests.py::CommandOptionTests::test_that_janitor_defines_dist_command", "tests.py::CommandOptionTests::test_that_janitor_user_options_are_not_clean_options", "tests.py::PycacheCleanupTests::test_that_janitor_does_not_fail_when_cache_parent_is_removed", "tests.py::RemoveAllTests::test_that_distdir_is_removed", "tests.py::RemoveAllTests::test_that_eggdir_is_removed", "tests.py::RemoveAllTests::test_that_envdir_is_removed", "tests.py::RemoveAllTests::test_that_pycache_is_removed" ]
[]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_removed_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2019-02-07 23:36:43+00:00
bsd-3-clause
1,849
dave-shawley__setupext-janitor-8
diff --git a/README.rst b/README.rst index 6a767de..c6a8596 100644 --- a/README.rst +++ b/README.rst @@ -38,7 +38,7 @@ imported into *setup.py* so that it can be passed as a keyword parameter import setuptools try: - from setupext import janitor + from setupext_janitor import janitor CleanCommand = janitor.CleanCommand except ImportError: CleanCommand = None @@ -49,8 +49,13 @@ imported into *setup.py* so that it can be passed as a keyword parameter setup( # normal parameters - setup_requires=['setupext.janitor'], + setup_requires=['setupext_janitor'], cmdclass=cmd_classes, + entry_points={ + # normal parameters, ie. console_scripts[] + 'distutils.commands': [ + ' clean = setupext_janitor.janitor:CleanCommand'] + } ) You can use a different approach if you are simply a developer that wants diff --git a/docs/conf.py b/docs/conf.py index 718339e..f1efef7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,7 +3,7 @@ import sphinx_rtd_theme -from setupext import janitor +from setupext_janitor import janitor project = 'Setupext: janitor' diff --git a/setup.py b/setup.py index d564df8..a267c85 100755 --- a/setup.py +++ b/setup.py @@ -3,7 +3,7 @@ import codecs import setuptools import sys -from setupext import janitor +from setupext_janitor import janitor with codecs.open('README.rst', 'rb', encoding='utf-8') as file_obj: @@ -26,7 +26,6 @@ setuptools.setup( description='Making setup.py clean more useful.', long_description=long_description, packages=setuptools.find_packages(exclude=['tests', 'tests.*']), - namespace_packages=['setupext'], zip_safe=True, platforms='any', install_requires=install_requirements, @@ -41,7 +40,7 @@ setuptools.setup( ], entry_points={ 'distutils.commands': [ - 'clean = setupext.janitor:CleanCommand', + 'clean = setupext_janitor.janitor:CleanCommand', ], }, cmdclass={ diff --git a/setupext/__init__.py b/setupext/__init__.py deleted file mode 100644 index de40ea7..0000000 --- a/setupext/__init__.py +++ /dev/null @@ -1,1 +0,0 @@ -__import__('pkg_resources').declare_namespace(__name__) diff --git a/setupext_janitor/__init__.py b/setupext_janitor/__init__.py new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/setupext_janitor/__init__.py @@ -0,0 +1,1 @@ +
dave-shawley/setupext-janitor
801d4e51b10c8880be16c99fd6316051808141fa
diff --git a/setupext/janitor.py b/setupext_janitor/janitor.py similarity index 100% rename from setupext/janitor.py rename to setupext_janitor/janitor.py diff --git a/tests.py b/tests.py index 39af958..a1d6b72 100644 --- a/tests.py +++ b/tests.py @@ -12,7 +12,7 @@ if sys.version_info >= (2, 7): else: # noinspection PyPackageRequirements,PyUnresolvedReferences import unittest2 as unittest -from setupext import janitor +from setupext_janitor import janitor def run_setup(*command_line):
Breaks matplotlib's setup.py It appears that matplotlib has a setupext.py file, for whatever reason, and that breaks if setupext-janitor is installed. Is the setupext nspackage thing really necessary?
0.0
801d4e51b10c8880be16c99fd6316051808141fa
[ "tests.py::DistDirectoryCleanupTests::test_that_multiple_dist_directories_with_be_removed", "tests.py::DistDirectoryCleanupTests::test_that_dist_directory_is_removed_for_bdist_dumb", "tests.py::DistDirectoryCleanupTests::test_that_directories_are_not_removed_without_parameter", "tests.py::DistDirectoryCleanupTests::test_that_dist_directory_is_removed_for_sdist", "tests.py::DistDirectoryCleanupTests::test_that_directories_are_not_removed_in_dry_run_mode" ]
[ "tests.py::CommandOptionTests::test_that_distutils_options_are_present", "tests.py::CommandOptionTests::test_that_janitor_user_options_are_not_clean_options", "tests.py::CommandOptionTests::test_that_janitor_defines_dist_command", "tests.py::RemoveAllTests::test_that_envdir_is_removed", "tests.py::RemoveAllTests::test_that_distdir_is_removed", "tests.py::RemoveAllTests::test_that_eggdir_is_removed", "tests.py::RemoveAllTests::test_that_pycache_is_removed", "tests.py::EggDirectoryCleanupTests::test_that_directories_are_not_removed_in_dry_run_mode", "tests.py::EggDirectoryCleanupTests::test_that_egg_directories_are_removed", "tests.py::EggDirectoryCleanupTests::test_that_egg_info_directories_are_removed", "tests.py::PycacheCleanupTests::test_that_janitor_does_not_fail_when_cache_parent_is_removed" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_removed_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2015-11-16 22:59:02+00:00
bsd-3-clause
1,850
davidchall__topas2numpy-13
diff --git a/topas2numpy/binned.py b/topas2numpy/binned.py index dac1dfe..2b65a6d 100644 --- a/topas2numpy/binned.py +++ b/topas2numpy/binned.py @@ -47,15 +47,15 @@ class BinnedResult(object): dimensions: list of BinnedDimension objects data: dict of scored data """ - def __init__(self, filepath): + def __init__(self, filepath, dtype=float): self.path = filepath _, ext = os.path.splitext(self.path) if ext == '.bin': - self._read_binary() + self._read_binary(dtype) elif ext == '.csv': - self._read_ascii() + self._read_ascii(dtype) - def _read_binary(self): + def _read_binary(self, dtype): """Reads data and metadata from binary format.""" # NOTE: binary files store binned data using Fortran-like ordering. # Dimensions are iterated like z, y, x (so x changes fastest) @@ -64,7 +64,7 @@ class BinnedResult(object): with open(header_path) as f_header: self._read_header(f_header.read()) - data = np.fromfile(self.path) + data = np.fromfile(self.path, dtype=dtype) # separate data by statistic data = data.reshape((len(self.statistics), -1), order='F') @@ -76,7 +76,7 @@ class BinnedResult(object): self.data = data - def _read_ascii(self): + def _read_ascii(self, dtype): """Reads data and metadata from ASCII format.""" # NOTE: ascii files store binned data using C-like ordering. # Dimensions are iterated like x, y, z (so z changes fastest) @@ -88,7 +88,7 @@ class BinnedResult(object): header_str += line self._read_header(header_str) - data = np.loadtxt(self.path, delimiter=',', unpack=True, ndmin=1) + data = np.loadtxt(self.path, dtype=dtype, delimiter=',', unpack=True, ndmin=1) # separate data by statistic (neglecting bin columns when necessary) n_dim = len(self.dimensions)
davidchall/topas2numpy
f20177d6930798e317033ab0e66117bb65ee08d6
diff --git a/tests/test_binned.py b/tests/test_binned.py index 19e68b3..04e7a37 100644 --- a/tests/test_binned.py +++ b/tests/test_binned.py @@ -12,6 +12,9 @@ Tests for TOPAS binned reading. import unittest import os.path +# third-party imports +import numpy as np + # project imports from topas2numpy import BinnedResult @@ -55,6 +58,7 @@ class TestAscii1D(unittest.TestCase): assert self.result.statistics[0] == 'Sum' assert len(self.result.data) == 1 data = self.result.data['Sum'] + assert data.dtype == np.float64 assert data.shape[0] == self.result.dimensions[0].n_bins assert data.shape[1] == self.result.dimensions[1].n_bins assert data.shape[2] == self.result.dimensions[2].n_bins @@ -62,7 +66,7 @@ class TestAscii1D(unittest.TestCase): class TestAscii2D(unittest.TestCase): def setUp(self): - self.result = BinnedResult(ascii_2d_path) + self.result = BinnedResult(ascii_2d_path, dtype=np.uint32) def test_quantity(self): assert self.result.quantity == 'SurfaceTrackCount' @@ -88,6 +92,7 @@ class TestAscii2D(unittest.TestCase): assert self.result.statistics[0] == 'Sum' assert len(self.result.data) == 1 data = self.result.data['Sum'] + assert data.dtype == np.uint32 assert data.shape[0] == self.result.dimensions[0].n_bins assert data.shape[1] == self.result.dimensions[1].n_bins assert data.shape[2] == self.result.dimensions[2].n_bins
Detect best NumPy dtype (use unsigned int for SurfaceTrackCount) When the TOPAS scorer mode is set to 'SurfaceTrackCount' then the result is an integer. It would be best if the numpy dtype of the loaded data was set to an unsigned integer type in this case. It seems this library loads such arrrays as 'float64' type which uses only 53 of the 64 bits to store the mantissa, meaning 11/64 bits are wasted in the case of 'SurfaceTrackCount', which unecessarily increases filesize. It's also unexpected to receive a NumPy array of type 'float64' when the data consists of unsigned integers so this may have a usability impact also. Is it possible to change this library so that it bases the data type whether the scorer is 'SurfaceTrackCount' or something else?
0.0
f20177d6930798e317033ab0e66117bb65ee08d6
[ "tests/test_binned.py::TestAscii2D::test_data", "tests/test_binned.py::TestAscii2D::test_dimensions", "tests/test_binned.py::TestAscii2D::test_quantity" ]
[ "tests/test_binned.py::TestAscii1D::test_data", "tests/test_binned.py::TestAscii1D::test_dimensions", "tests/test_binned.py::TestAscii1D::test_quantity", "tests/test_binned.py::TestBinary1D::test_data", "tests/test_binned.py::TestBinary1D::test_dimensions", "tests/test_binned.py::TestBinary1D::test_quantity" ]
{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2022-06-22 05:16:22+00:00
mit
1,851
daviddrysdale__python-phonenumbers-182
diff --git a/python/phonenumbers/phonenumberutil.py b/python/phonenumbers/phonenumberutil.py index 8ff04afd..0948934d 100644 --- a/python/phonenumbers/phonenumberutil.py +++ b/python/phonenumbers/phonenumberutil.py @@ -3223,6 +3223,9 @@ class NumberParseException(UnicodeMixin, Exception): self.error_type = error_type self._msg = msg + def __reduce__(self): + return (type(self), (self.error_type, self._msg)) + def __unicode__(self): return unicod("(%s) %s") % (self.error_type, self._msg)
daviddrysdale/python-phonenumbers
5bcfeb70b6ae8d4ebe525999910f3180f6870807
diff --git a/python/tests/phonenumberutiltest.py b/python/tests/phonenumberutiltest.py index 592fec80..c9d2cedf 100755 --- a/python/tests/phonenumberutiltest.py +++ b/python/tests/phonenumberutiltest.py @@ -17,6 +17,7 @@ # See the License for the specific language governing permissions and # limitations under the License. import sys +import pickle import phonenumbers from phonenumbers import PhoneNumber, PhoneMetadata @@ -26,6 +27,7 @@ from phonenumbers import ValidationResult, NumberFormat, CountryCodeSource from phonenumbers import region_code_for_country_code # Access internal functions of phonenumberutil.py from phonenumbers import phonenumberutil, shortnumberinfo +from phonenumbers.phonenumberutil import NumberParseException from phonenumbers.util import u, to_long from .testmetadatatest import TestMetadataTestCase @@ -3165,6 +3167,12 @@ class PhoneNumberUtilTest(TestMetadataTestCase): 'register': True}) self.assertTrue(phonenumbers.example_number_for_type('XY', PhoneNumberType.PERSONAL_NUMBER) is None) + def testPickledException(self): + err = NumberParseException(NumberParseException.TOO_SHORT_AFTER_IDD, 'hello world') + pickled = pickle.dumps(err) + recovered = pickle.loads(pickled) + self.assertEqual("%r" % err, "%r" % recovered) + def testCoverage(self): # Python version extra tests self.assertTrue(phonenumberutil._region_code_for_number_from_list(GB_NUMBER, ("XX",)) is None)
NumberParseException is not picklable Hi, I noticed that `NumberParseException` is not picklable. It deviates from the `__init__` signature of `Exception`, which itself implements `__reduce__` s.t. only the `msg` argument is pickled. This program: ```python import pickle from phonenumbers.phonenumberutil import NumberParseException error = NumberParseException(NumberParseException.TOO_SHORT_AFTER_IDD, 'hello world') s = pickle.dumps(error) again = pickle.loads(s) ``` produces the output: ``` Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: __init__() missing 1 required positional argument: 'msg' ``` Adding a `__reduce__` method to `NumberParseException` seems to fix it: ```python def __reduce__(self): return (type(self), (self.error_type, self._msg)) ```
0.0
5bcfeb70b6ae8d4ebe525999910f3180f6870807
[ "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testPickledException" ]
[ "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testCanBeInternationallyDialled", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testConvertAlphaCharactersInNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testCountryWithNoNumberDesc", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testCoverage", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testExtractPossibleNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFailedParseOnInvalidNumbers", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatARNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatAUNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatBSNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatByPattern", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatDENumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatE164Number", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatGBNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatITNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatInOriginalFormat", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatMXNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatNumberForMobileDialing", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatNumberWithExtension", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatOutOfCountryCallingNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatOutOfCountryKeepingAlphaChars", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatOutOfCountryWithInvalidRegion", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatOutOfCountryWithPreferredIntlPrefix", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatUSNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatWithCarrierCode", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFormatWithPreferredCarrierCode", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testFrozenPhoneNumberImmutable", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetCountryCodeForRegion", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetCountryMobileToken", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetExampleNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetExampleNumberForNonGeoEntity", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetExampleNumberWithoutRegion", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetInstanceLoadARMetadata", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetInstanceLoadDEMetadata", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetInstanceLoadInternationalTollFreeMetadata", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetInstanceLoadUSMetadata", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetInvalidExampleNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetLengthOfGeographicalAreaCode", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetLengthOfNationalDestinationCode", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetNationalDiallingPrefixForRegion", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetNationalSignificantNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetNationalSignificantNumber_ManyLeadingZeros", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetRegionCodeForCountryCode", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetRegionCodeForNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetRegionCodesForCountryCode", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetSupportedCallingCodes", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetSupportedGlobalNetworkCallingCodes", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetSupportedTypesForNonGeoEntity", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testGetSupportedTypesForRegion", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsAlphaNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsFixedLine", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsFixedLineAndMobile", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsMobile", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsMobileNumberPortableRegion", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNANPACountry", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNotPossibleNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNotValidNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNumberGeographical", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNumberMatchAcceptsProtoDefaultsAsMatch", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNumberMatchIgnoresSomeFields", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNumberMatchMatches", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNumberMatchMatchesDiffLeadingZerosIfItalianLeadingZeroFalse", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNumberMatchNonMatches", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNumberMatchNsnMatches", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNumberMatchShortMatchIfDiffNumLeadingZeros", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsNumberMatchShortNsnMatches", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPersonalNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumberForTypeWithReason_DataMissingForSizeReasons", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumberForTypeWithReason_DifferentTypeLengths", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumberForTypeWithReason_FixedLineOrMobile", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumberForTypeWithReason_LocalOnly", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumberForTypeWithReason_NumberTypeNotSupportedForRegion", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumberForType_DataMissingForSizeReasons", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumberForType_DifferentTypeLengths", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumberForType_LocalOnly", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumberForType_NumberTypeNotSupportedForRegion", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPossibleNumberWithReason", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsPremiumRate", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsSharedCost", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsTollFree", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsUnknown", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsValidForRegion", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsValidNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsViablePhoneNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsViablePhoneNumberNonAscii", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testIsVoip", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testMaybeExtractCountryCode", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testMaybeStripInternationalPrefix", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testMaybeStripNationalPrefix", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testMetadataAsString", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testMetadataEquality", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testMetadataEval", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testMetadataImmutable", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testNormaliseOtherDigits", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testNormaliseRemovePunctuation", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testNormaliseReplaceAlphaCharacters", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testNormaliseStripAlphaCharacters", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testNormaliseStripNonDiallableCharacters", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseAndKeepRaw", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseExtensions", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseHandlesLongExtensionsWithAutoDiallingLabels", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseHandlesLongExtensionsWithExplicitLabels", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseHandlesShortExtensionsWhenNotSureOfLabel", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseHandlesShortExtensionsWithAmbiguousChar", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseItalianLeadingZeros", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseMaliciousInput", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseNationalNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseNationalNumberArgentina", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseNonAscii", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseNumberTooShortIfNationalPrefixStripped", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseNumberWithAlphaCharacters", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseNumbersMexico", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseNumbersWithPlusWithNoRegion", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseWithInternationalPrefixes", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseWithLeadingZero", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testParseWithXInNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testSupportedRegions", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testTruncateTooLongNumber", "python/tests/phonenumberutiltest.py::PhoneNumberUtilTest::testUnknownCountryCallingCode" ]
{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }
2020-12-15 19:03:52+00:00
apache-2.0
1,852
davidesarra__jupyter_spaces-15
diff --git a/README.md b/README.md index 398cbb9..222a688 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ Reloading the extension will remove all spaces. ```python %%space <space-name> alpha = 0.50 -print(alpha) +alpha ``` When you execute a cell within a space, all references are firstly searched in @@ -51,33 +51,6 @@ execution equivalent to not using such keyword. Mutable objects in the user namespace can be altered (e.g. appending an item to a list). -#### Console output - -Conversely to the standard usage of the Python console, you need to print -objects explicitly (e.g. by using `print`). - -- No output to console - ```python - %%space <space-name> - 100 - ``` -- Output to console - ```python - %%space <space-name> - print(100) - ``` - -If you want IPython to use more advanced representations, you can do so via -IPython's display library (e.g. display a Pandas dataframe as a HTML table). - -```python -%%space <space-name> -from IPython.display import display -from pandas import DataFrame -dataframe = DataFrame(data=[[1, 2]]) -display(dataframe) -``` - ### Remove a space ```python diff --git a/jupyter_spaces/space.py b/jupyter_spaces/space.py index 476a7a0..7c3b89e 100644 --- a/jupyter_spaces/space.py +++ b/jupyter_spaces/space.py @@ -1,3 +1,6 @@ +import ast +import sys + from jupyter_spaces.errors import RegistryError @@ -101,7 +104,16 @@ class Space: Args: source (str): Source code. """ - exec(source, self._execution_namespace) + tree = ast.parse(source=source) + + interactive_tree = ast.Interactive(body=tree.body) + if sys.version_info > (3, 8): + interactive_tree.type_ignores = tree.type_ignores + + compiled_interactive_tree = compile( + source=interactive_tree, filename="<string>", mode="single" + ) + exec(compiled_interactive_tree, self._execution_namespace) class ExecutionNamespace(dict):
davidesarra/jupyter_spaces
035e984dab3d6b29e46db982619a376c3c293b6a
diff --git a/tests/test_magics.py b/tests/test_magics.py index e24cc1b..22da064 100644 --- a/tests/test_magics.py +++ b/tests/test_magics.py @@ -152,6 +152,11 @@ def test_get_spaces_reflects_extension_reload(ip): assert not ip.user_global_ns["spaces"] +def test_space_outputs_to_console(ip, capsys): + ip.run_cell_magic(magic_name="space", line="tomato", cell="100") + assert capsys.readouterr().out == "100\n" + + def test_space_can_print_to_console(ip): with capture_output() as captured: ip.run_cell_magic(magic_name="space", line="tomato", cell="print(100)")
Automatic console output It would be great if space cells would automatically print their return result similar to a normal cell. Having to use the print statement for output is cumbersome.
0.0
035e984dab3d6b29e46db982619a376c3c293b6a
[ "tests/test_magics.py::test_space_outputs_to_console" ]
[ "tests/test_magics.py::test_space_can_access_user_namespace_references", "tests/test_magics.py::test_space_references_prioritized_over_user_namespace_references", "tests/test_magics.py::test_space_cannot_alter_user_namespace_immutable_references", "tests/test_magics.py::test_space_can_alter_user_namespace_mutable_references", "tests/test_magics.py::test_space_cannot_alter_user_namespace_references_using_global", "tests/test_magics.py::test_space_cannot_remove_user_namespace_references", "tests/test_magics.py::test_space_cannot_remove_user_namespace_references_using_global", "tests/test_magics.py::test_space_cannot_add_user_namespace_references", "tests/test_magics.py::test_space_cannot_add_user_namespace_references_using_global", "tests/test_magics.py::test_space_reference_assignments_persist_in_new_magic_call", "tests/test_magics.py::test_space_reference_deletions_persist_in_new_magic_call", "tests/test_magics.py::test_space_references_assignments_are_confined_in_one_space_only", "tests/test_magics.py::test_space_references_deletions_are_confined_in_one_space_only", "tests/test_magics.py::test_space_can_execute_newly_defined_lambda_functions", "tests/test_magics.py::test_space_can_execute_newly_defined_functions", "tests/test_magics.py::test_space_can_execute_top_level_non_closure_functions", "tests/test_magics.py::test_get_spaces_can_access_space_references", "tests/test_magics.py::test_get_spaces_can_alter_space_references", "tests/test_magics.py::test_get_spaces_can_remove_space_references", "tests/test_magics.py::test_get_spaces_reflects_space_references_changes", "tests/test_magics.py::test_get_spaces_reflects_space_removal", "tests/test_magics.py::test_get_spaces_reflects_extension_reload", "tests/test_magics.py::test_space_can_print_to_console" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2020-11-22 00:38:28+00:00
mit
1,853
dbcli__athenacli-42
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 0000000..4f20546 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,7 @@ +## Description +<!--- Describe your changes in detail. --> + +## Checklist +<!--- We appreciate your help and want to give you credit. Please take a moment to put an `x` in the boxes below as you complete them. --> +- [ ] I've added this contribution to the `changelog.md`. +- [ ] I've added my name to the `AUTHORS` file (or it's already there). diff --git a/AUTHORS.rst b/AUTHORS.rst index 93b5168..58ee8a4 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -14,6 +14,7 @@ Contributors: * Joe Block * Jash Gala * Hourann + * Paul Gross Creator: -------- diff --git a/athenacli/packages/completion_engine.py b/athenacli/packages/completion_engine.py index d4e7281..86b9abb 100644 --- a/athenacli/packages/completion_engine.py +++ b/athenacli/packages/completion_engine.py @@ -290,7 +290,7 @@ def suggest_based_on_last_token(token, text_before_cursor, full_text, identifier if parent: # "ON parent.<suggestion>" # parent can be either a schema name or table alias - tables = tuple(t for t in tables if identifies(parent, t)) + tables = tuple(t for t in tables if identifies(parent, *t)) return ( Column(tables=tables), Table(schema=parent), diff --git a/changelog.md b/changelog.md index b0eb065..fe2b505 100644 --- a/changelog.md +++ b/changelog.md @@ -1,6 +1,10 @@ (Unreleased; add upcoming change notes here) ============================================== +Bugfix +---------- +* Fix bug when completing `ON parent.` clauses. (Thanks @pgr0ss) + 1.1.2 ======== diff --git a/docs/develop.rst b/docs/develop.rst index 6c5d66d..084a312 100644 --- a/docs/develop.rst +++ b/docs/develop.rst @@ -20,12 +20,22 @@ The installation instructions in the README file are intended for users of athen It is highly recommended to use virtualenv for development. If you don't know what a virtualenv is, `this guide <https://docs.python-guide.org/dev/virtualenvs/#virtual-environments>`_ will help you get started. -Create a virtualenv (let's call it athenacli-dev). Activate it: +Create a virtualenv (let's call it athenacli-dev): + +.. code-block:: bash + + $ virtualenv athenacli-dev + +Activate it: + +.. code-block:: bash $ source ./athenacli-dev/bin/activate + Once the virtualenv is activated, cd into the local clone of athenacli folder and install athenacli using pip as follows: .. code-block:: bash + $ pip install -e . This will install the necessary dependencies as well as install athenacli from the working folder into a virtualenv. Athenacli is installed in an editable way, so any changes made to the code is immediately available in the installed version of athenacli. This makes it easy to change something in the code, launch athenacli and check the effects of your change. @@ -38,6 +48,7 @@ Currently we don't have enough tests for athenacli, because we haven't found an First, install the requirements for testing: .. code-block:: bash + $ pip install -r requirements-dev.txt After that, tests can be run with:
dbcli/athenacli
f413a24662cca6923b13563dedb7565e1e2b31a9
diff --git a/test/test_completion_engine.py b/test/test_completion_engine.py index 587fa6b..3a3c24a 100644 --- a/test/test_completion_engine.py +++ b/test/test_completion_engine.py @@ -2,7 +2,7 @@ import os import pytest from athenacli.packages.completion_engine import ( - suggest_type, Column, Function, Alias, Keyword + suggest_type, Column, Function, Alias, Keyword, Table, View ) @@ -28,6 +28,15 @@ def test_select_suggests_cols_with_qualified_table_scope(): Alias(aliases=['tabl']), Keyword(last_token='SELECT')) +def test_join_suggests_cols_with_qualified_table_scope(): + expression = 'SELECT * FROM tabl a JOIN tabl b on a.' + suggestions = suggest_type(expression, expression) + + assert suggestions == ( + Column(tables=((None, 'tabl', 'a'),), drop_unique=None), + Table(schema='a'), + View(schema='a'), + Function(schema='a', filter=None)) @pytest.mark.parametrize('expression', [ 'SELECT * FROM tabl WHERE ',
Error when typing a query I started writing this query: ``` SELECT d.* FROM doodads d JOIN trinkets t on d. ``` ## `JOIN` doesn't appear `JOIN` did not auto-complete as an option (I only saw `JSON`) ## Unhandled Exception When I type the `.` at the end (I'm trying to join on `d.trinket_id = doodad.id`) I get the following output: ``` Unhandled exception in event loop: File "/home/admin/.local/lib/python3.7/site-packages/prompt_toolkit/eventloop/coroutine.py", line 92, in step_next new_f = coroutine.throw(exc) File "/home/admin/.local/lib/python3.7/site-packages/prompt_toolkit/buffer.py", line 1654, in new_coroutine yield From(coroutine(*a, **kw)) File "/home/admin/.local/lib/python3.7/site-packages/prompt_toolkit/eventloop/coroutine.py", line 92, in step_next new_f = coroutine.throw(exc) File "/home/admin/.local/lib/python3.7/site-packages/prompt_toolkit/buffer.py", line 1506, in async_completer cancel=lambda: not proceed())) File "/home/admin/.local/lib/python3.7/site-packages/prompt_toolkit/eventloop/coroutine.py", line 88, in step_next new_f = coroutine.send(None) File "/home/admin/.local/lib/python3.7/site-packages/prompt_toolkit/eventloop/async_generator.py", line 117, in consume_async_generator item = iterator.send(send) File "/home/admin/.local/lib/python3.7/site-packages/prompt_toolkit/completion/base.py", line 176, in get_completions_async for item in self.get_completions(document, complete_event): File "/home/admin/.local/lib/python3.7/site-packages/athenacli/completer.py", line 210, in get_completions suggestions = suggest_type(document.text, document.text_before_cursor) File "/home/admin/.local/lib/python3.7/site-packages/athenacli/packages/completion_engine.py", line 121, in suggest_type full_text, identifier) File "/home/admin/.local/lib/python3.7/site-packages/athenacli/packages/completion_engine.py", line 293, in suggest_based_on_last_token tables = tuple(t for t in tables if identifies(parent, t)) File "/home/admin/.local/lib/python3.7/site-packages/athenacli/packages/completion_engine.py", line 293, in <genexpr> tables = tuple(t for t in tables if identifies(parent, t)) Exception identifies() missing 2 required positional arguments: 'table' and 'alias' ``` I also tried this without the table aliases, e.g.: ``` SELECT doodads.* FROM doodads JOIN trinkets on doodads. ``` and got the same "unhandled exception" error when typing the `.` at the end.
0.0
f413a24662cca6923b13563dedb7565e1e2b31a9
[ "test/test_completion_engine.py::test_join_suggests_cols_with_qualified_table_scope" ]
[ "test/test_completion_engine.py::test_select_suggests_cols_with_visible_table_scope", "test/test_completion_engine.py::test_select_suggests_cols_with_qualified_table_scope", "test/test_completion_engine.py::test_where_suggests_columns_functions[SELECT" ]
{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2020-02-14 21:42:59+00:00
bsd-3-clause
1,854
dbcli__athenacli-50
diff --git a/athenacli/packages/format_utils.py b/athenacli/packages/format_utils.py new file mode 100644 index 0000000..8450913 --- /dev/null +++ b/athenacli/packages/format_utils.py @@ -0,0 +1,34 @@ +# -*- coding: utf-8 -*- + + +def format_status(rows_length=None, cursor=None): + return rows_status(rows_length) + statistics(cursor) + +def rows_status(rows_length): + if rows_length: + return '%d row%s in set' % (rows_length, '' if rows_length == 1 else 's') + else: + return 'Query OK' + +def statistics(cursor): + if cursor: + # Most regions are $5 per TB: https://aws.amazon.com/athena/pricing/ + approx_cost = cursor.data_scanned_in_bytes / (1024 ** 4) * 5 + + return '\nExecution time: %d ms, Data scanned: %s, Approximate cost: $%.2f' % ( + cursor.execution_time_in_millis, + humanize_size(cursor.data_scanned_in_bytes), + approx_cost) + else: + return '' + +def humanize_size(num_bytes): + suffixes = ['B', 'KB', 'MB', 'GB', 'TB'] + + suffix_index = 0 + while num_bytes >= 1024 and suffix_index < len(suffixes) - 1: + num_bytes /= 1024.0 + suffix_index += 1 + + num = ('%.2f' % num_bytes).rstrip('0').rstrip('.') + return '%s %s' % (num, suffixes[suffix_index]) diff --git a/athenacli/sqlexecute.py b/athenacli/sqlexecute.py index 3a0d8c5..d560ecd 100644 --- a/athenacli/sqlexecute.py +++ b/athenacli/sqlexecute.py @@ -5,6 +5,7 @@ import sqlparse import pyathena from athenacli.packages import special +from athenacli.packages.format_utils import format_status logger = logging.getLogger(__name__) @@ -92,11 +93,11 @@ class SQLExecute(object): if cursor.description is not None: headers = [x[0] for x in cursor.description] rows = cursor.fetchall() - status = '%d row%s in set' % (len(rows), '' if len(rows) == 1 else 's') + status = format_status(rows_length=len(rows), cursor=cursor) else: logger.debug('No rows in result.') rows = None - status = 'Query OK' + status = format_status(rows_length=None, cursor=cursor) return (title, rows, headers, status) def tables(self): diff --git a/changelog.md b/changelog.md index 22d8273..cafd121 100644 --- a/changelog.md +++ b/changelog.md @@ -1,6 +1,13 @@ (Unreleased; add upcoming change notes here) ============================================== +1.3.0 +======== + +Features +---------- +* Show query execution statistics, such as the amount of data scanned and the approximate cost. (Thanks: @pgr0ss) + 1.2.0 ========
dbcli/athenacli
c0e6869d7c023c3c2a2bda7f40f09286f5d0c0c0
diff --git a/test/test_format_utils.py b/test/test_format_utils.py new file mode 100644 index 0000000..abe8d75 --- /dev/null +++ b/test/test_format_utils.py @@ -0,0 +1,26 @@ +# -*- coding: utf-8 -*- + + +from collections import namedtuple +from athenacli.packages.format_utils import format_status, humanize_size + + +def test_format_status_plural(): + assert format_status(rows_length=1) == "1 row in set" + assert format_status(rows_length=2) == "2 rows in set" + +def test_format_status_no_results(): + assert format_status(rows_length=None) == "Query OK" + +def test_format_status_with_stats(): + FakeCursor = namedtuple("FakeCursor", ["execution_time_in_millis", "data_scanned_in_bytes"]) + + assert format_status(rows_length=1, cursor=FakeCursor(10, 12345678900)) == "1 row in set\nExecution time: 10 ms, Data scanned: 11.5 GB, Approximate cost: $0.06" + assert format_status(rows_length=2, cursor=FakeCursor(1000, 1234)) == "2 rows in set\nExecution time: 1000 ms, Data scanned: 1.21 KB, Approximate cost: $0.00" + +def test_humanize_size(): + assert humanize_size(20) == "20 B" + assert humanize_size(2000) == "1.95 KB" + assert humanize_size(200000) == "195.31 KB" + assert humanize_size(20000000) == "19.07 MB" + assert humanize_size(200000000000) == "186.26 GB"
Feature request: output cost and size of query Something like: submission_date = stats['QueryExecution']['Status']['SubmissionDateTime'] completion_date = stats['QueryExecution']['Status']['CompletionDateTime'] execution_time = stats['QueryExecution']['Statistics']['EngineExecutionTimeInMillis'] data_scanned = stats['QueryExecution']['Statistics']['DataScannedInBytes'] query_cost = data_scanned / 1000000000000.0 * 5.0 print('Time: {}, CPU Time: {}ms total, Data Scanned: {}, Cost: ${:,.2f}\n'.format( str(completion_date - submission_date).split('.')[0], execution_time, human_readable(data_scanned), query_cost )) from https://github.com/guardian/athena-cli/blob/0d5cc98a1cac21094077ed29cf168686ca61f10d/athena_cli.py#L217-L228 (Currently we only print `Time`.)
0.0
c0e6869d7c023c3c2a2bda7f40f09286f5d0c0c0
[ "test/test_format_utils.py::test_format_status_plural", "test/test_format_utils.py::test_format_status_no_results", "test/test_format_utils.py::test_format_status_with_stats", "test/test_format_utils.py::test_humanize_size" ]
[]
{ "failed_lite_validators": [ "has_hyperlinks", "has_added_files", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2020-04-18 00:03:20+00:00
bsd-3-clause
1,855
dbcli__litecli-113
diff --git a/CHANGELOG.md b/CHANGELOG.md index b8c8122..0ccb53a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,5 @@ ## Unreleased - TBD -<!-- add upcoming change notes here --> - ### Features - Add verbose feature to `favorite_query` command. (Thanks: [Zhaolong Zhu]) @@ -12,6 +10,7 @@ ### Bug Fixes - Fix compatibility with sqlparse >= 0.4.0. (Thanks: [chocolateboy]) +- Fix invalid utf-8 exception. (Thanks: [Amjith]) ## 1.4.1 - 2020-07-27 diff --git a/litecli/sqlexecute.py b/litecli/sqlexecute.py index 7ef103c..93acd91 100644 --- a/litecli/sqlexecute.py +++ b/litecli/sqlexecute.py @@ -17,6 +17,13 @@ _logger = logging.getLogger(__name__) # }) +def utf8_resilient_decoder(s): + try: + return s.decode("utf-8") + except UnicodeDecodeError: + return s.decode("latin-1") + + class SQLExecute(object): databases_query = """ @@ -61,6 +68,7 @@ class SQLExecute(object): raise Exception("Path does not exist: {}".format(db_dir_name)) conn = sqlite3.connect(database=db_name, isolation_level=None) + conn.text_factory = utf8_resilient_decoder if self.conn: self.conn.close()
dbcli/litecli
a1a01c11d6154b6f841b81fbdeb6b8b887b697d3
diff --git a/tests/test_sqlexecute.py b/tests/test_sqlexecute.py index 03e7f19..0ddfb8f 100644 --- a/tests/test_sqlexecute.py +++ b/tests/test_sqlexecute.py @@ -101,6 +101,17 @@ def test_unicode_support_in_output(executor): assert_result_equal(results, headers=["t"], rows=[(u"é",)]) +@dbtest +def test_invalid_unicode_values_dont_choke(executor): + run(executor, "create table unicodechars(t text)") + # \xc3 is not a valid utf-8 char. But we can insert it into the database + # which can break querying if not handled correctly. + run(executor, u"insert into unicodechars (t) values (cast(x'c3' as text))") + + results = run(executor, u"select * from unicodechars") + assert_result_equal(results, headers=["t"], rows=[(u"Ã",)]) + + @dbtest def test_multiple_queries_same_line(executor): results = run(executor, "select 'foo'; select 'bar'") @@ -199,11 +210,7 @@ def test_verbose_feature_of_favorite_query(executor): results = run(executor, "\\f sh_param 1") assert_result_equal( - results, - title=None, - headers=["a", "id"], - rows=[("abc", 1)], - auto_status=False, + results, title=None, headers=["a", "id"], rows=[("abc", 1)], auto_status=False, ) results = run(executor, "\\f+ sh_param 1")
TabularOutputFormatter chokes on values that can't be converted to UTF-8 if it's a text column I don't know how to solve this. If there is a single record with a non-convertible column it won't print anything. `Could not decode to UTF-8 column 'verifier' with text '`'���U'` sqlite3 prints ``` 2bho15FMrSQhKAYnjBqRQ1x4LS3zcHANsRjKMJyiSwT9|GnyZktv2SaCehfNCGjoYdAgAirxpCjvBCUXH6MiEHEH7 `'ŜU|`'ŜU ``` Seeing this was actually helpful because it notified me that I had garbage data, but I still would've thought the other rows would print.
0.0
a1a01c11d6154b6f841b81fbdeb6b8b887b697d3
[ "tests/test_sqlexecute.py::test_invalid_unicode_values_dont_choke" ]
[ "tests/test_sqlexecute.py::test_conn", "tests/test_sqlexecute.py::test_bools", "tests/test_sqlexecute.py::test_binary", "tests/test_sqlexecute.py::test_database_list", "tests/test_sqlexecute.py::test_invalid_syntax", "tests/test_sqlexecute.py::test_invalid_column_name", "tests/test_sqlexecute.py::test_unicode_support_in_output", "tests/test_sqlexecute.py::test_multiple_queries_same_line", "tests/test_sqlexecute.py::test_multiple_queries_same_line_syntaxerror", "tests/test_sqlexecute.py::test_favorite_query", "tests/test_sqlexecute.py::test_bind_parameterized_favorite_query", "tests/test_sqlexecute.py::test_verbose_feature_of_favorite_query", "tests/test_sqlexecute.py::test_shell_parameterized_favorite_query", "tests/test_sqlexecute.py::test_favorite_query_multiple_statement", "tests/test_sqlexecute.py::test_favorite_query_expanded_output", "tests/test_sqlexecute.py::test_special_command", "tests/test_sqlexecute.py::test_cd_command_without_a_folder_name", "tests/test_sqlexecute.py::test_system_command_not_found", "tests/test_sqlexecute.py::test_system_command_output", "tests/test_sqlexecute.py::test_cd_command_current_dir", "tests/test_sqlexecute.py::test_unicode_support", "tests/test_sqlexecute.py::test_timestamp_null", "tests/test_sqlexecute.py::test_datetime_null", "tests/test_sqlexecute.py::test_date_null", "tests/test_sqlexecute.py::test_time_null" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2021-03-14 20:14:14+00:00
bsd-3-clause
1,856
dbcli__mssql-cli-396
diff --git a/build.py b/build.py index d8c7ce3..8a82eca 100644 --- a/build.py +++ b/build.py @@ -173,6 +173,7 @@ def get_active_test_filepaths(): 'tests/test_config.py ' 'tests/test_naive_completion.py ' 'tests/test_main.py ' + 'tests/test_multiline.py ' 'tests/test_fuzzy_completion.py ' 'tests/test_rowlimit.py ' 'tests/test_sqlcompletion.py ' diff --git a/mssqlcli/mssqlbuffer.py b/mssqlcli/mssqlbuffer.py index 581010c..d0fdced 100644 --- a/mssqlcli/mssqlbuffer.py +++ b/mssqlcli/mssqlbuffer.py @@ -1,5 +1,6 @@ from __future__ import unicode_literals - +import re +import sqlparse from prompt_toolkit.enums import DEFAULT_BUFFER from prompt_toolkit.filters import Condition from prompt_toolkit.application import get_app @@ -21,10 +22,31 @@ def mssql_is_multiline(mssql_cli): def _is_complete(sql): - # A complete command is an sql statement that ends with a semicolon, unless + # A complete command is an sql statement that ends with a 'GO', unless # there's an open quote surrounding it, as is common when writing a # CREATE FUNCTION command - return sql.endswith(';') and not is_open_quote(sql) + if sql is not None and sql != "": + # remove comments + sql = sqlparse.format(sql, strip_comments=True) + + # check for open comments + # remove all closed quotes to isolate instances of open comments + sql_no_quotes = re.sub(r'".*?"|\'.*?\'', '', sql) + is_open_comment = len(re.findall(r'\/\*', sql_no_quotes)) > 0 + + # check that 'go' is only token on newline + lines = sql.split('\n') + lastline = lines[len(lines) - 1].lower().strip() + is_valid_go_on_lastline = lastline == 'go' + + # check that 'go' is on last line, not in open quotes, and there's no open + # comment with closed comments and quotes removed. + # NOTE: this method fails when GO follows a closing '*/' block comment on the same line, + # we've taken a dependency with sqlparse + # (https://github.com/andialbrecht/sqlparse/issues/484) + return not is_open_quote(sql) and not is_open_comment and is_valid_go_on_lastline + + return False def _multiline_exception(text): diff --git a/mssqlcli/mssqlcliclient.py b/mssqlcli/mssqlcliclient.py index d7019cb..f4e26b0 100644 --- a/mssqlcli/mssqlcliclient.py +++ b/mssqlcli/mssqlcliclient.py @@ -230,7 +230,8 @@ class MssqlCliClient: query_has_exception = query_response.exception_message query_has_error_messages = query_messages[0].is_error if query_messages else False query_has_batch_error = query_response.batch_summaries[0].has_error \ - if hasattr(query_response, 'batch_summaries') else False + if hasattr(query_response, 'batch_summaries') \ + and len(query_response.batch_summaries) > 0 else False query_failed = query_has_exception or query_has_batch_error or query_has_error_messages @@ -277,7 +278,8 @@ class MssqlCliClient: @staticmethod def _no_results_found_in(query_response): - return not query_response.batch_summaries[0].result_set_summaries + return not query_response.batch_summaries \ + or not query_response.batch_summaries[0].result_set_summaries @staticmethod def _no_rows_found_in(query_response): diff --git a/mssqlcli/mssqlclirc b/mssqlcli/mssqlclirc index 75e8b38..fc8deeb 100644 --- a/mssqlcli/mssqlclirc +++ b/mssqlcli/mssqlclirc @@ -10,13 +10,13 @@ smart_completion = True wider_completion_menu = False # Multi-line mode allows breaking up the sql statements into multiple lines. If -# this is set to True, then the end of the statements must have a semi-colon. +# this is set to True, then the end of the statements must have 'GO'. # If this is set to False then sql statements can't be split into multiple # lines. End of line (return) is considered as the end of the statement. multi_line = False # If multi_line_mode is set to "tsql", in multi-line mode, [Enter] will execute -# the current input if the input ends in a semicolon. +# the current input if the input ends in 'GO'. # If multi_line_mode is set to "safe", in multi-line mode, [Enter] will always # insert a newline, and [Esc] [Enter] or [Alt]-[Enter] must be used to execute # a command. diff --git a/mssqlcli/mssqltoolbar.py b/mssqlcli/mssqltoolbar.py index 38cca71..7ee5e2d 100644 --- a/mssqlcli/mssqltoolbar.py +++ b/mssqlcli/mssqltoolbar.py @@ -39,7 +39,7 @@ def create_toolbar_tokens_func(mssql_cli): if mssql_cli.multiline_mode == 'safe': result.append((token, ' ([Esc] [Enter] to execute]) ')) else: - result.append((token, ' (Semi-colon [;] will end the line) ')) + result.append((token, ' ([GO] statement will end the line) ')) if mssql_cli.vi_mode: result.append( diff --git a/mssqlcli/packages/parseutils/utils.py b/mssqlcli/packages/parseutils/utils.py index 1376019..1f14772 100644 --- a/mssqlcli/packages/parseutils/utils.py +++ b/mssqlcli/packages/parseutils/utils.py @@ -113,7 +113,7 @@ def is_open_quote(sql): def _parsed_is_open_quote(parsed): # Look for unmatched single quotes, or unmatched dollar sign quotes - return any(tok.match(Token.Error, ("'", "$")) for tok in parsed.flatten()) + return any(tok.match(Token.Error, ("'", '"', "$")) for tok in parsed.flatten()) def parse_partial_identifier(word):
dbcli/mssql-cli
341fead174a009474af31fd2e7849ea07b66b251
diff --git a/tests/test_multiline.py b/tests/test_multiline.py new file mode 100644 index 0000000..81577d0 --- /dev/null +++ b/tests/test_multiline.py @@ -0,0 +1,37 @@ +import pytest +from mssqlcli.mssqlbuffer import _is_complete + + +class TestMssqlCliMultiline: + testdata = [ + (None, False), + ('', False), + ('select 1 /* open comment!\ngo', False), + ('select 1\ngo -- another comment', True), + ('select 1; select 2, "open quote: go', False), + ('select 1\n"go"', False), + ('select 1; GO', False), + ('SELECT 4;\nGO', True), + ('select 1\n select 2;\ngo', True), + ('select 1;', False), + ('select 1 go', False), + ('select 1\ngo go go', False), + ('GO select 1', False), + ('GO', True) + # tests below to be enabled when sqlparse supports retaining newlines + # when stripping comments (tracking here: + # https://github.com/andialbrecht/sqlparse/issues/484): + # ('select 3 /* another open comment\n*/ GO', True), + # ('select 1\n*/go', False), + # ('select 1 /*\nmultiple lines!\n*/go', True) + ] + + @staticmethod + @pytest.mark.parametrize("query_str, is_complete", testdata) + def test_multiline_completeness(query_str, is_complete): + """ + Tests the _is_complete helper method, which parses a T-SQL multiline + statement on each newline and determines whether the script should + execute. + """ + assert _is_complete(query_str) == is_complete
Do not use a semicolon to end a multi-line query Currently when editing a multiline query, we use use a semicolon+<enter> to delineate the query should be executed. Feedback from the MVP summit: in multiline query mode, users like to enter more that one statement, which are delineated by semicolons, so using a semicolon is a bad choice. We should consider using the 'GO' keyword to execute the query, which aligns with sqlcmd.
0.0
341fead174a009474af31fd2e7849ea07b66b251
[ "tests/test_multiline.py::TestMssqlCliMultiline::test_multiline_completeness[None-False]", "tests/test_multiline.py::TestMssqlCliMultiline::test_multiline_completeness[select", "tests/test_multiline.py::TestMssqlCliMultiline::test_multiline_completeness[SELECT", "tests/test_multiline.py::TestMssqlCliMultiline::test_multiline_completeness[GO-True]" ]
[ "tests/test_multiline.py::TestMssqlCliMultiline::test_multiline_completeness[-False]", "tests/test_multiline.py::TestMssqlCliMultiline::test_multiline_completeness[GO" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2019-12-17 18:17:23+00:00
bsd-3-clause
1,857
deardurham__ciprs-reader-21
diff --git a/ciprs/parsers.py b/ciprs/parsers.py index 9f2bfec..c648277 100644 --- a/ciprs/parsers.py +++ b/ciprs/parsers.py @@ -113,6 +113,25 @@ class OffenseRecordRow(Parser): report["Offense Record"]["Records"].append(record) +class OffenseRecordRowWithNumber(Parser): + """ + Extract offense row like: + 54 CHARGED SPEEDING INFRACTION G.S. 20-141(B) + """ + + # pylint: disable=line-too-long + pattern = r"(?:\d*)?\s*(?P<action>\w+)\s+(?P<desc>[\w \-\(\)]+)[ ]{2,}(?P<severity>\w+)[ ]{2,}(?P<law>[\w. \-\(\)]+)" + + def extract(self, matches, report): + record = { + "Action": matches["action"], + "Description": matches["desc"], + "Severity": matches["severity"], + "Law": matches["law"], + } + report["Offense Record"]["Records"].append(record) + + class OffenseDisposedDate(Parser): pattern = r".*Disposed on:\s*(?P<value>[\d/:]+)" diff --git a/ciprs/reader.py b/ciprs/reader.py index b084926..81f9faa 100644 --- a/ciprs/reader.py +++ b/ciprs/reader.py @@ -6,6 +6,7 @@ from ciprs.parsers import ( CaseDetails, CaseStatus, OffenseRecordRow, + OffenseRecordRowWithNumber, OffenseDateTime, OffenseDisposedDate, CaseWasServedOnDate, @@ -35,6 +36,7 @@ class PDFToTextReader: CaseDetails(self.report), CaseStatus(self.report), OffenseRecordRow(self.report), + OffenseRecordRowWithNumber(self.report), OffenseDateTime(self.report), OffenseDisposedDate(self.report), CaseWasServedOnDate(self.report),
deardurham/ciprs-reader
a052cb447ca15183f6fb0eb2ac0b7cbd3d699f25
diff --git a/tests/test_parsers.py b/tests/test_parsers.py index ca14731..efa4bb8 100644 --- a/tests/test_parsers.py +++ b/tests/test_parsers.py @@ -39,6 +39,16 @@ def test_offense_record_charged(): assert matches["code"] == "4450" +def test_offense_record_charged_with_number(): + string = "54 CHARGED SPEEDING(80 mph in a 65 mph zone) INFRACTION G.S. 20-141(B)" # noqa + matches = parsers.OffenseRecordRowWithNumber().match(string) + assert matches is not None, "Regex match failed" + assert matches["action"] == "CHARGED" + assert matches["desc"] == "SPEEDING(80 mph in a 65 mph zone)" + assert matches["severity"] == "INFRACTION" + assert matches["law"] == "G.S. 20-141(B)" + + def test_offense_record_arrainged(): string = "ARRAIGNED SPEEDING(80 mph in a 65 mph zone) INFRACTION G.S. 20-141(B) 4450" # noqa matches = parsers.OffenseRecordRow().match(string)
Parsers do not catch numbered offense rows The offense row parser is designed to capture data from offense rows that look like this: ACTION DESCRIPTION SEVERITY LAW CODE However, on some records they look like this: \# ACTION DESCRIPTION SEVERITY LAW With # being either a zero padded number or blank
0.0
a052cb447ca15183f6fb0eb2ac0b7cbd3d699f25
[ "tests/test_parsers.py::test_offense_record_charged_with_number" ]
[ "tests/test_parsers.py::test_case_details[expected0-", "tests/test_parsers.py::test_case_details[expected1-", "tests/test_parsers.py::test_case_status", "tests/test_parsers.py::test_offense_record_charged", "tests/test_parsers.py::test_offense_record_arrainged", "tests/test_parsers.py::test_offense_record_convicted", "tests/test_parsers.py::test_offense_date_time", "tests/test_parsers.py::test_defendent_name", "tests/test_parsers.py::test_defendent_name_no_middle", "tests/test_parsers.py::test_defendent_race", "tests/test_parsers.py::test_defendent_sex_male", "tests/test_parsers.py::test_defendent_sex_female", "tests/test_parsers.py::test_defendent_sex_bad", "tests/test_parsers.py::test_defendent_dob", "tests/test_parsers.py::test_offense_disposed_date[2000-01-01-", "tests/test_parsers.py::test_offense_disposed_date[2016-07-20-", "tests/test_parsers.py::test_case_was_served_on_date[2000-09-09-", "tests/test_parsers.py::test_case_was_served_on_date[2015-05-17-Case", "tests/test_parsers.py::test_known_offense_disposition_method", "tests/test_parsers.py::test_unknown_offense_disposition_method", "tests/test_parsers.py::test_court_type_other", "tests/test_parsers.py::test_court_type_cr", "tests/test_parsers.py::test_court_type_crs" ]
{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2020-02-19 01:01:30+00:00
bsd-3-clause
1,859
deardurham__ciprs-reader-38
diff --git a/ciprs_reader/parser/section/header.py b/ciprs_reader/parser/section/header.py index 1f18711..34edc94 100644 --- a/ciprs_reader/parser/section/header.py +++ b/ciprs_reader/parser/section/header.py @@ -13,7 +13,7 @@ class CaseDetails(HeaderParser): """Extract County and File No from header on top of first page""" pattern = ( - r"\s*Case (Details|Summary) for Court Case[\s:]+(?P<county>\w+) (?P<fileno>\w+)" + r"\s*Case (Details|Summary) for Court Case[\s:]+(?P<county>(\w\s*)+) (?P<fileno>\w+)" ) def extract(self, matches, report):
deardurham/ciprs-reader
a39ef64b3e2ee9c14b377262c64230cce9bc2681
diff --git a/tests/parsers/test_header.py b/tests/parsers/test_header.py index 3610ac9..5fb3138 100644 --- a/tests/parsers/test_header.py +++ b/tests/parsers/test_header.py @@ -12,6 +12,14 @@ CASE_DETAIL_DATA = [ {"county": "ORANGE", "fileno": "99FN9999999"}, " Case Summary for Court Case: ORANGE 99FN9999999", ), + ( + {"county": "NEW HANOVER", "fileno": "00GR000000"}, + " Case Details for Court Case NEW HANOVER 00GR000000 ", + ), + ( + {"county": "OLD HANOVER", "fileno": "99FN9999999"}, + " Case Summary for Court Case: OLD HANOVER 99FN9999999", + ), ]
County names with spaces are not parsed properly The [CaseDetails](https://github.com/deardurham/ciprs-reader/blob/master/ciprs_reader/parser/section/header.py#L12) parser doesn't expect county names to contain spaces, so a line like ``` Case Summary for Court Case: NEW HANOVER 20CR000000 ``` will result in a county name of ``NEW``. AC - [CaseDetails](https://github.com/deardurham/ciprs-reader/blob/master/ciprs_reader/parser/section/header.py#L12) parser updated to expect spaces - A test is added wi spaces in the county name
0.0
a39ef64b3e2ee9c14b377262c64230cce9bc2681
[ "tests/parsers/test_header.py::test_case_details[expected2-", "tests/parsers/test_header.py::test_case_details[expected3-" ]
[ "tests/parsers/test_header.py::test_case_details[expected0-", "tests/parsers/test_header.py::test_case_details[expected1-", "tests/parsers/test_header.py::test_defendent_name", "tests/parsers/test_header.py::test_defendent_name_no_middle", "tests/parsers/test_header.py::test_defendent_name_special_character" ]
{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }
2020-06-26 03:08:23+00:00
bsd-3-clause
1,860
decargroup__pykoop-132
diff --git a/LICENSE b/LICENSE index e8d5947..a4df98f 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2022 DECAR Systems Group +Copyright (c) 2022 DECAR Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/pykoop/koopman_pipeline.py b/pykoop/koopman_pipeline.py index 18f1d8b..80ad541 100644 --- a/pykoop/koopman_pipeline.py +++ b/pykoop/koopman_pipeline.py @@ -2821,7 +2821,9 @@ class KoopmanPipeline(metaestimators._BaseComposition, KoopmanLiftingFn): an error has occured in estimator fitting. If set to ``'raise'``, a :class:`ValueError` is raised. If a numerical value is given, a :class:`sklearn.exceptions.FitFailedWarning` warning is raised and - the specified score is returned. + the specified score is returned. The error score defines the worst + possible score. If a score is finite but lower than the error + score, the error score will be returned instead. multistep : bool If true, predict using :func:`predict_trajectory`. Otherwise, @@ -3204,7 +3206,9 @@ def score_trajectory( error has occured in estimator fitting. If set to ``'raise'``, a :class:`ValueError` is raised. If a numerical value is given, a :class:`sklearn.exceptions.FitFailedWarning` warning is raised and the - specified score is returned. + specified score is returned. The error score defines the worst possible + score. If a score is finite but lower than the error score, the error + score will be returned instead. min_samples : int Number of samples in initial condition. @@ -3298,6 +3302,13 @@ def score_trajectory( # Invert losses if regression_metric not in greater_is_better: score *= -1 + # If score is worse than error score, return that. + if np.isfinite(error_score) and (score < error_score): + warnings.warn( + f'Score `score={score}` is finite, but is lower than error ' + f'score `error_score={error_score}`. Returning error score.', + sklearn.exceptions.FitFailedWarning) + return error_score return score
decargroup/pykoop
a9f1f516ca6dc273f96d2165d195c648417067c1
diff --git a/tests/test_koopman_pipeline.py b/tests/test_koopman_pipeline.py index 2762359..9d8c34a 100644 --- a/tests/test_koopman_pipeline.py +++ b/tests/test_koopman_pipeline.py @@ -560,6 +560,22 @@ class TestKoopmanPipelineScore: False, None, ), + # Finite score worse than error score should return error score. + ( + np.array([ + [1e-2, 1e-3], + ]).T, + np.array([ + [1e5, 1e6], + ]).T, + None, + 1, + 'neg_mean_squared_error', + -100, + 1, + False, + -100, + ), ], ) def test_score_trajectory(
Change name in license file DECAR Systems Group -> DECAR Group or just DECAR
0.0
a9f1f516ca6dc273f96d2165d195c648417067c1
[ "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted16-X_expected16-None-1-neg_mean_squared_error--100-1-False--100]" ]
[ "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_koopman_pipeline_attrs[lf0-names_in0-X0-names_out0-Xt_exp0-1-False-attr_exp0]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_koopman_pipeline_attrs[lf1-names_in1-X1-names_out1-Xt_exp1-1-False-attr_exp1]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_koopman_pipeline_attrs[lf2-names_in2-X2-names_out2-Xt_exp2-1-False-attr_exp2]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_koopman_pipeline_attrs[lf3-names_in3-X3-names_out3-Xt_exp3-1-False-attr_exp3]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_transform[lf0-names_in0-X0-names_out0-Xt_exp0-1-False-attr_exp0]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_transform[lf1-names_in1-X1-names_out1-Xt_exp1-1-False-attr_exp1]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_transform[lf2-names_in2-X2-names_out2-Xt_exp2-1-False-attr_exp2]", 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"tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_feature_names_in[lf2-names_in2-X2-names_out2-Xt_exp2-1-False-attr_exp2]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_feature_names_in[lf3-names_in3-X3-names_out3-Xt_exp3-1-False-attr_exp3]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_feature_names_out[lf0-names_in0-X0-names_out0-Xt_exp0-1-False-attr_exp0]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_feature_names_out[lf1-names_in1-X1-names_out1-Xt_exp1-1-False-attr_exp1]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_feature_names_out[lf2-names_in2-X2-names_out2-Xt_exp2-1-False-attr_exp2]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineTransform::test_feature_names_out[lf3-names_in3-X3-names_out3-Xt_exp3-1-False-attr_exp3]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineFit::test_fit", 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"tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted5-X_expected5-2-1-neg_mean_squared_error-nan-1-False-0]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted6-X_expected6-None-0.5-neg_mean_squared_error-nan-1-False--0.14285714285714285]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted7-X_expected7-None-1-neg_mean_squared_error-nan-1-True--0.5]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted8-X_expected8-1-1-neg_mean_squared_error-nan-1-True--0.5]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted9-X_expected9-None-0.5-neg_mean_squared_error-nan-1-True--0.5]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted10-X_expected10-1-0.5-neg_mean_squared_error-nan-1-True--0.5]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted11-X_expected11-None-1-neg_mean_squared_error-nan-1-False-nan]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted12-X_expected12-None-1-neg_mean_squared_error--100-1-False--100]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted13-X_expected13-None-1-neg_mean_squared_error-raise-1-False-None]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted14-X_expected14-None-1-neg_mean_squared_error--100-1-False--100]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_score_trajectory[X_predicted15-X_expected15-None-1-neg_mean_squared_error-raise-1-False-None]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_weights_from_data_matrix[X0-w_exp0-2-1-False]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_weights_from_data_matrix[X1-w_exp1-3-0.5-False]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_weights_from_data_matrix[X2-w_exp2-2-0.5-True]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_weights_from_data_matrix[X3-w_exp3-10-1-True]", "tests/test_koopman_pipeline.py::TestKoopmanPipelineScore::test_weights_from_data_matrix[X4-w_exp4-10-0.1-True]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_shift_episodes[X0-X_unsh_exp0-X_sh_exp0-0-False]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_shift_episodes[X1-X_unsh_exp1-X_sh_exp1-1-False]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_shift_episodes[X2-X_unsh_exp2-X_sh_exp2-0-True]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_shift_episodes[X3-X_unsh_exp3-X_sh_exp3-1-True]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_extract_initial_conditions[X0-ic_exp0-1-0-False]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_extract_initial_conditions[X1-ic_exp1-2-0-False]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_extract_initial_conditions[X2-ic_exp2-1-1-False]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_extract_initial_conditions[X3-ic_exp3-1-0-True]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_extract_initial_conditions[X4-ic_exp4-1-1-True]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_extract_initial_conditions[X5-ic_exp5-2-1-True]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_extract_input[X0-u_exp0-1-False]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_extract_input[X1-u_exp1-0-False]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_extract_input[X2-u_exp2-1-True]", "tests/test_koopman_pipeline.py::TestEpisodeManipulation::test_strip_initial_conditons", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_trajectory[kp0]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_trajectory[kp1]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_trajectory[kp2]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_trajectory[kp3]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_trajectory[kp4]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_trajectory_no_U[kp0]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_trajectory_no_U[kp1]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_trajectory_no_U[kp2]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_trajectory_no_U[kp3]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_trajectory_no_U[kp4]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_multistep[kp0]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_multistep[kp1]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_multistep[kp2]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_multistep[kp3]", "tests/test_koopman_pipeline.py::TestPrediction::test_predict_multistep[kp4]", "tests/test_koopman_pipeline.py::TestSplitCombineEpisodes::test_split_episodes[X0-episodes0-True]", "tests/test_koopman_pipeline.py::TestSplitCombineEpisodes::test_split_episodes[X1-episodes1-True]", "tests/test_koopman_pipeline.py::TestSplitCombineEpisodes::test_split_episodes[X2-episodes2-False]", "tests/test_koopman_pipeline.py::TestSplitCombineEpisodes::test_split_episodes[X3-episodes3-True]", "tests/test_koopman_pipeline.py::TestSplitCombineEpisodes::test_combine_episodes[X0-episodes0-True]", "tests/test_koopman_pipeline.py::TestSplitCombineEpisodes::test_combine_episodes[X1-episodes1-True]", "tests/test_koopman_pipeline.py::TestSplitCombineEpisodes::test_combine_episodes[X2-episodes2-False]", "tests/test_koopman_pipeline.py::TestSplitCombineEpisodes::test_combine_episodes[X3-episodes3-True]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_attrs[lf0-names_in0-X0-names_out0-Xt_exp0-2-False-attr_exp0]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_attrs[lf1-names_in1-X1-names_out1-Xt_exp1-2-True-attr_exp1]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_attrs[lf2-names_in2-X2-names_out2-Xt_exp2-2-False-attr_exp2]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_attrs[lf3-names_in3-X3-names_out3-Xt_exp3-2-False-attr_exp3]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_attrs[lf4-names_in4-X4-names_out4-Xt_exp4-2-False-attr_exp4]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_transform[lf0-names_in0-X0-names_out0-Xt_exp0-2-False-attr_exp0]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_transform[lf1-names_in1-X1-names_out1-Xt_exp1-2-True-attr_exp1]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_transform[lf2-names_in2-X2-names_out2-Xt_exp2-2-False-attr_exp2]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_transform[lf3-names_in3-X3-names_out3-Xt_exp3-2-False-attr_exp3]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_transform[lf4-names_in4-X4-names_out4-Xt_exp4-2-False-attr_exp4]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_inverse_transform[lf0-names_in0-X0-names_out0-Xt_exp0-2-False-attr_exp0]", "tests/test_koopman_pipeline.py::TestSplitPipeline::test_split_lifting_fn_inverse_transform[lf1-names_in1-X1-names_out1-Xt_exp1-2-True-attr_exp1]", 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"tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_parameters_default_constructible]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_methods_sample_order_invariance]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_methods_subset_invariance]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_fit2d_1sample]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_fit2d_1feature]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_get_params_invariance]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_set_params]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_dict_unchanged]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_dont_overwrite_parameters]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_fit_idempotent]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_fit_check_is_fitted]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_n_features_in]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_fit1d]", "tests/test_koopman_pipeline.py::TestSkLearn::test_compatible_estimator[SplitPipeline(lifting_functions_state=[('pl',PolynomialLiftingFn())])-check_fit2d_predict1d]", "tests/test_koopman_pipeline.py::TestDeepParams::test_get_set", "tests/test_koopman_pipeline.py::TestDeepParams::test_nested_get_set", "tests/test_koopman_pipeline.py::TestDeepParams::test_invalid_set" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-01-18 16:51:15+00:00
mit
1,861
dedupeio__dedupe-837
diff --git a/dedupe/predicates.py b/dedupe/predicates.py index 1934811..e796a6d 100644 --- a/dedupe/predicates.py +++ b/dedupe/predicates.py @@ -329,9 +329,14 @@ class CompoundPredicate(tuple): def __call__(self, record, **kwargs): predicate_keys = [predicate(record, **kwargs) for predicate in self] - return [u':'.join(block_key) - for block_key - in itertools.product(*predicate_keys)] + return [ + u':'.join( + # must escape : to avoid confusion with : join separator + b.replace(u':', u'\\:') for b in block_key + ) + for block_key + in itertools.product(*predicate_keys) + ] def wholeFieldPredicate(field: Any) -> Tuple[str]:
dedupeio/dedupe
5092f2598f1f2bcb4f3b1f0ec85f88b95ce7454b
diff --git a/tests/test_predicates.py b/tests/test_predicates.py index deca290..714ac31 100644 --- a/tests/test_predicates.py +++ b/tests/test_predicates.py @@ -80,5 +80,47 @@ class TestNumericPredicates(unittest.TestCase): assert predicates.roundTo1(-22315) == (u'-20000',) +class TestCompoundPredicate(unittest.TestCase): + def test_escapes_colon(self): + ''' + Regression test for issue #836 + ''' + predicate_1 = predicates.SimplePredicate( + predicates.commonSetElementPredicate, 'col_1') + predicate_2 = predicates.SimplePredicate( + predicates.commonSetElementPredicate, 'col_2') + record = { + 'col_1': ['foo:', 'foo'], + 'col_2': [':bar', 'bar'] + } + + block_val = predicates.CompoundPredicate([ + predicate_1, + predicate_2 + ])(record) + assert len(set(block_val)) == 4 + assert block_val == ['foo\\::\\:bar', 'foo\\::bar', 'foo:\\:bar', 'foo:bar'] + + def test_escapes_escaped_colon(self): + ''' + Regression test for issue #836 + ''' + predicate_1 = predicates.SimplePredicate( + predicates.commonSetElementPredicate, 'col_1') + predicate_2 = predicates.SimplePredicate( + predicates.commonSetElementPredicate, 'col_2') + record = { + 'col_1': ['foo\\:', 'foo'], + 'col_2': ['\\:bar', 'bar'] + } + + block_val = predicates.CompoundPredicate([ + predicate_1, + predicate_2 + ])(record) + assert len(set(block_val)) == 4 + assert block_val == ['foo\\\\::\\\\:bar', 'foo\\\\::bar', 'foo:\\\\:bar', 'foo:bar'] + + if __name__ == '__main__': unittest.main()
CompoundPredicate should escape `:` to avoid wrong block_keys I've found an issue on `CompoundPredicate` caused by the lack of escaping `:` chars inside fields. This causes two problems. First, it can generate duplicate `block_key`s for the same `id`. Here's the example: ``` (SimplePredicate: (commonSetElementPredicate, name), SimplePredicate: (commonSetElementPredicate, address)) ``` ``` id | name | address --------------------------------------- 1 | {'foo:', 'foo'} | {':bar', 'bar'} ``` ``` id | block_key --------------- 1 | foo::bar:0 1 | foo::bar:0 ``` That's probably not problematic for Dedupe 2, but that breaks [this line](https://github.com/dedupeio/dedupe-examples/blob/83dbf872674a5c3f6a209c367f46c7e6ef78e9a3/pgsql_big_dedupe_example/pgsql_big_dedupe_example.py#L246-L247) of the old `smaller_id`-based big Dedupe I still use. Second, it can group together under the same `block_key` records that shouldn't be blocked together. See: ``` (SimplePredicate: (wholeFieldPredicate, name), SimplePredicate: (wholeFieldPredicate, address)) ``` ``` id | name | address --------------------------- 1 | flavio: | one street 2 | flavio | :one street ``` ``` id | blocking_key ------------------------- 1 | flavio::one street:0 2 | flavio::one street:0 ``` The solution is to escape `:` right before performing the `join` at this line: https://github.com/dedupeio/dedupe/blob/5092f2598f1f2bcb4f3b1f0ec85f88b95ce7454b/dedupe/predicates.py#L332 Something like `u':'.join(block_key.replace(u':', u'\\:'))` would work, because the examples above would become this: ``` id | block_key --------------- 1 | foo\::bar:0 1 | foo:\:bar:0 ``` ``` id | blocking_key ------------------------- 1 | flavio\::one street:0 2 | flavio:\:one street:0 ``` I'll open a PR for this.
0.0
5092f2598f1f2bcb4f3b1f0ec85f88b95ce7454b
[ "tests/test_predicates.py::TestCompoundPredicate::test_escapes_colon", "tests/test_predicates.py::TestCompoundPredicate::test_escapes_escaped_colon" ]
[ "tests/test_predicates.py::TestPuncStrip::test_set", "tests/test_predicates.py::TestPuncStrip::test_sevenchar", "tests/test_predicates.py::TestMetaphone::test_metaphone_token", "tests/test_predicates.py::TestWholeSet::test_full_set", "tests/test_predicates.py::TestSetElement::test_empty_set", "tests/test_predicates.py::TestSetElement::test_first_last", "tests/test_predicates.py::TestSetElement::test_long_set", "tests/test_predicates.py::TestSetElement::test_magnitude", "tests/test_predicates.py::TestLatLongGrid::test_precise_latlong", "tests/test_predicates.py::TestNumericPredicates::test_order_of_magnitude", "tests/test_predicates.py::TestNumericPredicates::test_round_to_1" ]
{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }
2020-07-13 17:49:49+00:00
mit
1,862
deepchem__deepchem-2664
diff --git a/README.md b/README.md index fec472dbe..54d1c06d7 100644 --- a/README.md +++ b/README.md @@ -109,6 +109,10 @@ If GPU support is required, then make sure CUDA is installed and then install th 2. pytorch - https://pytorch.org/get-started/locally/#start-locally 3. jax - https://github.com/google/jax#pip-installation-gpu-cuda +In `zsh` square brackets are used for globbing/pattern matching. This means you +need to escape the square brackets in the above installation. You can do so +by including the dependencies in quotes like `pip install --pre 'deepchem[jax]'` + ### Docker If you want to install deepchem using a docker, you can pull two kinds of images. diff --git a/deepchem/data/datasets.py b/deepchem/data/datasets.py index 1abdde3e7..27427927a 100644 --- a/deepchem/data/datasets.py +++ b/deepchem/data/datasets.py @@ -1500,10 +1500,10 @@ class DiskDataset(Dataset): """Gets size of shards on disk.""" if not len(self.metadata_df): raise ValueError("No data in dataset.") - sample_y = load_from_disk( + sample_ids = load_from_disk( os.path.join(self.data_dir, - next(self.metadata_df.iterrows())[1]['y'])) - return len(sample_y) + next(self.metadata_df.iterrows())[1]['ids'])) + return len(sample_ids) def _get_metadata_filename(self) -> Tuple[str, str]: """Get standard location for metadata file.""" @@ -2369,11 +2369,11 @@ class DiskDataset(Dataset): if y is not None: y_sel = y[shard_inds] else: - y_sel = None + y_sel = np.array([]) if w is not None: w_sel = w[shard_inds] else: - w_sel = None + w_sel = np.array([]) ids_sel = ids[shard_inds] Xs.append(X_sel) ys.append(y_sel) @@ -2399,9 +2399,16 @@ class DiskDataset(Dataset): np.where(sorted_indices == orig_index)[0][0] for orig_index in select_shard_indices ]) - X, y, w, ids = X[reverted_indices], y[reverted_indices], w[ - reverted_indices], ids[reverted_indices] - yield (X, y, w, ids) + if y.size == 0: + tup_y = y + else: + tup_y = y[reverted_indices] + if w.size == 0: + tup_w = w + else: + tup_w = w[reverted_indices] + X, ids = X[reverted_indices], ids[reverted_indices] + yield (X, tup_y, tup_w, ids) start = end select_shard_num += 1 diff --git a/docs/source/get_started/installation.rst b/docs/source/get_started/installation.rst index 198d1020c..1c9a0cd68 100644 --- a/docs/source/get_started/installation.rst +++ b/docs/source/get_started/installation.rst @@ -66,6 +66,9 @@ If GPU support is required, then make sure CUDA is installed and then install th 2. pytorch - https://pytorch.org/get-started/locally/#start-locally 3. jax - https://github.com/google/jax#pip-installation-gpu-cuda +In :code:`zsh` square brackets are used for globbing/pattern matching. This means +you need to escape the square brackets in the above installation. You can do so by +including the dependencies in quotes like :code:`pip install --pre 'deepchem[jax]'` Google Colab ------------
deepchem/deepchem
22a8fbd7350540d6e0410223c0c75d744c241495
diff --git a/deepchem/data/tests/reaction_smiles.csv b/deepchem/data/tests/reaction_smiles.csv new file mode 100644 index 000000000..ce90ba563 --- /dev/null +++ b/deepchem/data/tests/reaction_smiles.csv @@ -0,0 +1,5 @@ +reactions +CCS(=O)(=O)Cl.OCCBr>CCN(CC)CC.CCOCC>CCS(=O)(=O)OCCBr +CC(C)CS(=O)(=O)Cl.OCCCl>CCN(CC)CC.CCOCC>CC(C)CS(=O)(=O)OCCCl +O=[N+]([O-])c1cccc2cnc(Cl)cc12>CC(=O)O.O.[Fe].[Na+].[OH-]>Nc1cccc2cnc(Cl)cc12 +Cc1cc2c([N+](=O)[O-])cccc2c[n+]1[O-].O=P(Cl)(Cl)Cl>>Cc1cc2c([N+](=O)[O-])cccc2c(Cl)n1 \ No newline at end of file diff --git a/deepchem/data/tests/test_shape.py b/deepchem/data/tests/test_shape.py index 346c7da31..aca120dbe 100644 --- a/deepchem/data/tests/test_shape.py +++ b/deepchem/data/tests/test_shape.py @@ -106,3 +106,29 @@ def test_disk_dataset_get_legacy_shape_multishard(): assert y_shape == (num_datapoints, num_tasks) assert w_shape == (num_datapoints, num_tasks) assert ids_shape == (num_datapoints,) + + +def test_get_shard_size(): + """ + Test that using ids for getting the shard size does not break the method. + The issue arises when attempting to load a dataset that does not have a labels + column. The create_dataset method of the DataLoader class sets the y to None + in this case, which causes the existing implementation of the get_shard_size() + method to fail, as it relies on the dataset having a not None y column. This + consequently breaks all methods depending on this, like the splitters for + example. + + Note + ---- + DiskDatasets without labels cannot be resharded! + """ + + current_dir = os.path.dirname(os.path.abspath(__file__)) + file_path = os.path.join(current_dir, "reaction_smiles.csv") + + featurizer = dc.feat.DummyFeaturizer() + loader = dc.data.CSVLoader( + tasks=[], feature_field="reactions", featurizer=featurizer) + + dataset = loader.create_dataset(file_path) + assert dataset.get_shard_size() == 4
Clarification for installation issues I was working with a new source install for deepchem following the new lightweight guide and tried ``` pip install -e .[jax] ``` And got the following error ``` zsh: no matches found: [jax] ``` I googled this and found https://stackoverflow.com/questions/30539798/zsh-no-matches-found-requestssecurity. The basic issue is we need to do something like ``` noglob pip install -e .[jax] ``` We should modify the install directions to clarify.
0.0
22a8fbd7350540d6e0410223c0c75d744c241495
[ "deepchem/data/tests/test_shape.py::test_get_shard_size" ]
[ "deepchem/data/tests/test_shape.py::test_numpy_dataset_get_shape", "deepchem/data/tests/test_shape.py::test_disk_dataset_get_shape_single_shard", "deepchem/data/tests/test_shape.py::test_disk_dataset_get_shape_multishard", "deepchem/data/tests/test_shape.py::test_disk_dataset_get_legacy_shape_single_shard", "deepchem/data/tests/test_shape.py::test_disk_dataset_get_legacy_shape_multishard" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2021-08-18 09:54:21+00:00
mit
1,863
deepchem__deepchem-2741
diff --git a/deepchem/dock/pose_generation.py b/deepchem/dock/pose_generation.py index 97af3f929..59af72747 100644 --- a/deepchem/dock/pose_generation.py +++ b/deepchem/dock/pose_generation.py @@ -5,10 +5,8 @@ import platform import logging import os import tempfile -import tarfile import numpy as np -from subprocess import call, Popen, PIPE -from subprocess import check_output +from subprocess import Popen, PIPE from typing import List, Optional, Tuple, Union from deepchem.dock.binding_pocket import BindingPocketFinder @@ -244,87 +242,50 @@ class VinaPoseGenerator(PoseGenerator): """Uses Autodock Vina to generate binding poses. This class uses Autodock Vina to make make predictions of - binding poses. It downloads the Autodock Vina executable for - your system to your specified DEEPCHEM_DATA_DIR (remember this - is an environment variable you set) and invokes the executable - to perform pose generation for you. + binding poses. + + Example + ------- + >> import deepchem as dc + >> vpg = dc.dock.VinaPoseGenerator(pocket_finder=None) + >> protein_file = '1jld_protein.pdb' + >> ligand_file = '1jld_ligand.sdf' + >> poses, scores = vpg.generate_poses( + .. (protein_file, ligand_file), + .. exhaustiveness=1, + .. num_modes=1, + .. out_dir=tmp, + .. generate_scores=True) Note ---- - This class requires RDKit to be installed. + This class requires RDKit and vina to be installed. """ - def __init__(self, - sixty_four_bits: bool = True, - pocket_finder: Optional[BindingPocketFinder] = None): + def __init__(self, pocket_finder: Optional[BindingPocketFinder] = None): """Initializes Vina Pose Generator Parameters ---------- - sixty_four_bits: bool, optional (default True) - Specifies whether this is a 64-bit machine. Needed to download - the correct executable. pocket_finder: BindingPocketFinder, optional (default None) If specified should be an instance of `dc.dock.BindingPocketFinder`. """ - data_dir = get_data_dir() - if platform.system() == 'Linux': - url = "http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz" - filename = "autodock_vina_1_1_2_linux_x86.tgz" - dirname = "autodock_vina_1_1_2_linux_x86" - self.vina_dir = os.path.join(data_dir, dirname) - self.vina_cmd = os.path.join(self.vina_dir, "bin/vina") - elif platform.system() == 'Darwin': - if sixty_four_bits: - url = "http://vina.scripps.edu/download/autodock_vina_1_1_2_mac_64bit.tar.gz" - filename = "autodock_vina_1_1_2_mac_64bit.tar.gz" - dirname = "autodock_vina_1_1_2_mac_catalina_64bit" - else: - url = "http://vina.scripps.edu/download/autodock_vina_1_1_2_mac.tgz" - filename = "autodock_vina_1_1_2_mac.tgz" - dirname = "autodock_vina_1_1_2_mac" - self.vina_dir = os.path.join(data_dir, dirname) - self.vina_cmd = os.path.join(self.vina_dir, "bin/vina") - elif platform.system() == 'Windows': - url = "http://vina.scripps.edu/download/autodock_vina_1_1_2_win32.msi" - filename = "autodock_vina_1_1_2_win32.msi" - self.vina_dir = "\\Program Files (x86)\\The Scripps Research Institute\\Vina" - self.vina_cmd = os.path.join(self.vina_dir, "vina.exe") - else: - raise ValueError( - "Unknown operating system. Try using a cloud platform to run this code instead." - ) self.pocket_finder = pocket_finder - if not os.path.exists(self.vina_dir): - logger.info("Vina not available. Downloading") - download_url(url, data_dir) - downloaded_file = os.path.join(data_dir, filename) - logger.info("Downloaded Vina. Extracting") - if platform.system() == 'Windows': - msi_cmd = "msiexec /i %s" % downloaded_file - check_output(msi_cmd.split()) - else: - with tarfile.open(downloaded_file) as tar: - tar.extractall(data_dir) - logger.info("Cleanup: removing downloaded vina tar.gz") - os.remove(downloaded_file) - def generate_poses(self, - molecular_complex: Tuple[str, str], - centroid: Optional[np.ndarray] = None, - box_dims: Optional[np.ndarray] = None, - exhaustiveness: int = 10, - num_modes: int = 9, - num_pockets: Optional[int] = None, - out_dir: Optional[str] = None, - generate_scores: Optional[bool] = False - ) -> Union[Tuple[DOCKED_POSES, List[float]], DOCKED_POSES]: + def generate_poses( + self, + molecular_complex: Tuple[str, str], + centroid: Optional[np.ndarray] = None, + box_dims: Optional[np.ndarray] = None, + exhaustiveness: int = 10, + num_modes: int = 9, + num_pockets: Optional[int] = None, + out_dir: Optional[str] = None, + generate_scores: Optional[bool] = False, + **kwargs) -> Union[Tuple[DOCKED_POSES, List[float]], DOCKED_POSES]: """Generates the docked complex and outputs files for docked complex. - TODO: How can this work on Windows? We need to install a .msi file and - invoke it correctly from Python for this to work. - Parameters ---------- molecular_complexes: Tuple[str, str] @@ -337,8 +298,9 @@ class VinaPoseGenerator(PoseGenerator): A numpy array of shape `(3,)` holding the size of the box to dock. If not specified is set to size of molecular complex plus 5 angstroms. exhaustiveness: int, optional (default 10) - Tells Autodock Vina how exhaustive it should be with pose - generation. + Tells Autodock Vina how exhaustive it should be with pose generation. A + higher value of exhaustiveness implies more computation effort for the + docking experiment. num_modes: int, optional (default 9) Tells Autodock Vina how many binding modes it should generate at each invocation. @@ -352,6 +314,9 @@ class VinaPoseGenerator(PoseGenerator): If `True`, the pose generator will return scores for complexes. This is used typically when invoking external docking programs that compute scores. + kwargs: + Any args supported by VINA as documented in + https://autodock-vina.readthedocs.io/en/latest/vina.html Returns ------- @@ -365,6 +330,28 @@ class VinaPoseGenerator(PoseGenerator): ------ `ValueError` if `num_pockets` is set but `self.pocket_finder is None`. """ + if "cpu" in kwargs: + cpu = kwargs["cpu"] + else: + cpu = 0 + if "min_rmsd" in kwargs: + min_rmsd = kwargs["min_rmsd"] + else: + min_rmsd = 1.0 + if "max_evals" in kwargs: + max_evals = kwargs["max_evals"] + else: + max_evals = 0 + if "energy_range" in kwargs: + energy_range = kwargs["energy_range"] + else: + energy_range = 3.0 + + try: + from vina import Vina + except ModuleNotFoundError: + raise ImportError("This function requires vina to be installed") + if out_dir is None: out_dir = tempfile.mkdtemp() @@ -435,6 +422,7 @@ class VinaPoseGenerator(PoseGenerator): docked_complexes = [] all_scores = [] + vpg = Vina(sf_name='vina', cpu=cpu, seed=0, no_refine=False, verbosity=1) for i, (protein_centroid, box_dims) in enumerate( zip(centroids, dimensions)): logger.info("Docking in pocket %d/%d" % (i + 1, len(centroids))) @@ -451,23 +439,25 @@ class VinaPoseGenerator(PoseGenerator): num_modes=num_modes, exhaustiveness=exhaustiveness) - # Define locations of log and output files - log_file = os.path.join(out_dir, "%s_log.txt" % ligand_name) + # Define locations of output files out_pdbqt = os.path.join(out_dir, "%s_docked.pdbqt" % ligand_name) logger.info("About to call Vina") - if platform.system() == 'Windows': - args = [ - self.vina_cmd, "--config", conf_file, "--log", log_file, "--out", - out_pdbqt - ] - else: - # I'm not sure why specifying the args as a list fails on other platforms, - # but for some reason it only works if I pass it as a string. - # FIXME: Incompatible types in assignment - args = "%s --config %s --log %s --out %s" % ( # type: ignore - self.vina_cmd, conf_file, log_file, out_pdbqt) - # FIXME: We should use `subprocess.run` instead of `call` - call(args, shell=True) + + vpg.set_receptor(protein_pdbqt) + vpg.set_ligand_from_file(ligand_pdbqt) + + vpg.compute_vina_maps(center=protein_centroid, box_size=box_dims) + vpg.dock( + exhaustiveness=exhaustiveness, + n_poses=num_modes, + min_rmsd=min_rmsd, + max_evals=max_evals) + vpg.write_poses( + out_pdbqt, + n_poses=num_modes, + energy_range=energy_range, + overwrite=True) + ligands, scores = load_docked_ligands(out_pdbqt) docked_complexes += [(protein_mol[1], ligand) for ligand in ligands] all_scores += scores diff --git a/env.common.yml b/env.common.yml index 46417eeb3..c94d13b49 100644 --- a/env.common.yml +++ b/env.common.yml @@ -30,3 +30,4 @@ dependencies: - transformers==4.6.* - xgboost==1.* - git+https://github.com/samoturk/mol2vec + - vina diff --git a/requirements/env_common.yml b/requirements/env_common.yml index b1c6868df..45f78aac5 100644 --- a/requirements/env_common.yml +++ b/requirements/env_common.yml @@ -1,6 +1,5 @@ name: deepchem channels: - - omnia - conda-forge - defaults dependencies: @@ -24,3 +23,4 @@ dependencies: - transformers==4.6.* - xgboost==1.* - git+https://github.com/samoturk/mol2vec + - vina
deepchem/deepchem
7740d91e185b411c65b06c5d3aea647b0b6dee66
diff --git a/deepchem/dock/tests/test_pose_generation.py b/deepchem/dock/tests/test_pose_generation.py index 79b21d667..66387f367 100644 --- a/deepchem/dock/tests/test_pose_generation.py +++ b/deepchem/dock/tests/test_pose_generation.py @@ -19,7 +19,6 @@ class TestPoseGeneration(unittest.TestCase): Does sanity checks on pose generation. """ - @unittest.skipIf(IS_WINDOWS, 'Skip the test on Windows') def test_vina_initialization(self): """Test that VinaPoseGenerator can be initialized.""" dc.dock.VinaPoseGenerator() @@ -29,7 +28,6 @@ class TestPoseGeneration(unittest.TestCase): """Test that GninaPoseGenerator can be initialized.""" dc.dock.GninaPoseGenerator() - @unittest.skipIf(IS_WINDOWS, 'Skip the test on Windows') def test_pocket_vina_initialization(self): """Test that VinaPoseGenerator can be initialized.""" pocket_finder = dc.dock.ConvexHullPocketFinder()
Error in intializing VinaPoseGenerator ## 🐛 Bug ## To Reproduce Steps to reproduce the behavior: 1. Install deepchem latest version in colab `pip install --pre deepchem` 2. Run the following code sample: ``` import deepchem as dc vpg = dc.dock.VinaPoseGenerator() ``` The above raises a`SSLCertVerificationError` but it is expected to initialize `vpg`. There are two points regarding this: - The download location of autodock vina executables was updated from the side of Vina team. Previously, DeepChem referenced them from [here](http://vina.scripps.edu/download/autodock_vina_1_1_2_mac_64bit.tar.gz) but now it is referenced from [here](https://vina.scripps.edu/wp-content/uploads/sites/55/2020/12/autodock_vina_1_1_2_mac_64bit.tar.gz) - There is some problem in the server side which is causing `SSLCertVerificationError`, probably an expired SSL Certificate. Some possible fixes: - Move the executables to DeepChem's infrastructure - Upgrade to the latest version of Autodock vina - 1.2.2
0.0
7740d91e185b411c65b06c5d3aea647b0b6dee66
[ "deepchem/dock/tests/test_pose_generation.py::TestPoseGeneration::test_gnina_initialization", "deepchem/dock/tests/test_pose_generation.py::TestPoseGeneration::test_pocket_vina_initialization", "deepchem/dock/tests/test_pose_generation.py::TestPoseGeneration::test_vina_initialization" ]
[]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2021-11-04 16:57:48+00:00
mit
1,864
deepchem__deepchem-2802
diff --git a/deepchem/data/datasets.py b/deepchem/data/datasets.py index f80a399ca..dd5ba637f 100644 --- a/deepchem/data/datasets.py +++ b/deepchem/data/datasets.py @@ -2286,6 +2286,7 @@ class DiskDataset(Dataset): basename = "shard-%d" % shard_num DiskDataset.write_data_to_disk(self.data_dir, basename, X, y, w, ids) self._cached_shards = None + self.legacy_metadata = True def select(self, indices: Sequence[int],
deepchem/deepchem
9ef6c58eefd4e5f9bee40743ca14defa6f764f80
diff --git a/deepchem/data/tests/test_setshard.py b/deepchem/data/tests/test_setshard.py new file mode 100644 index 000000000..0fcf4b03e --- /dev/null +++ b/deepchem/data/tests/test_setshard.py @@ -0,0 +1,21 @@ +import deepchem as dc +import numpy as np + + +def test_setshard_with_X_y(): + """Test setsharding on a simple example""" + X = np.random.rand(10, 3) + y = np.random.rand(10,) + dataset = dc.data.DiskDataset.from_numpy(X, y) + X_shape, y_shape, _, _ = dataset.get_shape() + assert X_shape[0] == 10 + assert y_shape[0] == 10 + for i, (X, y, w, ids) in enumerate(dataset.itershards()): + X = X[1:] + y = y[1:] + w = w[1:] + ids = ids[1:] + dataset.set_shard(i, X, y, w, ids) + X_shape, y_shape, _, _ = dataset.get_shape() + assert X_shape[0] == 9 + assert y_shape[0] == 9
Bug in dataset.get_shape() when used after dataset.set_shard() ## 🐛 Bug ## To Reproduce <!-- If you have a code sample, error messages, stack traces, please provide it here as well. --> ## Expected behavior ``` import deepchem as dc import numpy as np X = np.random.randn(10, 3) y = np.random.randn(10) dataset = dc.data.DiskDataset.from_numpy(X, y) dataset.get_shape() # Output: ((10, 3), (10,), (10,), (10,)) for i, (X, y, w, ids) in enumerate(dataset.itershards()): X = X[1:] y = y[1:] w = w[1:] ids = ids[1:] dataset.set_shard(i, X, y, w, ids) dataset.get_shape() # Output: ((10, 3), (10,), (10,), (10,)) # Expected output: ((9, 3), (9, ), (9, ), (9,)) ``` Edit 1: This prints correctly: ``` for i, (X, y, w, ids) in enumerate(dataset.itershards()): print (X.shape) # Output: (9, 3) ``` ## Environment * DeepChem version: 2.6.0.dev ## Additional context The fix is probably a simple one.
0.0
9ef6c58eefd4e5f9bee40743ca14defa6f764f80
[ "deepchem/data/tests/test_setshard.py::test_setshard_with_X_y" ]
[]
{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }
2022-01-01 16:38:29+00:00
mit
1,865
deepchem__deepchem-2979
diff --git a/deepchem/feat/graph_data.py b/deepchem/feat/graph_data.py index b9d037e95..000b4d750 100644 --- a/deepchem/feat/graph_data.py +++ b/deepchem/feat/graph_data.py @@ -69,7 +69,9 @@ class GraphData: raise ValueError('edge_index.dtype must contains integers.') elif edge_index.shape[0] != 2: raise ValueError('The shape of edge_index is [2, num_edges].') - elif np.max(edge_index) >= len(node_features): + + # np.max() method works only for a non-empty array, so size of the array should be non-zero + elif (edge_index.size != 0) and (np.max(edge_index) >= len(node_features)): raise ValueError('edge_index contains the invalid node number.') if edge_features is not None:
deepchem/deepchem
ba780d3d21013b2924fd3301913ff530939a2ccb
diff --git a/deepchem/feat/tests/test_graph_data.py b/deepchem/feat/tests/test_graph_data.py index 4f28809c0..1d13cc76b 100644 --- a/deepchem/feat/tests/test_graph_data.py +++ b/deepchem/feat/tests/test_graph_data.py @@ -20,12 +20,11 @@ class TestGraph(unittest.TestCase): # z is kwargs z = np.random.random(5) - graph = GraphData( - node_features=node_features, - edge_index=edge_index, - edge_features=edge_features, - node_pos_features=node_pos_features, - z=z) + graph = GraphData(node_features=node_features, + edge_index=edge_index, + edge_features=edge_features, + node_pos_features=node_pos_features, + z=z) assert graph.num_nodes == num_nodes assert graph.num_node_features == num_node_features @@ -97,13 +96,12 @@ class TestGraph(unittest.TestCase): ] graph_list = [ - GraphData( - node_features=np.random.random_sample((num_nodes_list[i], - num_node_features)), - edge_index=edge_index_list[i], - edge_features=np.random.random_sample((num_edge_list[i], - num_edge_features)), - node_pos_features=None) for i in range(len(num_edge_list)) + GraphData(node_features=np.random.random_sample( + (num_nodes_list[i], num_node_features)), + edge_index=edge_index_list[i], + edge_features=np.random.random_sample( + (num_edge_list[i], num_edge_features)), + node_pos_features=None) for i in range(len(num_edge_list)) ] batch = BatchGraphData(graph_list) @@ -112,3 +110,22 @@ class TestGraph(unittest.TestCase): assert batch.num_edges == sum(num_edge_list) assert batch.num_edge_features == num_edge_features assert batch.graph_index.shape == (sum(num_nodes_list),) + + @pytest.mark.torch + def test_graph_data_single_atom_mol(self): + """ + Test for graph data when no edges in the graph (example: single atom mol) + """ + num_nodes, num_node_features = 1, 32 + num_edges = 0 + node_features = np.random.random_sample((num_nodes, num_node_features)) + edge_index = np.empty((2, 0), dtype=int) + + graph = GraphData(node_features=node_features, edge_index=edge_index) + + assert graph.num_nodes == num_nodes + assert graph.num_node_features == num_node_features + assert graph.num_edges == num_edges + assert str( + graph + ) == 'GraphData(node_features=[1, 32], edge_index=[2, 0], edge_features=None)'
GraphData class not working for single atom mols ## 🐛 Bug `GraphData` class checks if the `edge_index` contains the invalid node number, using the condition `np.max(edge_index) >= len(node_features)`. In case of single atom mols, `edge_index` in an empty array of `shape = (2, 0)` and np.max() method raises error for empty array : `Error: zero-size array to reduction operation maximum which has no identity`. ## To Reproduce Steps to reproduce the behaviour: code to check the error: ``` num_nodes, num_node_features = 1, 32 num_edges = 0 node_features = np.random.random_sample((num_nodes, num_node_features)) edge_index = np.empty((2, 0), dtype=int) graph = GraphData(node_features=node_features, edge_index=edge_index) assert graph.num_nodes == num_nodes assert graph.num_edges == num_edges assert str(graph) == 'GraphData(node_features=[1, 32], edge_index=[2, 0], edge_features=None)' ``` error message: `py::TestGraph::test_graph_data_single_atom_mol Failed with Error: zero-size array to reduction operation maximum which has no identity` ## Expected behaviour No error should have raised and `str(graph)` should return `'GraphData(node_features=[1, 32], edge_index=[2, 0], edge_features=None)'` ## Environment * OS: Ubuntu 20.04.3 LTS * Python version: Python 3.8.8 * DeepChem version: 2.6.1 * RDKit version (optional): * TensorFlow version (optional): * PyTorch version (optional): * Any other relevant information: NA ## Additional context This is how Deepchem generally computes edge index: ``` # construct edge (bond) index src, dest = [], [] for bond in datapoint.GetBonds(): # add edge list considering a directed graph start, end = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx() src += [start, end] dest += [end, start] ```
0.0
ba780d3d21013b2924fd3301913ff530939a2ccb
[ "deepchem/feat/tests/test_graph_data.py::TestGraph::test_graph_data_single_atom_mol" ]
[ "deepchem/feat/tests/test_graph_data.py::TestGraph::test_batch_graph_data", "deepchem/feat/tests/test_graph_data.py::TestGraph::test_invalid_graph_data" ]
{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }
2022-07-06 08:15:57+00:00
mit
1,866
deepset-ai__haystack-6594
diff --git a/haystack/components/writers/document_writer.py b/haystack/components/writers/document_writer.py index f4debb17..170ee24d 100644 --- a/haystack/components/writers/document_writer.py +++ b/haystack/components/writers/document_writer.py @@ -15,11 +15,15 @@ class DocumentWriter: A component for writing documents to a DocumentStore. """ - def __init__(self, document_store: DocumentStore, policy: DuplicatePolicy = DuplicatePolicy.FAIL): + def __init__(self, document_store: DocumentStore, policy: DuplicatePolicy = DuplicatePolicy.NONE): """ Create a DocumentWriter component. - :param policy: The policy to use when encountering duplicate documents (default is DuplicatePolicy.FAIL). + :param policy: the policy to apply when a Document with the same id already exists in the DocumentStore. + - `DuplicatePolicy.NONE`: Default policy, behaviour depends on the Document Store. + - `DuplicatePolicy.SKIP`: If a Document with the same id already exists, it is skipped and not written. + - `DuplicatePolicy.OVERWRITE`: If a Document with the same id already exists, it is overwritten. + - `DuplicatePolicy.FAIL`: If a Document with the same id already exists, an error is raised. """ self.document_store = document_store self.policy = policy diff --git a/haystack/core/component/connection.py b/haystack/core/component/connection.py index c84c9b5b..c3118aa4 100644 --- a/haystack/core/component/connection.py +++ b/haystack/core/component/connection.py @@ -116,21 +116,24 @@ class Connection: name_matches = [ (out_sock, in_sock) for out_sock, in_sock in possible_connections if in_sock.name == out_sock.name ] - if len(name_matches) != 1: - # TODO allow for multiple connections at once if there is no ambiguity? - # TODO give priority to sockets that have no default values? - connections_status_str = _connections_status( - sender_node=sender_node, - sender_sockets=sender_sockets, - receiver_node=receiver_node, - receiver_sockets=receiver_sockets, - ) - raise PipelineConnectError( - f"Cannot connect '{sender_node}' with '{receiver_node}': more than one connection is possible " - "between these components. Please specify the connection name, like: " - f"pipeline.connect('{sender_node}.{possible_connections[0][0].name}', " - f"'{receiver_node}.{possible_connections[0][1].name}').\n{connections_status_str}" - ) + if len(name_matches) == 1: + # Sockets match by type and name, let's use this + return Connection(sender_node, name_matches[0][0], receiver_node, name_matches[0][1]) + + # TODO allow for multiple connections at once if there is no ambiguity? + # TODO give priority to sockets that have no default values? + connections_status_str = _connections_status( + sender_node=sender_node, + sender_sockets=sender_sockets, + receiver_node=receiver_node, + receiver_sockets=receiver_sockets, + ) + raise PipelineConnectError( + f"Cannot connect '{sender_node}' with '{receiver_node}': more than one connection is possible " + "between these components. Please specify the connection name, like: " + f"pipeline.connect('{sender_node}.{possible_connections[0][0].name}', " + f"'{receiver_node}.{possible_connections[0][1].name}').\n{connections_status_str}" + ) match = possible_connections[0] return Connection(sender_node, match[0], receiver_node, match[1]) diff --git a/releasenotes/notes/document-writer-default-policy-693027781629fc73.yaml b/releasenotes/notes/document-writer-default-policy-693027781629fc73.yaml new file mode 100644 index 00000000..b90629fe --- /dev/null +++ b/releasenotes/notes/document-writer-default-policy-693027781629fc73.yaml @@ -0,0 +1,6 @@ +--- +enhancements: + - | + Change `DocumentWriter` default `policy` from `DuplicatePolicy.FAIL` to `DuplicatePolicy.NONE`. + The `DocumentStore` protocol uses the same default so that different Document Stores can choose + the default policy that better fit. diff --git a/releasenotes/notes/fix-connect-with-same-name-5ce470f7f0451362.yaml b/releasenotes/notes/fix-connect-with-same-name-5ce470f7f0451362.yaml new file mode 100644 index 00000000..529cd69a --- /dev/null +++ b/releasenotes/notes/fix-connect-with-same-name-5ce470f7f0451362.yaml @@ -0,0 +1,4 @@ +--- +fixes: + - | + Fix `Pipeline.connect()` so it connects sockets with same name if multiple sockets with compatible types are found.
deepset-ai/haystack
f877704839dc585cf47305d97fd5011be367b907
diff --git a/test/components/writers/test_document_writer.py b/test/components/writers/test_document_writer.py index 9858538f..623d5ee5 100644 --- a/test/components/writers/test_document_writer.py +++ b/test/components/writers/test_document_writer.py @@ -16,7 +16,7 @@ class TestDocumentWriter: "type": "haystack.components.writers.document_writer.DocumentWriter", "init_parameters": { "document_store": {"type": "haystack.testing.factory.MockedDocumentStore", "init_parameters": {}}, - "policy": "FAIL", + "policy": "NONE", }, } diff --git a/test/core/pipeline/test_connections.py b/test/core/pipeline/test_connections.py index ba4d70ca..a28a038a 100644 --- a/test/core/pipeline/test_connections.py +++ b/test/core/pipeline/test_connections.py @@ -386,3 +386,18 @@ def test_parse_connection(): assert parse_connect_string("foobar") == ("foobar", None) assert parse_connect_string("foo.bar") == ("foo", "bar") assert parse_connect_string("foo.bar.baz") == ("foo", "bar.baz") + + +def test_connect_with_same_socket_names(): + SimpleComponent = factory.component_class("SimpleComponent", output_types={"documents": List}) + ComponentWithMultipleInputs = factory.component_class( + "ComponentWithMultipleInputs", input_types={"question": Any, "documents": Any} + ) + + pipe = Pipeline() + pipe.add_component("simple", SimpleComponent()) + pipe.add_component("multiple", ComponentWithMultipleInputs()) + + pipe.connect("simple", "multiple") + + assert list(pipe.graph.edges) == [("simple", "multiple", "documents/documents")]
Auto-connect between pipeline components intermittently failing **Describe the bug** The connections between components when using the `.connect()` method of a pipeline are non-deterministic. We did find that *explicitly* defining the connection (as showcased in the documentation found [here](https://docs.haystack.deepset.ai/v2.0/docs/transformerssimilarityranker)) worked to resolve this issue, however it seems like it might be possible to ensure that if there *are* default connections that share a name, they be preferentially connected during graph construction. Hopefully all this makes sense - if not, I'm happy to follow-up! **Error message** There is no specific error. **Expected behavior** The logic should not connect two components by incompatible IDs or should not default to a random selection/decision. **Additional context** Creating connections like this will lead to a semi-random incidence of the pipeline graph being constructed incorrectly: ```python pipeline.connect("tgi_fetcher", "tgi_converter") pipeline.connect("tgi_converter", "tgi_splitter") pipeline.connect("tgi_splitter", "tgi_ranker") pipeline.connect("tgi_ranker", "tgi_prompt_builder") pipeline.connect("tgi_prompt_builder", "tgi_llm") ``` ![image](https://i.imgur.com/zUBwJaB.png) As you can hopefully see, the output of `ranker` (documents) is being connected to the `question` input of the `prompt_builder`. This is despite the fact that the `prompt_builder` has a `documents` input. You can get around the error by keying `documents` in your input - and swapping any potential prompt-templates, but this seems like undesirable behaviour. ```python pipeline.connect("tgi_fetcher", "tgi_converter") pipeline.connect("tgi_converter", "tgi_splitter") pipeline.connect("tgi_splitter", "tgi_ranker") pipeline.connect("tgi_ranker.documents", "tgi_prompt_builder.documents") pipeline.connect("tgi_prompt_builder", "tgi_llm") ``` **To Reproduce** ```python prompt_template = """ According to these documents: {% for doc in documents %} {{ doc.content }} {% endfor %} Answer the given question: {{question}} Answer: """ prompt_builder = PromptBuilder(template=prompt_template) fetcher = LinkContentFetcher() converter = HTMLToDocument() splitter = DocumentSplitter(split_length=100, split_overlap=5) llm = GPTGenerator(api_key = openai_api_key, model_name = "gpt-4") ranker = TransformersSimilarityRanker() pipeline = Pipeline() pipeline.add_component(name="fetcher", instance=fetcher) pipeline.add_component(name="converter", instance=converter) pipeline.add_component(name="splitter", instance=splitter) pipeline.add_component(name="ranker", instance=ranker) pipeline.add_component(name="prompt_builder", instance=prompt_builder) pipeline.add_component(name="llm", instance=llm) pipeline.connect("fetcher", "converter") pipeline.connect("converter", "splitter") pipeline.connect("splitter", "ranker") pipeline.connect("ranker", "prompt_builder") pipeline.connect("prompt_builder", "llm") question = "What is our favorite animal?" result = pipeline.run({"prompt_builder": {"question": question}, "ranker": {"query": question}, "fetcher": {"urls": ["https://haystack.deepset.ai/advent-of-haystack/day-1#challenge"]}}) print(result['llm']['replies'][0]) ``` **FAQ Check** - [x ] Have you had a look at [our new FAQ page](https://docs.haystack.deepset.ai/docs/faq)? **System:** - OS: Linux - GPU/CPU: CPU - Haystack version (commit or version number): 2.0.0b2 - DocumentStore: N/A - Reader: N/A - Retriever: N/A
0.0
f877704839dc585cf47305d97fd5011be367b907
[ "test/components/writers/test_document_writer.py::TestDocumentWriter::test_to_dict", "test/core/pipeline/test_connections.py::test_connect_with_same_socket_names" ]
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"test/core/pipeline/test_connections.py::test_connect_many_outputs_to_the_same_input", "test/core/pipeline/test_connections.py::test_connect_many_connections_possible_name_matches", "test/core/pipeline/test_connections.py::test_connect_many_connections_possible_no_name_matches", "test/core/pipeline/test_connections.py::test_parse_connection" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_media", "has_added_files", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2023-12-19 15:44:45+00:00
apache-2.0
1,867
deepset-ai__haystack-6717
diff --git a/haystack/core/component/component.py b/haystack/core/component/component.py index 4a082873..7d5eb00d 100644 --- a/haystack/core/component/component.py +++ b/haystack/core/component/component.py @@ -139,7 +139,10 @@ class ComponentMeta(type): instance.__canals_input__ = {} run_signature = inspect.signature(getattr(cls, "run")) for param in list(run_signature.parameters)[1:]: # First is 'self' and it doesn't matter. - if run_signature.parameters[param].kind == inspect.Parameter.POSITIONAL_OR_KEYWORD: # ignore `**kwargs` + if run_signature.parameters[param].kind not in ( + inspect.Parameter.VAR_POSITIONAL, + inspect.Parameter.VAR_KEYWORD, + ): # ignore variable args socket_kwargs = {"name": param, "type": run_signature.parameters[param].annotation} if run_signature.parameters[param].default != inspect.Parameter.empty: socket_kwargs["default_value"] = run_signature.parameters[param].default diff --git a/haystack/document_stores/in_memory/document_store.py b/haystack/document_stores/in_memory/document_store.py index 027e9c4b..44b2f6d5 100644 --- a/haystack/document_stores/in_memory/document_store.py +++ b/haystack/document_stores/in_memory/document_store.py @@ -212,8 +212,11 @@ class InMemoryDocumentStore: return_documents = [] for i in top_docs_positions: doc = all_documents[i] + score = docs_scores[i] + if score <= 0.0: + continue doc_fields = doc.to_dict() - doc_fields["score"] = docs_scores[i] + doc_fields["score"] = score return_document = Document.from_dict(doc_fields) return_documents.append(return_document) return return_documents diff --git a/releasenotes/notes/component-kw-only-run-args-eedee8907232d2d4.yaml b/releasenotes/notes/component-kw-only-run-args-eedee8907232d2d4.yaml new file mode 100644 index 00000000..68ef50fb --- /dev/null +++ b/releasenotes/notes/component-kw-only-run-args-eedee8907232d2d4.yaml @@ -0,0 +1,4 @@ +--- +fixes: + - | + Fix ComponentMeta ignoring keyword-only parameters in the `run` method. ComponentMeta.__call__ handles the creation of InputSockets for the component's inputs when the latter has not explicitly called _Component.set_input_types(). This logic was not correctly handling keyword-only parameters. diff --git a/releasenotes/notes/inmemorybm25retriever-zero-score-docs-67406062a76aa7f4.yaml b/releasenotes/notes/inmemorybm25retriever-zero-score-docs-67406062a76aa7f4.yaml new file mode 100644 index 00000000..3ae44016 --- /dev/null +++ b/releasenotes/notes/inmemorybm25retriever-zero-score-docs-67406062a76aa7f4.yaml @@ -0,0 +1,3 @@ +--- +fixes: + - Prevent InMemoryBM25Retriever from returning documents with a score of 0.0.
deepset-ai/haystack
0616197b44ae95da03aad7e5ac3997b243bd735d
diff --git a/test/components/retrievers/test_in_memory_bm25_retriever.py b/test/components/retrievers/test_in_memory_bm25_retriever.py index db5e82a3..4c1df2f2 100644 --- a/test/components/retrievers/test_in_memory_bm25_retriever.py +++ b/test/components/retrievers/test_in_memory_bm25_retriever.py @@ -113,15 +113,14 @@ class TestMemoryBM25Retriever: InMemoryBM25Retriever.from_dict(data) def test_retriever_valid_run(self, mock_docs): - top_k = 5 ds = InMemoryDocumentStore() ds.write_documents(mock_docs) - retriever = InMemoryBM25Retriever(ds, top_k=top_k) + retriever = InMemoryBM25Retriever(ds, top_k=5) result = retriever.run(query="PHP") assert "documents" in result - assert len(result["documents"]) == top_k + assert len(result["documents"]) == 1 assert result["documents"][0].content == "PHP is a popular programming language" def test_invalid_run_wrong_store_type(self): @@ -174,5 +173,5 @@ class TestMemoryBM25Retriever: assert "retriever" in result results_docs = result["retriever"]["documents"] assert results_docs - assert len(results_docs) == top_k + assert len(results_docs) == 1 assert results_docs[0].content == query_result diff --git a/test/core/component/test_component.py b/test/core/component/test_component.py index cba6fc42..f2835e62 100644 --- a/test/core/component/test_component.py +++ b/test/core/component/test_component.py @@ -176,3 +176,17 @@ def test_input_has_default_value(): comp = MockComponent() assert comp.__canals_input__["value"].default_value == 42 assert not comp.__canals_input__["value"].is_mandatory + + +def test_keyword_only_args(): + @component + class MockComponent: + def __init__(self): + component.set_output_types(self, value=int) + + def run(self, *, arg: int): + return {"value": arg} + + comp = MockComponent() + component_inputs = {name: {"type": socket.type} for name, socket in comp.__canals_input__.items()} + assert component_inputs == {"arg": {"type": int}} diff --git a/test/document_stores/test_in_memory.py b/test/document_stores/test_in_memory.py index 1d3a3613..9ebcae41 100644 --- a/test/document_stores/test_in_memory.py +++ b/test/document_stores/test_in_memory.py @@ -5,8 +5,8 @@ import pandas as pd import pytest from haystack import Document -from haystack.document_stores.in_memory import InMemoryDocumentStore from haystack.document_stores.errors import DocumentStoreError, DuplicateDocumentError +from haystack.document_stores.in_memory import InMemoryDocumentStore from haystack.testing.document_store import DocumentStoreBaseTests @@ -17,7 +17,7 @@ class TestMemoryDocumentStore(DocumentStoreBaseTests): # pylint: disable=R0904 @pytest.fixture def document_store(self) -> InMemoryDocumentStore: - return InMemoryDocumentStore() + return InMemoryDocumentStore(bm25_algorithm="BM25L") def test_to_dict(self): store = InMemoryDocumentStore() @@ -73,7 +73,6 @@ class TestMemoryDocumentStore(DocumentStoreBaseTests): # pylint: disable=R0904 document_store.write_documents(docs) def test_bm25_retrieval(self, document_store: InMemoryDocumentStore): - document_store = InMemoryDocumentStore() # Tests if the bm25_retrieval method returns the correct document based on the input query. docs = [Document(content="Hello world"), Document(content="Haystack supports multiple languages")] document_store.write_documents(docs) @@ -106,7 +105,7 @@ class TestMemoryDocumentStore(DocumentStoreBaseTests): # pylint: disable=R0904 document_store.write_documents(docs) # top_k = 2 - results = document_store.bm25_retrieval(query="languages", top_k=2) + results = document_store.bm25_retrieval(query="language", top_k=2) assert len(results) == 2 # top_k = 3 @@ -141,7 +140,7 @@ class TestMemoryDocumentStore(DocumentStoreBaseTests): # pylint: disable=R0904 document_store.write_documents(docs) results = document_store.bm25_retrieval(query="Python", top_k=1) - assert len(results) == 1 + assert len(results) == 0 document_store.write_documents([Document(content="Python is a popular programming language")]) results = document_store.bm25_retrieval(query="Python", top_k=1) @@ -199,10 +198,10 @@ class TestMemoryDocumentStore(DocumentStoreBaseTests): # pylint: disable=R0904 docs = [Document(), Document(content="Gardening"), Document(content="Bird watching")] document_store.write_documents(docs) results = document_store.bm25_retrieval(query="doesn't matter, top_k is 10", top_k=10) - assert len(results) == 2 + assert len(results) == 0 def test_bm25_retrieval_with_filters(self, document_store: InMemoryDocumentStore): - selected_document = Document(content="Gardening", meta={"selected": True}) + selected_document = Document(content="Java is, well...", meta={"selected": True}) docs = [Document(), selected_document, Document(content="Bird watching")] document_store.write_documents(docs) results = document_store.bm25_retrieval(query="Java", top_k=10, filters={"selected": True}) @@ -224,10 +223,10 @@ class TestMemoryDocumentStore(DocumentStoreBaseTests): # pylint: disable=R0904 assert results[0].id == document.id def test_bm25_retrieval_with_documents_with_mixed_content(self, document_store: InMemoryDocumentStore): - double_document = Document(content="Gardening", embedding=[1.0, 2.0, 3.0]) + double_document = Document(content="Gardening is a hobby", embedding=[1.0, 2.0, 3.0]) docs = [Document(embedding=[1.0, 2.0, 3.0]), double_document, Document(content="Bird watching")] document_store.write_documents(docs) - results = document_store.bm25_retrieval(query="Java", top_k=10, filters={"embedding": {"$not": None}}) + results = document_store.bm25_retrieval(query="Gardening", top_k=10, filters={"embedding": {"$not": None}}) assert len(results) == 1 assert results[0].id == double_document.id
MemoryBM25Retriever returns non relevant documents **Describe the bug** `MemoryBM25Retriever` currently always returns `top_k` number of `Document` even if they're not relevant. The [`test_retriever_valid_run`](https://github.com/deepset-ai/haystack/blob/ccc9f010bbdc75e1c5f1d269a43a5f06f36acba1/test/preview/components/retrievers/test_memory_bm25_retriever.py#L119-L129) is a good example of the current behavior. A simple fix would be to filter out `Document`s with `score==0.0` before scaling the score. **Expected behavior** Non relevant `Document`, those with score `0.0`, are not returned. **Additional context** @tstadel confirmed that it's unexpected we're returning `Document`s with a score of `0.0`. **To Reproduce** ``` from haystack.preview.document_stores import MemoryDocumentStore from haystack.preview.dataclasses import Document from haystack.preview.components.retrievers import MemoryBM25Retriever docs = [ Document(text="Javascript is a popular programming language"), Document(text="Java is a popular programming language"), Document(text="Python is a popular programming language"), Document(text="Ruby is a popular programming language"), Document(text="PHP is a popular programming language"), ] ds = MemoryDocumentStore() ds.write_documents(docs) retriever = MemoryBM25Retriever(ds, top_k=5, scale_score=False) result = retriever.run(query="PHP") # This is wrong assert len(result["documents"]) == 5 assert result["documents"][0].text == "PHP is a popular programming language" assert result["documents"][1].score == 0.0 assert result["documents"][2].score == 0.0 assert result["documents"][3].score == 0.0 assert result["documents"][4].score == 0.0 # This is the expected behaviour assert len(result["documents"]) == 1 assert result["documents"][0].text == "PHP is a popular programming language" assert result["documents"][0].score > 0.0 ```
0.0
0616197b44ae95da03aad7e5ac3997b243bd735d
[ "test/components/retrievers/test_in_memory_bm25_retriever.py::TestMemoryBM25Retriever::test_retriever_valid_run", "test/components/retrievers/test_in_memory_bm25_retriever.py::TestMemoryBM25Retriever::test_run_with_pipeline_and_top_k[Java-Java", "test/components/retrievers/test_in_memory_bm25_retriever.py::TestMemoryBM25Retriever::test_run_with_pipeline_and_top_k[Ruby-Ruby", "test/core/component/test_component.py::test_keyword_only_args", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_updated_docs", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_default_filter_for_text_and_dataframes" ]
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"test/components/retrievers/test_in_memory_bm25_retriever.py::TestMemoryBM25Retriever::test_from_dict_nonexisting_docstore", "test/components/retrievers/test_in_memory_bm25_retriever.py::TestMemoryBM25Retriever::test_invalid_run_wrong_store_type", "test/components/retrievers/test_in_memory_bm25_retriever.py::TestMemoryBM25Retriever::test_run_with_pipeline[Javascript-Javascript", "test/components/retrievers/test_in_memory_bm25_retriever.py::TestMemoryBM25Retriever::test_run_with_pipeline[Java-Java", "test/components/retrievers/test_in_memory_bm25_retriever.py::TestMemoryBM25Retriever::test_run_with_pipeline_and_top_k[Javascript-Javascript", "test/core/component/test_component.py::test_correct_declaration", "test/core/component/test_component.py::test_correct_declaration_with_additional_readonly_property", "test/core/component/test_component.py::test_correct_declaration_with_additional_writable_property", "test/core/component/test_component.py::test_missing_run", "test/core/component/test_component.py::test_set_input_types", "test/core/component/test_component.py::test_set_output_types", "test/core/component/test_component.py::test_output_types_decorator_with_compatible_type", "test/core/component/test_component.py::test_component_decorator_set_it_as_component", "test/core/component/test_component.py::test_input_has_default_value", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_no_filters", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_equal", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_equal_with_dataframe", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_equal_with_none", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_not_equal", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_not_equal_with_dataframe", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_not_equal_with_none", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_with_iso_date", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_with_string", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_with_dataframe", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_with_list", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_with_none", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_equal", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_equal_with_iso_date", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_equal_with_string", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_equal_with_dataframe", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_equal_with_list", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_greater_than_equal_with_none", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_with_iso_date", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_with_string", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_with_dataframe", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_with_list", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_with_none", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_equal", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_equal_with_iso_date", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_equal_with_string", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_equal_with_dataframe", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_equal_with_list", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_less_than_equal_with_none", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_in", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_in_with_with_non_list", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_in_with_with_non_list_iterable", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_not_in", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_not_in_with_with_non_list", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_comparison_not_in_with_with_non_list_iterable", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_and_operator", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_or_operator", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_not_operator", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_missing_top_level_operator_key", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_missing_top_level_conditions_key", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_missing_condition_field_key", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_missing_condition_operator_key", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_missing_condition_value_key", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_delete_documents", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_delete_documents_empty_document_store", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_delete_documents_non_existing_document", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_write_documents_duplicate_fail", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_write_documents_duplicate_skip", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_write_documents_duplicate_overwrite", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_write_documents_invalid_input", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_count_empty", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_count_not_empty", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_to_dict", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_to_dict_with_custom_init_parameters", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_from_dict", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_write_documents", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_empty_document_store", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_empty_query", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_different_top_k", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_two_queries", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_scale_score", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_table_content", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_text_and_table_content", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_filters", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_filters_keeps_default_filters", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_filters_on_text_or_dataframe", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_bm25_retrieval_with_documents_with_mixed_content", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_embedding_retrieval", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_embedding_retrieval_invalid_query", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_embedding_retrieval_no_embeddings", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_embedding_retrieval_some_documents_wo_embeddings", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_embedding_retrieval_documents_different_embedding_sizes", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_embedding_retrieval_query_documents_different_embedding_sizes", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_embedding_retrieval_with_different_top_k", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_embedding_retrieval_with_scale_score", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_embedding_retrieval_return_embedding", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_compute_cosine_similarity_scores", "test/document_stores/test_in_memory.py::TestMemoryDocumentStore::test_compute_dot_product_similarity_scores" ]
{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2024-01-10 10:15:54+00:00
apache-2.0
1,868
deepset-ai__haystack-6941
diff --git a/haystack/components/extractors/named_entity_extractor.py b/haystack/components/extractors/named_entity_extractor.py index 6ca988fa..f8d8d717 100644 --- a/haystack/components/extractors/named_entity_extractor.py +++ b/haystack/components/extractors/named_entity_extractor.py @@ -126,6 +126,9 @@ class NamedEntityExtractor: raise ComponentError(f"Unknown NER backend '{type(backend).__name__}' for extractor") def warm_up(self): + """ + Initialize the named entity extractor backend. + """ try: self._backend.initialize() except Exception as e: @@ -135,6 +138,16 @@ class NamedEntityExtractor: @component.output_types(documents=List[Document]) def run(self, documents: List[Document], batch_size: int = 1) -> Dict[str, Any]: + """ + Run the named-entity extractor. + + :param documents: + Documents to process. + :param batch_size: + Batch size used for processing the documents. + :returns: + The processed documents. + """ texts = [doc.content if doc.content is not None else "" for doc in documents] annotations = self._backend.annotate(texts, batch_size=batch_size) @@ -150,6 +163,9 @@ class NamedEntityExtractor: return {"documents": documents} def to_dict(self) -> Dict[str, Any]: + """ + Serialize this component to a dictionary. + """ return default_to_dict( self, backend=self._backend.type, @@ -160,6 +176,12 @@ class NamedEntityExtractor: @classmethod def from_dict(cls, data: Dict[str, Any]) -> "NamedEntityExtractor": + """ + Deserialize the component from a dictionary. + + :param data: + The dictionary to deserialize from. + """ try: init_params = data["init_parameters"] init_params["device"] = ComponentDevice.from_dict(init_params["device"]) diff --git a/haystack/core/component/component.py b/haystack/core/component/component.py index 95ae87d7..c231e41d 100644 --- a/haystack/core/component/component.py +++ b/haystack/core/component/component.py @@ -160,6 +160,21 @@ class ComponentMeta(type): return instance +def _component_repr(component: Component) -> str: + """ + All Components override their __repr__ method with this one. + It prints the component name and the input/output sockets. + """ + result = object.__repr__(component) + if pipeline := getattr(component, "__haystack_added_to_pipeline__"): + # This Component has been added in a Pipeline, let's get the name from there. + result += f"\n{pipeline.get_component_name(component)}" + + # We're explicitly ignoring the type here because we're sure that the component + # has the __haystack_input__ and __haystack_output__ attributes at this point + return f"{result}\n{component.__haystack_input__}\n{component.__haystack_output__}" # type: ignore[attr-defined] + + class _Component: """ See module's docstring. @@ -332,6 +347,9 @@ class _Component: self.registry[class_path] = class_ logger.debug("Registered Component %s", class_) + # Override the __repr__ method with a default one + class_.__repr__ = _component_repr + return class_ def __call__(self, class_): diff --git a/haystack/core/component/sockets.py b/haystack/core/component/sockets.py index 25bf4fdc..374ae630 100644 --- a/haystack/core/component/sockets.py +++ b/haystack/core/component/sockets.py @@ -82,8 +82,9 @@ class Sockets: return pipeline.get_component_name(self._component) # This Component has not been added to a Pipeline yet, so we can't know its name. - # Let's use the class name instead. - return str(self._component) + # Let's use default __repr__. We don't call repr() directly as Components have a custom + # __repr__ method and that would lead to infinite recursion since we call Sockets.__repr__ in it. + return object.__repr__(self._component) def __getattribute__(self, name): try: @@ -96,12 +97,10 @@ class Sockets: return object.__getattribute__(self, name) def __repr__(self) -> str: - result = self._component_name() + result = "" if self._sockets_io_type == InputSocket: - result += " inputs:\n" + result = "Inputs:\n" elif self._sockets_io_type == OutputSocket: - result += " outputs:\n" + result = "Outputs:\n" - result += "\n".join([f" - {n}: {_type_name(s.type)}" for n, s in self._sockets_dict.items()]) - - return result + return result + "\n".join([f" - {n}: {_type_name(s.type)}" for n, s in self._sockets_dict.items()]) diff --git a/releasenotes/notes/component-repr-a6486af81530bc3b.yaml b/releasenotes/notes/component-repr-a6486af81530bc3b.yaml new file mode 100644 index 00000000..3a7439e9 --- /dev/null +++ b/releasenotes/notes/component-repr-a6486af81530bc3b.yaml @@ -0,0 +1,6 @@ +--- +enhancements: + - | + Add `__repr__` to all Components to print their I/O. + This can also be useful in Jupyter notebooks as this will be shown as a cell output + if the it's the last expression in a cell.
deepset-ai/haystack
74683fe74d400820a442cca03bb69473824e841a
diff --git a/e2e/pipelines/test_rag_pipelines_e2e.py b/e2e/pipelines/test_rag_pipelines_e2e.py index fa3aeb8c..d38053c9 100644 --- a/e2e/pipelines/test_rag_pipelines_e2e.py +++ b/e2e/pipelines/test_rag_pipelines_e2e.py @@ -30,7 +30,7 @@ def test_bm25_rag_pipeline(tmp_path): rag_pipeline = Pipeline() rag_pipeline.add_component(instance=InMemoryBM25Retriever(document_store=InMemoryDocumentStore()), name="retriever") rag_pipeline.add_component(instance=PromptBuilder(template=prompt_template), name="prompt_builder") - rag_pipeline.add_component(instance=OpenAIGenerator(api_key=os.environ.get("OPENAI_API_KEY")), name="llm") + rag_pipeline.add_component(instance=OpenAIGenerator(), name="llm") rag_pipeline.add_component(instance=AnswerBuilder(), name="answer_builder") rag_pipeline.connect("retriever", "prompt_builder.documents") rag_pipeline.connect("prompt_builder", "llm") @@ -101,7 +101,7 @@ def test_embedding_retrieval_rag_pipeline(tmp_path): instance=InMemoryEmbeddingRetriever(document_store=InMemoryDocumentStore()), name="retriever" ) rag_pipeline.add_component(instance=PromptBuilder(template=prompt_template), name="prompt_builder") - rag_pipeline.add_component(instance=OpenAIGenerator(api_key=os.environ.get("OPENAI_API_KEY")), name="llm") + rag_pipeline.add_component(instance=OpenAIGenerator(), name="llm") rag_pipeline.add_component(instance=AnswerBuilder(), name="answer_builder") rag_pipeline.connect("text_embedder", "retriever") rag_pipeline.connect("retriever", "prompt_builder.documents") diff --git a/test/core/component/test_component.py b/test/core/component/test_component.py index bbe2605f..b093c32b 100644 --- a/test/core/component/test_component.py +++ b/test/core/component/test_component.py @@ -4,6 +4,7 @@ import pytest from haystack.core.component import Component, InputSocket, OutputSocket, component from haystack.core.errors import ComponentError +from haystack.core.pipeline import Pipeline def test_correct_declaration(): @@ -189,3 +190,31 @@ def test_keyword_only_args(): comp = MockComponent() component_inputs = {name: {"type": socket.type} for name, socket in comp.__haystack_input__._sockets_dict.items()} assert component_inputs == {"arg": {"type": int}} + + +def test_repr(): + @component + class MockComponent: + def __init__(self): + component.set_output_types(self, value=int) + + def run(self, value: int): + return {"value": value} + + comp = MockComponent() + assert repr(comp) == f"{object.__repr__(comp)}\nInputs:\n - value: int\nOutputs:\n - value: int" + + +def test_repr_added_to_pipeline(): + @component + class MockComponent: + def __init__(self): + component.set_output_types(self, value=int) + + def run(self, value: int): + return {"value": value} + + pipe = Pipeline() + comp = MockComponent() + pipe.add_component("my_component", comp) + assert repr(comp) == f"{object.__repr__(comp)}\nmy_component\nInputs:\n - value: int\nOutputs:\n - value: int" diff --git a/test/core/component/test_sockets.py b/test/core/component/test_sockets.py index ac3b01bd..6e942b84 100644 --- a/test/core/component/test_sockets.py +++ b/test/core/component/test_sockets.py @@ -23,19 +23,6 @@ class TestSockets: assert io._component == comp assert io._sockets_dict == {} - def test_component_name(self): - comp = component_class("SomeComponent")() - io = Sockets(component=comp, sockets_dict={}, sockets_io_type=InputSocket) - assert io._component_name() == str(comp) - - def test_component_name_added_to_pipeline(self): - comp = component_class("SomeComponent")() - pipeline = Pipeline() - pipeline.add_component("my_component", comp) - - io = Sockets(component=comp, sockets_dict={}, sockets_io_type=InputSocket) - assert io._component_name() == "my_component" - def test_getattribute(self): comp = component_class("SomeComponent", input_types={"input_1": int, "input_2": int})() io = Sockets(component=comp, sockets_dict=comp.__haystack_input__._sockets_dict, sockets_io_type=InputSocket) @@ -54,4 +41,4 @@ class TestSockets: comp = component_class("SomeComponent", input_types={"input_1": int, "input_2": int})() io = Sockets(component=comp, sockets_dict=comp.__haystack_input__._sockets_dict, sockets_io_type=InputSocket) res = repr(io) - assert res == f"{comp} inputs:\n - input_1: int\n - input_2: int" + assert res == "Inputs:\n - input_1: int\n - input_2: int"
RAG pipeline e2e test fails to resolve api key **Describe the bug** `e2e/pipelines/test_rag_pipelines_e2e.py` fails resolving the OpenAI api key after the PR that changed the secret management. https://github.com/deepset-ai/haystack/pull/6887 Here is the failing test run: https://github.com/deepset-ai/haystack/actions/runs/7792596449/job/21250892136 **Error message** ```python self.client = OpenAI(api_key=api_key.resolve_value(), organization=organization, base_url=api_base_url) E AttributeError: 'str' object has no attribute 'resolve_value' ```
0.0
74683fe74d400820a442cca03bb69473824e841a
[ "test/core/component/test_component.py::test_repr", "test/core/component/test_component.py::test_repr_added_to_pipeline", "test/core/component/test_sockets.py::TestSockets::test_repr" ]
[ "test/core/component/test_component.py::test_correct_declaration", "test/core/component/test_component.py::test_correct_declaration_with_additional_readonly_property", "test/core/component/test_component.py::test_correct_declaration_with_additional_writable_property", "test/core/component/test_component.py::test_missing_run", "test/core/component/test_component.py::test_set_input_types", "test/core/component/test_component.py::test_set_output_types", "test/core/component/test_component.py::test_output_types_decorator_with_compatible_type", "test/core/component/test_component.py::test_component_decorator_set_it_as_component", "test/core/component/test_component.py::test_input_has_default_value", "test/core/component/test_component.py::test_keyword_only_args", "test/core/component/test_sockets.py::TestSockets::test_init", "test/core/component/test_sockets.py::TestSockets::test_init_with_empty_sockets", "test/core/component/test_sockets.py::TestSockets::test_getattribute", "test/core/component/test_sockets.py::TestSockets::test_getattribute_non_existing_socket" ]
{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2024-02-08 09:38:11+00:00
apache-2.0
1,869
deepset-ai__haystack-6963
diff --git a/haystack/core/pipeline/pipeline.py b/haystack/core/pipeline/pipeline.py index 632cc73e..98ba8df8 100644 --- a/haystack/core/pipeline/pipeline.py +++ b/haystack/core/pipeline/pipeline.py @@ -71,6 +71,34 @@ class Pipeline: return False return self.to_dict() == other.to_dict() + def __repr__(self) -> str: + """ + Returns a text representation of the Pipeline. + If this runs in a Jupyter notebook, it will instead display the Pipeline image. + """ + if is_in_jupyter(): + # If we're in a Jupyter notebook we want to display the image instead of the text repr. + self.show() + return "" + + res = f"{object.__repr__(self)}\n" + if self.metadata: + res += "🧱 Metadata\n" + for k, v in self.metadata.items(): + res += f" - {k}: {v}\n" + + res += "🚅 Components\n" + for name, instance in self.graph.nodes(data="instance"): + res += f" - {name}: {instance.__class__.__name__}\n" + + res += "🛤️ Connections\n" + for sender, receiver, edge_data in self.graph.edges(data=True): + sender_socket = edge_data["from_socket"].name + receiver_socket = edge_data["to_socket"].name + res += f" - {sender}.{sender_socket} -> {receiver}.{receiver_socket} ({edge_data['conn_type']})\n" + + return res + def to_dict(self) -> Dict[str, Any]: """ Returns this Pipeline instance as a dictionary. diff --git a/releasenotes/notes/enhance-repr-0c5efa1e2ca6bafa.yaml b/releasenotes/notes/enhance-repr-0c5efa1e2ca6bafa.yaml new file mode 100644 index 00000000..a9f1914e --- /dev/null +++ b/releasenotes/notes/enhance-repr-0c5efa1e2ca6bafa.yaml @@ -0,0 +1,5 @@ +--- +enhancements: + - | + Customize `Pipeline.__repr__()` to return a nice text representation of it. + If run on a Jupyter notebook it will instead have the same behaviour as `Pipeline.show()`.
deepset-ai/haystack
a7f36fdd3226cd822c600c724c2b72005180269a
diff --git a/test/core/pipeline/test_pipeline.py b/test/core/pipeline/test_pipeline.py index c6dec132..4e66f38f 100644 --- a/test/core/pipeline/test_pipeline.py +++ b/test/core/pipeline/test_pipeline.py @@ -79,6 +79,49 @@ def test_get_component_name_not_added_to_pipeline(): assert pipe.get_component_name(some_component) == "" +@patch("haystack.core.pipeline.pipeline.is_in_jupyter") +def test_repr(mock_is_in_jupyter): + pipe = Pipeline(metadata={"test": "test"}, max_loops_allowed=42) + pipe.add_component("add_two", AddFixedValue(add=2)) + pipe.add_component("add_default", AddFixedValue()) + pipe.add_component("double", Double()) + pipe.connect("add_two", "double") + pipe.connect("double", "add_default") + + expected_repr = ( + f"{object.__repr__(pipe)}\n" + "🧱 Metadata\n" + " - test: test\n" + "🚅 Components\n" + " - add_two: AddFixedValue\n" + " - add_default: AddFixedValue\n" + " - double: Double\n" + "🛤️ Connections\n" + " - add_two.result -> double.value (int)\n" + " - double.value -> add_default.value (int)\n" + ) + # Simulate not being in a notebook + mock_is_in_jupyter.return_value = False + assert repr(pipe) == expected_repr + + +@patch("haystack.core.pipeline.pipeline.is_in_jupyter") +def test_repr_in_notebook(mock_is_in_jupyter): + pipe = Pipeline(metadata={"test": "test"}, max_loops_allowed=42) + pipe.add_component("add_two", AddFixedValue(add=2)) + pipe.add_component("add_default", AddFixedValue()) + pipe.add_component("double", Double()) + pipe.connect("add_two", "double") + pipe.connect("double", "add_default") + + # Simulate being in a notebook + mock_is_in_jupyter.return_value = True + + with patch.object(Pipeline, "show") as mock_show: + assert repr(pipe) == "" + mock_show.assert_called_once_with() + + def test_run_with_component_that_does_not_return_dict(): BrokenComponent = component_class( "BrokenComponent", input_types={"a": int}, output_types={"b": int}, output=1 # type:ignore
`Pipeline.__repr__` should display an easy to understand representation of the Pipeline When working and creating a `Pipeline` it's useful to quickly get an easy to understand text representation of it. This should display connections between components, the I/O of the Pipeline, missing mandatory connections and other useful information. This is also useful when working in a Jupyter notebook, if the `Pipeline` is the last statement in a cell the user will get a nice representation of the `Pipeline` for free. Some examples: Pandas' DataFrame ![Pandas' DataFrame](https://github.com/deepset-ai/haystack/assets/3314350/0703ecdb-2e4c-4db0-92da-27709c1a3d80) DocArray document ![DocArray document](https://github.com/deepset-ai/haystack/assets/3314350/1e8054d0-06f6-4a20-82ee-74fecada8000)
0.0
a7f36fdd3226cd822c600c724c2b72005180269a
[ "test/core/pipeline/test_pipeline.py::test_repr", "test/core/pipeline/test_pipeline.py::test_repr_in_notebook" ]
[ "test/core/pipeline/test_pipeline.py::test_show_in_notebook", "test/core/pipeline/test_pipeline.py::test_show_not_in_notebook", "test/core/pipeline/test_pipeline.py::test_draw", "test/core/pipeline/test_pipeline.py::test_add_component_to_different_pipelines", "test/core/pipeline/test_pipeline.py::test_get_component_name", "test/core/pipeline/test_pipeline.py::test_get_component_name_not_added_to_pipeline", "test/core/pipeline/test_pipeline.py::test_run_with_component_that_does_not_return_dict", "test/core/pipeline/test_pipeline.py::test_to_dict", "test/core/pipeline/test_pipeline.py::test_from_dict", "test/core/pipeline/test_pipeline.py::test_from_dict_with_empty_dict", "test/core/pipeline/test_pipeline.py::test_from_dict_with_components_instances", "test/core/pipeline/test_pipeline.py::test_from_dict_without_component_type", "test/core/pipeline/test_pipeline.py::test_from_dict_without_registered_component_type", "test/core/pipeline/test_pipeline.py::test_from_dict_without_connection_sender", "test/core/pipeline/test_pipeline.py::test_from_dict_without_connection_receiver", "test/core/pipeline/test_pipeline.py::test_falsy_connection", "test/core/pipeline/test_pipeline.py::test_describe_input_only_no_inputs_components", "test/core/pipeline/test_pipeline.py::test_describe_input_some_components_with_no_inputs", "test/core/pipeline/test_pipeline.py::test_describe_input_all_components_have_inputs", "test/core/pipeline/test_pipeline.py::test_describe_output_multiple_possible", "test/core/pipeline/test_pipeline.py::test_describe_output_single", "test/core/pipeline/test_pipeline.py::test_describe_no_outputs" ]
{ "failed_lite_validators": [ "has_added_files" ], "has_test_patch": true, "is_lite": false }
2024-02-08 17:34:44+00:00
apache-2.0
1,870
deepset-ai__haystack-7038
diff --git a/haystack/components/evaluators/statistical_evaluator.py b/haystack/components/evaluators/statistical_evaluator.py index 6f65fc10..a6c00964 100644 --- a/haystack/components/evaluators/statistical_evaluator.py +++ b/haystack/components/evaluators/statistical_evaluator.py @@ -1,4 +1,5 @@ import collections +import itertools from enum import Enum from typing import Any, Dict, List, Union @@ -16,6 +17,8 @@ class StatisticalMetric(Enum): F1 = "f1" EM = "exact_match" + RECALL_SINGLE_HIT = "recall_single_hit" + RECALL_MULTI_HIT = "recall_multi_hit" @classmethod def from_str(cls, metric: str) -> "StatisticalMetric": @@ -47,7 +50,12 @@ class StatisticalEvaluator: metric = StatisticalMetric.from_str(metric) self._metric = metric - self._metric_function = {StatisticalMetric.F1: self._f1, StatisticalMetric.EM: self._exact_match}[self._metric] + self._metric_function = { + StatisticalMetric.F1: self._f1, + StatisticalMetric.EM: self._exact_match, + StatisticalMetric.RECALL_SINGLE_HIT: self._recall_single_hit, + StatisticalMetric.RECALL_MULTI_HIT: self._recall_multi_hit, + }[self._metric] def to_dict(self) -> Dict[str, Any]: return default_to_dict(self, metric=self._metric.value) @@ -68,9 +76,6 @@ class StatisticalEvaluator: :returns: A dictionary with the following outputs: * `result` - Calculated result of the chosen metric. """ - if len(labels) != len(predictions): - raise ValueError("The number of predictions and labels must be the same.") - return {"result": self._metric_function(labels, predictions)} @staticmethod @@ -78,6 +83,9 @@ class StatisticalEvaluator: """ Measure word overlap between predictions and labels. """ + if len(labels) != len(predictions): + raise ValueError("The number of predictions and labels must be the same.") + if len(predictions) == 0: # We expect callers of this function already checked if predictions and labels are equal length return 0.0 @@ -105,8 +113,40 @@ class StatisticalEvaluator: """ Measure the proportion of cases where predictiond is identical to the the expected label. """ + if len(labels) != len(predictions): + raise ValueError("The number of predictions and labels must be the same.") + if len(predictions) == 0: # We expect callers of this function already checked if predictions and labels are equal length return 0.0 score_list = np_array(predictions) == np_array(labels) return np_mean(score_list) + + @staticmethod + def _recall_single_hit(labels: List[str], predictions: List[str]) -> float: + """ + Measures how many times a label is present in at least one prediction. + If the same label is found in multiple predictions it is only counted once. + """ + if len(labels) == 0: + return 0.0 + + # In Recall Single Hit we only consider if a label is present in at least one prediction. + # No need to count multiple occurrences of the same label in different predictions + retrieved_labels = {l for l, p in itertools.product(labels, predictions) if l in p} + return len(retrieved_labels) / len(labels) + + @staticmethod + def _recall_multi_hit(labels: List[str], predictions: List[str]) -> float: + """ + Measures how many times a label is present in at least one or more predictions. + """ + if len(labels) == 0: + return 0.0 + + correct_retrievals = 0 + for label, prediction in itertools.product(labels, predictions): + if label in prediction: + correct_retrievals += 1 + + return correct_retrievals / len(labels)
deepset-ai/haystack
5910b4adc9b2688155abb8d2290e5cf56833eb0b
diff --git a/test/components/evaluators/test_statistical_evaluator.py b/test/components/evaluators/test_statistical_evaluator.py index e98899cb..619b2584 100644 --- a/test/components/evaluators/test_statistical_evaluator.py +++ b/test/components/evaluators/test_statistical_evaluator.py @@ -121,3 +121,71 @@ class TestStatisticalEvaluatorExactMatch: result = evaluator.run(labels=labels, predictions=predictions) assert len(result) == 1 assert result["result"] == 2 / 3 + + +class TestStatisticalEvaluatorRecallSingleHit: + def test_run(self): + evaluator = StatisticalEvaluator(metric=StatisticalMetric.RECALL_SINGLE_HIT) + labels = ["Eiffel Tower", "Louvre Museum", "Colosseum", "Trajan's Column"] + predictions = [ + "The Eiffel Tower, completed in 1889, symbolizes Paris's cultural magnificence.", + "The Eiffel Tower max height is 330 meters.", + "Louvre Museum is the world's largest art museum and a historic monument in Paris, France.", + "The Leaning Tower of Pisa is the campanile, or freestanding bell tower, of Pisa Cathedral.", + ] + result = evaluator.run(labels=labels, predictions=predictions) + assert len(result) == 1 + assert result["result"] == 2 / 4 + + def test_run_with_empty_labels(self): + evaluator = StatisticalEvaluator(metric=StatisticalMetric.RECALL_SINGLE_HIT) + predictions = [ + "The Eiffel Tower, completed in 1889, symbolizes Paris's cultural magnificence.", + "The Eiffel Tower max height is 330 meters.", + "Louvre Museum is the world's largest art museum and a historic monument in Paris, France.", + "The Leaning Tower of Pisa is the campanile, or freestanding bell tower, of Pisa Cathedral.", + ] + result = evaluator.run(labels=[], predictions=predictions) + assert len(result) == 1 + assert result["result"] == 0.0 + + def test_run_with_empty_predictions(self): + evaluator = StatisticalEvaluator(metric=StatisticalMetric.RECALL_SINGLE_HIT) + labels = ["Eiffel Tower", "Louvre Museum", "Colosseum", "Trajan's Column"] + result = evaluator.run(labels=labels, predictions=[]) + assert len(result) == 1 + assert result["result"] == 0.0 + + +class TestStatisticalEvaluatorRecallMultiHit: + def test_run(self): + evaluator = StatisticalEvaluator(metric=StatisticalMetric.RECALL_MULTI_HIT) + labels = ["Eiffel Tower", "Louvre Museum", "Colosseum", "Trajan's Column"] + predictions = [ + "The Eiffel Tower, completed in 1889, symbolizes Paris's cultural magnificence.", + "The Eiffel Tower max height is 330 meters.", + "Louvre Museum is the world's largest art museum and a historic monument in Paris, France.", + "The Leaning Tower of Pisa is the campanile, or freestanding bell tower, of Pisa Cathedral.", + ] + result = evaluator.run(labels=labels, predictions=predictions) + assert len(result) == 1 + assert result["result"] == 0.75 + + def test_run_with_empty_labels(self): + evaluator = StatisticalEvaluator(metric=StatisticalMetric.RECALL_MULTI_HIT) + predictions = [ + "The Eiffel Tower, completed in 1889, symbolizes Paris's cultural magnificence.", + "The Eiffel Tower max height is 330 meters.", + "Louvre Museum is the world's largest art museum and a historic monument in Paris, France.", + "The Leaning Tower of Pisa is the campanile, or freestanding bell tower, of Pisa Cathedral.", + ] + result = evaluator.run(labels=[], predictions=predictions) + assert len(result) == 1 + assert result["result"] == 0.0 + + def test_run_with_empty_predictions(self): + evaluator = StatisticalEvaluator(metric=StatisticalMetric.RECALL_MULTI_HIT) + labels = ["Eiffel Tower", "Louvre Museum", "Colosseum", "Trajan's Column"] + result = evaluator.run(labels=labels, predictions=[]) + assert len(result) == 1 + assert result["result"] == 0.0
Implement function to calculate Recall metric As specified in proposal #5794 we need to implement a function to calculate the Recall metric. Ideally the function should be part of the private interface and called only through the `calculate_metrics` function (see #6063). `_calculate_recall()` could be a nice name. For more detailed information check out the original proposal.
0.0
5910b4adc9b2688155abb8d2290e5cf56833eb0b
[ "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorRecallSingleHit::test_run", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorRecallSingleHit::test_run_with_empty_labels", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorRecallSingleHit::test_run_with_empty_predictions", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorRecallMultiHit::test_run", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorRecallMultiHit::test_run_with_empty_labels", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorRecallMultiHit::test_run_with_empty_predictions" ]
[ "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluator::test_init_default", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluator::test_init_with_string", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluator::test_to_dict", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluator::test_from_dict", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorF1::test_run_with_empty_inputs", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorF1::test_run_with_different_lengths", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorF1::test_run_with_matching_predictions", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorF1::test_run_with_single_prediction", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorF1::test_run_with_mismatched_predictions", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorExactMatch::test_run_with_empty_inputs", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorExactMatch::test_run_with_different_lengths", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorExactMatch::test_run_with_matching_predictions", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorExactMatch::test_run_with_single_prediction", "test/components/evaluators/test_statistical_evaluator.py::TestStatisticalEvaluatorExactMatch::test_run_with_mismatched_predictions" ]
{ "failed_lite_validators": [ "has_issue_reference", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2024-02-19 15:37:23+00:00
apache-2.0
1,871
deepset-ai__haystack-7381
diff --git a/haystack/components/evaluators/__init__.py b/haystack/components/evaluators/__init__.py new file mode 100644 index 00000000..9550a5f4 --- /dev/null +++ b/haystack/components/evaluators/__init__.py @@ -0,0 +1,3 @@ +from .answer_exact_match import AnswerExactMatchEvaluator + +__all__ = ["AnswerExactMatchEvaluator"] diff --git a/haystack/components/evaluators/answer_exact_match.py b/haystack/components/evaluators/answer_exact_match.py new file mode 100644 index 00000000..4927f4e1 --- /dev/null +++ b/haystack/components/evaluators/answer_exact_match.py @@ -0,0 +1,59 @@ +from typing import Dict, List + +from haystack.core.component import component + + +@component +class AnswerExactMatchEvaluator: + """ + Evaluator that checks if the predicted answers matches any of the ground truth answers exactly. + The result is a number from 0.0 to 1.0, it represents the proportion of questions where any predicted answer + matched one of the ground truth answers. + Each question can have multiple ground truth answers and multiple predicted answers. + + Usage example: + ```python + from haystack.components.evaluators import AnswerExactMatchEvaluator + + evaluator = AnswerExactMatchEvaluator() + result = evaluator.run( + questions=["What is the capital of Germany?", "What is the capital of France?"], + ground_truth_answers=[["Berlin"], ["Paris"]], + predicted_answers=[["Berlin"], ["Paris"]], + ) + print(result["result"]) + # 1.0 + ``` + """ + + @component.output_types(result=float) + def run( + self, questions: List[str], ground_truth_answers: List[List[str]], predicted_answers: List[List[str]] + ) -> Dict[str, float]: + """ + Run the AnswerExactMatchEvaluator on the given inputs. + All lists must have the same length. + + :param questions: + A list of questions. + :param ground_truth_answers: + A list of expected answers for each question. + :param predicted_answers: + A list of predicted answers for each question. + :returns: + A dictionary with the following outputs: + - `result` - A number from 0.0 to 1.0 that represents the proportion of questions where any predicted + answer matched one of the ground truth answers. + """ + if not len(questions) == len(ground_truth_answers) == len(predicted_answers): + raise ValueError("The length of questions, ground_truth_answers, and predicted_answers must be the same.") + + matches = 0 + for truths, extracted in zip(ground_truth_answers, predicted_answers): + if set(truths) & set(extracted): + matches += 1 + + # The proportion of questions where any predicted answer matched one of the ground truth answers + result = matches / len(questions) + + return {"result": result} diff --git a/releasenotes/notes/exact-match-evaluator-197bb87b65e19d0c.yaml b/releasenotes/notes/exact-match-evaluator-197bb87b65e19d0c.yaml new file mode 100644 index 00000000..ad380617 --- /dev/null +++ b/releasenotes/notes/exact-match-evaluator-197bb87b65e19d0c.yaml @@ -0,0 +1,6 @@ +--- +features: + - | + Add `AnswerExactMatchEvaluator`, a Component that can be used to calculate the Exact Match metric + given a list of questions, a list of expected answers for each question and the list of predicted + answers for each question.
deepset-ai/haystack
f69c3e5cd26046b826927a39cad02af93b2ccbbf
diff --git a/test/components/evaluators/test_answer_exact_match.py b/test/components/evaluators/test_answer_exact_match.py new file mode 100644 index 00000000..c179c74a --- /dev/null +++ b/test/components/evaluators/test_answer_exact_match.py @@ -0,0 +1,61 @@ +import pytest + +from haystack.components.evaluators import AnswerExactMatchEvaluator + + +def test_run_with_all_matching(): + evaluator = AnswerExactMatchEvaluator() + result = evaluator.run( + questions=["What is the capital of Germany?", "What is the capital of France?"], + ground_truth_answers=[["Berlin"], ["Paris"]], + predicted_answers=[["Berlin"], ["Paris"]], + ) + + assert result["result"] == 1.0 + + +def test_run_with_no_matching(): + evaluator = AnswerExactMatchEvaluator() + result = evaluator.run( + questions=["What is the capital of Germany?", "What is the capital of France?"], + ground_truth_answers=[["Berlin"], ["Paris"]], + predicted_answers=[["Paris"], ["London"]], + ) + + assert result["result"] == 0.0 + + +def test_run_with_partial_matching(): + evaluator = AnswerExactMatchEvaluator() + result = evaluator.run( + questions=["What is the capital of Germany?", "What is the capital of France?"], + ground_truth_answers=[["Berlin"], ["Paris"]], + predicted_answers=[["Berlin"], ["London"]], + ) + + assert result["result"] == 0.5 + + +def test_run_with_different_lengths(): + evaluator = AnswerExactMatchEvaluator() + + with pytest.raises(ValueError): + evaluator.run( + questions=["What is the capital of Germany?"], + ground_truth_answers=[["Berlin"], ["Paris"]], + predicted_answers=[["Berlin"], ["London"]], + ) + + with pytest.raises(ValueError): + evaluator.run( + questions=["What is the capital of Germany?", "What is the capital of France?"], + ground_truth_answers=[["Berlin"]], + predicted_answers=[["Berlin"], ["London"]], + ) + + with pytest.raises(ValueError): + evaluator.run( + questions=["What is the capital of Germany?", "What is the capital of France?"], + ground_truth_answers=[["Berlin"], ["Paris"]], + predicted_answers=[["Berlin"]], + )
Implement function to calculate Exact Match metric As specified in proposal #5794 we need to implement a function to calculate the Exact Match metric. Ideally the function should be part of the private interface and called only through the `calculate_metrics` function (see #6063). `_calculate_em()` could be a nice name. For more detailed information check out the original proposal.
0.0
f69c3e5cd26046b826927a39cad02af93b2ccbbf
[ "test/components/evaluators/test_answer_exact_match.py::test_run_with_all_matching", "test/components/evaluators/test_answer_exact_match.py::test_run_with_no_matching", "test/components/evaluators/test_answer_exact_match.py::test_run_with_partial_matching", "test/components/evaluators/test_answer_exact_match.py::test_run_with_different_lengths" ]
[]
{ "failed_lite_validators": [ "has_issue_reference", "has_added_files", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }
2024-03-19 14:33:17+00:00
apache-2.0
1,872
deepset-ai__haystack-7424
diff --git a/haystack/components/evaluators/__init__.py b/haystack/components/evaluators/__init__.py index 479cd500..0da03f91 100644 --- a/haystack/components/evaluators/__init__.py +++ b/haystack/components/evaluators/__init__.py @@ -2,6 +2,7 @@ from .answer_exact_match import AnswerExactMatchEvaluator from .document_map import DocumentMAPEvaluator from .document_mrr import DocumentMRREvaluator from .document_recall import DocumentRecallEvaluator +from .faithfulness import FaithfulnessEvaluator from .llm_evaluator import LLMEvaluator from .sas_evaluator import SASEvaluator @@ -10,6 +11,7 @@ __all__ = [ "DocumentMAPEvaluator", "DocumentMRREvaluator", "DocumentRecallEvaluator", + "FaithfulnessEvaluator", "LLMEvaluator", "SASEvaluator", ] diff --git a/haystack/components/evaluators/faithfulness.py b/haystack/components/evaluators/faithfulness.py new file mode 100644 index 00000000..9ceb9973 --- /dev/null +++ b/haystack/components/evaluators/faithfulness.py @@ -0,0 +1,161 @@ +from typing import Any, Dict, List, Optional + +from numpy import mean as np_mean + +from haystack import default_from_dict +from haystack.components.evaluators.llm_evaluator import LLMEvaluator +from haystack.core.component import component +from haystack.utils import Secret, deserialize_secrets_inplace + + +class FaithfulnessEvaluator(LLMEvaluator): + """ + Evaluator that checks if a generated answer can be inferred from the provided contexts. + + An LLM separates the answer into multiple statements and checks whether the statement can be inferred from the + context or not. The final score for the full answer is a number from 0.0 to 1.0. It represents the proportion of + statements that can be inferred from the provided contexts. + + Usage example: + ```python + from haystack.components.evaluators import FaithfulnessEvaluator + + questions = ["Who created the Python language?"] + contexts = [ + [ + "Python, created by Guido van Rossum in the late 1980s, is a high-level general-purpose programming language. Its design philosophy emphasizes code readability, and its language constructs aim to help programmers write clear, logical code for both small and large-scale software projects." + ], + ] + responses = ["Python is a high-level general-purpose programming language that was created by George Lucas."] + evaluator = FaithfulnessEvaluator() + result = evaluator.run(questions=questions, contexts=contexts, responses=responses) + print(results["evaluator"]) + # {'results': [{'statements': ['Python is a high-level general-purpose programming language.', + # 'Python was created by George Lucas.'], 'statement_scores': + # [1, 0], 'score': 0.5}], 'score': 0.5, 'individual_scores': [0.5]} + + ``` + """ + + def __init__( + self, + examples: Optional[List[Dict[str, Any]]] = None, + api: str = "openai", + api_key: Secret = Secret.from_env_var("OPENAI_API_KEY"), + ): + """ + Creates an instance of LLMEvaluator. + + :param examples: + Few-shot examples conforming to the expected input and output format of FaithfulnessEvaluator. + Each example must be a dictionary with keys "inputs" and "outputs". + "inputs" must be a dictionary with keys "questions", "contexts", and "responses". + "outputs" must be a dictionary with "statements" and "statement_scores". + Expected format: + [{ + "inputs": { + "questions": "What is the capital of Italy?", "contexts": ["Rome is the capital of Italy."], + "responses": "Rome is the capital of Italy with more than 4 million inhabitants.", + }, + "outputs": { + "statements": ["Rome is the capital of Italy.", "Rome has more than 4 million inhabitants."], + "statement_scores": [1, 0], + }, + }] + :param api: + The API to use for calling an LLM through a Generator. + Supported APIs: "openai". + :param api_key: + The API key. + + """ + self.instructions = ( + "Your task is to judge the faithfulness or groundedness of statements based " + "on context information. First, please extract statements from a provided " + "response to a question. Second, calculate a faithfulness score for each " + "statement made in the response. The score is 1 if the statement can be " + "inferred from the provided context or 0 if it cannot be inferred." + ) + self.inputs = [("questions", List[str]), ("contexts", List[List[str]]), ("responses", List[str])] + self.outputs = ["statements", "statement_scores"] + self.examples = examples or [ + { + "inputs": { + "questions": "What is the capital of Germany and when was it founded?", + "contexts": ["Berlin is the capital of Germany and was founded in 1244."], + "responses": "The capital of Germany, Berlin, was founded in the 13th century.", + }, + "outputs": { + "statements": ["Berlin is the capital of Germany.", "Berlin was founded in 1244."], + "statement_scores": [1, 1], + }, + }, + { + "inputs": { + "questions": "What is the capital of France?", + "contexts": ["Berlin is the capital of Germany."], + "responses": "Paris", + }, + "outputs": {"statements": ["Paris is the capital of France."], "statement_scores": [0]}, + }, + { + "inputs": { + "questions": "What is the capital of Italy?", + "contexts": ["Rome is the capital of Italy."], + "responses": "Rome is the capital of Italy with more than 4 million inhabitants.", + }, + "outputs": { + "statements": ["Rome is the capital of Italy.", "Rome has more than 4 million inhabitants."], + "statement_scores": [1, 0], + }, + }, + ] + self.api = api + self.api_key = api_key + + super().__init__( + instructions=self.instructions, + inputs=self.inputs, + outputs=self.outputs, + examples=self.examples, + api=self.api, + api_key=self.api_key, + ) + + @component.output_types(results=List[Dict[str, Any]]) + def run(self, **inputs) -> Dict[str, Any]: + """ + Run the LLM evaluator. + + :param inputs: + The input values to evaluate. The keys are the input names and the values are lists of input values. + :returns: + A dictionary with the following outputs: + - `score`: Mean faithfulness score over all the provided input answers. + - `individual_scores`: A list of faithfulness scores for each input answer. + - `results`: A list of dictionaries with `statements` and `statement_scores` for each input answer. + """ + result = super().run(**inputs) + + # calculate average statement faithfulness score per query + for res in result["results"]: + res["score"] = np_mean(res["statement_scores"]) + + # calculate average answer faithfulness score over all queries + result["score"] = np_mean([res["score"] for res in result["results"]]) + result["individual_scores"] = [res["score"] for res in result["results"]] + + return result + + @classmethod + def from_dict(cls, data: Dict[str, Any]) -> "FaithfulnessEvaluator": + """ + Deserialize this component from a dictionary. + + :param data: + The dictionary representation of this component. + :returns: + The deserialized component instance. + """ + deserialize_secrets_inplace(data["init_parameters"], keys=["api_key"]) + return default_from_dict(cls, data) diff --git a/releasenotes/notes/faithfulness-evaluator-2e039a697c847d1c.yaml b/releasenotes/notes/faithfulness-evaluator-2e039a697c847d1c.yaml new file mode 100644 index 00000000..5279d0d9 --- /dev/null +++ b/releasenotes/notes/faithfulness-evaluator-2e039a697c847d1c.yaml @@ -0,0 +1,6 @@ +--- +features: + - | + Add a new FaithfulnessEvaluator component that can be used to evaluate faithfulness / groundedness / hallucinations of LLMs in a RAG pipeline. + Given a question, a list of retrieved document contents (contexts), and a predicted answer, FaithfulnessEvaluator returns a score ranging from 0 (poor faithfulness) to 1 (perfect faithfulness). + The score is the proportion of statements in the predicted answer that could by inferred from the documents.
deepset-ai/haystack
189dfaf640caf7993d4ba367d6ea3bcb1b4eca11
diff --git a/test/components/evaluators/test_faithfulness_evaluator.py b/test/components/evaluators/test_faithfulness_evaluator.py new file mode 100644 index 00000000..57764373 --- /dev/null +++ b/test/components/evaluators/test_faithfulness_evaluator.py @@ -0,0 +1,129 @@ +from typing import List + +import pytest + +from haystack.components.evaluators import FaithfulnessEvaluator +from haystack.utils.auth import Secret + + +class TestFaithfulnessEvaluator: + def test_init_default(self, monkeypatch): + monkeypatch.setenv("OPENAI_API_KEY", "test-api-key") + component = FaithfulnessEvaluator() + assert component.api == "openai" + assert component.generator.client.api_key == "test-api-key" + assert component.instructions == ( + "Your task is to judge the faithfulness or groundedness of statements based " + "on context information. First, please extract statements from a provided " + "response to a question. Second, calculate a faithfulness score for each " + "statement made in the response. The score is 1 if the statement can be " + "inferred from the provided context or 0 if it cannot be inferred." + ) + assert component.inputs == [("questions", List[str]), ("contexts", List[List[str]]), ("responses", List[str])] + assert component.outputs == ["statements", "statement_scores"] + assert component.examples == [ + { + "inputs": { + "questions": "What is the capital of Germany and when was it founded?", + "contexts": ["Berlin is the capital of Germany and was founded in 1244."], + "responses": "The capital of Germany, Berlin, was founded in the 13th century.", + }, + "outputs": { + "statements": ["Berlin is the capital of Germany.", "Berlin was founded in 1244."], + "statement_scores": [1, 1], + }, + }, + { + "inputs": { + "questions": "What is the capital of France?", + "contexts": ["Berlin is the capital of Germany."], + "responses": "Paris", + }, + "outputs": {"statements": ["Paris is the capital of France."], "statement_scores": [0]}, + }, + { + "inputs": { + "questions": "What is the capital of Italy?", + "contexts": ["Rome is the capital of Italy."], + "responses": "Rome is the capital of Italy with more than 4 million inhabitants.", + }, + "outputs": { + "statements": ["Rome is the capital of Italy.", "Rome has more than 4 million inhabitants."], + "statement_scores": [1, 0], + }, + }, + ] + + def test_init_fail_wo_openai_api_key(self, monkeypatch): + monkeypatch.delenv("OPENAI_API_KEY", raising=False) + with pytest.raises(ValueError, match="None of the .* environment variables are set"): + FaithfulnessEvaluator() + + def test_init_with_parameters(self): + component = FaithfulnessEvaluator( + api_key=Secret.from_token("test-api-key"), + api="openai", + examples=[ + {"inputs": {"responses": "Damn, this is straight outta hell!!!"}, "outputs": {"custom_score": 1}}, + {"inputs": {"responses": "Football is the most popular sport."}, "outputs": {"custom_score": 0}}, + ], + ) + assert component.generator.client.api_key == "test-api-key" + assert component.api == "openai" + assert component.examples == [ + {"inputs": {"responses": "Damn, this is straight outta hell!!!"}, "outputs": {"custom_score": 1}}, + {"inputs": {"responses": "Football is the most popular sport."}, "outputs": {"custom_score": 0}}, + ] + + def test_from_dict(self, monkeypatch): + monkeypatch.setenv("OPENAI_API_KEY", "test-api-key") + + data = { + "type": "haystack.components.evaluators.faithfulness.FaithfulnessEvaluator", + "init_parameters": { + "api_key": {"env_vars": ["OPENAI_API_KEY"], "strict": True, "type": "env_var"}, + "api": "openai", + "examples": [{"inputs": {"responses": "Football is the most popular sport."}, "outputs": {"score": 0}}], + }, + } + component = FaithfulnessEvaluator.from_dict(data) + assert component.api == "openai" + assert component.generator.client.api_key == "test-api-key" + assert component.examples == [ + {"inputs": {"responses": "Football is the most popular sport."}, "outputs": {"score": 0}} + ] + + def test_run_calculates_mean_score(self, monkeypatch): + monkeypatch.setenv("OPENAI_API_KEY", "test-api-key") + component = FaithfulnessEvaluator() + + def generator_run(self, *args, **kwargs): + if "Football" in kwargs["prompt"]: + return {"replies": ['{"statements": ["a", "b"], "statement_scores": [1, 0]}']} + else: + return {"replies": ['{"statements": ["c", "d"], "statement_scores": [1, 1]}']} + + monkeypatch.setattr("haystack.components.generators.openai.OpenAIGenerator.run", generator_run) + + questions = ["Which is the most popular global sport?", "Who created the Python language?"] + contexts = [ + [ + "The popularity of sports can be measured in various ways, including TV viewership, social media presence, number of participants, and economic impact. Football is undoubtedly the world's most popular sport with major events like the FIFA World Cup and sports personalities like Ronaldo and Messi, drawing a followership of more than 4 billion people." + ], + [ + "Python, created by Guido van Rossum in the late 1980s, is a high-level general-purpose programming language. Its design philosophy emphasizes code readability, and its language constructs aim to help programmers write clear, logical code for both small and large-scale software projects." + ], + ] + responses = [ + "Football is the most popular sport with around 4 billion followers worldwide.", + "Python is a high-level general-purpose programming language that was created by George Lucas.", + ] + results = component.run(questions=questions, contexts=contexts, responses=responses) + assert results == { + "individual_scores": [0.5, 1], + "results": [ + {"score": 0.5, "statement_scores": [1, 0], "statements": ["a", "b"]}, + {"score": 1, "statement_scores": [1, 1], "statements": ["c", "d"]}, + ], + "score": 0.75, + }
LLM Eval - Implement Faithfulness/Factual Accuracy metric Depends on https://github.com/deepset-ai/haystack/issues/7022. Wrap `LLMEvaluator` to provide a component that calculates the "Faithfulness" or "Factual accuracy" based on the following inputs: - Questions - Contexts - Responses This component is meant to be plug-n-play, meaning it will provide a good enough starting prompt and examples. These should also be customizable by the user. A requirement for this component is that the LLM is expected to return a binary value for each input tuple. This will let us calculate a final score for the dataset ourselves.
0.0
189dfaf640caf7993d4ba367d6ea3bcb1b4eca11
[ "test/components/evaluators/test_faithfulness_evaluator.py::TestFaithfulnessEvaluator::test_init_default", "test/components/evaluators/test_faithfulness_evaluator.py::TestFaithfulnessEvaluator::test_init_fail_wo_openai_api_key", "test/components/evaluators/test_faithfulness_evaluator.py::TestFaithfulnessEvaluator::test_init_with_parameters", "test/components/evaluators/test_faithfulness_evaluator.py::TestFaithfulnessEvaluator::test_from_dict", "test/components/evaluators/test_faithfulness_evaluator.py::TestFaithfulnessEvaluator::test_run_calculates_mean_score" ]
[]
{ "failed_lite_validators": [ "has_added_files", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }
2024-03-26 10:10:20+00:00
apache-2.0
1,873
deepset-ai__haystack-7519
diff --git a/docs/pydoc/config/evaluators_api.yml b/docs/pydoc/config/evaluators_api.yml index 9acd64ef..b24b3003 100644 --- a/docs/pydoc/config/evaluators_api.yml +++ b/docs/pydoc/config/evaluators_api.yml @@ -4,6 +4,7 @@ loaders: modules: [ "answer_exact_match", + "context_relevance", "document_map", "document_mrr", "document_recall", diff --git a/haystack/components/evaluators/__init__.py b/haystack/components/evaluators/__init__.py index f69c8257..631691c5 100644 --- a/haystack/components/evaluators/__init__.py +++ b/haystack/components/evaluators/__init__.py @@ -1,4 +1,5 @@ from .answer_exact_match import AnswerExactMatchEvaluator +from .context_relevance import ContextRelevanceEvaluator from .document_map import DocumentMAPEvaluator from .document_mrr import DocumentMRREvaluator from .document_recall import DocumentRecallEvaluator @@ -9,6 +10,7 @@ from .sas_evaluator import SASEvaluator __all__ = [ "AnswerExactMatchEvaluator", + "ContextRelevanceEvaluator", "DocumentMAPEvaluator", "DocumentMRREvaluator", "DocumentRecallEvaluator", diff --git a/haystack/components/evaluators/context_relevance.py b/haystack/components/evaluators/context_relevance.py new file mode 100644 index 00000000..d78ccfc7 --- /dev/null +++ b/haystack/components/evaluators/context_relevance.py @@ -0,0 +1,154 @@ +from typing import Any, Dict, List, Optional + +from numpy import mean as np_mean + +from haystack import default_from_dict +from haystack.components.evaluators.llm_evaluator import LLMEvaluator +from haystack.core.component import component +from haystack.utils import Secret, deserialize_secrets_inplace + +# Private global variable for default examples to include in the prompt if the user does not provide any examples +_DEFAULT_EXAMPLES = [ + { + "inputs": { + "questions": "What is the capital of Germany?", + "contexts": ["Berlin is the capital of Germany and was founded in 1244."], + }, + "outputs": { + "statements": ["Berlin is the capital of Germany.", "Berlin was founded in 1244."], + "statement_scores": [1, 0], + }, + }, + { + "inputs": {"questions": "What is the capital of France?", "contexts": ["Berlin is the capital of Germany."]}, + "outputs": {"statements": ["Berlin is the capital of Germany."], "statement_scores": [0]}, + }, + { + "inputs": {"questions": "What is the capital of Italy?", "contexts": ["Rome is the capital of Italy."]}, + "outputs": {"statements": ["Rome is the capital of Italy."], "statement_scores": [1]}, + }, +] + + +class ContextRelevanceEvaluator(LLMEvaluator): + """ + Evaluator that checks if a provided context is relevant to the question. + + An LLM separates the answer into multiple statements and checks whether the statement can be inferred from the + context or not. The final score for the full answer is a number from 0.0 to 1.0. It represents the proportion of + statements that can be inferred from the provided contexts. + + Usage example: + ```python + from haystack.components.evaluators import ContextRelevanceEvaluator + + questions = ["Who created the Python language?"] + contexts = [ + [ + "Python, created by Guido van Rossum in the late 1980s, is a high-level general-purpose programming language. Its design philosophy emphasizes code readability, and its language constructs aim to help programmers write clear, logical code for both small and large-scale software projects." + ], + ] + + evaluator = ContextRelevanceEvaluator() + result = evaluator.run(questions=questions, contexts=contexts) + print(result["score"]) + # 1.0 + print(result["individual_scores"]) + # [1.0] + print(result["results"]) + # [{'statements': ['Python, created by Guido van Rossum in the late 1980s.'], 'statement_scores': [1], 'score': 1.0}] + ``` + """ + + def __init__( + self, + examples: Optional[List[Dict[str, Any]]] = None, + api: str = "openai", + api_key: Secret = Secret.from_env_var("OPENAI_API_KEY"), + ): + """ + Creates an instance of ContextRelevanceEvaluator. + + :param examples: + Optional few-shot examples conforming to the expected input and output format of ContextRelevanceEvaluator. + Default examples will be used if none are provided. + Each example must be a dictionary with keys "inputs" and "outputs". + "inputs" must be a dictionary with keys "questions" and "contexts". + "outputs" must be a dictionary with "statements" and "statement_scores". + Expected format: + [{ + "inputs": { + "questions": "What is the capital of Italy?", "contexts": ["Rome is the capital of Italy."], + }, + "outputs": { + "statements": ["Rome is the capital of Italy."], + "statement_scores": [1], + }, + }] + :param api: + The API to use for calling an LLM through a Generator. + Supported APIs: "openai". + :param api_key: + The API key. + + """ + self.instructions = ( + "Your task is to judge how relevant the provided context is for answering a question. " + "First, please extract statements from the provided context. " + "Second, calculate a relevance score for each statement in the context. " + "The score is 1 if the statement is relevant to answer the question or 0 if it is not relevant." + ) + self.inputs = [("questions", List[str]), ("contexts", List[List[str]])] + self.outputs = ["statements", "statement_scores"] + self.examples = examples or _DEFAULT_EXAMPLES + self.api = api + self.api_key = api_key + + super().__init__( + instructions=self.instructions, + inputs=self.inputs, + outputs=self.outputs, + examples=self.examples, + api=self.api, + api_key=self.api_key, + ) + + @component.output_types(results=List[Dict[str, Any]]) + def run(self, questions: List[str], contexts: List[List[str]]) -> Dict[str, Any]: + """ + Run the LLM evaluator. + + :param questions: + A list of questions. + :param contexts: + A list of lists of contexts. Each list of contexts corresponds to one question. + :returns: + A dictionary with the following outputs: + - `score`: Mean context relevance score over all the provided input questions. + - `individual_scores`: A list of context relevance scores for each input question. + - `results`: A list of dictionaries with `statements` and `statement_scores` for each input context. + """ + result = super().run(questions=questions, contexts=contexts) + + # calculate average statement relevance score per query + for res in result["results"]: + res["score"] = np_mean(res["statement_scores"]) + + # calculate average context relevance score over all queries + result["score"] = np_mean([res["score"] for res in result["results"]]) + result["individual_scores"] = [res["score"] for res in result["results"]] + + return result + + @classmethod + def from_dict(cls, data: Dict[str, Any]) -> "ContextRelevanceEvaluator": + """ + Deserialize this component from a dictionary. + + :param data: + The dictionary representation of this component. + :returns: + The deserialized component instance. + """ + deserialize_secrets_inplace(data["init_parameters"], keys=["api_key"]) + return default_from_dict(cls, data) diff --git a/pyproject.toml b/pyproject.toml index b2e9202f..3c3833c8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -139,18 +139,18 @@ extra-dependencies = [ [tool.hatch.envs.test.scripts] e2e = "pytest e2e" -unit = 'pytest --cov-report xml:coverage.xml --cov="haystack" -m "not integration" test {args:test}' -integration = 'pytest --maxfail=5 -m "integration" test' -integration-mac = 'pytest --maxfail=5 -m "integration" test -k "not tika"' -integration-windows = 'pytest --maxfail=5 -m "integration" test -k "not tika"' +unit = 'pytest --cov-report xml:coverage.xml --cov="haystack" -m "not integration" {args:test}' +integration = 'pytest --maxfail=5 -m "integration" {args:test}' +integration-mac = 'pytest --maxfail=5 -m "integration" -k "not tika" {args:test}' +integration-windows = 'pytest --maxfail=5 -m "integration" -k "not tika" {args:test}' types = "mypy --install-types --non-interactive --cache-dir=.mypy_cache/ {args:haystack}" lint = [ - "ruff {args:haystack}", + "ruff check {args:haystack}", "pylint -ry -j 0 {args:haystack}" ] lint-fix = [ "black .", - "ruff {args:haystack} --fix", + "ruff check {args:haystack} --fix", ] [tool.hatch.envs.readme] @@ -303,12 +303,10 @@ select = [ "ASYNC", # flake8-async "C4", # flake8-comprehensions "C90", # McCabe cyclomatic complexity - "CPY", # flake8-copyright "DJ", # flake8-django "E501", # Long lines "EXE", # flake8-executable "F", # Pyflakes - "FURB", # refurb "INT", # flake8-gettext "PERF", # Perflint "PL", # Pylint diff --git a/releasenotes/notes/context-relevance-04063b9dc9fe7379.yaml b/releasenotes/notes/context-relevance-04063b9dc9fe7379.yaml new file mode 100644 index 00000000..2ab79f87 --- /dev/null +++ b/releasenotes/notes/context-relevance-04063b9dc9fe7379.yaml @@ -0,0 +1,5 @@ +--- +features: + - | + Add a new ContextRelevanceEvaluator component that can be used to evaluate whether retrieved documents are relevant to answer a question with a RAG pipeline. + Given a question and a list of retrieved document contents (contexts), an LLM is used to score to what extent the provided context is relevant. The score ranges from 0 to 1.
deepset-ai/haystack
3d0f7affed7b192d32d295a6c92bdff5e8f97de4
diff --git a/test/components/evaluators/test_context_relevance_evaluator.py b/test/components/evaluators/test_context_relevance_evaluator.py new file mode 100644 index 00000000..8bd1a3cf --- /dev/null +++ b/test/components/evaluators/test_context_relevance_evaluator.py @@ -0,0 +1,142 @@ +import os +from typing import List + +import pytest + +from haystack.components.evaluators import ContextRelevanceEvaluator +from haystack.utils.auth import Secret + + +class TestContextRelevanceEvaluator: + def test_init_default(self, monkeypatch): + monkeypatch.setenv("OPENAI_API_KEY", "test-api-key") + component = ContextRelevanceEvaluator() + assert component.api == "openai" + assert component.generator.client.api_key == "test-api-key" + assert component.instructions == ( + "Your task is to judge how relevant the provided context is for answering a question. " + "First, please extract statements from the provided context. " + "Second, calculate a relevance score for each statement in the context. " + "The score is 1 if the statement is relevant to answer the question or 0 if it is not relevant." + ) + assert component.inputs == [("questions", List[str]), ("contexts", List[List[str]])] + assert component.outputs == ["statements", "statement_scores"] + assert component.examples == [ + { + "inputs": { + "questions": "What is the capital of Germany?", + "contexts": ["Berlin is the capital of Germany and was founded in 1244."], + }, + "outputs": { + "statements": ["Berlin is the capital of Germany.", "Berlin was founded in 1244."], + "statement_scores": [1, 0], + }, + }, + { + "inputs": { + "questions": "What is the capital of France?", + "contexts": ["Berlin is the capital of Germany."], + }, + "outputs": {"statements": ["Berlin is the capital of Germany."], "statement_scores": [0]}, + }, + { + "inputs": {"questions": "What is the capital of Italy?", "contexts": ["Rome is the capital of Italy."]}, + "outputs": {"statements": ["Rome is the capital of Italy."], "statement_scores": [1]}, + }, + ] + + def test_init_fail_wo_openai_api_key(self, monkeypatch): + monkeypatch.delenv("OPENAI_API_KEY", raising=False) + with pytest.raises(ValueError, match="None of the .* environment variables are set"): + ContextRelevanceEvaluator() + + def test_init_with_parameters(self): + component = ContextRelevanceEvaluator( + api_key=Secret.from_token("test-api-key"), + api="openai", + examples=[ + {"inputs": {"questions": "Damn, this is straight outta hell!!!"}, "outputs": {"custom_score": 1}}, + {"inputs": {"questions": "Football is the most popular sport."}, "outputs": {"custom_score": 0}}, + ], + ) + assert component.generator.client.api_key == "test-api-key" + assert component.api == "openai" + assert component.examples == [ + {"inputs": {"questions": "Damn, this is straight outta hell!!!"}, "outputs": {"custom_score": 1}}, + {"inputs": {"questions": "Football is the most popular sport."}, "outputs": {"custom_score": 0}}, + ] + + def test_from_dict(self, monkeypatch): + monkeypatch.setenv("OPENAI_API_KEY", "test-api-key") + + data = { + "type": "haystack.components.evaluators.context_relevance.ContextRelevanceEvaluator", + "init_parameters": { + "api_key": {"env_vars": ["OPENAI_API_KEY"], "strict": True, "type": "env_var"}, + "api": "openai", + "examples": [{"inputs": {"questions": "What is football?"}, "outputs": {"score": 0}}], + }, + } + component = ContextRelevanceEvaluator.from_dict(data) + assert component.api == "openai" + assert component.generator.client.api_key == "test-api-key" + assert component.examples == [{"inputs": {"questions": "What is football?"}, "outputs": {"score": 0}}] + + def test_run_calculates_mean_score(self, monkeypatch): + monkeypatch.setenv("OPENAI_API_KEY", "test-api-key") + component = ContextRelevanceEvaluator() + + def generator_run(self, *args, **kwargs): + if "Football" in kwargs["prompt"]: + return {"replies": ['{"statements": ["a", "b"], "statement_scores": [1, 0]}']} + else: + return {"replies": ['{"statements": ["c", "d"], "statement_scores": [1, 1]}']} + + monkeypatch.setattr("haystack.components.generators.openai.OpenAIGenerator.run", generator_run) + + questions = ["Which is the most popular global sport?", "Who created the Python language?"] + contexts = [ + [ + "The popularity of sports can be measured in various ways, including TV viewership, social media " + "presence, number of participants, and economic impact. Football is undoubtedly the world's most " + "popular sport with major events like the FIFA World Cup and sports personalities like Ronaldo and " + "Messi, drawing a followership of more than 4 billion people." + ], + [ + "Python, created by Guido van Rossum in the late 1980s, is a high-level general-purpose programming " + "language. Its design philosophy emphasizes code readability, and its language constructs aim to help " + "programmers write clear, logical code for both small and large-scale software projects." + ], + ] + results = component.run(questions=questions, contexts=contexts) + assert results == { + "individual_scores": [0.5, 1], + "results": [ + {"score": 0.5, "statement_scores": [1, 0], "statements": ["a", "b"]}, + {"score": 1, "statement_scores": [1, 1], "statements": ["c", "d"]}, + ], + "score": 0.75, + } + + def test_run_missing_parameters(self, monkeypatch): + monkeypatch.setenv("OPENAI_API_KEY", "test-api-key") + component = ContextRelevanceEvaluator() + with pytest.raises(TypeError, match="missing 2 required positional arguments"): + component.run() + + @pytest.mark.skipif( + not os.environ.get("OPENAI_API_KEY", None), + reason="Export an env var called OPENAI_API_KEY containing the OpenAI API key to run this test.", + ) + @pytest.mark.integration + def test_live_run(self): + questions = ["Who created the Python language?"] + contexts = [["Python, created by Guido van Rossum, is a high-level general-purpose programming language."]] + + evaluator = ContextRelevanceEvaluator() + result = evaluator.run(questions=questions, contexts=contexts) + assert result["score"] == 1.0 + assert result["individual_scores"] == [1.0] + assert result["results"][0]["score"] == 1.0 + assert result["results"][0]["statement_scores"] == [1.0] + assert "Guido van Rossum" in result["results"][0]["statements"][0]
Custom LLM-based evaluator in Haystack core Now that we have integrations for third party LLM eval frameworks, we need to add support for a handful of LLM-based metrics that we officially support as part of core. This will be done by implementing a custom `LLMEvaluator` component that wraps around one or more of our generator APIs. We'll then build a small section of curated metrics on top of this component, all the while allowing the user to change the underlying service (OpenAI, Cohere, etc) and the associated prompts at will ```[tasklist] ### Tasks - [ ] LLM Eval - Implement custom LLM evaluator component in core - [ ] LLM Eval - Implement Faithfulness/Factual Accuracy metric - [ ] LLM Eval - Implement Context Relevance metric ```
0.0
3d0f7affed7b192d32d295a6c92bdff5e8f97de4
[ "test/components/evaluators/test_context_relevance_evaluator.py::TestContextRelevanceEvaluator::test_init_default", "test/components/evaluators/test_context_relevance_evaluator.py::TestContextRelevanceEvaluator::test_init_fail_wo_openai_api_key", "test/components/evaluators/test_context_relevance_evaluator.py::TestContextRelevanceEvaluator::test_init_with_parameters", "test/components/evaluators/test_context_relevance_evaluator.py::TestContextRelevanceEvaluator::test_from_dict", "test/components/evaluators/test_context_relevance_evaluator.py::TestContextRelevanceEvaluator::test_run_calculates_mean_score", "test/components/evaluators/test_context_relevance_evaluator.py::TestContextRelevanceEvaluator::test_run_missing_parameters" ]
[]
{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }
2024-04-09 15:52:30+00:00
apache-2.0
1,874
deepset-ai__haystack-7599
diff --git a/haystack/components/preprocessors/document_splitter.py b/haystack/components/preprocessors/document_splitter.py index adea7cc3..033f55a8 100644 --- a/haystack/components/preprocessors/document_splitter.py +++ b/haystack/components/preprocessors/document_splitter.py @@ -1,5 +1,5 @@ from copy import deepcopy -from typing import List, Literal +from typing import Dict, List, Literal, Tuple from more_itertools import windowed @@ -53,7 +53,7 @@ class DocumentSplitter: :returns: A dictionary with the following key: - `documents`: List of documents with the split texts. A metadata field "source_id" is added to each - document to keep track of the original document that was split. Other metadata are copied from the original + document to keep track of the original document that was split. Another metadata field "page_number" is added to each number to keep track of the page it belonged to in the original document. Other metadata are copied from the original document. :raises TypeError: if the input is not a list of Documents. @@ -70,10 +70,12 @@ class DocumentSplitter: f"DocumentSplitter only works with text documents but document.content for document ID {doc.id} is None." ) units = self._split_into_units(doc.content, self.split_by) - text_splits = self._concatenate_units(units, self.split_length, self.split_overlap) + text_splits, splits_pages = self._concatenate_units(units, self.split_length, self.split_overlap) metadata = deepcopy(doc.meta) metadata["source_id"] = doc.id - split_docs += [Document(content=txt, meta=metadata) for txt in text_splits] + split_docs += self._create_docs_from_splits( + text_splits=text_splits, splits_pages=splits_pages, meta=metadata + ) return {"documents": split_docs} def _split_into_units(self, text: str, split_by: Literal["word", "sentence", "passage", "page"]) -> List[str]: @@ -95,15 +97,40 @@ class DocumentSplitter: units[i] += split_at return units - def _concatenate_units(self, elements: List[str], split_length: int, split_overlap: int) -> List[str]: + def _concatenate_units( + self, elements: List[str], split_length: int, split_overlap: int + ) -> Tuple[List[str], List[int]]: """ - Concatenates the elements into parts of split_length units. + Concatenates the elements into parts of split_length units keeping track of the original page number that each element belongs. """ text_splits = [] + splits_pages = [] + cur_page = 1 segments = windowed(elements, n=split_length, step=split_length - split_overlap) for seg in segments: current_units = [unit for unit in seg if unit is not None] txt = "".join(current_units) if len(txt) > 0: text_splits.append(txt) - return text_splits + splits_pages.append(cur_page) + processed_units = current_units[: split_length - split_overlap] + if self.split_by == "page": + num_page_breaks = len(processed_units) + else: + num_page_breaks = sum(processed_unit.count("\f") for processed_unit in processed_units) + cur_page += num_page_breaks + return text_splits, splits_pages + + @staticmethod + def _create_docs_from_splits(text_splits: List[str], splits_pages: List[int], meta: Dict) -> List[Document]: + """ + Creates Document objects from text splits enriching them with page number and the metadata of the original document. + """ + documents: List[Document] = [] + + for i, txt in enumerate(text_splits): + meta = deepcopy(meta) + doc = Document(content=txt, meta=meta) + doc.meta["page_number"] = splits_pages[i] + documents.append(doc) + return documents diff --git a/releasenotes/notes/add-page-number-to-document-splitter-162e9dc7443575f0.yaml b/releasenotes/notes/add-page-number-to-document-splitter-162e9dc7443575f0.yaml new file mode 100644 index 00000000..8c97663c --- /dev/null +++ b/releasenotes/notes/add-page-number-to-document-splitter-162e9dc7443575f0.yaml @@ -0,0 +1,7 @@ +--- +highlights: > + Add the "page_number" field to the metadata of all output documents. + +enhancements: + - | + Now the DocumentSplitter adds the "page_number" field to the metadata of all output documents to keep track of the page of the original document it belongs to.
deepset-ai/haystack
8d04e530da24b5e5c8c11af29829714eeea47db2
diff --git a/test/components/preprocessors/test_document_splitter.py b/test/components/preprocessors/test_document_splitter.py index 479f0d50..4874c25b 100644 --- a/test/components/preprocessors/test_document_splitter.py +++ b/test/components/preprocessors/test_document_splitter.py @@ -141,3 +141,98 @@ class TestDocumentSplitter: for doc, split_doc in zip(documents, result["documents"]): assert doc.meta.items() <= split_doc.meta.items() assert split_doc.content == "Text." + + def test_add_page_number_to_metadata_with_no_overlap_word_split(self): + splitter = DocumentSplitter(split_by="word", split_length=2) + doc1 = Document(content="This is some text.\f This text is on another page.") + doc2 = Document(content="This content has two.\f\f page brakes.") + result = splitter.run(documents=[doc1, doc2]) + + expected_pages = [1, 1, 2, 2, 2, 1, 1, 3] + for doc, p in zip(result["documents"], expected_pages): + assert doc.meta["page_number"] == p + + def test_add_page_number_to_metadata_with_no_overlap_sentence_split(self): + splitter = DocumentSplitter(split_by="sentence", split_length=1) + doc1 = Document(content="This is some text.\f This text is on another page.") + doc2 = Document(content="This content has two.\f\f page brakes.") + result = splitter.run(documents=[doc1, doc2]) + + expected_pages = [1, 1, 1, 1] + for doc, p in zip(result["documents"], expected_pages): + assert doc.meta["page_number"] == p + + def test_add_page_number_to_metadata_with_no_overlap_passage_split(self): + splitter = DocumentSplitter(split_by="passage", split_length=1) + doc1 = Document( + content="This is a text with some words.\f There is a second sentence.\n\nAnd there is a third sentence.\n\nAnd more passages.\n\n\f And another passage." + ) + result = splitter.run(documents=[doc1]) + + expected_pages = [1, 2, 2, 2] + for doc, p in zip(result["documents"], expected_pages): + assert doc.meta["page_number"] == p + + def test_add_page_number_to_metadata_with_no_overlap_page_split(self): + splitter = DocumentSplitter(split_by="page", split_length=1) + doc1 = Document( + content="This is a text with some words. There is a second sentence.\f And there is a third sentence.\f And another passage." + ) + result = splitter.run(documents=[doc1]) + expected_pages = [1, 2, 3] + for doc, p in zip(result["documents"], expected_pages): + assert doc.meta["page_number"] == p + + splitter = DocumentSplitter(split_by="page", split_length=2) + doc1 = Document( + content="This is a text with some words. There is a second sentence.\f And there is a third sentence.\f And another passage." + ) + result = splitter.run(documents=[doc1]) + expected_pages = [1, 3] + + for doc, p in zip(result["documents"], expected_pages): + assert doc.meta["page_number"] == p + + def test_add_page_number_to_metadata_with_overlap_word_split(self): + splitter = DocumentSplitter(split_by="word", split_length=3, split_overlap=1) + doc1 = Document(content="This is some text. And\f this text is on another page.") + doc2 = Document(content="This content has two.\f\f page brakes.") + result = splitter.run(documents=[doc1, doc2]) + + expected_pages = [1, 1, 1, 2, 2, 1, 1, 3] + for doc, p in zip(result["documents"], expected_pages): + print(doc.content, doc.meta, p) + assert doc.meta["page_number"] == p + + def test_add_page_number_to_metadata_with_overlap_sentence_split(self): + splitter = DocumentSplitter(split_by="sentence", split_length=2, split_overlap=1) + doc1 = Document(content="This is some text. And this is more text.\f This text is on another page. End.") + doc2 = Document(content="This content has two.\f\f page brakes. More text.") + result = splitter.run(documents=[doc1, doc2]) + + expected_pages = [1, 1, 1, 2, 1, 1] + for doc, p in zip(result["documents"], expected_pages): + print(doc.content, doc.meta, p) + assert doc.meta["page_number"] == p + + def test_add_page_number_to_metadata_with_overlap_passage_split(self): + splitter = DocumentSplitter(split_by="passage", split_length=2, split_overlap=1) + doc1 = Document( + content="This is a text with some words.\f There is a second sentence.\n\nAnd there is a third sentence.\n\nAnd more passages.\n\n\f And another passage." + ) + result = splitter.run(documents=[doc1]) + + expected_pages = [1, 2, 2] + for doc, p in zip(result["documents"], expected_pages): + assert doc.meta["page_number"] == p + + def test_add_page_number_to_metadata_with_overlap_page_split(self): + splitter = DocumentSplitter(split_by="page", split_length=2, split_overlap=1) + doc1 = Document( + content="This is a text with some words. There is a second sentence.\f And there is a third sentence.\f And another passage." + ) + result = splitter.run(documents=[doc1]) + expected_pages = [1, 2, 3] + + for doc, p in zip(result["documents"], expected_pages): + assert doc.meta["page_number"] == p
feat: Add `page_number` to meta of Documents in `DocumentSplitter` **Is your feature request related to a problem? Please describe.** In Haystack v1 we had an option in the Preprocessor to add the original `page_number` to a Document's meta data when it was split into a chunk. This feature made down stream applications of visualizing the retrieved text from original files (e.g. PDFs) very easy and straightforward, so I'd like to see it in Haystack v2 as well. **Describe the solution you'd like** I would like to add the option to store the `page_number` in the meta info of the Document in the DocumentSplitter component. I believe we can use a similar/same implementation of calculating this like we did for the Preprocessor.
0.0
8d04e530da24b5e5c8c11af29829714eeea47db2
[ "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_add_page_number_to_metadata_with_no_overlap_word_split", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_add_page_number_to_metadata_with_no_overlap_sentence_split", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_add_page_number_to_metadata_with_no_overlap_passage_split", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_add_page_number_to_metadata_with_no_overlap_page_split", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_add_page_number_to_metadata_with_overlap_word_split", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_add_page_number_to_metadata_with_overlap_sentence_split", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_add_page_number_to_metadata_with_overlap_passage_split", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_add_page_number_to_metadata_with_overlap_page_split" ]
[ "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_non_text_document", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_single_doc", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_empty_list", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_unsupported_split_by", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_unsupported_split_length", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_unsupported_split_overlap", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_split_by_word", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_split_by_word_multiple_input_docs", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_split_by_sentence", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_split_by_passage", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_split_by_page", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_split_by_word_with_overlap", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_source_id_stored_in_metadata", "test/components/preprocessors/test_document_splitter.py::TestDocumentSplitter::test_copy_metadata" ]
{ "failed_lite_validators": [ "has_added_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2024-04-25 19:09:50+00:00
apache-2.0
1,875
delph-in__pydelphin-359
diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml index 2a5298f..0ef3a60 100644 --- a/.github/workflows/checks.yml +++ b/.github/workflows/checks.yml @@ -37,4 +37,4 @@ jobs: pytest . - name: Type-check with mypy run: | - mypy delphin --namespace-packages --explicit-package-bases --ignore-missing-imports + mypy delphin --namespace-packages --explicit-package-bases --ignore-missing-imports --implicit-optional diff --git a/CHANGELOG.md b/CHANGELOG.md index e7ef17a..b11f97b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,14 @@ # Change Log +## Unreleased + +### Fixed + +* `delphin.tdl.ConsList.values()` and `delphin.tdl.DiffList.values()` + now treat explicit sublists as regular items instead of descending + into their structures ([#357]) + + ## [v1.7.0] **Release date: 2022-10-13** @@ -1556,3 +1565,4 @@ information about changes, except for [#343]: https://github.com/delph-in/pydelphin/issues/343 [#344]: https://github.com/delph-in/pydelphin/issues/344 [#352]: https://github.com/delph-in/pydelphin/issues/352 +[#357]: https://github.com/delph-in/pydelphin/issues/357 diff --git a/delphin/cli/convert.py b/delphin/cli/convert.py index 5d50e28..4dadf80 100644 --- a/delphin/cli/convert.py +++ b/delphin/cli/convert.py @@ -9,9 +9,7 @@ with "-lines" to enable line-based reading/writing, in which case the import sys import argparse -import warnings -from delphin.exceptions import PyDelphinWarning from delphin.commands import convert from delphin import util diff --git a/delphin/cli/repp.py b/delphin/cli/repp.py index f47571c..ed0cdb8 100644 --- a/delphin/cli/repp.py +++ b/delphin/cli/repp.py @@ -11,9 +11,7 @@ useful for debugging REPP modules. import sys import argparse -import warnings -from delphin.exceptions import PyDelphinWarning from delphin.commands import repp diff --git a/delphin/tdl.py b/delphin/tdl.py index aa7a18a..ec330f4 100644 --- a/delphin/tdl.py +++ b/delphin/tdl.py @@ -253,6 +253,10 @@ class AVM(FeatureStructure, Term): return fs +class _ImplicitAVM(AVM): + """AVM implicitly constructed by list syntax.""" + + class ConsList(AVM): """ AVM subclass for cons-lists (``< ... >``) @@ -308,12 +312,7 @@ class ConsList(AVM): if self._avm is None: return [] else: - vals = [val for _, val in _collect_list_items(self)] - # the < a . b > notation puts b on the last REST path, - # which is not returned by _collect_list_items() - if self.terminated and self[self._last_path] is not None: - vals.append(self[self._last_path]) - return vals + return [val for _, val in _collect_list_items(self)] def append(self, value): """ @@ -330,7 +329,7 @@ class ConsList(AVM): path += '.' self[path + LIST_HEAD] = value self._last_path = path + LIST_TAIL - self[self._last_path] = AVM() + self[self._last_path] = _ImplicitAVM() else: raise TDLError('Cannot append to a closed list.') @@ -395,7 +394,7 @@ class DiffList(AVM): if values: # use ConsList to construct the list, but discard the class tmplist = ConsList(values, end=cr) - dl_list = AVM() + dl_list = _ImplicitAVM() dl_list._avm.update(tmplist._avm) dl_list._feats = tmplist._feats self.last = 'LIST.' + tmplist._last_path @@ -416,16 +415,25 @@ class DiffList(AVM): """ Return the list of values in the DiffList feature structure. """ - return [val for _, val - in _collect_list_items(self.get(DIFF_LIST_LIST))] + if isinstance(self[DIFF_LIST_LIST], Coreference): + vals = [] + else: + vals = [val for _, val + in _collect_list_items(self.get(DIFF_LIST_LIST))] + vals.pop() # last item of diff list is coreference + return vals def _collect_list_items(d): - if d is None or not isinstance(d, AVM) or d.get(LIST_HEAD) is None: + if not isinstance(d, AVM) or d.get(LIST_HEAD) is None: return [] vals = [(LIST_HEAD, d[LIST_HEAD])] - vals.extend((LIST_TAIL + '.' + path, val) - for path, val in _collect_list_items(d.get(LIST_TAIL))) + rest = d[LIST_TAIL] + if isinstance(rest, _ImplicitAVM): + vals.extend((LIST_TAIL + '.' + path, val) + for path, val in _collect_list_items(rest)) + elif rest is not None: + vals.append((LIST_TAIL, rest)) return vals
delph-in/pydelphin
b5c7094691f01a161983224fe78b2ad26e7fea9b
diff --git a/tests/tdl_test.py b/tests/tdl_test.py index b4b88d2..5cae05c 100644 --- a/tests/tdl_test.py +++ b/tests/tdl_test.py @@ -960,3 +960,18 @@ def test_format_environments(): ' :end :instance.\n' ' :include "another.tdl".\n' ':end :type.') + + +def test_issue_357(): + # https://github.com/delph-in/pydelphin/issues/357 + t = TypeDefinition( + 'id', + ConsList( + [TypeIdentifier('a')], + end=ConsList([TypeIdentifier('b')], end=TypeIdentifier('c')) + ) + ) + c = t.conjunction.terms[0] + assert isinstance(c, ConsList) + assert len(c.values()) == 2 + assert tdl.format(t) == 'id := < a . < b . c > >.'
format function for TypeDefinition seems to mess up some of the Lists If I `iterparse` this TypeDefinition ``` main-vprn := basic-main-verb & norm-pronominal-verb & [ SYNSEM.LOCAL.CAT.VAL [ SUBJ < #subj >, COMPS < #comps >, CLTS #clt ], ARG-ST < #subj . < #comps . #clt > > ]. ``` and then print it back out using the `format` function, I get this: ``` main-vprn := basic-main-verb & norm-pronominal-verb & [ SYNSEM.LOCAL.CAT.VAL [ SUBJ < #subj >, COMPS < #comps >, CLTS #clt ], ARG-ST < #subj, #comps . < #comps . #clt > > ]. <----- Note the extra `,#comps`which used to not be there before ```
0.0
b5c7094691f01a161983224fe78b2ad26e7fea9b
[ "tests/tdl_test.py::test_issue_357" ]
[ "tests/tdl_test.py::test_Term", "tests/tdl_test.py::test_TypeIdentifier", "tests/tdl_test.py::test_String", "tests/tdl_test.py::test_Regex", "tests/tdl_test.py::test_AVM", "tests/tdl_test.py::test_ConsList", "tests/tdl_test.py::test_DiffList", "tests/tdl_test.py::test_Coreference", "tests/tdl_test.py::TestConjunction::test_init", "tests/tdl_test.py::TestConjunction::test_and", "tests/tdl_test.py::TestConjunction::test_eq", "tests/tdl_test.py::TestConjunction::test__contains__", "tests/tdl_test.py::TestConjunction::test__getitem__", "tests/tdl_test.py::TestConjunction::test__setitem__", "tests/tdl_test.py::TestConjunction::test__setitem__issue293", "tests/tdl_test.py::TestConjunction::test__delitem__", "tests/tdl_test.py::TestConjunction::test_get", "tests/tdl_test.py::TestConjunction::test_normalize", "tests/tdl_test.py::TestConjunction::test_terms", "tests/tdl_test.py::TestConjunction::test_add", "tests/tdl_test.py::TestConjunction::test_types", "tests/tdl_test.py::TestConjunction::test_features", "tests/tdl_test.py::TestConjunction::test_string", "tests/tdl_test.py::test_TypeDefinition", "tests/tdl_test.py::test_TypeAddendum", "tests/tdl_test.py::test_LexicalRuleDefinition", "tests/tdl_test.py::test_parse_identifiers", "tests/tdl_test.py::test_parse_supertypes", "tests/tdl_test.py::test_parse_no_features", "tests/tdl_test.py::test_parse_string_features", "tests/tdl_test.py::test_quoted_symbol", "tests/tdl_test.py::test_parse_type_features", "tests/tdl_test.py::test_parse_cons_list", "tests/tdl_test.py::test_issue_294", "tests/tdl_test.py::test_parse_diff_list", "tests/tdl_test.py::test_parse_multiple_features", "tests/tdl_test.py::test_parse_multiple_avms", "tests/tdl_test.py::test_parse_feature_path", "tests/tdl_test.py::test_parse_coreferences", "tests/tdl_test.py::test_parse_typedef", "tests/tdl_test.py::test_parse_typeaddendum", "tests/tdl_test.py::test_parse_lexicalruledefinition", "tests/tdl_test.py::test_parse_docstrings", "tests/tdl_test.py::test_parse_letterset", "tests/tdl_test.py::test_parse_wildcard", "tests/tdl_test.py::test_parse_linecomment", "tests/tdl_test.py::test_parse_blockcomment", "tests/tdl_test.py::test_parse_environments", "tests/tdl_test.py::test_format_TypeTerms", "tests/tdl_test.py::test_format_AVM", "tests/tdl_test.py::test_format_lists", "tests/tdl_test.py::test_format_docstring_terms", "tests/tdl_test.py::test_format_Conjunction", "tests/tdl_test.py::test_format_typedefs", "tests/tdl_test.py::test_format_morphsets", "tests/tdl_test.py::test_format_environments" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-01-03 07:08:39+00:00
mit
1,876
delph-in__pydelphin-362
diff --git a/CHANGELOG.md b/CHANGELOG.md index b99690f..1163e8a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,11 @@ ## Unreleased +### Added + +* `delphin.tdl.LineComment` class ([#356]) +* `delphin.tdl.BlockComment` class ([#356]) + ### Fixed * `delphin.tdl.ConsList.values()` and `delphin.tdl.DiffList.values()` @@ -9,6 +14,11 @@ into their structures ([#357]) * Implicit optional types are made explicit ([#360]) +### Changed + +* TDL parsing now models line and block comments ([#356]) +* TDL formatting now formats `LineComment` and `BlockComment` classes ([#356]) + ## [v1.7.0] @@ -1566,5 +1576,6 @@ information about changes, except for [#343]: https://github.com/delph-in/pydelphin/issues/343 [#344]: https://github.com/delph-in/pydelphin/issues/344 [#352]: https://github.com/delph-in/pydelphin/issues/352 +[#356]: https://github.com/delph-in/pydelphin/issues/356 [#357]: https://github.com/delph-in/pydelphin/issues/357 [#360]: https://github.com/delph-in/pydelphin/issues/360 diff --git a/delphin/tdl.py b/delphin/tdl.py index ec330f4..4bb0ae5 100644 --- a/delphin/tdl.py +++ b/delphin/tdl.py @@ -853,6 +853,14 @@ class FileInclude: self.path = Path(basedir, value).with_suffix('.tdl') +class LineComment(str): + """Single-line comments in TDL.""" + + +class BlockComment(str): + """Multi-line comments in TDL.""" + + # NOTE: be careful rearranging subpatterns in _tdl_lex_re; some must # appear before others, e.g., """ before ", <! before <, etc., # to prevent short-circuiting from blocking the larger patterns @@ -1055,9 +1063,9 @@ def _parse_tdl(tokens, path): except StopIteration: # normal EOF break if gid == 2: - yield ('BlockComment', token, line_no) + yield ('BlockComment', BlockComment(token), line_no) elif gid == 3: - yield ('LineComment', token, line_no) + yield ('LineComment', LineComment(token), line_no) elif gid == 20: obj = _parse_letterset(token, line_no) yield (obj.__class__.__name__, obj, line_no) @@ -1371,6 +1379,10 @@ def format(obj, indent=0): return _format_environment(obj, indent) elif isinstance(obj, FileInclude): return _format_include(obj, indent) + elif isinstance(obj, LineComment): + return _format_linecomment(obj, indent) + elif isinstance(obj, BlockComment): + return _format_blockcomment(obj, indent) else: raise ValueError(f'cannot format object as TDL: {obj!r}') @@ -1584,3 +1596,11 @@ def _format_environment(env, indent): def _format_include(fi, indent): return '{}:include "{}".'.format(' ' * indent, fi.value) + + +def _format_linecomment(obj, indent): + return '{};{}'.format(' ' * indent, str(obj)) + + +def _format_blockcomment(obj, indent): + return '{}#|{}|#'.format(' ' * indent, str(obj)) diff --git a/docs/api/delphin.tdl.rst b/docs/api/delphin.tdl.rst index 2d45274..f07b863 100644 --- a/docs/api/delphin.tdl.rst +++ b/docs/api/delphin.tdl.rst @@ -166,6 +166,16 @@ Environments and File Inclusion :members: +Comments +'''''''' + +.. autoclass:: LineComment + :members: + +.. autoclass:: BlockComment + :members: + + Exceptions and Warnings -----------------------
delph-in/pydelphin
4f71897b21f19be1c7efe219c02495cea911714b
diff --git a/tests/tdl_test.py b/tests/tdl_test.py index 5cae05c..968691d 100644 --- a/tests/tdl_test.py +++ b/tests/tdl_test.py @@ -24,6 +24,8 @@ from delphin.tdl import ( TypeEnvironment, InstanceEnvironment, FileInclude, + LineComment, + BlockComment, TDLError, TDLSyntaxError, TDLWarning) @@ -721,11 +723,13 @@ def test_parse_wildcard(): def test_parse_linecomment(): lc = tdlparse('; this is a comment\n') assert lc == ' this is a comment' + assert isinstance(lc, LineComment) def test_parse_blockcomment(): bc = tdlparse('#| this is a comment\n on multiple lines|#') assert bc == ' this is a comment\n on multiple lines' + assert isinstance(bc, BlockComment) def test_parse_environments(): @@ -962,6 +966,24 @@ def test_format_environments(): ':end :type.') +def test_format_fileinclude(): + assert tdl.format(FileInclude('foo.tdl')) == ':include "foo.tdl".' + + +def test_format_linecomment(): + assert tdl.format(LineComment(' a comment')) == '; a comment' + assert tdl.format(LineComment('; two semicolons')) == ';; two semicolons' + + +def test_format_blockcomment(): + assert tdl.format( + BlockComment(' a block comment ') + ) == '#| a block comment |#' + assert tdl.format( + BlockComment('\n one\n two\n') + ) == '#|\n one\n two\n|#' + + def test_issue_357(): # https://github.com/delph-in/pydelphin/issues/357 t = TypeDefinition(
format function for LineComment and BlockComment If I understand right, the `format` method is not currently implemented for all Events, in particular it is not implemented for LineComment and BlockComment? This would be useful in scenarios when someone is automatically updating part of a large TDL file and wants to copy large parts of it without modifying them (while modifying other parts).
0.0
4f71897b21f19be1c7efe219c02495cea911714b
[ "tests/tdl_test.py::test_Term", "tests/tdl_test.py::test_TypeIdentifier", "tests/tdl_test.py::test_String", "tests/tdl_test.py::test_Regex", "tests/tdl_test.py::test_AVM", "tests/tdl_test.py::test_ConsList", "tests/tdl_test.py::test_DiffList", "tests/tdl_test.py::test_Coreference", "tests/tdl_test.py::TestConjunction::test_init", "tests/tdl_test.py::TestConjunction::test_and", "tests/tdl_test.py::TestConjunction::test_eq", "tests/tdl_test.py::TestConjunction::test__contains__", "tests/tdl_test.py::TestConjunction::test__getitem__", "tests/tdl_test.py::TestConjunction::test__setitem__", "tests/tdl_test.py::TestConjunction::test__setitem__issue293", "tests/tdl_test.py::TestConjunction::test__delitem__", "tests/tdl_test.py::TestConjunction::test_get", "tests/tdl_test.py::TestConjunction::test_normalize", "tests/tdl_test.py::TestConjunction::test_terms", "tests/tdl_test.py::TestConjunction::test_add", "tests/tdl_test.py::TestConjunction::test_types", "tests/tdl_test.py::TestConjunction::test_features", "tests/tdl_test.py::TestConjunction::test_string", "tests/tdl_test.py::test_TypeDefinition", "tests/tdl_test.py::test_TypeAddendum", "tests/tdl_test.py::test_LexicalRuleDefinition", "tests/tdl_test.py::test_parse_identifiers", "tests/tdl_test.py::test_parse_supertypes", "tests/tdl_test.py::test_parse_no_features", "tests/tdl_test.py::test_parse_string_features", "tests/tdl_test.py::test_quoted_symbol", "tests/tdl_test.py::test_parse_type_features", "tests/tdl_test.py::test_parse_cons_list", "tests/tdl_test.py::test_issue_294", "tests/tdl_test.py::test_parse_diff_list", "tests/tdl_test.py::test_parse_multiple_features", "tests/tdl_test.py::test_parse_multiple_avms", "tests/tdl_test.py::test_parse_feature_path", "tests/tdl_test.py::test_parse_coreferences", "tests/tdl_test.py::test_parse_typedef", "tests/tdl_test.py::test_parse_typeaddendum", "tests/tdl_test.py::test_parse_lexicalruledefinition", "tests/tdl_test.py::test_parse_docstrings", "tests/tdl_test.py::test_parse_letterset", "tests/tdl_test.py::test_parse_wildcard", "tests/tdl_test.py::test_parse_linecomment", "tests/tdl_test.py::test_parse_blockcomment", "tests/tdl_test.py::test_parse_environments", "tests/tdl_test.py::test_format_TypeTerms", "tests/tdl_test.py::test_format_AVM", "tests/tdl_test.py::test_format_lists", "tests/tdl_test.py::test_format_docstring_terms", "tests/tdl_test.py::test_format_Conjunction", "tests/tdl_test.py::test_format_typedefs", "tests/tdl_test.py::test_format_morphsets", "tests/tdl_test.py::test_format_environments", "tests/tdl_test.py::test_format_fileinclude", "tests/tdl_test.py::test_format_linecomment", "tests/tdl_test.py::test_format_blockcomment", "tests/tdl_test.py::test_issue_357" ]
[]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-01-08 02:33:35+00:00
mit
1,877
deppen8__pandas-vet-127
diff --git a/src/pandas_vet/__init__.py b/src/pandas_vet/__init__.py index 9060511..2a4f0e0 100644 --- a/src/pandas_vet/__init__.py +++ b/src/pandas_vet/__init__.py @@ -173,7 +173,11 @@ def check_inplace_false(node: ast.Call) -> List: """ errors = [] for kw in node.keywords: - if kw.arg == "inplace" and kw.value.value is True: + if ( + kw.arg == "inplace" + and hasattr(kw.value, "value") + and kw.value.value is True + ): errors.append(PD002(node.lineno, node.col_offset)) return errors
deppen8/pandas-vet
b45e2283b2d880f88401992424c59682d0e4c380
diff --git a/tests/test_PD002.py b/tests/test_PD002.py index 7034674..f34fb1b 100644 --- a/tests/test_PD002.py +++ b/tests/test_PD002.py @@ -24,3 +24,16 @@ def test_PD002_fail(): actual = list(VetPlugin(tree).run()) expected = [PD002(1, 0)] assert actual == expected + + +def test_PD002_with_variable_does_not_crash(): + """ + Test that using inplace=<some variable> does not raise Exceptions. + + It will not be able to infer the value of the variable, so no errors either. + """ + statement = """use_inplace=True; df.drop(['a'], axis=1, inplace=use_inplace)""" + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [] + assert actual == expected
inplace set to a variable raises exception **Describe the bug** raised exception **To Reproduce** Steps to reproduce the behavior: Have the following code in a file ```python def some_function(dataFrame, in_place=False): return dataFrame.drop([], inplace=in_place) ``` **Expected behavior** Allow `flake8` to report violations and not throw exceptions. **Screenshots** <img width="732" alt="Screen Shot 2021-09-11 at 11 42 54 AM" src="https://user-images.githubusercontent.com/82820859/132955083-596471df-a18d-4b6d-b45b-afbdaae3596d.png"> **Additional context** ``` bash-5.1# cat /usr/lib/python3.9/site-packages/pandas_vet/version.py __version__ = "0.2.2" ``` This is running on a docker container based on alpine:3.14.1. Same results obtained on a mac. Things work if we do not provide a variable: ```python def some_function(dataFrame, in_place=False): return dataFrame.drop([], inplace=False) ```
0.0
b45e2283b2d880f88401992424c59682d0e4c380
[ "tests/test_PD002.py::test_PD002_with_variable_does_not_crash" ]
[ "tests/test_PD002.py::test_PD002_pass", "tests/test_PD002.py::test_PD002_fail" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_media" ], "has_test_patch": true, "is_lite": false }
2023-08-09 03:15:39+00:00
mit
1,878
deppen8__pandas-vet-39
diff --git a/pandas_vet/__init__.py b/pandas_vet/__init__.py index b675fd8..3e5e351 100644 --- a/pandas_vet/__init__.py +++ b/pandas_vet/__init__.py @@ -33,6 +33,7 @@ class Visitor(ast.NodeVisitor): self.errors.extend(check_for_unstack(node)) self.errors.extend(check_for_arithmetic_methods(node)) self.errors.extend(check_for_comparison_methods(node)) + self.errors.extend(check_for_read_table(node)) def visit_Subscript(self, node): self.generic_visit(node) # continue checking children @@ -136,19 +137,19 @@ def check_for_comparison_methods(node: ast.Call) -> List: def check_for_ix(node: ast.Subscript) -> List: - if node.value.attr == "ix": + if isinstance(node.value, ast.Attribute) and node.value.attr == "ix": return [PD007(node.lineno, node.col_offset)] return [] -def check_for_at(node: ast.Call) -> List: - if node.value.attr == "at": +def check_for_at(node: ast.Subscript) -> List: + if isinstance(node.value, ast.Attribute) and node.value.attr == "at": return [PD008(node.lineno, node.col_offset)] return [] -def check_for_iat(node: ast.Call) -> List: - if node.value.attr == "iat": +def check_for_iat(node: ast.Subscript) -> List: + if isinstance(node.value, ast.Attribute) and node.value.attr == "iat": return [PD009(node.lineno, node.col_offset)] return [] @@ -177,6 +178,17 @@ def check_for_unstack(node: ast.Call) -> List: return [] +def check_for_read_table(node: ast.Call) -> List: + """ + Check AST for occurence of the `.read_table()` method on the pandas object. + + Error/warning message to recommend use of `.read_csv()` method instead. + """ + if isinstance(node.func, ast.Attribute) and node.func.attr == "read_table": + return [PD012(node.lineno, node.col_offset)] + return [] + + error = namedtuple("Error", ["lineno", "col", "message", "type"]) VetError = partial(partial, error, type=VetPlugin) @@ -210,3 +222,6 @@ PD009 = VetError( PD010 = VetError( message="PD010 '.pivot_table' is preferred to '.pivot' or '.unstack'; provides same functionality" ) +PD012 = VetError( + message="PDO12 '.read_csv' is preferred to '.read_table'; provides same functionality" +)
deppen8/pandas-vet
f0865882b8f857ae38fc1c0e42e671418d8bb3ee
diff --git a/tests/test_PD012.py b/tests/test_PD012.py new file mode 100644 index 0000000..ee45e2e --- /dev/null +++ b/tests/test_PD012.py @@ -0,0 +1,41 @@ +""" +Test to check for use of the pandas soon-to-be-deprecated `.read_table()` +method. +""" +import ast + +from pandas_vet import VetPlugin +from pandas_vet import PD012 + + +def test_PD012_pass_read_csv(): + """ + Test that using .read_csv() explicitly does not result in an error. + """ + statement = "df = pd.read_csv(input_file)" + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [] + assert actual == expected + + +def test_PD012_fail_read_table(): + """ + Test that using .read_table() method results in an error. + """ + statement = "df = pd.read_table(input_file)" + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [PD012(1, 5)] + assert actual == expected + + +def test_PD012_node_Name_pass(): + """ + Test that where 'read_table' is a Name does NOT raise an error + """ + statement = "df = read_table" + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [] + assert actual == expected
Check for pd.read_table Check for `pd.read_table` function call. [See flashcard here](https://deppen8.github.io/pandas-bw/reading-data/). Give error message: > 'pd.read_table' is deprecated. Use 'pd.read_csv' for all delimited files.
0.0
f0865882b8f857ae38fc1c0e42e671418d8bb3ee
[ "tests/test_PD012.py::test_PD012_pass_read_csv", "tests/test_PD012.py::test_PD012_fail_read_table", "tests/test_PD012.py::test_PD012_node_Name_pass" ]
[]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2019-02-28 21:33:20+00:00
mit
1,879
deppen8__pandas-vet-42
diff --git a/pandas_vet/__init__.py b/pandas_vet/__init__.py index 8c286e0..b675fd8 100644 --- a/pandas_vet/__init__.py +++ b/pandas_vet/__init__.py @@ -14,6 +14,9 @@ class Visitor(ast.NodeVisitor): ast.NodeVisitor will automatically call the appropriate method for a given node type i.e. calling self.visit on an Import node calls visit_import + + The `check` functions should be called from the `visit_` method that + would produce a 'fail' condition. """ errors = attr.ib(default=attr.Factory(list)) @@ -28,6 +31,8 @@ class Visitor(ast.NodeVisitor): self.errors.extend(check_for_notnull(node)) self.errors.extend(check_for_pivot(node)) self.errors.extend(check_for_unstack(node)) + self.errors.extend(check_for_arithmetic_methods(node)) + self.errors.extend(check_for_comparison_methods(node)) def visit_Subscript(self, node): self.generic_visit(node) # continue checking children @@ -86,6 +91,50 @@ def check_for_notnull(node: ast.Call) -> List: return [PD004(node.lineno, node.col_offset)] return [] +def check_for_arithmetic_methods(node: ast.Call) -> List: + """ + Check AST for occurence of explicit arithmetic methods. + + Error/warning message to recommend use of binary arithmetic operators instead. + """ + arithmetic_methods = [ + 'add', + 'sub', 'subtract', + 'mul', 'multiply', + 'div', 'divide', 'truediv', + 'pow', + 'floordiv', + 'mod', + ] + arithmetic_operators = [ + '+', + '-', + '*', + '/', + '**', + '//', + '%', + ] + + if isinstance(node.func, ast.Attribute) and node.func.attr in arithmetic_methods: + return [PD005(node.lineno, node.col_offset)] + return [] + + +def check_for_comparison_methods(node: ast.Call) -> List: + """ + Check AST for occurence of explicit comparison methods. + + Error/warning message to recommend use of binary comparison operators instead. + """ + comparison_methods = ['gt', 'lt', 'ge', 'le', 'eq', 'ne'] + comparison_operators = ['>', '<', '>=', '<=', '==', '!='] + + if isinstance(node.func, ast.Attribute) and node.func.attr in comparison_methods: + return [PD006(node.lineno, node.col_offset)] + return [] + + def check_for_ix(node: ast.Subscript) -> List: if node.value.attr == "ix": return [PD007(node.lineno, node.col_offset)]
deppen8/pandas-vet
128232a43e8dd2819e77da5a03f494691e494da1
diff --git a/tests/test_PD005.py b/tests/test_PD005.py new file mode 100644 index 0000000..9c68e0e --- /dev/null +++ b/tests/test_PD005.py @@ -0,0 +1,51 @@ +""" +Test to check for use of explicit arithmetic methods. + +Recommend use of binary arithmetic operators instead. +""" +import ast + +from pandas_vet import VetPlugin +from pandas_vet import PD005 + + +def test_PD005_pass_arithmetic_operator(): + """ + Test that using binary arithmetic operator explicitly does not result in an error. + """ + arithmetic_operators = [ + '+', + '-', + '*', + '/', + '**', + '//', + '%', + ] + for op in arithmetic_operators: + statement = 'C = A {0} B'.format(op) + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [] + assert actual == expected + + +def test_PD005_fail_arithmetic_method(): + """ + Test that using arithmetic method results in an error. + """ + arithmetic_methods = [ + 'add', + 'sub', 'subtract', + 'mul', 'multiply', + 'div', 'divide', 'truediv', + 'pow', + 'floordiv', + 'mod', + ] + for op in arithmetic_methods: + statement = 'C = A.{0}(B)'.format(op) + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [PD005(1, 4)] + assert actual == expected diff --git a/tests/test_PD006.py b/tests/test_PD006.py new file mode 100644 index 0000000..cb30365 --- /dev/null +++ b/tests/test_PD006.py @@ -0,0 +1,35 @@ +""" +Test to check for use of explicit comparison methods. + +Recommend use of binary comparison operators instead. +""" +import ast + +from pandas_vet import VetPlugin +from pandas_vet import PD006 + + +def test_PD006_pass_comparison_operator(): + """ + Test that using binary comparison operator explicitly does not result in an error. + """ + comparison_operators = ['>', '<', '>=', '<=', '==', '!='] + for op in comparison_operators: + statement = 'C = A {0} B'.format(op) + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [] + assert actual == expected + + +def test_PD006_fail_comparison_method(): + """ + Test that using comparison method results in an error. + """ + comparison_methods = ['gt', 'lt', 'ge', 'le', 'eq', 'ne'] + for op in comparison_methods: + statement = 'C = A.{0}(B)'.format(op) + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [PD006(1, 4)] + assert actual == expected
Arithmetic and comparison operators We should implement checks for all of the text-based arithmetic and comparison operators. If found, recommend using the operator itself. Something like: > Use <operator> instead of <text method> | use | check for | | --- | ---------- | | `+` | `.add` | | `-` | `.sub` and `.subtract` | | `*` | `.mul` and `.multiply` | | `/` | `.div`, `.divide` and `.truediv` | | `**` | `.pow` | | `//` | `.floordiv` | | `%` | `.mod` | | `>` | `.gt` | | `<` | `.lt` | | `>=` | `.ge` | | `<=` | `.le` | | `==` | `.eq` | | `!=` | `.ne` |
0.0
128232a43e8dd2819e77da5a03f494691e494da1
[ "tests/test_PD005.py::test_PD005_fail_arithmetic_method", "tests/test_PD006.py::test_PD006_fail_comparison_method" ]
[ "tests/test_PD005.py::test_PD005_pass_arithmetic_operator", "tests/test_PD006.py::test_PD006_pass_comparison_operator" ]
{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }
2019-03-03 00:22:37+00:00
mit
1,880
deppen8__pandas-vet-52
diff --git a/pandas_vet/__init__.py b/pandas_vet/__init__.py index 1b54d23..6237dd5 100644 --- a/pandas_vet/__init__.py +++ b/pandas_vet/__init__.py @@ -37,6 +37,7 @@ class Visitor(ast.NodeVisitor): self.errors.extend(check_for_notnull(node)) self.errors.extend(check_for_pivot(node)) self.errors.extend(check_for_unstack(node)) + self.errors.extend(check_for_stack(node)) self.errors.extend(check_for_arithmetic_methods(node)) self.errors.extend(check_for_comparison_methods(node)) self.errors.extend(check_for_read_table(node)) @@ -193,6 +194,17 @@ def check_for_unstack(node: ast.Call) -> List: return [] +def check_for_stack(node: ast.Call) -> List: + """ + Check AST for occurence of the `.stack()` method on the pandas data frame. + + Error/warning message to recommend use of `.melt()` method instead. + """ + if isinstance(node.func, ast.Attribute) and node.func.attr == "stack": + return [PD013(node.lineno, node.col_offset)] + return [] + + def check_for_values(node: ast.Attribute) -> List: """ Check AST for occurence of the `.values` attribute on the pandas data frame. @@ -255,3 +267,6 @@ PD011 = VetError( PD012 = VetError( message="PDO12 '.read_csv' is preferred to '.read_table'; provides same functionality" ) +PD013 = VetError( + message="PD013 '.melt' is preferred to '.stack'; provides same functionality" +)
deppen8/pandas-vet
8605bebf1cb5b59b9fa0c541ed5c026a9d3acbed
diff --git a/tests/test_PD005.py b/tests/test_PD005.py index 9c68e0e..1fcc596 100644 --- a/tests/test_PD005.py +++ b/tests/test_PD005.py @@ -11,7 +11,8 @@ from pandas_vet import PD005 def test_PD005_pass_arithmetic_operator(): """ - Test that using binary arithmetic operator explicitly does not result in an error. + Test that explicit use of binary arithmetic operator does not + result in an error. """ arithmetic_operators = [ '+', diff --git a/tests/test_PD006.py b/tests/test_PD006.py index cb30365..7dae856 100644 --- a/tests/test_PD006.py +++ b/tests/test_PD006.py @@ -11,7 +11,8 @@ from pandas_vet import PD006 def test_PD006_pass_comparison_operator(): """ - Test that using binary comparison operator explicitly does not result in an error. + Test that explicit use of binary comparison operator does not + result in an error. """ comparison_operators = ['>', '<', '>=', '<=', '==', '!='] for op in comparison_operators: diff --git a/tests/test_PD010.py b/tests/test_PD010.py index d3ec020..1e897bd 100644 --- a/tests/test_PD010.py +++ b/tests/test_PD010.py @@ -12,7 +12,15 @@ def test_PD010_pass(): """ Test that using .pivot_table() explicitly does not result in an error. """ - statement = "table = df.pivot_table(df, values='D', index=['A', 'B'], columns=['C'], aggfunc=np.sum, fill_value=0)" + statement = """table = df.pivot_table( + df, + values='D', + index=['A', 'B'], + columns=['C'], + aggfunc=np.sum, + fill_value=0 + ) + """ tree = ast.parse(statement) actual = list(VetPlugin(tree).run()) expected = [] @@ -21,9 +29,16 @@ def test_PD010_pass(): def test_PD010_fail_pivot(): """ - Test that using either pd.pivot(df) or df.pivot() methods results in an error. + Test that using either pd.pivot(df) or df.pivot() methods + results in an error. + """ + statement = """table = pd.pivot( + df, + index='foo', + columns='bar', + values='baz' + ) """ - statement = "table = pd.pivot(df, index='foo', columns='bar', values='baz')" tree = ast.parse(statement) actual = list(VetPlugin(tree).run()) expected = [PD010(1, 8)] diff --git a/tests/test_PD011.py b/tests/test_PD011.py index b8f9cf1..6a671e2 100644 --- a/tests/test_PD011.py +++ b/tests/test_PD011.py @@ -1,6 +1,6 @@ """ -Test to check for use of the pandas dataframe `.array` attribute -or `.to_array()` method in preference to `.values` attribute. +Test to check for use of the pandas dataframe `.array` attribute +or `.to_array()` method in preference to `.values` attribute. """ import ast @@ -40,6 +40,7 @@ def test_PD011_fail_values(): expected = [PD011(1, 9)] assert actual == expected + def test_PD011_pass_node_Name(): """ Test that where 'values' is a Name does NOT raise an error diff --git a/tests/test_PD012.py b/tests/test_PD012.py index ee45e2e..176b2d4 100644 --- a/tests/test_PD012.py +++ b/tests/test_PD012.py @@ -1,6 +1,6 @@ """ Test to check for use of the pandas soon-to-be-deprecated `.read_table()` -method. +method. """ import ast diff --git a/tests/test_PD013.py b/tests/test_PD013.py new file mode 100644 index 0000000..dededc0 --- /dev/null +++ b/tests/test_PD013.py @@ -0,0 +1,35 @@ +""" +Test to check functionality for use of the `.melt()` data frame +method in preference to `.stack()` method. +""" +import ast + +from pandas_vet import VetPlugin +from pandas_vet import PD013 + + +def test_PD013_pass(): + """ + Test that using .melt() explicitly does not result in an error. + """ + statement = """table = df.melt( + id_vars='airline', + value_vars=['ATL', 'DEN', 'DFW'], + value_name='airline delay' + ) + """ + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [] + assert actual == expected + + +def test_PD013_fail_stack(): + """ + Test that using .stack() results in an error. + """ + statement = "table = df.stack(level=-1, dropna=True)" + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [PD013(1, 8)] + assert actual == expected
Check for .stack Check for `.stack` method. [See flashcard](https://deppen8.github.io/pandas-bw/reshape-split-apply-combine/melt-vs-stack.png). Give error message: > Prefer '.melt' to '.stack'. '.melt' allows direct column renaming and avoids a MultiIndex
0.0
8605bebf1cb5b59b9fa0c541ed5c026a9d3acbed
[ "tests/test_PD005.py::test_PD005_pass_arithmetic_operator", "tests/test_PD005.py::test_PD005_fail_arithmetic_method", "tests/test_PD006.py::test_PD006_pass_comparison_operator", "tests/test_PD006.py::test_PD006_fail_comparison_method", "tests/test_PD010.py::test_PD010_pass", "tests/test_PD010.py::test_PD010_fail_pivot", "tests/test_PD010.py::test_PD010_fail_unstack", "tests/test_PD011.py::test_PD011_pass_to_array", "tests/test_PD011.py::test_PD011_pass_array", "tests/test_PD011.py::test_PD011_fail_values", "tests/test_PD011.py::test_PD011_pass_node_Name", "tests/test_PD012.py::test_PD012_pass_read_csv", "tests/test_PD012.py::test_PD012_fail_read_table", "tests/test_PD012.py::test_PD012_node_Name_pass", "tests/test_PD013.py::test_PD013_pass", "tests/test_PD013.py::test_PD013_fail_stack" ]
[]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks", "has_media" ], "has_test_patch": true, "is_lite": false }
2019-03-07 18:36:43+00:00
mit
1,881
deppen8__pandas-vet-69
diff --git a/CHANGELOG.md b/CHANGELOG.md index 6b26e92..fb5f7e5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,12 +5,42 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) (to the best of our ability). +## Unreleased + +### Added + +- New check `PD901 'df' is a bad variable name. Be kinder to your future self.` ([#69](https://github.com/deppen8/pandas-vet/pull/69)) +- An `--annoy` flag that can be used to activate checks that set to "off" by default. The off-by-default checks should use the convention `PD9xx` ([#69](https://github.com/deppen8/pandas-vet/pull/69)) +- Added `PD901` to README along with an example use of the `--annoy` flag ([#69](https://github.com/deppen8/pandas-vet/pull/69)) + +### Changed + +- `test_PD012.py` had test cases that used `df = <something>`, which conflicted with the new `PD901` check. These were changed to `employees = <something>` ([#69](https://github.com/deppen8/pandas-vet/pull/69)) +- Applied the `black` formatter to the entire pandas-vet package. + +### Deprecated + +- None + +### Removed + +- A few extraneous variables ([455d1f0](https://github.com/deppen8/pandas-vet/pull/69/commits/455d1f0525dd4e9590cd10efdcd39c9d9a7923a2)) + +### Fixed + +- None + +### Security + +- None + + ## [0.2.1] - 2019-07-27 ### Added -- Leandro Leites added as contributor (#66) -- This CHANGELOG.md added +- Leandro Leites added as contributor ([#66](https://github.com/deppen8/pandas-vet/pull/66)) +- This CHANGELOG.md added ([#68](https://github.com/deppen8/pandas-vet/pull/68)) ### Changed @@ -22,12 +52,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed -- Unnecessary commented line from `setup.py` (#67) +- Unnecessary commented line from `setup.py` ([#67](https://github.com/deppen8/pandas-vet/pull/67)) ### Fixed -- PD015 would fail if `node.func.value` did not have an `id`. Fixed with #65 -- `version.py` now correctly uses v0.2.x. This version file was not bumped with the last release. (#67) +- PD015 would fail if `node.func.value` did not have an `id`. Fixed with [#65](https://github.com/deppen8/pandas-vet/pull/65) +- `version.py` now correctly uses v0.2.x. This version file was not bumped with the last release. ([#67](https://github.com/deppen8/pandas-vet/pull/67)) ### Security diff --git a/README.md b/README.md index bf5cb1c..f875ae7 100644 --- a/README.md +++ b/README.md @@ -138,3 +138,13 @@ flake8 pandas_vet setup.py tests --exclude tests/data **PD013** '.melt' is preferred to '.stack'; provides same functionality **PD015** Use '.merge' method instead of 'pd.merge' function. They have equivalent functionality. + +### *Very* Opinionated Warnings + +These warnings are turned off by default. To enable them, add the `-annoy` flag to your command, e.g., + +```bash +$ flake8 --annoy my_file.py +``` + +**PD901** 'df' is a bad variable name. Be kinder to your future self. diff --git a/pandas_vet/__init__.py b/pandas_vet/__init__.py index af81139..fd7bee9 100644 --- a/pandas_vet/__init__.py +++ b/pandas_vet/__init__.py @@ -18,6 +18,7 @@ class Visitor(ast.NodeVisitor): The `check` functions should be called from the `visit_` method that would produce a 'fail' condition. """ + errors = attr.ib(default=attr.Factory(list)) def visit_Import(self, node): @@ -56,8 +57,16 @@ class Visitor(ast.NodeVisitor): """ Called for `.attribute` nodes. """ + self.generic_visit(node) # continue checking children self.errors.extend(check_for_values(node)) + def visit_Name(self, node): + """ + Called for `Assignment` nodes. + """ + self.generic_visit(node) # continue checking children + self.errors.extend(check_for_df(node)) + def check(self, node): self.errors = [] self.visit(node) @@ -81,6 +90,22 @@ class VetPlugin: except Exception as e: raise PandasVetException(e) + @staticmethod + def add_options(optmanager): + """Informs flake8 to ignore PD9xx by default.""" + optmanager.extend_default_ignore(disabled_by_default) + + optmanager.add_option( + long_option_name="--annoy", + action="store_true", + dest="annoy", + default=False, + ) + + options, xargs = optmanager.parse_args() + if options.annoy: + optmanager.remove_from_default_ignore(disabled_by_default) + def check_import_name(node: ast.Import) -> List: """Check AST for imports of pandas not using the preferred alias 'pd'. @@ -163,26 +188,23 @@ def check_for_arithmetic_methods(node: ast.Call) -> List: Error/warning message to recommend use of binary arithmetic operators. """ arithmetic_methods = [ - 'add', - 'sub', 'subtract', - 'mul', 'multiply', - 'div', 'divide', 'truediv', - 'pow', - 'floordiv', - 'mod', - ] - arithmetic_operators = [ - '+', - '-', - '*', - '/', - '**', - '//', - '%', - ] - - if isinstance(node.func, ast.Attribute) and \ - node.func.attr in arithmetic_methods: + "add", + "sub", + "subtract", + "mul", + "multiply", + "div", + "divide", + "truediv", + "pow", + "floordiv", + "mod", + ] + + if ( + isinstance(node.func, ast.Attribute) + and node.func.attr in arithmetic_methods + ): return [PD005(node.lineno, node.col_offset)] return [] @@ -193,11 +215,12 @@ def check_for_comparison_methods(node: ast.Call) -> List: Error/warning message to recommend use of binary comparison operators. """ - comparison_methods = ['gt', 'lt', 'ge', 'le', 'eq', 'ne'] - comparison_operators = ['>', '<', '>=', '<=', '==', '!='] + comparison_methods = ["gt", "lt", "ge", "le", "eq", "ne"] - if isinstance(node.func, ast.Attribute) and \ - node.func.attr in comparison_methods: + if ( + isinstance(node.func, ast.Attribute) + and node.func.attr in comparison_methods + ): return [PD006(node.lineno, node.col_offset)] return [] @@ -304,42 +327,55 @@ def check_for_merge(node: ast.Call) -> List: # object. If the object name is `pd`, and if the `.merge()` method has at # least two arguments (left, right, ... ) we will assume that it matches # the pattern that we are trying to check, `pd.merge(left, right)` - if not hasattr(node.func, 'value'): - return [] # ignore functions - elif not hasattr(node.func.value, 'id'): - return [] # it could be the case that id is not present + if not hasattr(node.func, "value"): + return [] # ignore functions + elif not hasattr(node.func.value, "id"): + return [] # it could be the case that id is not present - if node.func.value.id != 'pd': return[] # assume object name is `pd` + if node.func.value.id != "pd": + return [] # assume object name is `pd` - if not len(node.args) >= 2: return [] # at least two arguments + if not len(node.args) >= 2: + return [] # at least two arguments - if isinstance(node.func, ast.Attribute) and \ - node.func.attr == "merge": + if isinstance(node.func, ast.Attribute) and node.func.attr == "merge": return [PD015(node.lineno, node.col_offset)] return [] +def check_for_df(node: ast.Name) -> List: + """ + Check for variables named `df` + """ + if node.id == "df" and isinstance(node.ctx, ast.Store): + return [PD901(node.lineno, node.col_offset)] + return [] + + error = namedtuple("Error", ["lineno", "col", "message", "type"]) VetError = partial(partial, error, type=VetPlugin) +disabled_by_default = ["PD9"] + PD001 = VetError( message="PD001 pandas should always be imported as 'import pandas as pd'" ) + PD002 = VetError( message="PD002 'inplace = True' should be avoided; it has inconsistent behavior" ) + PD003 = VetError( message="PD003 '.isna' is preferred to '.isnull'; functionality is equivalent" ) + PD004 = VetError( message="PD004 '.notna' is preferred to '.notnull'; functionality is equivalent" ) -PD005 = VetError( - message="PD005 Use arithmetic operator instead of method" -) -PD006 = VetError( - message="PD006 Use comparison operator instead of method" -) +PD005 = VetError(message="PD005 Use arithmetic operator instead of method") + +PD006 = VetError(message="PD006 Use comparison operator instead of method") + PD007 = VetError( message="PD007 '.ix' is deprecated; use more explicit '.loc' or '.iloc'" ) @@ -364,3 +400,7 @@ PD013 = VetError( PD015 = VetError( message="PD015 Use '.merge' method instead of 'pd.merge' function. They have equivalent functionality." ) + +PD901 = VetError( + message="PD901 'df' is a bad variable name. Be kinder to your future self." +) diff --git a/setup.py b/setup.py index 96c1e4c..10e1b69 100644 --- a/setup.py +++ b/setup.py @@ -1,15 +1,10 @@ import setuptools -requires = [ - "flake8 > 3.0.0", - "attrs", -] +requires = ["flake8 > 3.0.0", "attrs"] -tests_requires = [ - "pytest > 4.0.0" -] +tests_requires = ["pytest > 4.0.0"] -flake8_entry_point = 'flake8.extension' +flake8_entry_point = "flake8.extension" with open("README.md", "rt") as f: long_description = f.read() @@ -26,16 +21,10 @@ setuptools.setup( author="Jacob Deppen", author_email="[email protected]", url="https://github.com/deppen8/pandas-vet", - packages=[ - "pandas_vet", - ], + packages=["pandas_vet"], install_requires=requires, tests_require=tests_requires, - entry_points={ - flake8_entry_point: [ - 'PD = pandas_vet:VetPlugin', - ], - }, + entry_points={flake8_entry_point: ["PD = pandas_vet:VetPlugin"]}, classifiers=[ "Development Status :: 4 - Beta", "Environment :: Console",
deppen8/pandas-vet
4d0611ec5fb91fa9fc8c00a3bcc94e3d8beb94f7
diff --git a/tests/test_PD005.py b/tests/test_PD005.py index 1fcc596..78b3eca 100644 --- a/tests/test_PD005.py +++ b/tests/test_PD005.py @@ -14,17 +14,9 @@ def test_PD005_pass_arithmetic_operator(): Test that explicit use of binary arithmetic operator does not result in an error. """ - arithmetic_operators = [ - '+', - '-', - '*', - '/', - '**', - '//', - '%', - ] + arithmetic_operators = ["+", "-", "*", "/", "**", "//", "%"] for op in arithmetic_operators: - statement = 'C = A {0} B'.format(op) + statement = "C = A {0} B".format(op) tree = ast.parse(statement) actual = list(VetPlugin(tree).run()) expected = [] @@ -36,16 +28,20 @@ def test_PD005_fail_arithmetic_method(): Test that using arithmetic method results in an error. """ arithmetic_methods = [ - 'add', - 'sub', 'subtract', - 'mul', 'multiply', - 'div', 'divide', 'truediv', - 'pow', - 'floordiv', - 'mod', - ] + "add", + "sub", + "subtract", + "mul", + "multiply", + "div", + "divide", + "truediv", + "pow", + "floordiv", + "mod", + ] for op in arithmetic_methods: - statement = 'C = A.{0}(B)'.format(op) + statement = "C = A.{0}(B)".format(op) tree = ast.parse(statement) actual = list(VetPlugin(tree).run()) expected = [PD005(1, 4)] diff --git a/tests/test_PD006.py b/tests/test_PD006.py index 7dae856..b1e1b62 100644 --- a/tests/test_PD006.py +++ b/tests/test_PD006.py @@ -14,9 +14,9 @@ def test_PD006_pass_comparison_operator(): Test that explicit use of binary comparison operator does not result in an error. """ - comparison_operators = ['>', '<', '>=', '<=', '==', '!='] + comparison_operators = [">", "<", ">=", "<=", "==", "!="] for op in comparison_operators: - statement = 'C = A {0} B'.format(op) + statement = "C = A {0} B".format(op) tree = ast.parse(statement) actual = list(VetPlugin(tree).run()) expected = [] @@ -27,9 +27,9 @@ def test_PD006_fail_comparison_method(): """ Test that using comparison method results in an error. """ - comparison_methods = ['gt', 'lt', 'ge', 'le', 'eq', 'ne'] + comparison_methods = ["gt", "lt", "ge", "le", "eq", "ne"] for op in comparison_methods: - statement = 'C = A.{0}(B)'.format(op) + statement = "C = A.{0}(B)".format(op) tree = ast.parse(statement) actual = list(VetPlugin(tree).run()) expected = [PD006(1, 4)] diff --git a/tests/test_PD012.py b/tests/test_PD012.py index 176b2d4..d669b42 100644 --- a/tests/test_PD012.py +++ b/tests/test_PD012.py @@ -12,7 +12,7 @@ def test_PD012_pass_read_csv(): """ Test that using .read_csv() explicitly does not result in an error. """ - statement = "df = pd.read_csv(input_file)" + statement = "employees = pd.read_csv(input_file)" tree = ast.parse(statement) actual = list(VetPlugin(tree).run()) expected = [] @@ -23,10 +23,10 @@ def test_PD012_fail_read_table(): """ Test that using .read_table() method results in an error. """ - statement = "df = pd.read_table(input_file)" + statement = "employees = pd.read_table(input_file)" tree = ast.parse(statement) actual = list(VetPlugin(tree).run()) - expected = [PD012(1, 5)] + expected = [PD012(1, 12)] assert actual == expected @@ -34,7 +34,7 @@ def test_PD012_node_Name_pass(): """ Test that where 'read_table' is a Name does NOT raise an error """ - statement = "df = read_table" + statement = "employees = read_table" tree = ast.parse(statement) actual = list(VetPlugin(tree).run()) expected = [] diff --git a/tests/test_PD901.py b/tests/test_PD901.py new file mode 100644 index 0000000..f4093f1 --- /dev/null +++ b/tests/test_PD901.py @@ -0,0 +1,36 @@ +import ast + +from pandas_vet import VetPlugin +from pandas_vet import PD901 + + +def test_PD901_pass_non_df(): + statement = "employees = pd.DataFrame(employee_dict)" + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [] + assert actual == expected + + +def test_PD901_pass_part_df(): + statement = "employees_df = pd.DataFrame(employee_dict)" + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [] + assert actual == expected + + +def test_PD901_pass_df_param(): + statement = "my_function(df=data)" + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [] + assert actual == expected + + +def test_PD901_fail_df_var(): + statement = "df = pd.DataFrame()" + tree = ast.parse(statement) + actual = list(VetPlugin(tree).run()) + expected = [PD901(1, 0)] + assert actual == expected
Method for off-by-default linter checks As discussed in #64, it would be good to have some checks that can be implemented but are "off" by default. These would be the most opinionated checks that would be a bit too strict to be activated out-of-the-box.
0.0
4d0611ec5fb91fa9fc8c00a3bcc94e3d8beb94f7
[ "tests/test_PD005.py::test_PD005_pass_arithmetic_operator", "tests/test_PD005.py::test_PD005_fail_arithmetic_method", "tests/test_PD006.py::test_PD006_pass_comparison_operator", "tests/test_PD006.py::test_PD006_fail_comparison_method", "tests/test_PD012.py::test_PD012_pass_read_csv", "tests/test_PD012.py::test_PD012_fail_read_table", "tests/test_PD012.py::test_PD012_node_Name_pass", "tests/test_PD901.py::test_PD901_pass_non_df", "tests/test_PD901.py::test_PD901_pass_part_df", "tests/test_PD901.py::test_PD901_pass_df_param", "tests/test_PD901.py::test_PD901_fail_df_var" ]
[]
{ "failed_lite_validators": [ "has_issue_reference", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2019-08-03 21:46:13+00:00
mit
1,882
deshima-dev__decode-132
diff --git a/decode/__init__.py b/decode/__init__.py index 4ea797c..1646883 100644 --- a/decode/__init__.py +++ b/decode/__init__.py @@ -8,6 +8,7 @@ __all__ = [ "plot", "qlook", "select", + "utils", ] __version__ = "2.7.2" @@ -22,3 +23,4 @@ from . import make from . import plot from . import qlook from . import select +from . import utils diff --git a/decode/qlook.py b/decode/qlook.py index 7e5305a..388160b 100644 --- a/decode/qlook.py +++ b/decode/qlook.py @@ -1,4 +1,4 @@ -__all__ = ["raster", "skydip", "zscan"] +__all__ = ["pswsc", "raster", "skydip", "zscan"] # standard library @@ -11,7 +11,7 @@ import numpy as np import xarray as xr import matplotlib.pyplot as plt from fire import Fire -from . import assign, convert, load, make, plot, select +from . import assign, convert, load, make, plot, select, utils # constants @@ -22,6 +22,98 @@ BAD_MKID_IDS = ( 283, 296, 297, 299, 301, 313, ) # fmt: on +DFOF_TO_TSKY = -(300 - 77) / 3e-5 +TSKY_TO_DFOF = -3e-5 / (300 - 77) + + +def pswsc( + dems: Path, + /, + *, + include_mkid_ids: Optional[Sequence[int]] = None, + exclude_mkid_ids: Optional[Sequence[int]] = BAD_MKID_IDS, + data_type: Literal["df/f", "brightness"] = "brightness", + frequency_units: str = "GHz", + outdir: Path = Path(), + format: str = "png", +) -> None: + """Quick-look at a PSW observation with sky chopper. + + Args: + dems: Input DEMS file (netCDF or Zarr). + include_mkid_ids: MKID IDs to be included in analysis. + Defaults to all MKID IDs. + exclude_mkid_ids: MKID IDs to be excluded in analysis. + Defaults to bad MKID IDs found on 2023-11-07. + data_type: Data type of the input DEMS file. + frequency_units: Units of the frequency axis. + outdir: Output directory for the analysis result. + format: Output data format of the analysis result. + + """ + dems = Path(dems) + out = Path(outdir) / dems.with_suffix(f".pswsc.{format}").name + + # load DEMS + da = load.dems(dems, chunks=None) + da = assign.scan(da) + da = convert.frame(da, "relative") + da = convert.coord_units(da, "frequency", frequency_units) + da = convert.coord_units(da, "d2_mkid_frequency", frequency_units) + + if data_type == "df/f": + da = cast(xr.DataArray, np.abs(da)) + da.attrs.update(long_name="|df/f|", units="dimensionless") + + # select DEMS + da = select.by(da, "d2_mkid_type", include="filter") + da = select.by( + da, + "d2_mkid_id", + include=include_mkid_ids, + exclude=exclude_mkid_ids, + ) + da = select.by(da, "state", include=["ON", "OFF"]) + da_sub = da.groupby("scan").map(subtract_per_scan) + + # export output + spec = da_sub.mean("scan") + mad = utils.mad(spec) + + if format == "csv": + spec.to_dataset(name=data_type).to_pandas().to_csv(out) + elif format == "nc": + spec.to_netcdf(out) + elif format.startswith("zarr"): + spec.to_zarr(out) + else: + fig, axes = plt.subplots(1, 2, figsize=(12, 4)) + + ax = axes[0] + plot.data(da.scan, ax=ax) + ax.set_title(Path(dems).name) + ax.grid(True) + + ax = axes[1] + plot.data(spec, x="frequency", s=5, hue=None, ax=ax) + ax.set_ylim(-mad, spec.max() + mad) + ax.set_title(Path(dems).name) + ax.grid(True) + + if data_type == "df/f": + ax = ax.secondary_yaxis( + "right", + functions=( + lambda x: -DFOF_TO_TSKY * x, + lambda x: -TSKY_TO_DFOF * x, + ), + ) + ax.set_ylabel("Approx. brightness [K]") + + fig.tight_layout() + fig.savefig(out) + + print(str(out)) def raster( @@ -341,11 +433,30 @@ def mean_in_time(dems: xr.DataArray) -> xr.DataArray: return xr.zeros_like(middle) + dems.mean("time") +def subtract_per_scan(dems: xr.DataArray) -> xr.DataArray: + """Apply source-sky subtraction to a single-scan DEMS.""" + if len(states := np.unique(dems.state)) != 1: + raise ValueError("State must be unique.") + + if (state := states[0]) == "ON": + src = select.by(dems, "beam", include="B") + sky = select.by(dems, "beam", include="A") + return src.mean("time") - sky.mean("time").data + + if state == "OFF": + src = select.by(dems, "beam", include="A") + sky = select.by(dems, "beam", include="B") + return src.mean("time") - sky.mean("time").data + + raise ValueError("State must be either ON or OFF.") + + def main() -> None: """Entry point of the decode-qlook command.""" with xr.set_options(keep_attrs=True): Fire( { + "pswsc": pswsc, "raster": raster, "skydip": skydip, "zscan": zscan, diff --git a/decode/utils.py b/decode/utils.py new file mode 100644 index 0000000..53e4f74 --- /dev/null +++ b/decode/utils.py @@ -0,0 +1,40 @@ +__all__ = ["mad"] + + +# dependencies +from typing import Any, Optional, cast +import numpy as np +import xarray as xr +from xarray.core.types import Dims + + +def mad( + da: xr.DataArray, + dim: Dims = None, + skipna: Optional[bool] = None, + keep_attrs: Optional[bool] = None, + **kwargs: Any, +) -> xr.DataArray: + """Calculate median absolute deviation (MAD) of a DataArray. + + Args: + da: Input DataArray. + dim: Name of dimension(s) along which MAD is calculated. + skipna: Same-name option to be passed to ``DataArray.median``. + keep_attrs: Same-name option to be passed to ``DataArray.median``. + kwargs: Same-name option(s) to be passed to ``DataArray.median``. + + Returns: + MAD of the input DataArray. + + """ + + def median(da: xr.DataArray) -> xr.DataArray: + return da.median( + dim=dim, + skipna=skipna, + keep_attrs=keep_attrs, + **kwargs, + ) + + return median(cast(xr.DataArray, np.abs(da - median(da))))
deshima-dev/decode
15c93d59f42a9b3ad367d687de2ea24190213511
diff --git a/tests/test_utils.py b/tests/test_utils.py new file mode 100644 index 0000000..177a62c --- /dev/null +++ b/tests/test_utils.py @@ -0,0 +1,10 @@ +# dependencies +import numpy as np +import xarray as xr +from decode import utils +from dems.d2 import MS + + +def test_mad() -> None: + dems = MS.new(np.arange(25).reshape(5, 5)) + assert (utils.mad(dems, "time") == 5.0).all()
Add qlook command for PSW + Sky chopper (pswsc)
0.0
15c93d59f42a9b3ad367d687de2ea24190213511
[ "tests/test_utils.py::test_mad" ]
[]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-11-12 18:56:23+00:00
mit
1,883
desihub__desitransfer-10
diff --git a/bin/desi_transfer_status_restore b/bin/desi_transfer_status_restore new file mode 100755 index 0000000..4766fc8 --- /dev/null +++ b/bin/desi_transfer_status_restore @@ -0,0 +1,71 @@ +#!/usr/bin/env python +""" +Quick and dirty script to restore raw data transfer status. + +1. Obtain rsync time from modification time of exposure directory. +2. Set checksum time to rsync time. +3. Ignore pipeline time (as of early 2020). +4. Obtain backup time from HPSS backup files. + +This script is deliberately kept separate from the package because it +uses hpsspy. +""" +from sys import exit +import json +import os +import hpsspy.os as hpos + + +def backup_times(path='desi/spectro/data'): + """Obtain backup times from HPSS files. + + Parameters + ---------- + path : :class:`str` + The HPSS path to the raw data backup files. + + Returns + ------- + :class:`dict` + A mapping of night to backup time. The backup time is in milliseconds + for compatibility with JavaScript. + """ + ls = hpos.listdir(path) + return dict([(os.path.splitext(f.name)[0].split('_')[-1], f.st_mtime*1000) + for f in ls if f.name.endswith('.tar')]) + + +def main(): + """Entry point for :command:`desi_transfer_status_restore`. + + Returns + ------- + :class:`int` + An integer suitable for passing to :func:`sys.exit`. + """ + bt = backup_times() + nights = os.listdir(os.environ['DESI_SPECTRO_DATA']) + status = list() + for night in nights: + if night != 'README.html': + exposures = os.listdir(os.path.join(os.environ['DESI_SPECTRO_DATA'], night)) + for exp in exposures: + rt = int(os.stat(os.path.join(os.environ['DESI_SPECTRO_DATA'], night, exp)).st_mtime * 1000) + status.append([int(night), int(exp), 'rsync', True, '', rt]) + status.append([int(night), int(exp), 'checksum', True, '', rt]) + try: + status.append([int(night), int(exp), 'backup', True, '', bt[night]]) + except KeyError: + pass + status = sorted(status, key=lambda x: x[0]*10000000 + x[1], reverse=True) + with open('desi_transfer_status_restore.json', 'w') as j: + json.dump(status, j, indent=None, separators=(',', ':')) + return 0 + + +if __name__ == '__main__': + try: + foo = os.environ['HPSS_DIR'] + except KeyError: + os.environ['HPSS_DIR'] = '/usr/common/mss' + exit(main()) diff --git a/doc/api.rst b/doc/api.rst index 418593d..9ee155f 100644 --- a/doc/api.rst +++ b/doc/api.rst @@ -5,6 +5,9 @@ desitransfer API .. automodule:: desitransfer :members: +.. automodule:: desitransfer.common + :members: + .. automodule:: desitransfer.daemon :members: diff --git a/doc/changes.rst b/doc/changes.rst index c55f0ac..44903e1 100644 --- a/doc/changes.rst +++ b/doc/changes.rst @@ -5,7 +5,10 @@ Change Log 0.3.4 (unreleased) ------------------ -* No changes yet. +* Guard against corrupted status JSON files; restore transfer status; + additional daily transfers (PR `#10`_). + +.. _`#10`: https://github.com/desihub/desitransfer/pull/10 0.3.3 (2019-12-18) ------------------ diff --git a/py/desitransfer/daily.py b/py/desitransfer/daily.py index 94b63d5..d27b1f7 100644 --- a/py/desitransfer/daily.py +++ b/py/desitransfer/daily.py @@ -98,6 +98,8 @@ def _config(): # os.path.join(engineering, 'fxc')), DailyDirectory('/data/focalplane/logs/calib_logs', os.path.join(engineering, 'focalplane', 'logs', 'calib_logs')), + DailyDirectory('/data/focalplane/logs/kpno', + os.path.join(engineering, 'focalplane', 'logs', 'kpno')), DailyDirectory('/data/focalplane/logs/xytest_data', os.path.join(engineering, 'focalplane', 'logs', 'xytest_data')), DailyDirectory('/data/fvc/data', diff --git a/py/desitransfer/status.py b/py/desitransfer/status.py index 21cb7a9..e92998f 100644 --- a/py/desitransfer/status.py +++ b/py/desitransfer/status.py @@ -14,10 +14,6 @@ import time from argparse import ArgumentParser from pkg_resources import resource_filename from . import __version__ as dtVersion -# from desiutil.log import get_logger - - -# log = None class TransferStatus(object): @@ -47,11 +43,44 @@ class TransferStatus(object): return try: with open(self.json) as j: - self.status = json.load(j) + try: + self.status = json.load(j) + except json.JSONDecodeError: + self._handle_malformed() except FileNotFoundError: pass return + def _handle_malformed(self): + """Handle malformed JSON files. + + This function will save the malformed file to a .bad file for + later analysis, and write an empty array to a new status file. + """ + from .daemon import log + bad = self.json + '.bad' + m = "Malformed JSON file detected: %s; saving original file as %s." + try: + log.error(m, self.json, bad) + except AttributeError: + # If the status code is running stand-alone, the log object + # will be None. + print("ERROR: " + (m % (self.json, bad))) + m = "shutil.copy2('%s', '%s')" + try: + log.debug(m, self.json, bad) + except AttributeError: + print("DEBUG: " + (m % (self.json, bad))) + shutil.copy2(self.json, bad) + m = "Writing empty array to %s." + try: + log.info(m, self.json) + except AttributeError: + print("INFO: " + (m % (self.json,))) + with open(self.json, 'w') as j: + j.write('[]') + return + def update(self, night, exposure, stage, failure=False, last=''): """Update the transfer status. @@ -92,6 +121,14 @@ class TransferStatus(object): self.status.insert(0, row) self.status = sorted(self.status, key=lambda x: x[0]*10000000 + x[1], reverse=True) + # + # Copy the original file before modifying. + # This will overwrite any existing .bak file + # + try: + shutil.copy2(self.json, self.json + '.bak') + except FileNotFoundError: + pass with open(self.json, 'w') as j: json.dump(self.status, j, indent=None, separators=(',', ':')) diff --git a/requirements.txt b/requirements.txt index 345f714..98fc19f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,3 @@ setuptools pytz -git+https://github.com/desihub/[email protected]#egg=desiutil +git+https://github.com/desihub/[email protected]#egg=desiutil
desihub/desitransfer
9e0011389a87b6e881c99349dfb03ef4c9f3d85c
diff --git a/py/desitransfer/test/t/bad.json b/py/desitransfer/test/t/bad.json new file mode 100644 index 0000000..0f25ee4 --- /dev/null +++ b/py/desitransfer/test/t/bad.json @@ -0,0 +1,1 @@ +This is a bad JSON file! diff --git a/py/desitransfer/test/test_daemon.py b/py/desitransfer/test/test_daemon.py index f6247df..ab51215 100644 --- a/py/desitransfer/test/test_daemon.py +++ b/py/desitransfer/test/test_daemon.py @@ -135,10 +135,10 @@ class TestDaemon(unittest.TestCase): @patch('desitransfer.daemon.SMTPHandler') @patch('desitransfer.daemon.RotatingFileHandler') @patch('desitransfer.daemon.get_logger') - def test_TransferDaemon_configure_log(self, gl, rfh, smtp): + @patch('desitransfer.daemon.log') # Needed to restore the module-level log object after test. + def test_TransferDaemon_configure_log(self, mock_log, gl, rfh, smtp): """Test logging configuration. """ - ll = gl.return_value = MagicMock() with patch.dict('os.environ', {'CSCRATCH': self.tmp.name, 'DESI_ROOT': '/desi/root', @@ -149,7 +149,7 @@ class TestDaemon(unittest.TestCase): rfh.assert_called_once_with('/desi/root/spectro/staging/logs/desi_transfer_daemon.log', backupCount=100, maxBytes=100000000) gl.assert_called_once_with(timestamp=True) - ll.setLevel.assert_called_once_with(logging.DEBUG) + gl().setLevel.assert_called_once_with(logging.DEBUG) @patch.object(TransferDaemon, 'checksum_lock') @patch.object(TransferDaemon, 'directory') diff --git a/py/desitransfer/test/test_daily.py b/py/desitransfer/test/test_daily.py index 1d8c180..9089131 100644 --- a/py/desitransfer/test/test_daily.py +++ b/py/desitransfer/test/test_daily.py @@ -110,7 +110,7 @@ class TestDaily(unittest.TestCase): call().__exit__(None, None, None)]) mock_popen.assert_has_calls([call(), call(['fix_permissions.sh', '-a', '/dst/d0'], - stdout=mo(), stderr=-2), + stdout=mo(), stderr=-2), call().wait()]) diff --git a/py/desitransfer/test/test_status.py b/py/desitransfer/test/test_status.py index 0194031..23adbe1 100644 --- a/py/desitransfer/test/test_status.py +++ b/py/desitransfer/test/test_status.py @@ -4,9 +4,10 @@ """ import json import os +import shutil import sys import unittest -from unittest.mock import patch +from unittest.mock import patch, call from tempfile import TemporaryDirectory from pkg_resources import resource_filename from ..status import TransferStatus, _options @@ -85,6 +86,45 @@ class TestStatus(unittest.TestCase): cp.assert_called_once_with(j, d) cf.assert_called_once_with(h, os.path.join(d, 'index.html')) + @patch('desitransfer.daemon.log') + def test_TransferStatus_handle_malformed_with_log(self, mock_log): + """Test handling of malformed JSON files. + """ + bad = resource_filename('desitransfer.test', 't/bad.json') + with TemporaryDirectory() as d: + shutil.copy(bad, os.path.join(d, 'desi_transfer_status.json')) + s = TransferStatus(d) + self.assertTrue(os.path.exists(os.path.join(d, 'desi_transfer_status.json.bad'))) + self.assertListEqual(s.status, []) + self.assertListEqual(os.listdir(d), ['desi_transfer_status.json.bad', + 'desi_transfer_status.json']) + mock_log.error.assert_called_once_with('Malformed JSON file detected: %s; saving original file as %s.', + os.path.join(d, 'desi_transfer_status.json'), + os.path.join(d, 'desi_transfer_status.json.bad')) + mock_log.debug.assert_called_once_with("shutil.copy2('%s', '%s')", + os.path.join(d, 'desi_transfer_status.json'), + os.path.join(d, 'desi_transfer_status.json.bad')) + mock_log.info.assert_called_once_with('Writing empty array to %s.', + os.path.join(d, 'desi_transfer_status.json')) + + @patch('builtins.print') + def test_TransferStatus_handle_malformed_without_log(self, mock_print): + """Test handling of malformed JSON files (no log object). + """ + bad = resource_filename('desitransfer.test', 't/bad.json') + with TemporaryDirectory() as d: + shutil.copy(bad, os.path.join(d, 'desi_transfer_status.json')) + s = TransferStatus(d) + self.assertTrue(os.path.exists(os.path.join(d, 'desi_transfer_status.json.bad'))) + self.assertListEqual(s.status, []) + self.assertListEqual(os.listdir(d), ['desi_transfer_status.json.bad', + 'desi_transfer_status.json']) + mock_print.assert_has_calls([call('ERROR: Malformed JSON file detected: %s; saving original file as %s.' % (os.path.join(d, 'desi_transfer_status.json'), + os.path.join(d, 'desi_transfer_status.json.bad'))), + call("DEBUG: shutil.copy2('%s', '%s')" % (os.path.join(d, 'desi_transfer_status.json'), + os.path.join(d, 'desi_transfer_status.json.bad'))), + call("INFO: Writing empty array to %s." % (os.path.join(d, 'desi_transfer_status.json'),))]) + @patch('time.time') def test_TransferStatus_update(self, mock_time): """Test status reporting mechanism updates. @@ -98,6 +138,7 @@ class TestStatus(unittest.TestCase): json.dump(st, f, indent=None, separators=(',', ':')) s = TransferStatus(d) s.update('20200703', '12345678', 'checksum') + self.assertTrue(os.path.exists(js + '.bak')) self.assertEqual(s.status[0], [20200703, 12345678, 'checksum', True, '', 1565300090000]) s.update('20200703', '12345680', 'rsync') self.assertEqual(s.status[0], [20200703, 12345680, 'rsync', True, '', 1565300090000]) @@ -112,6 +153,35 @@ class TestStatus(unittest.TestCase): self.assertTrue(all(b)) self.assertEqual(len(b), 4) + @patch('time.time') + def test_TransferStatus_update_empty(self, mock_time): + """Test status reporting mechanism updates (with no initial JSON file). + """ + mock_time.return_value = 1565300090 + # st = [[20200703, 12345678, 'rsync', True, '', 1565300074664], + # [20200703, 12345677, 'rsync', True, '', 1565300073000]] + with TemporaryDirectory() as d: + js = os.path.join(d, 'desi_transfer_status.json') + # with open(js, 'w') as f: + # json.dump(st, f, indent=None, separators=(',', ':')) + s = TransferStatus(d) + s.update('20200703', '12345678', 'checksum') + self.assertFalse(os.path.exists(js + '.bak')) + self.assertEqual(s.status[0], [20200703, 12345678, 'checksum', True, '', 1565300090000]) + s.update('20200703', '12345680', 'rsync') + self.assertTrue(os.path.exists(js + '.bak')) + self.assertEqual(s.status[0], [20200703, 12345680, 'rsync', True, '', 1565300090000]) + s.update('20200703', '12345678', 'checksum', failure=True) + self.assertEqual(s.status[1], [20200703, 12345678, 'checksum', False, '', 1565300090000]) + s.update('20200703', '12345681', 'pipeline') + self.assertEqual(s.status[0], [20200703, 12345681, 'pipeline', True, '', 1565300090000]) + s.update('20200703', '12345681', 'pipeline', last='arcs') + self.assertEqual(s.status[0], [20200703, 12345681, 'pipeline', True, 'arcs', 1565300090000]) + s.update('20200703', 'all', 'backup') + b = [i[3] for i in s.status if i[2] == 'backup'] + self.assertTrue(all(b)) + self.assertEqual(len(b), 3) + def test_TransferStatus_find(self): """Test status search. """
Guard against truncated status file At 2020-01-09 01:00 PST, the desi_transfer_status.json file was truncated, causing the transfer daemon to crash when it subsequently tried to read the empty file. Workaround for quick restart: Add `[]` (an array) to the empty file. dtn04.nersc.gov was rebooted sometime after the file was truncated (approximately 02:30 PST), suggesting transient problems with the filesystem.
0.0
9e0011389a87b6e881c99349dfb03ef4c9f3d85c
[ "py/desitransfer/test/test_status.py::TestStatus::test_TransferStatus_handle_malformed_with_log", "py/desitransfer/test/test_status.py::TestStatus::test_TransferStatus_handle_malformed_without_log", "py/desitransfer/test/test_status.py::TestStatus::test_TransferStatus_update", "py/desitransfer/test/test_status.py::TestStatus::test_TransferStatus_update_empty" ]
[ "py/desitransfer/test/test_daemon.py::TestDaemon::test_lock_directory", "py/desitransfer/test/test_daemon.py::TestDaemon::test_popen", "py/desitransfer/test/test_daemon.py::TestDaemon::test_rsync_night", "py/desitransfer/test/test_daemon.py::TestDaemon::test_unlock_directory", "py/desitransfer/test/test_daemon.py::TestDaemon::test_verify_checksum", "py/desitransfer/test/test_daemon.py::test_suite", "py/desitransfer/test/test_daily.py::TestDaily::test_apache", "py/desitransfer/test/test_daily.py::TestDaily::test_config", "py/desitransfer/test/test_daily.py::TestDaily::test_lock", "py/desitransfer/test/test_daily.py::TestDaily::test_transfer", "py/desitransfer/test/test_daily.py::test_suite", "py/desitransfer/test/test_status.py::TestStatus::test_TransferStatus_find", "py/desitransfer/test/test_status.py::TestStatus::test_TransferStatus_init", "py/desitransfer/test/test_status.py::TestStatus::test_options", "py/desitransfer/test/test_status.py::test_suite" ]
{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2020-01-10 05:53:30+00:00
bsd-3-clause
1,884
desihub__desitransfer-21
diff --git a/bin/desi_tucson_transfer.sh b/bin/desi_tucson_transfer.sh index 94f1cc0..77cb2d5 100755 --- a/bin/desi_tucson_transfer.sh +++ b/bin/desi_tucson_transfer.sh @@ -29,7 +29,7 @@ set -o noglob # # Static data sets don't need to be updated as frequently. # -static='protodesi public/ets spectro/redux/andes spectro/redux/minisv2 spectro/redux/oak1' +static='protodesi public/epo public/ets spectro/redux/andes spectro/redux/minisv2 spectro/redux/oak1' # # Dynamic data sets may change daily. # diff --git a/doc/changes.rst b/doc/changes.rst index 81a4637..f41a9af 100644 --- a/doc/changes.rst +++ b/doc/changes.rst @@ -5,7 +5,12 @@ Change Log 0.3.9 (unreleased) ------------------ -* No changes yet. +* Deprecate continuous nightwatch transfers; nightwatch is now part of the + daily engineering transfer (PR `#21`_). +* Allow alternate scratch directory to be chosen if :envvar:`CSCRATCH` is + unavailable (PR `#21`_). + +.. _`#21`: https://github.com/desihub/desitransfer/pull/21 0.3.8 (2020-10-26) ------------------ diff --git a/py/desitransfer/common.py b/py/desitransfer/common.py index 0b9bb1b..6eba487 100644 --- a/py/desitransfer/common.py +++ b/py/desitransfer/common.py @@ -81,6 +81,35 @@ def stamp(zone='US/Pacific'): return n.astimezone(tz).strftime('%Y-%m-%d %H:%M:%S %Z') +def ensure_scratch(primary, alternate): + """Try an alternate temporary directory if the primary temporary directory + is unavilable. + + Parameters + ---------- + primary : :class:`str` + Primary temporary directory. + alternate : :class:`list` + A list of alternate directories. + + Returns + ------- + The first available temporary directory found. + """ + if not isinstance(alternate, list): + alternate = [alternate] + try: + l = os.listdir(primary) + except FileNotFoundError: + for a in alternate: + try: + l = os.listdir(a) + except FileNotFoundError: + continue + return a + return primary + + def yesterday(): """Yesterday's date in DESI "NIGHT" format, YYYYMMDD. """ diff --git a/py/desitransfer/daemon.py b/py/desitransfer/daemon.py index a3b5813..7113f27 100644 --- a/py/desitransfer/daemon.py +++ b/py/desitransfer/daemon.py @@ -24,7 +24,7 @@ from socket import getfqdn from tempfile import TemporaryFile from pkg_resources import resource_filename from desiutil.log import get_logger -from .common import dir_perm, file_perm, rsync, yesterday, empty_rsync +from .common import dir_perm, file_perm, rsync, yesterday, empty_rsync, ensure_scratch from .status import TransferStatus from . import __version__ as dtVersion @@ -94,7 +94,7 @@ class TransferDaemon(object): self.conf[s].getlist('expected_files'), self.conf[s]['checksum_file']) for s in self.sections] - self.scratch = self.conf['common']['scratch'] + self.scratch = ensure_scratch(self.conf['common']['scratch'], self.conf['common']['alternate_scratch'].split(',')) self._configure_log(options.debug) return @@ -365,7 +365,7 @@ The DESI Collaboration Account # pass else: - log.error('rsync problem detected!') + log.error('rsync problem detected for %s/%s!', night, exposure) log.debug("status.update('%s', '%s', 'rsync', failure=True)", night, exposure) status.update(night, exposure, 'rsync', failure=True) diff --git a/py/desitransfer/daily.py b/py/desitransfer/daily.py index 642825d..0ce4c30 100644 --- a/py/desitransfer/daily.py +++ b/py/desitransfer/daily.py @@ -11,6 +11,7 @@ import subprocess as sub import sys import time from argparse import ArgumentParser +from pkg_resources import resource_filename from .common import dir_perm, file_perm, rsync, stamp from . import __version__ as dtVersion @@ -24,20 +25,26 @@ class DailyDirectory(object): Source directory. destination : :class:`str` Desitination directory. + extra : :class:`list`, optional + Extra :command:`rsync` arguments to splice into command. + dirlinks : :class:`bool`, optional + If ``True``, convert source links into linked directory. """ - def __init__(self, source, destination): + def __init__(self, source, destination, extra=[], dirlinks=False): self.source = source self.destination = destination self.log = self.destination + '.log' + self.extra = extra + self.dirlinks = dirlinks - def transfer(self, apache=True): + def transfer(self, permission=True): """Data transfer operations for a single destination directory. Parameters ---------- - apache : :class:`bool` - If ``True`` set file ACLs for Apache httpd access. + permission : :class:`bool`, optional + If ``True``, set permissions for DESI collaboration access. Returns ------- @@ -45,6 +52,11 @@ class DailyDirectory(object): The status returned by :command:`rsync`. """ cmd = rsync(self.source, self.destination) + if not self.dirlinks: + cmd[cmd.index('--copy-dirlinks')] = '--links' + if self.extra: + for i, e in enumerate(self.extra): + cmd.insert(cmd.index('--omit-dir-times') + 1 + i, e) with open(self.log, 'ab') as l: l.write(("DEBUG: desi_daily_transfer %s\n" % dtVersion).encode('utf-8')) l.write(("DEBUG: %s\n" % stamp()).encode('utf-8')) @@ -54,8 +66,8 @@ class DailyDirectory(object): status = p.wait() if status == 0: self.lock() - if apache: - s = self.apache() + if permission: + s = self.permission() return status def lock(self): @@ -66,8 +78,8 @@ class DailyDirectory(object): for f in filenames: os.chmod(os.path.join(dirpath, f), file_perm) - def apache(self): - """Grant apache/www read access. + def permission(self): + """Set permissions for DESI collaboration access. In theory this should not change any permissions set by :meth:`~DailyDirectory.lock`. @@ -90,16 +102,20 @@ def _config(): """Wrap configuration so that module can be imported without environment variables set. """ + nightwatch_exclude = resource_filename('desitransfer', + 'data/desi_nightwatch_transfer_exclude.txt') engineering = os.path.realpath(os.path.join(os.environ['DESI_ROOT'], 'engineering')) spectro = os.path.realpath(os.path.join(os.environ['DESI_ROOT'], 'spectro')) return [DailyDirectory('/exposures/desi/sps', os.path.join(engineering, 'spectrograph', 'sps')), - # DailyDirectory('/exposures/nightwatch', - # os.path.join(spectro, 'nightwatch', 'kpno')), + DailyDirectory('/exposures/nightwatch', + os.path.join(spectro, 'nightwatch', 'kpno'), + extra=['--exclude-from', nightwatch_exclude]), DailyDirectory('/data/dts/exposures/lost+found', - os.path.join(spectro, 'staging', 'lost+found')), + os.path.join(spectro, 'staging', 'lost+found'), + dirlinks=True), # DailyDirectory('/data/fxc', # os.path.join(engineering, 'fxc')), DailyDirectory('/data/focalplane/logs/calib_logs', @@ -127,8 +143,6 @@ def _options(*args): """ desc = "Transfer non-critical DESI data from KPNO to NERSC." prsr = ArgumentParser(description=desc) - prsr.add_argument('-A', '--no-apache', action='store_false', dest='apache', - help='Do not set ACL for Apache httpd access.') # prsr.add_argument('-b', '--backup', metavar='H', type=int, default=20, # help='UTC time in hours to trigger HPSS backups (default %(default)s:00 UTC).') # prsr.add_argument('-d', '--debug', action='store_true', @@ -142,8 +156,8 @@ def _options(*args): help="Exit the script when FILE is detected (default %(default)s).") # prsr.add_argument('-n', '--nersc', default='cori', metavar='NERSC_HOST', # help="Trigger DESI pipeline on this NERSC system (default %(default)s).") - # prsr.add_argument('-P', '--no-pipeline', action='store_false', dest='pipeline', - # help="Only transfer files, don't start the DESI pipeline.") + prsr.add_argument('-P', '--no-permission', action='store_false', dest='permission', + help='Do not set permissions for DESI collaboration access.') prsr.add_argument('-s', '--sleep', metavar='H', type=int, default=24, help='In daemon mode, sleep H hours before checking for new data (default %(default)s hours).') # prsr.add_argument('-S', '--shadow', action='store_true', @@ -167,7 +181,7 @@ def main(): print("INFO: %s detected, shutting down daily transfer script." % options.kill) return 0 for d in _config(): - status = d.transfer(apache=options.apache) + status = d.transfer(permission=options.permission) if status != 0: print("ERROR: rsync problem detected for {0.source} -> {0.destination}!".format(d)) return status diff --git a/py/desitransfer/data/desi_nightwatch_transfer_exclude.txt b/py/desitransfer/data/desi_nightwatch_transfer_exclude.txt index 2f1f1fa..446d0a0 100644 --- a/py/desitransfer/data/desi_nightwatch_transfer_exclude.txt +++ b/py/desitransfer/data/desi_nightwatch_transfer_exclude.txt @@ -1,3 +1,9 @@ -*/preproc*.fits -*/qsky-*.fits -*/*.tmp +preproc*.fits +qsky-*.fits +*.tmp +nightwatch.* +nightwatch-debug.* +nightwatch-webapp.* +webapp.log +redux +test diff --git a/py/desitransfer/data/desi_transfer_daemon.ini b/py/desitransfer/data/desi_transfer_daemon.ini index c1a8ade..222baed 100644 --- a/py/desitransfer/data/desi_transfer_daemon.ini +++ b/py/desitransfer/data/desi_transfer_daemon.ini @@ -22,7 +22,7 @@ checksum_file = checksum-{exposure}.sha256sum [common] # Use this directory for temporary files. scratch = ${CSCRATCH} -# scratch = ${HOME}/tmp +alternate_scratch = ${HOME}/tmp # The presence of this file indicates checksums are being computed. checksum_lock = /tmp/checksum-running # UTC time in hours to look for delayed files.
desihub/desitransfer
e6e6d9ee728d4525608213214f00ff6127ccb376
diff --git a/py/desitransfer/test/test_common.py b/py/desitransfer/test/test_common.py index 1642616..8be6d5e 100644 --- a/py/desitransfer/test/test_common.py +++ b/py/desitransfer/test/test_common.py @@ -6,7 +6,8 @@ import datetime import os import unittest from unittest.mock import patch -from ..common import dir_perm, file_perm, empty_rsync, rsync, stamp, yesterday, today +from tempfile import TemporaryDirectory +from ..common import dir_perm, file_perm, empty_rsync, rsync, stamp, ensure_scratch, yesterday, today class TestCommon(unittest.TestCase): @@ -22,10 +23,14 @@ class TestCommon(unittest.TestCase): pass def setUp(self): - pass + """Create a temporary directory to simulate CSCRATCH. + """ + self.tmp = TemporaryDirectory() def tearDown(self): - pass + """Clean up temporary directory. + """ + self.tmp.cleanup() def test_permissions(self): """Ensure that file and directory permissions do not change. @@ -72,6 +77,19 @@ total size is 118,417,836,324 speedup is 494,367.55 s = stamp('US/Arizona') self.assertEqual(s, '2019-07-03 05:00:00 MST') + def test_ensure_scratch(self): + """Test ensure_scratch. + """ + tmp = self.tmp.name + t = ensure_scratch(tmp, ['/foo', '/bar']) + self.assertEqual(t, tmp) + t = ensure_scratch('/foo', tmp) + self.assertEqual(t, tmp) + t = ensure_scratch('/foo', ['/bar', tmp]) + self.assertEqual(t, tmp) + t = ensure_scratch('/foo', ['/bar', '/abcdefg', tmp]) + self.assertEqual(t, tmp) + @patch('desitransfer.common.dt') def test_yesterday(self, mock_dt): """Test yesterday's date. diff --git a/py/desitransfer/test/test_daemon.py b/py/desitransfer/test/test_daemon.py index 0944a75..fa0551e 100644 --- a/py/desitransfer/test/test_daemon.py +++ b/py/desitransfer/test/test_daemon.py @@ -288,7 +288,7 @@ class TestDaemon(unittest.TestCase): mock_popen.assert_called_once_with(['/bin/rsync', '--verbose', '--recursive', '--copy-dirlinks', '--times', '--omit-dir-times', 'dts:/data/dts/exposures/raw/20190703/00000127/', '/desi/root/spectro/staging/raw/20190703/00000127/']) - mock_log.error.assert_called_once_with('rsync problem detected!') + mock_log.error.assert_called_once_with('rsync problem detected for %s/%s!', '20190703', '00000127') mock_status.update.assert_called_once_with('20190703', '00000127', 'rsync', failure=True) # # Actually run the pipeline diff --git a/py/desitransfer/test/test_daily.py b/py/desitransfer/test/test_daily.py index 863f9e9..18feddd 100644 --- a/py/desitransfer/test/test_daily.py +++ b/py/desitransfer/test/test_daily.py @@ -37,6 +37,8 @@ class TestDaily(unittest.TestCase): self.assertEqual(c[0].source, '/exposures/desi/sps') self.assertEqual(c[0].destination, os.path.join(os.environ['DESI_ROOT'], 'engineering', 'spectrograph', 'sps')) + self.assertEqual(c[1].extra[0], '--exclude-from') + self.assertTrue(c[2].dirlinks) def test_options(self): """Test command-line arguments. @@ -45,7 +47,7 @@ class TestDaily(unittest.TestCase): ['desi_daily_transfer', '--daemon', '--kill', os.path.expanduser('~/stop_daily_transfer')]): options = _options() - self.assertTrue(options.apache) + self.assertTrue(options.permission) self.assertEqual(options.sleep, 24) self.assertTrue(options.daemon) self.assertEqual(options.kill, @@ -69,7 +71,7 @@ class TestDaily(unittest.TestCase): call().__enter__(), call().write(('DEBUG: desi_daily_transfer {}\n'.format(dtVersion)).encode('utf-8')), call().write(b'DEBUG: 2019-07-03\n'), - call().write(b'DEBUG: /bin/rsync --verbose --recursive --copy-dirlinks --times --omit-dir-times dts:/src/d0/ /dst/d0/\n'), + call().write(b'DEBUG: /bin/rsync --verbose --recursive --links --times --omit-dir-times dts:/src/d0/ /dst/d0/\n'), call().flush(), call().__exit__(None, None, None)]) mock_walk.assert_called_once_with('/dst/d0') @@ -79,6 +81,30 @@ class TestDaily(unittest.TestCase): @patch('os.walk') @patch('os.chmod') + @patch('subprocess.Popen') + @patch('desitransfer.daily.stamp') + @patch('builtins.open', new_callable=mock_open) + def test_transfer_extra(self, mo, mock_stamp, mock_popen, mock_chmod, mock_walk): + """Test the transfer functions in DailyDirectory.transfer() with extra options. + """ + mock_walk.return_value = [('/dst/d0', [], ['f1', 'f2'])] + mock_stamp.return_value = '2019-07-03' + mock_popen().wait.return_value = 0 + d = DailyDirectory('/src/d0', '/dst/d0', extra=['--exclude-from', 'foo']) + d.transfer() + mo.assert_has_calls([call('/dst/d0.log', 'ab'), + call().__enter__(), + call().write(('DEBUG: desi_daily_transfer {}\n'.format(dtVersion)).encode('utf-8')), + call().write(b'DEBUG: 2019-07-03\n'), + call().write(b'DEBUG: /bin/rsync --verbose --recursive --links --times --omit-dir-times --exclude-from foo dts:/src/d0/ /dst/d0/\n'), + call().flush(), + call().__exit__(None, None, None)]) + mock_walk.assert_called_once_with('/dst/d0') + mock_chmod.assert_has_calls([call('/dst/d0', 1512), + call('/dst/d0/f1', 288), + call('/dst/d0/f2', 288)]) + @patch('os.walk') + @patch('os.chmod') def test_lock(self, mock_chmod, mock_walk): """Test the lock functions in DailyDirectory.lock(). """ @@ -98,12 +124,12 @@ class TestDaily(unittest.TestCase): @patch('subprocess.Popen') @patch('builtins.open', new_callable=mock_open) - def test_apache(self, mo, mock_popen): - """Test granting apache/www permissions. + def test_permission(self, mo, mock_popen): + """Test granting permissions. """ mock_popen().wait.return_value = 0 d = DailyDirectory('/src/d0', '/dst/d0') - d.apache() + d.permission() mo.assert_has_calls([call('/dst/d0.log', 'ab'), call().__enter__(), call().write(b'DEBUG: fix_permissions.sh /dst/d0\n'),
Shift nightwatch transfer to daily engineering data transfer Nightwatch is now primarily being run at NERSC, so there is no need for near-real-time transfers of nightwatch data produced at KPNO.
0.0
e6e6d9ee728d4525608213214f00ff6127ccb376
[ "py/desitransfer/test/test_common.py::TestCommon::test_empty_rsync", "py/desitransfer/test/test_common.py::TestCommon::test_ensure_scratch", "py/desitransfer/test/test_common.py::TestCommon::test_permissions", "py/desitransfer/test/test_common.py::TestCommon::test_rsync", "py/desitransfer/test/test_common.py::TestCommon::test_stamp", "py/desitransfer/test/test_common.py::TestCommon::test_today", "py/desitransfer/test/test_common.py::TestCommon::test_yesterday", "py/desitransfer/test/test_common.py::test_suite", "py/desitransfer/test/test_daemon.py::TestDaemon::test_lock_directory", "py/desitransfer/test/test_daemon.py::TestDaemon::test_popen", "py/desitransfer/test/test_daemon.py::TestDaemon::test_rsync_night", "py/desitransfer/test/test_daemon.py::TestDaemon::test_unlock_directory", "py/desitransfer/test/test_daemon.py::TestDaemon::test_verify_checksum", "py/desitransfer/test/test_daemon.py::test_suite", "py/desitransfer/test/test_daily.py::TestDaily::test_config", "py/desitransfer/test/test_daily.py::TestDaily::test_lock", "py/desitransfer/test/test_daily.py::TestDaily::test_permission", "py/desitransfer/test/test_daily.py::TestDaily::test_transfer", "py/desitransfer/test/test_daily.py::TestDaily::test_transfer_extra", "py/desitransfer/test/test_daily.py::test_suite" ]
[]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2020-11-20 18:43:42+00:00
bsd-3-clause
1,885
desihub__desiutil-125
diff --git a/doc/changes.rst b/doc/changes.rst index f154327..6f23c11 100644 --- a/doc/changes.rst +++ b/doc/changes.rst @@ -10,7 +10,11 @@ Change Log 1.9.15 (unreleased) ------------------- -* Draw ecliptic in all-sky plots. +* Set read-only permissions on all Module files, and unlock them as needed (PR `#125`_). +* Draw ecliptic in all-sky plots (PR `#124`_). + +.. _`#125`: https://github.com/desihub/desiutil/pull/125 +.. _`#124`: https://github.com/desihub/desiutil/pull/124 1.9.14 (2018-10-05) ------------------- diff --git a/py/desiutil/install.py b/py/desiutil/install.py index 11f22e1..1f7077f 100644 --- a/py/desiutil/install.py +++ b/py/desiutil/install.py @@ -720,7 +720,6 @@ class DesiInstall(object): outfile = os.path.join(module_directory, self.module_keywords['name'], self.module_keywords['version']) - os.chmod(outfile, 0o440) except OSError as ose: self.log.critical(ose.strerror) raise DesiInstallException(ose.strerror) diff --git a/py/desiutil/io.py b/py/desiutil/io.py index 4a9d2a5..b515e43 100644 --- a/py/desiutil/io.py +++ b/py/desiutil/io.py @@ -9,6 +9,8 @@ Module for I/O related code. """ from __future__ import (print_function, absolute_import, division, unicode_literals) +from contextlib import contextmanager + try: basestring @@ -218,3 +220,55 @@ def decode_table(data, encoding='ascii', native=True): table.meta['ENCODING'] = encoding return table + + +@contextmanager +def unlock_file(*args, **kwargs): + """Unlock a read-only file, return a file-like object, and restore the + read-only state when done. Arguments are the same as :func:`open`. + + Returns + ------- + file-like + A file-like object, as returned by :func:`open`. + + Notes + ----- + * This assumes that the user of this function is also the owner of the + file. :func:`os.chmod` would not be expected to work in any other + circumstance. + * Technically, this restores the *original* permissions of the file, it + does not care what the original permissions were. + * If the named file does not exist, this function effectively does not + attempt to guess what the final permissions of the file would be. In + other words, it just does whatever :func:`open` would do. In this case + it is the user's responsibilty to change permissions as needed after + creating the file. + + Examples + -------- + >>> with unlock_file('read-only.txt', 'w') as f: + ... f.write(new_data) + """ + import os + import stat + w = stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH + # + # Get original permissions, unlock permissions + # + # uid = os.getuid() + old_mode = None + if os.path.exists(args[0]): + old_mode = stat.S_IMODE(os.stat(args[0]).st_mode) + os.chmod(args[0], old_mode | stat.S_IWUSR) + f = open(*args, **kwargs) + try: + yield f + finally: + # + # Restore permissions to read-only state. + # + f.close() + if old_mode is None: + old_mode = stat.S_IMODE(os.stat(args[0]).st_mode) + os.chmod(args[0], old_mode & ~w) diff --git a/py/desiutil/modules.py b/py/desiutil/modules.py index f8be62f..97aebb4 100644 --- a/py/desiutil/modules.py +++ b/py/desiutil/modules.py @@ -253,8 +253,7 @@ def process_module(module_file, module_keywords, module_dir): module_keywords['version']) with open(module_file) as m: mod = m.read().format(**module_keywords) - with open(install_module_file, 'w') as m: - m.write(mod) + _write_module_data(install_module_file, mod) return mod @@ -278,6 +277,18 @@ def default_module(module_keywords, module_dir): install_version_file = join(module_dir, module_keywords['name'], '.version') dot_version = dot_template.format(**module_keywords) - with open(install_version_file, 'w') as v: - v.write(dot_version) + _write_module_data(install_version_file, dot_version) return dot_version + + +def _write_module_data(filename, data): + """Write and permission-lock Module file data. This is intended + to consolidate some duplicated code. + """ + from os import chmod + from stat import S_IRUSR, S_IRGRP + from .io import unlock_file + with unlock_file(filename, 'w') as f: + f.write(data) + chmod(filename, S_IRUSR | S_IRGRP) + return
desihub/desiutil
07df949c0cd4e94db02a8941b369899245df5af0
diff --git a/py/desiutil/test/test_io.py b/py/desiutil/test/test_io.py index a8b17dd..4c75f51 100644 --- a/py/desiutil/test/test_io.py +++ b/py/desiutil/test/test_io.py @@ -6,16 +6,24 @@ from __future__ import (absolute_import, division, print_function, unicode_literals) # The line above will help with 2to3 support. import unittest +import os +import stat import sys import numpy as np from astropy.table import Table -from ..io import combine_dicts, decode_table, encode_table, yamlify +from ..io import combine_dicts, decode_table, encode_table, yamlify, unlock_file try: basestring except NameError: # For Python 3 basestring = str +skipTemp = False +try: + from tempfile import TemporaryDirectory +except ImportError: + skipTemp = True + class TestIO(unittest.TestCase): """Test desiutil.io @@ -178,6 +186,33 @@ class TestIO(unittest.TestCase): self.assertEqual(dict1, {'a': {'b': {'x': 1, 'y': 2}}}) self.assertEqual(dict2, {'a': {'b': {'p': 3, 'q': 4}}}) + @unittest.skipIf(skipTemp, "Skipping test that requires tempfile.TemporaryDirectory.") + def test_unlock_file(self): + """Test the permission unlock file manager. + """ + fff = stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH + www = stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH + with TemporaryDirectory() as dirname: + filename = os.path.join(dirname, 'tempfile') + with open(filename, 'wb') as f: + f.write(b'Content\n') + s0 = os.stat(filename) + ro = stat.S_IFMT(s0.st_mode) | fff + os.chmod(filename, ro) + s1 = os.stat(filename) + self.assertEqual(stat.S_IMODE(s1.st_mode), fff) + with unlock_file(filename, 'ab') as f: + f.write(b'More content\n') + s2 = os.stat(filename) + self.assertEqual(stat.S_IMODE(s2.st_mode), fff | stat.S_IWUSR) + s3 = os.stat(filename) + self.assertEqual(stat.S_IMODE(s3.st_mode), fff) + filename = os.path.join(dirname, 'newfile') + with unlock_file(filename, 'wb') as f: + f.write(b'Some content\n') + s0 = os.stat(filename) + self.assertEqual(stat.S_IMODE(s0.st_mode) & www, 0) + def test_suite(): """Allows testing of only this module with the command:: diff --git a/py/desiutil/test/test_modules.py b/py/desiutil/test/test_modules.py index a05a62c..72c073a 100644 --- a/py/desiutil/test/test_modules.py +++ b/py/desiutil/test/test_modules.py @@ -12,6 +12,8 @@ from os import chmod, environ, mkdir, pathsep, remove, rmdir from os.path import dirname, exists, isdir, join from sys import version_info from shutil import rmtree +from tempfile import mkdtemp +from pkg_resources import resource_filename from ..modules import (init_modules, configure_module, process_module, default_module) @@ -23,7 +25,7 @@ class TestModules(unittest.TestCase): @classmethod def setUpClass(cls): # Data directory - cls.data_dir = join(dirname(__file__), 't') + cls.data_dir = mkdtemp() cls.bin_dir = join(cls.data_dir, 'libexec') cls.orig_env_cache = dict() cls.env_cache = dict() @@ -56,7 +58,7 @@ class TestModules(unittest.TestCase): del environ[e] else: environ[e] = cls.orig_env_cache[e] - rmtree(cls.bin_dir) + rmtree(cls.data_dir) def cache_env(self, envs): """Store existing environment variables in a cache and delete them. @@ -227,7 +229,7 @@ class TestModules(unittest.TestCase): def test_process_module(self): """Test processing of module file templates. """ - module_file = join(self.data_dir, 'test.module') + module_file = resource_filename('desiutil.test', 't/test.module') module_keywords = {'name': 'foo', 'version': 'bar'} process_module(module_file, module_keywords, self.data_dir) self.assertTrue(isdir(join(self.data_dir, 'foo')))
desiInstall can't alter .version files with new permissions settings. So, I tagged 1.9.14, and went to install it with `desiInstall -d desiutil 1.9.14`. In the process of restricting write access, even to the desi user, I also made .version files read-only. However, `desiInstall` expects to be able to write to such files. For now, I am going to restore user-read to all .version files in 20180709-1.2.6-spec.
0.0
07df949c0cd4e94db02a8941b369899245df5af0
[ "py/desiutil/test/test_io.py::TestIO::test_combinedicts", "py/desiutil/test/test_io.py::TestIO::test_endecode_table", "py/desiutil/test/test_io.py::TestIO::test_unlock_file", "py/desiutil/test/test_io.py::test_suite", "py/desiutil/test/test_modules.py::TestModules::test_configure_module", "py/desiutil/test/test_modules.py::TestModules::test_default_module", "py/desiutil/test/test_modules.py::TestModules::test_init_modules", "py/desiutil/test/test_modules.py::TestModules::test_process_module", "py/desiutil/test/test_modules.py::test_suite" ]
[]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2018-10-30 16:59:46+00:00
bsd-3-clause
1,886
desihub__desiutil-173
diff --git a/doc/changes.rst b/doc/changes.rst index ef3bf1d..0fc8189 100644 --- a/doc/changes.rst +++ b/doc/changes.rst @@ -5,7 +5,10 @@ Change Log 3.2.2 (unreleased) ------------------ -* No changes yet. +* Add module config support for packages like QuasarNP where the GitHub + name is capitalized by the python package isn't (PR `#173`_). + +.. _`#173`: https://github.com/desihub/desiutil/pull/173 3.2.1 (2021-05-13) ------------------ diff --git a/py/desiutil/modules.py b/py/desiutil/modules.py index 33a2ca9..4accae3 100644 --- a/py/desiutil/modules.py +++ b/py/desiutil/modules.py @@ -199,7 +199,10 @@ def configure_module(product, version, product_root, working_dir=None, dev=False module_keywords['needs_ld_lib'] = '' if isdir(join(working_dir, 'pro')): module_keywords['needs_idl'] = '' - if (exists(join(working_dir, 'setup.py')) and isdir(join(working_dir, product))): + if (exists(join(working_dir, 'setup.py')) and + (isdir(join(working_dir, product)) or + isdir(join(working_dir, product.lower()))) + ): if dev: module_keywords['needs_trunk_py'] = '' module_keywords['trunk_py_dir'] = ''
desihub/desiutil
93f40ac22f0d5629bb80713e11918e1d1cd3f36b
diff --git a/py/desiutil/test/test_modules.py b/py/desiutil/test/test_modules.py index 3b5233b..4c710f0 100644 --- a/py/desiutil/test/test_modules.py +++ b/py/desiutil/test/test_modules.py @@ -222,6 +222,35 @@ class TestModules(unittest.TestCase): rmdir(join(self.data_dir, t)) for t in test_files: remove(join(self.data_dir, t)) + # + # Test mixed case product directory (Blat) vs. python package (blat) + # + test_dirs = ('blat',) + test_files = {'setup.py': '#!/usr/bin/env python\n'} + for t in test_dirs: + mkdir(join(self.data_dir, t)) + for t in test_files: + with open(join(self.data_dir, t), 'w') as s: + s.write(test_files[t]) + results['name'] = 'Blat' + results['version'] = '1.2.3' + results['needs_bin'] = '# ' + results['needs_python'] = '' + results['needs_trunk_py'] = '# ' + results['trunk_py_dir'] = '/py' + results['needs_ld_lib'] = '# ' + results['needs_idl'] = '# ' + + conf = configure_module('Blat', '1.2.3', '/my/product/root', + working_dir=self.data_dir) + + for key in results: + self.assertEqual(conf[key], results[key], key) + for t in test_dirs: + rmdir(join(self.data_dir, t)) + for t in test_files: + remove(join(self.data_dir, t)) + def test_process_module(self): """Test processing of module file templates.
desiInstall creates incorrect module file for QuasarNP QuasarNP is a semi-external package hosted in desihub. It doesn't have a boilerplate etc/quasarnp.module file, but it also doesn't require anything custom so I was expecting the desiInstall default module file to work. desiInstall does correctly identify the "py" install and pip installs QuasarNP, but the resulting module file doesn't add $PRODUCT_DIR/lib/python3.8/site-packages to $PYTHONPATH. ``` [cori06 ~] desiInstall -v -r $SCRATCH/desi/test QuasarNP 0.1.0 WARNING:install.py:183:get_options:2021-06-03T14:21:29: The environment variable LANG is not set! DEBUG:install.py:251:get_options:2021-06-03T14:21:29: Set log level to DEBUG. DEBUG:install.py:320:get_product_version:2021-06-03T14:21:29: Detected GitHub install. DEBUG:install.py:351:identify_branch:2021-06-03T14:21:29: Using https://github.com/desihub/QuasarNP/archive/0.1.0.tar.gz as the URL of this product. INFO:install.py:412:get_code:2021-06-03T14:21:29: Detected old working directory, /global/u2/s/sjbailey/QuasarNP-0.1.0. Deleting... DEBUG:install.py:414:get_code:2021-06-03T14:21:29: shutil.rmtree('/global/u2/s/sjbailey/QuasarNP-0.1.0') DEBUG:install.py:638:start_modules:2021-06-03T14:21:30: Initializing Modules with MODULESHOME=/opt/cray/pe/modules/3.2.11.4. DEBUG:install.py:538:build_type:2021-06-03T14:21:30: Detected build type: py DEBUG:install.py:700:install_module:2021-06-03T14:21:30: configure_module(QuasarNP, 0.1.0, working_dir=/global/u2/s/sjbailey/QuasarNP-0.1.0, dev=False) DEBUG:install.py:720:install_module:2021-06-03T14:21:30: process_module('/global/common/software/desi/cori/desiconda/20200801-1.4.0-spec/code/desiutil/3.2.1/lib/python3.8/site-packages/desiutil/data/desiutil.module', self.module_keywords, '/global/cscratch1/sd/sjbailey/desi/test/modulefiles') DEBUG:install.py:757:prepare_environment:2021-06-03T14:21:31: module('switch', 'QuasarNP/0.1.0') DEBUG:install.py:538:build_type:2021-06-03T14:21:31: Detected build type: py DEBUG:install.py:538:build_type:2021-06-03T14:21:31: Detected build type: py DEBUG:install.py:802:install:2021-06-03T14:21:31: os.makedirs('/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages') DEBUG:install.py:824:install:2021-06-03T14:21:31: /global/common/software/desi/cori/desiconda/20200801-1.4.0-spec/conda/bin/python -m pip install --no-deps --disable-pip-version-check --ignore-installed --prefix=/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0 . DEBUG:install.py:833:install:2021-06-03T14:21:33: Processing /global/u2/s/sjbailey/QuasarNP-0.1.0 Building wheels for collected packages: quasarnp Building wheel for quasarnp (setup.py): started Building wheel for quasarnp (setup.py): finished with status 'done' Created wheel for quasarnp: filename=quasarnp-0.1.0-py3-none-any.whl size=13407 sha256=17d7dbdf89520f3a0e5d751edd4b7591b45563425a190550ff31c71e48b1b855 Stored in directory: /global/u2/s/sjbailey/.cache/pip/wheels/b3/5d/19/08d052aecb141666e9fca7cef889a0c9393b18766c47f69300 Successfully built quasarnp Installing collected packages: quasarnp Successfully installed quasarnp-0.1.0 DEBUG:install.py:538:build_type:2021-06-03T14:21:33: Detected build type: py DEBUG:install.py:538:build_type:2021-06-03T14:21:33: Detected build type: py DEBUG:install.py:957:permissions:2021-06-03T14:21:33: fix_permissions.sh -v /global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0 DEBUG:install.py:962:permissions:2021-06-03T14:21:35: Fixing permissions on /global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0 ... /usr/bin/find /global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0 -user sjbailey -not -group desi -exec chgrp -c -h desi {} ; changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/model.py' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/io.py' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/__init__.py' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/__pycache__' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/__pycache__/layers.cpython-38.pyc' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/__pycache__/model.cpython-38.pyc' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/__pycache__/__init__.cpython-38.pyc' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/__pycache__/utils.cpython-38.pyc' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/__pycache__/io.cpython-38.pyc' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/layers.py' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/utils.py' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp-0.1.0.dist-info' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp-0.1.0.dist-info/INSTALLER' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp-0.1.0.dist-info/WHEEL' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp-0.1.0.dist-info/LICENSE' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp-0.1.0.dist-info/top_level.txt' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp-0.1.0.dist-info/METADATA' from sjbailey to desi changed group of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp-0.1.0.dist-info/RECORD' from sjbailey to desi /usr/bin/find /global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0 -user sjbailey -type f -not -perm /g+r -exec chmod -c g+r {} ; /usr/bin/find /global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0 -user sjbailey -type d -not -perm -g+rxs -exec chmod -c g+rxs {} ; mode of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0' changed from 0755 (rwxr-xr-x) to 2755 (rwxr-sr-x) mode of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib' changed from 0755 (rwxr-xr-x) to 2755 (rwxr-sr-x) mode of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8' changed from 0755 (rwxr-xr-x) to 2755 (rwxr-sr-x) mode of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages' changed from 0755 (rwxr-xr-x) to 2755 (rwxr-sr-x) mode of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp' changed from 0755 (rwxr-xr-x) to 2755 (rwxr-sr-x) mode of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp/__pycache__' changed from 0755 (rwxr-xr-x) to 2755 (rwxr-sr-x) mode of '/global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0/lib/python3.8/site-packages/quasarnp-0.1.0.dist-info' changed from 0755 (rwxr-xr-x) to 2755 (rwxr-sr-x) DEBUG:install.py:970:permissions:2021-06-03T14:21:35: chmod -R a-w /global/cscratch1/sd/sjbailey/desi/test/code/QuasarNP/0.1.0 DEBUG:install.py:975:permissions:2021-06-03T14:21:35: DEBUG:install.py:987:cleanup:2021-06-03T14:21:35: os.chdir('/global/u2/s/sjbailey') DEBUG:install.py:991:cleanup:2021-06-03T14:21:35: shutil.rmtree('/global/u2/s/sjbailey/QuasarNP-0.1.0') DEBUG:install.py:1024:run:2021-06-03T14:21:35: run() complete. [cori06 ~] tail -15 $SCRATCH/desi/test/modulefiles/QuasarNP/0.1.0 # setenv [string toupper $product] $PRODUCT_DIR # # The lines below set various other environment variables. They assume the # template product layout. These will be set or commented as needed by the # desiInstall script. # # prepend-path PATH $PRODUCT_DIR/bin # prepend-path PYTHONPATH $PRODUCT_DIR/lib/python3.8/site-packages # prepend-path PYTHONPATH $PRODUCT_DIR/py # prepend-path LD_LIBRARY_PATH $PRODUCT_DIR/lib # prepend-path IDL_PATH +$PRODUCT_DIR/pro # # Add any non-standard Module code below this point. # ```
0.0
93f40ac22f0d5629bb80713e11918e1d1cd3f36b
[ "py/desiutil/test/test_modules.py::TestModules::test_configure_module" ]
[ "py/desiutil/test/test_modules.py::TestModules::test_default_module", "py/desiutil/test/test_modules.py::TestModules::test_init_modules", "py/desiutil/test/test_modules.py::TestModules::test_process_module", "py/desiutil/test/test_modules.py::test_suite" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2021-06-03 22:34:52+00:00
bsd-3-clause
1,887
desihub__desiutil-188
diff --git a/doc/changes.rst b/doc/changes.rst index 8697970..93581d9 100644 --- a/doc/changes.rst +++ b/doc/changes.rst @@ -8,9 +8,14 @@ Change Log * :command:`desiInstall` uses desihub location of simqso fork (commit e963344_). * Allow :command:`desiInstall` to remove permission-locked directories; suppress certain :command:`pip` warnings (PR `#185`_). +* Allow :command:`desiInstall` to compile code in certain branch installs (PR `#188`_). +* Add `gpu_specter`_ to known packages (PR `#189`_). .. _e963344: https://github.com/desihub/desiutil/commit/e963344cd072255174187d2bd6da72d085745abd .. _`#185`: https://github.com/desihub/desiutil/pull/185 +.. _`#188`: https://github.com/desihub/desiutil/pull/188 +.. _`#189`: https://github.com/desihub/desiutil/pull/189 +.. _`gpu_specter`: https://github.com/desihub/gpu_specter 3.2.5 (2022-01-20) ------------------ diff --git a/doc/desiInstall.rst b/doc/desiInstall.rst index e433192..8c926f0 100644 --- a/doc/desiInstall.rst +++ b/doc/desiInstall.rst @@ -322,6 +322,23 @@ not bundled with the code. The script should download data *directly* to with :command:`desiInstall` and unit tests. Note that here are other, better ways to install and manipulate data that is bundled *with* a Python package. +Compile in Branch Installs +-------------------------- + +In a few cases (fiberassign_, specex_) code needs to be compiled even when +installing a branch. If :command:`desiInstall` detects a branch install *and* +the script ``etc/product_compile.sh`` exists, :command:`desiInstall` will run this +script, supplying the Python executable path as a single command-line argument. +The script itself is intended to be a thin wrapper on *e.g.*:: + + #!/bin/bash + py=$1 + ${py} setup.py build_ext --inplace + + +.. _fiberassign: https://github.com/desihub/fiberassign +.. _specex: https://github.com/desihub/specex + Fix Permissions --------------- diff --git a/py/desiutil/install.py b/py/desiutil/install.py index 28c92ad..7dfc4cf 100644 --- a/py/desiutil/install.py +++ b/py/desiutil/install.py @@ -910,6 +910,33 @@ class DesiInstall(object): raise DesiInstallException(message) return + def compile_branch(self): + """Certain packages need C/C++ code compiled even for a branch install. + """ + if self.is_branch: + compile_script = os.path.join(self.install_dir, 'etc', + '{0}_compile.sh'.format(self.baseproduct)) + if os.path.exists(compile_script): + self.log.debug("Detected compile script: %s.", compile_script) + if self.options.test: + self.log.debug('Test Mode. Skipping compile script.') + else: + current_dir = os.getcwd() + self.log.debug("os.chdir('%s')", self.install_dir) + os.chdir(self.install_dir) + proc = Popen([compile_script, sys.executable], universal_newlines=True, + stdout=PIPE, stderr=PIPE) + out, err = proc.communicate() + status = proc.returncode + self.log.debug(out) + self.log.debug("os.chdir('%s')", current_dir) + os.chdir(current_dir) + if status != 0 and len(err) > 0: + message = "Error compiling code: {0}".format(err) + self.log.critical(message) + raise DesiInstallException(message) + return + def verify_bootstrap(self): """Make sure that desiutil/desiInstall was installed with an explicit Python executable path. @@ -1027,6 +1054,7 @@ class DesiInstall(object): self.prepare_environment() self.install() self.get_extra() + self.compile_branch() self.verify_bootstrap() self.permissions() except DesiInstallException:
desihub/desiutil
4f910f407c4b7fa9636aa64fc65acd72c49a3cf7
diff --git a/py/desiutil/test/test_install.py b/py/desiutil/test/test_install.py index 73c18f7..a12433f 100644 --- a/py/desiutil/test/test_install.py +++ b/py/desiutil/test/test_install.py @@ -2,6 +2,7 @@ # -*- coding: utf-8 -*- """Test desiutil.install. """ +import sys import unittest from unittest.mock import patch, call, MagicMock, mock_open from os import chdir, environ, getcwd, mkdir, remove, rmdir @@ -507,6 +508,42 @@ class TestInstall(unittest.TestCase): self.assertLog(-1, message) self.assertEqual(str(cm.exception), message) + @patch('os.chdir') + @patch('os.path.exists') + @patch('desiutil.install.Popen') + def test_compile_branch(self, mock_popen, mock_exists, mock_chdir): + """Test compiling code in certain cases. + """ + current_dir = getcwd() + options = self.desiInstall.get_options(['fiberassign', 'branches/main']) + self.desiInstall.baseproduct = 'fiberassign' + self.desiInstall.is_branch = True + self.desiInstall.install_dir = join(self.data_dir, 'fiberassign') + mock_exists.return_value = True + mock_proc = mock_popen() + mock_proc.returncode = 0 + mock_proc.communicate.return_value = ('out', 'err') + self.desiInstall.compile_branch() + mock_chdir.assert_has_calls([call(self.desiInstall.install_dir), + call(current_dir)]) + mock_exists.assert_has_calls([call(join(self.desiInstall.install_dir, 'etc', 'fiberassign_compile.sh'))]) + mock_popen.assert_has_calls([call([join(self.desiInstall.install_dir, 'etc', 'fiberassign_compile.sh'), sys.executable], + stderr=-1, stdout=-1, universal_newlines=True)], any_order=True) + mock_popen.reset_mock() + self.desiInstall.options.test = True + self.desiInstall.compile_branch() + self.assertLog(-1, 'Test Mode. Skipping compile script.') + mock_popen.reset_mock() + self.desiInstall.options.test = False + mock_proc = mock_popen() + mock_proc.returncode = 1 + mock_proc.communicate.return_value = ('out', 'err') + with self.assertRaises(DesiInstallException) as cm: + self.desiInstall.compile_branch() + message = "Error compiling code: err" + self.assertLog(-1, message) + self.assertEqual(str(cm.exception), message) + def test_verify_bootstrap(self): """Test proper installation of the desiInstall executable. """
desiInstall of specex/main and fiberassign/main, which need compilation too desiInstall supports "in-place" installations of python repos that adds `$PRODUCT_DIR/py` to `$PYTHONPATH` and `$PRODUCT_DIR/bin` to `$PATH` so that any changes to the repo are automatically available without having to do a separate installation step. Good. specex and fiberassign, however, are hybrid repos that have python code with compiled extensions. An in-place install is handy when making changes to any of the python code, but if any of the C++ code changes it still has to be compiled using: ``` python setup.py build_ext --inplace ``` desiInstall doesn't know this, and this pattern doesn't fit any of the build types listed at https://desiutil.readthedocs.io/en/latest/desiInstall.html#determine-build-type . What's the best way to get desiInstall to know that it needs to run this extra step for these two repos? A somewhat hacky solution that may not require changing desiInstall is to leverage its special case of looking for an `etc/{productname}_data.sh` script and executing that, e.g. as used by desimodel to get the data from svn. specex and fiberassign could add their own `etc/*_data.sh` scripts to run `python setup.py build_ext --inplace`, but that is somewhat cryptically using a data-download hook for other purposes. It might be better to define another hook similar to `etc/*_data.sh`, and if desiInstall detects that it will run it for in-place branch installations, but not for regular installations. That requires an update to both desiInstall and the specex+fiberassign repos, but it might be more obvious and maintainable in the future. For context, both specex and fiberassign used to have a Makefile that desiInstall knew to run, but both have migrated to a python-first approach with compiled extensions without a Makefile. Current master (now main) installations have bootstrapped the `python setup.py build_ext --inplace` upon first installation, after which the desitest nightly update cronjob re-runs that every night after `git pull`. The point of this ticket is so that the end-user doesn't have to remember to do special steps whenever they make a fresh main installation. @weaverba137 thoughts?
0.0
4f910f407c4b7fa9636aa64fc65acd72c49a3cf7
[ "py/desiutil/test/test_install.py::TestInstall::test_compile_branch" ]
[ "py/desiutil/test/test_install.py::TestInstall::test_anaconda_version", "py/desiutil/test/test_install.py::TestInstall::test_build_type", "py/desiutil/test/test_install.py::TestInstall::test_cleanup", "py/desiutil/test/test_install.py::TestInstall::test_default_nersc_dir", "py/desiutil/test/test_install.py::TestInstall::test_dependencies", "py/desiutil/test/test_install.py::TestInstall::test_get_extra", "py/desiutil/test/test_install.py::TestInstall::test_get_product_version", "py/desiutil/test/test_install.py::TestInstall::test_identify_branch", "py/desiutil/test/test_install.py::TestInstall::test_install", "py/desiutil/test/test_install.py::TestInstall::test_install_module", "py/desiutil/test/test_install.py::TestInstall::test_module_dependencies", "py/desiutil/test/test_install.py::TestInstall::test_nersc_module_dir", "py/desiutil/test/test_install.py::TestInstall::test_permissions", "py/desiutil/test/test_install.py::TestInstall::test_prepare_environment", "py/desiutil/test/test_install.py::TestInstall::test_sanity_check", "py/desiutil/test/test_install.py::TestInstall::test_set_install_dir", "py/desiutil/test/test_install.py::TestInstall::test_unlock_permissions", "py/desiutil/test/test_install.py::TestInstall::test_verify_bootstrap", "py/desiutil/test/test_install.py::test_suite" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }
2022-08-18 00:08:44+00:00
bsd-3-clause
1,888
destag__at-date-17
diff --git a/atdate/api.py b/atdate/api.py index b42b2ac..7f1af8e 100644 --- a/atdate/api.py +++ b/atdate/api.py @@ -15,7 +15,9 @@ class AtDateParser: tree = self.parser.parse(string_to_parse.lower()) new_tree = transformer.transform(tree) - next_time_run = new_tree if isinstance(new_tree, datetime) else new_tree.children[-1] + next_time_run = new_tree + while not isinstance(next_time_run, datetime): + next_time_run = next_time_run.children[-1] if next_time_run < transformer.now: raise ValueError @@ -65,7 +67,7 @@ class AtDateTransformer(Transformer): self.datetime_params['second'] = 0 return datetime(**self.datetime_params) - def _hr24clock_hour_minute(self, matches): + def _iso_time(self, matches): hour = int(matches[0]) minute = int(matches[1]) next_day = self._check_if_next_day(hour, minute) @@ -152,6 +154,13 @@ class AtDateTransformer(Transformer): self.datetime_params['year'] = year return datetime(**self.datetime_params) + def _iso_date(self, matches): + year, month, day = map(int, matches) + self.datetime_params['day'] = day + self.datetime_params['month'] = month + self.datetime_params['year'] = year + return datetime(**self.datetime_params) + def _next(self, matches): inc_period = matches[0] if matches[0].endswith('s') else matches[0] + 's' dt = datetime(**self.datetime_params) diff --git a/atdate/atdate_format.py b/atdate/atdate_format.py index 42e910b..f163137 100644 --- a/atdate/atdate_format.py +++ b/atdate/atdate_format.py @@ -3,25 +3,30 @@ format_string = r''' | time date | time increment | time date increment + | date time + | isodate "t" isotime | date | date increment | nowspec | nowspec increment | increment -time: HR24CLOCK_HR_MIN -> _hr24clock_hr_min - | HR24CLOCK_HOUR ":" MINUTE -> _hr24clock_hour_minute - | WALLCLOCK_HR_MIN AM_PM -> _wallclock_hr_min_am_pm - | WALLCLOCK_HOUR ":" MINUTE AM_PM -> _wallclock_hour_minute_am_pm - | "noon" -> _noon - | "midnight" -> _midnight -date: MONTH_NAME DAY_NUMBER -> _month_name_day_number - | MONTH_NUMBER "/" DAY_NUMBER -> _month_number_day_number - | MONTH_NUMBER "/" DAY_NUMBER "/" YEAR_NUMBER -> _month_number_day_number_year_number - | DAY_NUMBER "." MONTH_NUMBER -> _day_number_month_number - | DAY_NUMBER "." MONTH_NUMBER "." YEAR_NUMBER -> _day_number_month_number_year_number -increment: "next" INC_PERIOD -> _next - | "+" INT INC_PERIOD -> _inc_number -nowspec: "now" -> _now +time: HR24CLOCK_HR_MIN -> _hr24clock_hr_min + | WALLCLOCK_HR_MIN AM_PM -> _wallclock_hr_min_am_pm + | WALLCLOCK_HOUR ":" MINUTE AM_PM -> _wallclock_hour_minute_am_pm + | "noon" -> _noon + | "midnight" -> _midnight + | isotime +date: MONTH_NAME DAY_NUMBER -> _month_name_day_number + | MONTH_NUMBER "/" DAY_NUMBER -> _month_number_day_number + | MONTH_NUMBER "/" DAY_NUMBER "/" YEAR_NUMBER -> _month_number_day_number_year_number + | DAY_NUMBER "." MONTH_NUMBER -> _day_number_month_number + | DAY_NUMBER "." MONTH_NUMBER "." YEAR_NUMBER -> _day_number_month_number_year_number + | isodate +isodate: YEAR_NUMBER "-" MONTH_NUMBER "-" DAY_NUMBER -> _iso_date +isotime: HR24CLOCK_HOUR ":" MINUTE -> _iso_time +increment: "next" INC_PERIOD -> _next + | "+" INT INC_PERIOD -> _inc_number +nowspec: "now" -> _now INC_PERIOD: "minutes" | "minute" | "hours" | "hour" | "days" | "day" diff --git a/docs/README.md b/docs/README.md index b33fdbd..ab82ea5 100644 --- a/docs/README.md +++ b/docs/README.md @@ -98,15 +98,18 @@ tokens|example [time] [increment]|17:32 next day [time] [date] [increment]|17:32 11/22/2033 next day [date]|11/22/2033 +[date] [time]|11/22/2033 17:32 [date] [increment]|11/22/2033 next month [now]|now [now] [increment]|now next day [increment]|next month +[isodatetime]|2033-11-22T17:32 [time]: #time [date]: #date [increment]: #increment [now]: #now +[isodatetime]: #isodatetime ### At date tokens @@ -135,6 +138,7 @@ format|example \[1-12\] / \[1-31\] / \[0-9999\]|10/27/2006 \[1-12\] . \[1-31\]|10.27 \[1-12\] . \[1-31\] . \[0-9999\]|10.27.2006 +\[0-9999\] - \[1-12\] - \[1-31\]|2006-10-27 #### increment @@ -145,6 +149,14 @@ format|example next \[[period](#period)\]|next month \+ \[0-9999\] \[[period](#period)\]|\+ 12 minutes +#### isodatetime + +Format for ISO 8601 date time. + +format|example +---|--- +\[0-9999\] - \[1-12\] - \[1-31\] T \[0-23\] : \[0-59\]|2033-11-22T17:32 + #### now Format for this token is literally `now`.
destag/at-date
3957d0b750ef1205adb0ba2fc3dccf34c3f0ce62
diff --git a/test/test_atdate.py b/test/test_atdate.py index fdbf0ce..8c23f7c 100644 --- a/test/test_atdate.py +++ b/test/test_atdate.py @@ -220,3 +220,31 @@ def test_plus_one_day_without_now(): test_string = '+1days' result = atdate.parse(test_string) assert result == datetime(2000, 7, 3, 3, 4, 5, 0) + + +@freeze_time('2000-07-02 03:04:05') +def test_isodate(): + test_string = '2011-09-22' + result = atdate.parse(test_string) + assert result == datetime(2011, 9, 22, 3, 4, 5, 0) + + +@freeze_time('2000-07-02 03:04:05') +def test_time_date(): + test_string = "12:24 01.02.2011" + result = atdate.parse(test_string) + assert result == datetime(2011, 2, 1, 12, 24, 0, 0) + + +@freeze_time('2000-07-02 03:04:05') +def test_isodatetime(): + test_string = '2011-09-22T11:44' + result = atdate.parse(test_string) + assert result == datetime(2011, 9, 22, 11, 44, 0, 0) + + +@freeze_time('2000-07-02 03:04:05') +def test_isodatetime_without_t(): + test_string = '2011-09-22 11:44' + result = atdate.parse(test_string) + assert result == datetime(2011, 9, 22, 11, 44, 0, 0)
ISO 8601 compatibility I think that it would be nice to support dates and times in ISO 8601 format.
0.0
3957d0b750ef1205adb0ba2fc3dccf34c3f0ce62
[ "test/test_atdate.py::test_isodate", "test/test_atdate.py::test_isodatetime_without_t", "test/test_atdate.py::test_isodatetime" ]
[ "test/test_atdate.py::test_at_midnight_month_change", "test/test_atdate.py::test_day_number_month_number_year_number", "test/test_atdate.py::test_at_now_next_week", "test/test_atdate.py::test_at_now_next_day", "test/test_atdate.py::test_at_midnight", "test/test_atdate.py::test_at_now_next_minutes", "test/test_atdate.py::test_at_noon_after_noon", "test/test_atdate.py::test_at_now_next_minute_change_minute", "test/test_atdate.py::test_next_month_without_now", "test/test_atdate.py::test_month_number_day_number", "test/test_atdate.py::test_at_now_next_minute_change_day", "test/test_atdate.py::test_wallclock_hour_minute_am_pm", "test/test_atdate.py::test_at_now_next_year", "test/test_atdate.py::test_at_now_next_hour", "test/test_atdate.py::test_at_noon_before_noon", "test/test_atdate.py::test_at_now_next_month", "test/test_atdate.py::test_hr24clock_hr_min", "test/test_atdate.py::test_at_date_has_atdateparser_attribute", "test/test_atdate.py::test_day_number_month_number", "test/test_atdate.py::test_month_name_day_number", "test/test_atdate.py::test_wallclock_hr_min_am_pm", "test/test_atdate.py::test_at_now_next_minute_change_hour", "test/test_atdate.py::test_plus_one_day_without_now", "test/test_atdate.py::test_at_noon_month_change", "test/test_atdate.py::test_at_noon_year_change", "test/test_atdate.py::test_parse_return_datetime_object", "test/test_atdate.py::test_at_now", "test/test_atdate.py::test_inc_period", "test/test_atdate.py::test_hr24clock_hour_minute", "test/test_atdate.py::test_month_number_day_number_year_number", "test/test_atdate.py::test_at_date_has_parse_attribute", "test/test_atdate.py::test_time_date", "test/test_atdate.py::test_at_midnight_year_change" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2018-10-17 19:42:01+00:00
mit
1,889
dev-cafe__parselglossy-52
diff --git a/parselglossy/documentation.py b/parselglossy/documentation.py index f101cb7..0b8ed79 100644 --- a/parselglossy/documentation.py +++ b/parselglossy/documentation.py @@ -51,14 +51,19 @@ def documentation_generator( """ comment = ( + ".. raw:: html\n\n" + " <style> .red {color:#aa0060; font-weight:bold; font-size:18px} </style>\n\n" # noqa: E501 + ".. role:: red\n\n" ".. This documentation was autogenerated using parselglossy." " Editing by hand is not recommended.\n" ) header_fmt = ( "{comment:s}\n{markup:s}\n{header:s}\n{markup:s}\n\n" - "Keywords without a default value are **required**.\n" - "Sections where all keywords have a default value can be omitted.\n" + "- Keywords without a default value are **required**.\n" + "- Default values are either explicit or computed from the value of other keywords in the input.\n" # noqa: E501 + "- Sections where all keywords have a default value can be omitted.\n" + "- Predicates, if present, are the functions run to validate user input.\n" ) docs = rec_documentation_generator(template=template) @@ -78,14 +83,26 @@ def document_keyword(keyword: JSONDict) -> str: **Type** ``{2:s}`` """ - doc = kw_fmt.format(keyword["name"], keyword["docstring"], keyword["type"]) + doc = kw_fmt.format( + keyword["name"], keyword["docstring"].replace("\n", " "), keyword["type"] + ) if "default" in keyword.keys(): doc += """ - **Default** {}""".format( + **Default** ``{}`` +""".format( keyword["default"] ) + if "predicates" in keyword.keys(): + preds = "\n ".join(("- ``{}``".format(x) for x in keyword["predicates"])) + doc += """ + **Predicates** + {} +""".format( + preds + ) + return doc @@ -106,20 +123,20 @@ def rec_documentation_generator(template, *, level: int = 0) -> str: keywords = template["keywords"] if "keywords" in template.keys() else [] if keywords: - doc = "\n**Keywords**" + docs.append(indent("\n:red:`Keywords`", level)) + for k in keywords: - doc += document_keyword(k) + doc = document_keyword(k) docs.extend(indent(doc, level)) sections = template["sections"] if "sections" in template.keys() else [] if sections: - doc = "\n" if level == 0 else "\n\n" - doc += "**Sections**" + docs.append(indent("\n:red:`Sections`", level)) fmt = r""" :{0:s}: {1:s} """ for s in sections: - doc += fmt.format(s["name"], s["docstring"]) + doc = fmt.format(s["name"], s["docstring"].replace("\n", " ")) doc += rec_documentation_generator(s, level=level + 1) docs.extend(indent(doc, level))
dev-cafe/parselglossy
b28084a6ca692dd1cecc2e07a229f20d1630e162
diff --git a/tests/api/docs_template.yml b/tests/api/docs_template.yml index 9966f26..2425855 100644 --- a/tests/api/docs_template.yml +++ b/tests/api/docs_template.yml @@ -1,20 +1,60 @@ keywords: -- docstring: Title of the calculation. +- docstring: | + Title of the calculation. I had to write an extremely long documentation + string for this one, as it is extremely important to let you know that this + keyword will define the title of the calculation and, not having a default, + you will be required to set it! name: title type: str +- docstring: Some integer + name: an_integer + type: int + default: 15 +- docstring: A list of floats + name: float_list + type: List[float] + default: [1.0, 2.0, 3.0] + predicates: + - "len(value) < 10" + - "max(value) < user['foo']['fooffa]['another_float']" sections: - docstring: brilliant + name: foo keywords: - default: Wham! Bang! Pow! Let's Rock Out! docstring: Title of the calculation. name: tragic type: str - name: foo + - name: a_float + type: float + docstring: A floating point number + predicates: + - "value < 35.0" + - "value in user['float_list']" sections: - docstring: A ba-bar section + name: Bar keywords: - default: Bobson Dugnutt docstring: Title of the calculation. name: amazing type: str - name: Bar + - name: coolio + type: bool + docstring: A cool bool + default: True +- docstring: | + Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec luctus elit + ut posuere dictum. Proin ipsum libero, maximus vitae placerat a, bibendum + viverra ante. + name: fooffa + keywords: + - name: dwigt + docstring: An unusual name + type: str + predicates: + - "len(value) < 80" + - name: another_float + type: float + docstring: Another floating point number + default: "user['foo']['a_float'] * 2" diff --git a/tests/cli/docs_template.yml b/tests/cli/docs_template.yml index 9966f26..2425855 100644 --- a/tests/cli/docs_template.yml +++ b/tests/cli/docs_template.yml @@ -1,20 +1,60 @@ keywords: -- docstring: Title of the calculation. +- docstring: | + Title of the calculation. I had to write an extremely long documentation + string for this one, as it is extremely important to let you know that this + keyword will define the title of the calculation and, not having a default, + you will be required to set it! name: title type: str +- docstring: Some integer + name: an_integer + type: int + default: 15 +- docstring: A list of floats + name: float_list + type: List[float] + default: [1.0, 2.0, 3.0] + predicates: + - "len(value) < 10" + - "max(value) < user['foo']['fooffa]['another_float']" sections: - docstring: brilliant + name: foo keywords: - default: Wham! Bang! Pow! Let's Rock Out! docstring: Title of the calculation. name: tragic type: str - name: foo + - name: a_float + type: float + docstring: A floating point number + predicates: + - "value < 35.0" + - "value in user['float_list']" sections: - docstring: A ba-bar section + name: Bar keywords: - default: Bobson Dugnutt docstring: Title of the calculation. name: amazing type: str - name: Bar + - name: coolio + type: bool + docstring: A cool bool + default: True +- docstring: | + Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec luctus elit + ut posuere dictum. Proin ipsum libero, maximus vitae placerat a, bibendum + viverra ante. + name: fooffa + keywords: + - name: dwigt + docstring: An unusual name + type: str + predicates: + - "len(value) < 80" + - name: another_float + type: float + docstring: Another floating point number + default: "user['foo']['a_float'] * 2" diff --git a/tests/ref/dwigt.rst b/tests/ref/dwigt.rst index 6d92abd..86670c0 100644 --- a/tests/ref/dwigt.rst +++ b/tests/ref/dwigt.rst @@ -1,33 +1,88 @@ +.. raw:: html + + <style> .red {color:#aa0060; font-weight:bold; font-size:18px} </style> + +.. role:: red + .. This documentation was autogenerated using parselglossy. Editing by hand is not recommended. ========================================== Dwigt Rortugal's guide to input parameters ========================================== -Keywords without a default value are **required**. -Sections where all keywords have a default value can be omitted. +- Keywords without a default value are **required**. +- Default values are either explicit or computed from the value of other keywords in the input. +- Sections where all keywords have a default value can be omitted. +- Predicates, if present, are the functions run to validate user input. -**Keywords** - :title: Title of the calculation. +:red:`Keywords` + :title: Title of the calculation. I had to write an extremely long documentation string for this one, as it is extremely important to let you know that this keyword will define the title of the calculation and, not having a default, you will be required to set it! **Type** ``str`` -**Sections** + :an_integer: Some integer + + **Type** ``int`` + + **Default** ``15`` + + :float_list: A list of floats + + **Type** ``List[float]`` + + **Default** ``[1.0, 2.0, 3.0]`` + + **Predicates** + - ``len(value) < 10`` + - ``max(value) < user['foo']['fooffa]['another_float']`` + +:red:`Sections` :foo: brilliant - **Keywords** + :red:`Keywords` :tragic: Title of the calculation. **Type** ``str`` - **Default** Wham! Bang! Pow! Let's Rock Out! + **Default** ``Wham! Bang! Pow! Let's Rock Out!`` + + :a_float: A floating point number + + **Type** ``float`` - **Sections** + **Predicates** + - ``value < 35.0`` + - ``value in user['float_list']`` + + :red:`Sections` :Bar: A ba-bar section - **Keywords** + :red:`Keywords` :amazing: Title of the calculation. **Type** ``str`` - **Default** Bobson Dugnutt \ No newline at end of file + **Default** ``Bobson Dugnutt`` + + :coolio: A cool bool + + **Type** ``bool`` + + **Default** ``True`` + + :fooffa: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec luctus elit ut posuere dictum. Proin ipsum libero, maximus vitae placerat a, bibendum viverra ante. + + :red:`Keywords` + :dwigt: An unusual name + + **Type** ``str`` + + **Predicates** + - ``len(value) < 80`` + + :another_float: Another floating point number + + **Type** ``float`` + + **Default** ``user['foo']['a_float'] * 2`` + \ No newline at end of file diff --git a/tests/ref/input.rst b/tests/ref/input.rst index 6217605..a5f9cea 100644 --- a/tests/ref/input.rst +++ b/tests/ref/input.rst @@ -1,33 +1,88 @@ +.. raw:: html + + <style> .red {color:#aa0060; font-weight:bold; font-size:18px} </style> + +.. role:: red + .. This documentation was autogenerated using parselglossy. Editing by hand is not recommended. ================ Input parameters ================ -Keywords without a default value are **required**. -Sections where all keywords have a default value can be omitted. +- Keywords without a default value are **required**. +- Default values are either explicit or computed from the value of other keywords in the input. +- Sections where all keywords have a default value can be omitted. +- Predicates, if present, are the functions run to validate user input. -**Keywords** - :title: Title of the calculation. +:red:`Keywords` + :title: Title of the calculation. I had to write an extremely long documentation string for this one, as it is extremely important to let you know that this keyword will define the title of the calculation and, not having a default, you will be required to set it! **Type** ``str`` -**Sections** + :an_integer: Some integer + + **Type** ``int`` + + **Default** ``15`` + + :float_list: A list of floats + + **Type** ``List[float]`` + + **Default** ``[1.0, 2.0, 3.0]`` + + **Predicates** + - ``len(value) < 10`` + - ``max(value) < user['foo']['fooffa]['another_float']`` + +:red:`Sections` :foo: brilliant - **Keywords** + :red:`Keywords` :tragic: Title of the calculation. **Type** ``str`` - **Default** Wham! Bang! Pow! Let's Rock Out! + **Default** ``Wham! Bang! Pow! Let's Rock Out!`` + + :a_float: A floating point number + + **Type** ``float`` - **Sections** + **Predicates** + - ``value < 35.0`` + - ``value in user['float_list']`` + + :red:`Sections` :Bar: A ba-bar section - **Keywords** + :red:`Keywords` :amazing: Title of the calculation. **Type** ``str`` - **Default** Bobson Dugnutt \ No newline at end of file + **Default** ``Bobson Dugnutt`` + + :coolio: A cool bool + + **Type** ``bool`` + + **Default** ``True`` + + :fooffa: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec luctus elit ut posuere dictum. Proin ipsum libero, maximus vitae placerat a, bibendum viverra ante. + + :red:`Keywords` + :dwigt: An unusual name + + **Type** ``str`` + + **Predicates** + - ``len(value) < 80`` + + :another_float: Another floating point number + + **Type** ``float`` + + **Default** ``user['foo']['a_float'] * 2`` + \ No newline at end of file diff --git a/tests/ref/simple.rst b/tests/ref/simple.rst new file mode 100644 index 0000000..fab7a8c --- /dev/null +++ b/tests/ref/simple.rst @@ -0,0 +1,42 @@ +.. raw:: html + + <style> .red {color:#aa0060; font-weight:bold; font-size:18px} </style> + +.. role:: red + +.. This documentation was autogenerated using parselglossy. Editing by hand is not recommended. + +================ +Input parameters +================ + +- Keywords without a default value are **required**. +- Default values are either explicit or computed from the value of other keywords in the input. +- Sections where all keywords have a default value can be omitted. +- Predicates, if present, are the functions run to validate user input. + +:red:`Keywords` + :title: Title of the calculation. + + **Type** ``str`` + +:red:`Sections` + :foo: brilliant + + :red:`Keywords` + :tragic: Title of the calculation. + + **Type** ``str`` + + **Default** ``Wham! Bang! Pow! Let's Rock Out!`` + + :red:`Sections` + :Bar: A ba-bar section + + :red:`Keywords` + :amazing: Title of the calculation. + + **Type** ``str`` + + **Default** ``Bobson Dugnutt`` + \ No newline at end of file diff --git a/tests/test_documentation.py b/tests/test_documentation.py index f8d3aca..fcbb12e 100644 --- a/tests/test_documentation.py +++ b/tests/test_documentation.py @@ -71,7 +71,7 @@ def template(): def test_documentation(template): - doc_ref = Path(__file__).parent / Path("ref/input.rst") + doc_ref = Path(__file__).parent / Path("ref/simple.rst") with doc_ref.open("r") as ref: stuff = ref.read().rstrip("\n")
Repeated keywords in the autogenerated documentation * parselglossy version: b28084a * Python version: 3.7.0 * Operating System: Ubuntu-18.10 ### What I Did The following `template.yml` ``` keywords: - name: foo type: int docstring: foo - name: bar type: int docstring: bar - name: baz type: int docstring: baz ``` is documented using the CLI command `parselglossy doc template.yml` to give: ``` **Keywords** :foo: foo **Type** ``int`` **Keywords** :foo: foo **Type** ``int`` :bar: bar **Type** ``int`` **Keywords** :foo: foo **Type** ``int`` :bar: bar **Type** ``int`` :baz: baz **Type** ``int`` ```
0.0
b28084a6ca692dd1cecc2e07a229f20d1630e162
[ "tests/test_documentation.py::test_documentation" ]
[]
{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }
2019-03-27 16:50:22+00:00
mit
1,890
developmentseed__cogeo-mosaic-228
diff --git a/CHANGES.md b/CHANGES.md index 12763d0..1ec014f 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,3 +1,6 @@ +## 7.1.0 + +* Automatically remove/add `asset_prefix` in Mosaic Backends ## 7.0.1 (2023-10-17) diff --git a/cogeo_mosaic/backends/base.py b/cogeo_mosaic/backends/base.py index 4fe4f64..7cb8a91 100644 --- a/cogeo_mosaic/backends/base.py +++ b/cogeo_mosaic/backends/base.py @@ -236,13 +236,17 @@ class BaseBackend(BaseReader): def get_assets(self, x: int, y: int, z: int) -> List[str]: """Find assets.""" quadkeys = self.find_quadkeys(Tile(x=x, y=y, z=z), self.quadkey_zoom) - return list( + assets = list( dict.fromkeys( itertools.chain.from_iterable( [self.mosaic_def.tiles.get(qk, []) for qk in quadkeys] ) ) ) + if self.mosaic_def.asset_prefix: + assets = [self.mosaic_def.asset_prefix + asset for asset in assets] + + return assets def find_quadkeys(self, tile: Tile, quadkey_zoom: int) -> List[str]: """ diff --git a/cogeo_mosaic/backends/dynamodb.py b/cogeo_mosaic/backends/dynamodb.py index 5a1e5f8..8c14e6a 100644 --- a/cogeo_mosaic/backends/dynamodb.py +++ b/cogeo_mosaic/backends/dynamodb.py @@ -222,13 +222,17 @@ class DynamoDBBackend(BaseBackend): def get_assets(self, x: int, y: int, z: int) -> List[str]: """Find assets.""" quadkeys = self.find_quadkeys(Tile(x=x, y=y, z=z), self.quadkey_zoom) - return list( + assets = list( dict.fromkeys( itertools.chain.from_iterable( [self._fetch_dynamodb(qk).get("assets", []) for qk in quadkeys] ) ) ) + if self.mosaic_def.asset_prefix: + assets = [self.mosaic_def.asset_prefix + asset for asset in assets] + + return assets @property def _quadkeys(self) -> List[str]: diff --git a/cogeo_mosaic/backends/sqlite.py b/cogeo_mosaic/backends/sqlite.py index d4ae7d7..d336c9e 100644 --- a/cogeo_mosaic/backends/sqlite.py +++ b/cogeo_mosaic/backends/sqlite.py @@ -316,11 +316,15 @@ class SQLiteBackend(BaseBackend): """Find assets.""" mercator_tile = morecantile.Tile(x=x, y=y, z=z) quadkeys = self.find_quadkeys(mercator_tile, self.quadkey_zoom) - return list( + assets = list( dict.fromkeys( itertools.chain.from_iterable([self._fetch(qk) for qk in quadkeys]) ) ) + if self.mosaic_def.asset_prefix: + assets = [self.mosaic_def.asset_prefix + asset for asset in assets] + + return assets @property def _quadkeys(self) -> List[str]: diff --git a/cogeo_mosaic/mosaic.py b/cogeo_mosaic/mosaic.py index 21d0dbc..4ba709c 100644 --- a/cogeo_mosaic/mosaic.py +++ b/cogeo_mosaic/mosaic.py @@ -1,6 +1,7 @@ """cogeo_mosaic.mosaic MosaicJSON models and helper functions.""" import os +import re import sys import warnings from contextlib import ExitStack @@ -230,9 +231,16 @@ class MosaicJSON(BaseModel, validate_assignment=True): ) if dataset: - mosaic_definition["tiles"][quadkey] = [ - accessor(f) for f in dataset - ] + assets = [accessor(f) for f in dataset] + if asset_prefix: + assets = [ + re.sub(rf"^{asset_prefix}", "", asset) + if asset.startswith(asset_prefix) + else asset + for asset in assets + ] + + mosaic_definition["tiles"][quadkey] = assets return cls(**mosaic_definition)
developmentseed/cogeo-mosaic
2e12ff197f3c64bd3ba36c99ce2f27597342881a
diff --git a/tests/test_backends.py b/tests/test_backends.py index c2e7d57..852157e 100644 --- a/tests/test_backends.py +++ b/tests/test_backends.py @@ -1217,3 +1217,15 @@ def test_point_crs_coordinates(): assert ptsR[0][0] == pts[0][0] assert ptsR[0][1].crs == "epsg:3857" assert ptsR[0][1].coordinates == (-8200051.8694, 5782905.49327) + + +def test_InMemoryReader_asset_prefix(): + """Test MemoryBackend.""" + assets = [asset1, asset2] + prefix = os.path.join(os.path.dirname(__file__), "fixtures") + mosaicdef = MosaicJSON.from_urls(assets, quiet=False, asset_prefix=prefix) + + assert mosaicdef.tiles["0302310"] == ["/cog1.tif", "/cog2.tif"] + with MemoryBackend(mosaic_def=mosaicdef) as mosaic: + assets = mosaic.assets_for_tile(150, 182, 9) + assert assets[0].startswith(prefix) diff --git a/tests/test_create.py b/tests/test_create.py index 6998267..4fb30e5 100644 --- a/tests/test_create.py +++ b/tests/test_create.py @@ -127,7 +127,7 @@ def test_mosaic_create_additional_metadata(): quiet=True, tilematrixset=tms_3857, asset_type="COG", - asset_prefix="s3://my-bucket/", + asset_prefix=basepath, data_type="uint16", layers={ "true-color": { @@ -137,6 +137,7 @@ def test_mosaic_create_additional_metadata(): }, ) assert mosaic.asset_type == "COG" - assert mosaic.asset_prefix == "s3://my-bucket/" + assert mosaic.asset_prefix == basepath assert mosaic.data_type == "uint16" assert mosaic.layers["true-color"] + assert mosaic.tiles["0302301"] == ["/cog1.tif", "/cog2.tif"]
add`asset_prefix` to assets ### Discussed in https://github.com/developmentseed/cogeo-mosaic/discussions/226 <div type='discussions-op-text'> <sup>Originally posted by **scottyhq** December 6, 2023</sup> I tired rendering the 0.0.3 example which uses public data: https://titiler.xyz/mosaicjson/map?url=https://raw.githubusercontent.com/developmentseed/mosaicjson-spec/main/0.0.3/example/dg_post_idai.json But get a lot of 500 errors, I also tried modifying the docs example to just use `"asset_prefix":"s3://noaa-eri-pds/2020_Nashville_Tornado/20200307a_RGB/"`: https://titiler.xyz/mosaicjson/map?url=https://gist.githubusercontent.com/scottyhq/4c288a2dbf7b97ef7833c5e0ee19d6d6/raw/636083cf7117a96e38d271eeef932a3ee507d7d1/NOAA_Nashville_Tornado_v3.json So I suspect titiler by default doesn't have logic to pick up the `asset_prefix` </div>
0.0
2e12ff197f3c64bd3ba36c99ce2f27597342881a
[ "tests/test_backends.py::test_InMemoryReader_asset_prefix", "tests/test_create.py::test_mosaic_create_additional_metadata" ]
[ "tests/test_backends.py::test_file_backend", "tests/test_backends.py::test_http_backend", "tests/test_backends.py::test_s3_backend", "tests/test_backends.py::test_gs_backend", "tests/test_backends.py::test_dynamoDB_backend", "tests/test_backends.py::test_stac_backend", "tests/test_backends.py::test_stac_search", "tests/test_backends.py::test_stac_accessor", "tests/test_backends.py::test_mosaic_crud_error[file:///path/to/mosaic.json]", "tests/test_backends.py::test_mosaic_crud_error[https://developmentseed.org/cogeo-mosaic/amosaic.json.gz]", "tests/test_backends.py::test_InMemoryReader", "tests/test_backends.py::test_sqlite_backend", "tests/test_backends.py::test_tms_and_coordinates", "tests/test_backends.py::test_point_crs_coordinates", "tests/test_create.py::test_mosaic_create", "tests/test_create.py::test_mosaic_create_tms" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-12-06 19:13:07+00:00
mit
1,891
devopshq__artifactory-439
diff --git a/artifactory.py b/artifactory.py index 4325018..69bc540 100755 --- a/artifactory.py +++ b/artifactory.py @@ -410,13 +410,13 @@ def quote_url(url): parsed_url = urllib3.util.parse_url(url) if parsed_url.port: quoted_path = requests.utils.quote( - url.rpartition(f"{parsed_url.host}:{parsed_url.port}")[2] + url.partition(f"{parsed_url.host}:{parsed_url.port}")[2] ) quoted_url = ( f"{parsed_url.scheme}://{parsed_url.host}:{parsed_url.port}{quoted_path}" ) else: - quoted_path = requests.utils.quote(url.rpartition(parsed_url.host)[2]) + quoted_path = requests.utils.quote(url.partition(parsed_url.host)[2]) quoted_url = f"{parsed_url.scheme}://{parsed_url.host}{quoted_path}" return quoted_url
devopshq/artifactory
2e9274273aefba744accb3d5a012c4dbdb111b49
diff --git a/tests/unit/test_artifactory_path.py b/tests/unit/test_artifactory_path.py index f2f57d9..16e528d 100644 --- a/tests/unit/test_artifactory_path.py +++ b/tests/unit/test_artifactory_path.py @@ -100,6 +100,10 @@ class ArtifactoryFlavorTest(unittest.TestCase): check( "https://example.com/artifactory/foo", "https://example.com/artifactory/foo" ) + check( + "https://example.com/artifactory/foo/example.com/bar", + "https://example.com/artifactory/foo/example.com/bar" + ) check( "https://example.com/artifactory/foo/#1", "https://example.com/artifactory/foo/%231",
path.stat() doesn't handle ArtifactoryPath() properly Hi, Here is my environment: ```` python 3.8.4 dohq-artifactory 0.8.4 ```` I want to get the stats of 2 files. I have a piece of code looking like this: ````python from artifactory import ArtifactoryPath path1 = ArtifactoryPath( "https://artifactory.domain.com/artifactory/repo-docker-local/rdl/rd-image/0.2.0/manifest.json", apikey=token ) path2 = ArtifactoryPath( "https://artifactory.domain.com/artifactory/repo-docker-local/rdl/artifactory.domain.com/repo-docker/rd/rd-image/0.2.0/manifest.json", apikey=token ) # Get FileStat stat1 = path1.stat() # works print(stat1) stat2 = path2.stat() # error print(stat2) ```` As you can see the path in `path2` is containing 2 times the artifactory host `artifactory.domain.com`. In the error message below I can see it tries to fetch the file but only using half the real path: it crops everything before the second `artifactory.domain.com`. ````bash $ python tests.py --token=**** ArtifactoryFileStat(ctime='[...]', mtime='[...]', created_by='[...]', modified_by='[...]') # print(stat1), shorted for libility Traceback (most recent call last): File "[...]/.env/lib/python3.8/site-packages/dohq_artifactory/exception.py", line 20, in raise_for_status response.raise_for_status() File "[...]/.env/lib/python3.8/site-packages/requests/models.py", line 1021, in raise_for_status raise HTTPError(http_error_msg, response=self) requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://artifactory.domain.com/repo-docker/rd/rd-image/0.2.0/manifest.json The above exception was the direct cause of the following exception: Traceback (most recent call last): File "tests.py", line 35, in <module> stats2 = path2.stat() File "[...]/.env/lib/python3.8/site-packages/artifactory.py", line 1610, in stat return self._accessor.stat(pathobj=pathobj) File "[...]/.env/lib/python3.8/site-packages/artifactory.py", line 878, in stat jsn = self.get_stat_json(pathobj) File "[...]/.env/lib/python3.8/site-packages/artifactory.py", line 869, in get_stat_json raise_for_status(response) File "[...]/.env/lib/python3.8/site-packages/dohq_artifactory/exception.py", line 28, in raise_for_status raise ArtifactoryException(str(exception)) from exception dohq_artifactory.exception.ArtifactoryException: 404 Client Error: Not Found for url: https://artifactory.domain.com/repo-docker/rd/rd-image/0.2.0/manifest.json ```` I cannot change the files names. It is not in my perimeter. To identify where the problem comes from I tried the same thing but using JFrog Web API and it works: ````bash $ curl -u user:passwd https://artifactory.domain.com/artifactory/api/storage/repo-docker-local/rdl/artifactory.domain.com/repo-docker/rdl/rd-image/0.2.0 -v * About to connect() to artifactory.domain.com port <port> (#0) * Trying <ip>... * Connected to artifactory.domain.com (<ip>) port <port> (#0) * [...] > GET /artifactory/api/storage/repo-docker-local/rdl/artifactory.domain.com/repo-docker/rdl/rd-image/0.2.0 HTTP/1.1 > Authorization: Basic xxxx > User-Agent: <user_agent> > Host: artifactory.domain.com > Accept: */* > < HTTP/1.1 200 < Date: Wed, 17 May 2023 11:45:28 GMT < Content-Type: application/vnd.org.jfrog.artifactory.storage.FolderInfo+json < Transfer-Encoding: chunked < Connection: keep-alive < X-JFrog-Version: <jfrog_version> < X-Artifactory-Id: <artifactory_id> < X-Artifactory-Node-Id: <artifactory_node_id> < Cache-Control: no-store < Set-Cookie: <cookie> < { "repo" : "repo-docker-local", "path" : "/rdl/artifactory.domain.com/repo-docker/rdl/rd-image/0.2.0", "created" : "<created>", "createdBy" : "<createdBy>", "lastModified" : "<lastModified>", "modifiedBy" : "<modifiedBy>", "lastUpdated" : "<lastUpdated>", "children" : [{ "uri" : "/manifest.json", "folder" : false, [...] }], "uri" : "https://artifactory.domain.com:<port>/artifactory/api/storage/repo-docker-local/rdl/artifactory.domain.com/repo-docker/rdl/rd-image/0.2.0" } * Connection #0 to host artifactory.domain.com left intact ```` For me the problem is from how the `stat()` method parses an ArtifactoryPath. Do you have any solutions ?
0.0
2e9274273aefba744accb3d5a012c4dbdb111b49
[ "tests/unit/test_artifactory_path.py::ArtifactoryFlavorTest::test_quote_url" ]
[ "tests/unit/test_artifactory_path.py::UtilTest::test_checksum", "tests/unit/test_artifactory_path.py::UtilTest::test_escape_chars", "tests/unit/test_artifactory_path.py::UtilTest::test_matrix_encode", "tests/unit/test_artifactory_path.py::UtilTest::test_properties_encode", "tests/unit/test_artifactory_path.py::UtilTest::test_properties_encode_multi", "tests/unit/test_artifactory_path.py::ArtifactoryFlavorTest::test_parse_parts", "tests/unit/test_artifactory_path.py::ArtifactoryFlavorTest::test_special_characters", "tests/unit/test_artifactory_path.py::ArtifactoryFlavorTest::test_splitroot", "tests/unit/test_artifactory_path.py::ArtifactoryFlavorTest::test_splitroot_custom_drv", "tests/unit/test_artifactory_path.py::ArtifactoryFlavorTest::test_splitroot_custom_root", "tests/unit/test_artifactory_path.py::PureArtifactoryPathTest::test_anchor", "tests/unit/test_artifactory_path.py::PureArtifactoryPathTest::test_join_endswith_slash", "tests/unit/test_artifactory_path.py::PureArtifactoryPathTest::test_join_endswithout_slash", "tests/unit/test_artifactory_path.py::PureArtifactoryPathTest::test_join_with_artifactory_folder", "tests/unit/test_artifactory_path.py::PureArtifactoryPathTest::test_join_with_multiple_folder_and_artifactory_substr_in_it", "tests/unit/test_artifactory_path.py::PureArtifactoryPathTest::test_join_with_repo", "tests/unit/test_artifactory_path.py::PureArtifactoryPathTest::test_join_with_repo_folder", "tests/unit/test_artifactory_path.py::PureArtifactoryPathTest::test_root", "tests/unit/test_artifactory_path.py::PureArtifactoryPathTest::test_with_suffix", "tests/unit/test_artifactory_path.py::ArtifactoryAccessorTest::test_get_properties", "tests/unit/test_artifactory_path.py::ArtifactoryAccessorTest::test_listdir", "tests/unit/test_artifactory_path.py::ArtifactoryAccessorTest::test_mkdir", "tests/unit/test_artifactory_path.py::ArtifactoryAccessorTest::test_set_properties", "tests/unit/test_artifactory_path.py::ArtifactoryAccessorTest::test_set_properties_without_remove", "tests/unit/test_artifactory_path.py::ArtifactoryAccessorTest::test_stat", "tests/unit/test_artifactory_path.py::ArtifactoryAccessorTest::test_stat_no_sha256", "tests/unit/test_artifactory_path.py::ArtifactoryAccessorTest::test_unlink", "tests/unit/test_artifactory_path.py::ArtifactoryAccessorTest::test_unlink_raises_not_found", "tests/unit/test_artifactory_path.py::ArtifactoryAccessorTest::test_unlink_raises_on_404", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_archive", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_archive_download", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_auth", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_auth_inheritance", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_basic", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_deploy_by_checksum_error", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_deploy_by_checksum_sha1", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_deploy_by_checksum_sha1_or_sha256", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_deploy_by_checksum_sha256", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_deploy_deb", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_deploy_file", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_joinpath_repo", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_path_in_repo", "tests/unit/test_artifactory_path.py::ArtifactoryPathTest::test_repo", "tests/unit/test_artifactory_path.py::ArtifactorySaaSPathTest::test_basic", "tests/unit/test_artifactory_path.py::ArtifactorySaaSPathTest::test_drive", "tests/unit/test_artifactory_path.py::ArtifactorySaaSPathTest::test_path_in_repo", "tests/unit/test_artifactory_path.py::ArtifactorySaaSPathTest::test_repo", "tests/unit/test_artifactory_path.py::TestArtifactoryConfig::test_artifactory_config", "tests/unit/test_artifactory_path.py::TestArtifactoryAql::test_create_aql_text_list", "tests/unit/test_artifactory_path.py::TestArtifactoryAql::test_create_aql_text_list_in_dict", "tests/unit/test_artifactory_path.py::TestArtifactoryAql::test_create_aql_text_simple", "tests/unit/test_artifactory_path.py::TestArtifactoryAql::test_from_aql_file", "tests/unit/test_artifactory_path.py::TestArtifactoryPathGetAll::test_get_groups", "tests/unit/test_artifactory_path.py::TestArtifactoryPathGetAll::test_get_groups_lazy", "tests/unit/test_artifactory_path.py::TestArtifactoryPathGetAll::test_get_projects", "tests/unit/test_artifactory_path.py::TestArtifactoryPathGetAll::test_get_projects_lazy", "tests/unit/test_artifactory_path.py::TestArtifactoryPathGetAll::test_get_users", "tests/unit/test_artifactory_path.py::TestArtifactoryPathGetAll::test_get_users_lazy" ]
{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }
2023-12-29 09:24:40+00:00
mit
1,892
devopshq__artifactory-cleanup-100
diff --git a/README.md b/README.md index c0a63ec..ee5afde 100644 --- a/README.md +++ b/README.md @@ -135,6 +135,12 @@ artifactory-cleanup --days-in-future=10 # Not satisfied with built-in rules? Write your own rules in python and connect them! artifactory-cleanup --load-rules=myrule.py docker run -v "$(pwd)":/app devopshq/artifactory-cleanup artifactory-cleanup --load-rules=myrule.py + +# Save the table summary in a file +artifactory-cleanup --output=myfile.txt + +# Save the summary in a Json file +artifactory-cleanup --output=myfile.txt --output-format=json ``` # Rules diff --git a/artifactory_cleanup/cli.py b/artifactory_cleanup/cli.py index 312c999..b168ecf 100644 --- a/artifactory_cleanup/cli.py +++ b/artifactory_cleanup/cli.py @@ -1,3 +1,4 @@ +import json import logging import sys from datetime import timedelta, date @@ -5,6 +6,7 @@ from datetime import timedelta, date import requests from hurry.filesize import size from plumbum import cli +from plumbum.cli.switches import Set from prettytable import PrettyTable from requests.auth import HTTPBasicAuth @@ -62,6 +64,19 @@ class ArtifactoryCleanupCLI(cli.Application): mandatory=False, ) + _output_file = cli.SwitchAttr( + "--output", help="Choose the output file", mandatory=False + ) + + _output_format = cli.SwitchAttr( + "--output-format", + Set("table", "json", case_sensitive=False), + help="Choose the output format", + default="table", + requires=["--output"], + mandatory=False, + ) + @property def VERSION(self): # To prevent circular imports @@ -83,6 +98,36 @@ class ArtifactoryCleanupCLI(cli.Application): print(f"Simulating cleanup actions that will occur on {today}") return today + def _format_table(self, result) -> PrettyTable: + table = PrettyTable() + table.field_names = ["Cleanup Policy", "Files count", "Size"] + table.align["Cleanup Policy"] = "l" + + for policy_result in result["policies"]: + row = [ + policy_result["name"], + policy_result["file_count"], + size(policy_result["size"]), + ] + table.add_row(row) + + table.add_row(["", "", ""]) + table.add_row(["Total size: {}".format(size(result["total_size"])), "", ""]) + return table + + def _print_table(self, result: dict): + print(self._format_table(result)) + + def _create_output_file(self, result, filename, format): + text = None + if format == "table": + text = self._format_table(result).get_string() + else: + text = json.dumps(result) + + with open(filename, "w") as file: + file.write(text) + def main(self): today = self._get_today() if self._load_rules: @@ -112,9 +157,7 @@ class ArtifactoryCleanupCLI(cli.Application): if self._policy: cleanup.only(self._policy) - table = PrettyTable() - table.field_names = ["Cleanup Policy", "Files count", "Size"] - table.align["Cleanup Policy"] = "l" + result = {"policies": [], "total_size": 0} total_size = 0 block_ctx_mgr, test_ctx_mgr = get_context_managers() @@ -124,16 +167,21 @@ class ArtifactoryCleanupCLI(cli.Application): if summary is None: continue total_size += summary.artifacts_size - row = [ - summary.policy_name, - summary.artifacts_removed, - size(summary.artifacts_size), - ] - table.add_row(row) - table.add_row(["", "", ""]) - table.add_row(["Total size: {}".format(size(total_size)), "", ""]) - print(table) + result["policies"].append( + { + "name": summary.policy_name, + "file_count": summary.artifacts_removed, + "size": summary.artifacts_size, + } + ) + + result["total_size"] = total_size + + self._print_table(result) + + if self._output_file: + self._create_output_file(result, self._output_file, self._output_format) if __name__ == "__main__":
devopshq/artifactory-cleanup
c523f319dc7835c5b3bd583f5ba187184df24dbc
diff --git a/tests/data/expected_output.txt b/tests/data/expected_output.txt new file mode 100644 index 0000000..2471489 --- /dev/null +++ b/tests/data/expected_output.txt @@ -0,0 +1,8 @@ ++--------------------------------------------------------+-------------+------+ +| Cleanup Policy | Files count | Size | ++--------------------------------------------------------+-------------+------+ +| Remove all files from repo-name-here older then 7 days | 1 | 528B | +| Use your own rules! | 1 | 528B | +| | | | +| Total size: 1K | | | ++--------------------------------------------------------+-------------+------+ \ No newline at end of file diff --git a/tests/test_cli.py b/tests/test_cli.py index f5c5afe..2869e23 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,4 +1,6 @@ +import json import pytest +from filecmp import cmp from artifactory_cleanup import ArtifactoryCleanupCLI @@ -69,3 +71,101 @@ def test_destroy(capsys, shared_datadir, requests_mock): last_request.url == "https://repo.example.com/artifactory/repo-name-here/path/to/file/filename1.json" ) + + [email protected]("requests_repo_name_here") +def test_output_table(capsys, shared_datadir, requests_mock): + _, code = ArtifactoryCleanupCLI.run( + [ + "ArtifactoryCleanupCLI", + "--config", + str(shared_datadir / "cleanup.yaml"), + "--load-rules", + str(shared_datadir / "myrule.py"), + ], + exit=False, + ) + stdout, stderr = capsys.readouterr() + print(stdout) + assert code == 0, stdout + assert ( + "| Cleanup Policy | Files count | Size |" + in stdout + ) + + [email protected]("requests_repo_name_here") +def test_output_table(capsys, shared_datadir, requests_mock, tmp_path): + output_file = tmp_path / "output.txt" + _, code = ArtifactoryCleanupCLI.run( + [ + "ArtifactoryCleanupCLI", + "--config", + str(shared_datadir / "cleanup.yaml"), + "--load-rules", + str(shared_datadir / "myrule.py"), + "--output-format", + "table", + "--output", + str(output_file), + ], + exit=False, + ) + stdout, stderr = capsys.readouterr() + print(stdout) + assert code == 0, stdout + assert cmp(output_file, shared_datadir / "expected_output.txt") is True + + [email protected]("requests_repo_name_here") +def test_output_json(capsys, shared_datadir, requests_mock, tmp_path): + output_json = tmp_path / "output.json" + _, code = ArtifactoryCleanupCLI.run( + [ + "ArtifactoryCleanupCLI", + "--config", + str(shared_datadir / "cleanup.yaml"), + "--load-rules", + str(shared_datadir / "myrule.py"), + "--output-format", + "json", + "--output", + str(output_json), + ], + exit=False, + ) + stdout, stderr = capsys.readouterr() + assert code == 0, stdout + with open(output_json, "r") as file: + assert json.load(file) == { + "policies": [ + { + "name": "Remove all files from repo-name-here older then 7 days", + "file_count": 1, + "size": 528, + }, + {"name": "Use your own rules!", "file_count": 1, "size": 528}, + ], + "total_size": 1056, + } + + [email protected]("requests_repo_name_here") +def test_require_output_json(capsys, shared_datadir, requests_mock): + _, code = ArtifactoryCleanupCLI.run( + [ + "ArtifactoryCleanupCLI", + "--config", + str(shared_datadir / "cleanup.yaml"), + "--load-rules", + str(shared_datadir / "myrule.py"), + "--output-format", + "json", + ], + exit=False, + ) + assert code == 2, stdout + stdout, stderr = capsys.readouterr() + assert ( + "Error: Given --output-format, the following are missing ['output']" in stdout + )
Output format to Json We would like a feature request to have the output table to Json format. The PrettyTable libraries can do it : https://pypi.org/project/prettytable/ If I have time, I would propose a PR
0.0
c523f319dc7835c5b3bd583f5ba187184df24dbc
[ "tests/test_cli.py::test_output_json", "tests/test_cli.py::test_require_output_json", "tests/test_cli.py::test_output_table" ]
[ "tests/test_cli.py::test_dry_mode", "tests/test_cli.py::test_destroy", "tests/test_cli.py::test_help" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-03-17 06:28:51+00:00
mit
1,893
devopsspiral__KubeLibrary-124
diff --git a/CHANGELOG.md b/CHANGELOG.md index b7b2f42..e8800dd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,8 +5,14 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](http://semver.org/). ## In progress + +## [0.8.1] - 2022-12-16 +### Added - Add proxy configuration fetched from `HTTP_PROXY` or `http_proxy` environment variable +### Fixed +Fix disabling cert validation [#124](https://github.com/devopsspiral/KubeLibrary/pull/124) + ## [0.8.0] - 2022-10-27 ### Added - Add function list_namespaced_stateful_set_by_pattern [#114](https://github.com/devopsspiral/KubeLibrary/pull/113) by [@siaomingjeng](https://github.com/siaomingjeng) diff --git a/src/KubeLibrary/KubeLibrary.py b/src/KubeLibrary/KubeLibrary.py index 3f73adc..ebff896 100755 --- a/src/KubeLibrary/KubeLibrary.py +++ b/src/KubeLibrary/KubeLibrary.py @@ -1,6 +1,5 @@ import json import re -import ssl import urllib3 from os import environ @@ -276,7 +275,7 @@ class KubeLibrary: def _add_api(self, reference, class_name): self.__dict__[reference] = class_name(self.api_client) if not self.cert_validation: - self.__dict__[reference].api_client.rest_client.pool_manager.connection_pool_kw['cert_reqs'] = ssl.CERT_NONE + self.__dict__[reference].api_client.configuration.verify_ssl = False def k8s_api_ping(self): """Performs GET on /api/v1/ for simple check of API availability. diff --git a/src/KubeLibrary/version.py b/src/KubeLibrary/version.py index 8675559..73baf8f 100644 --- a/src/KubeLibrary/version.py +++ b/src/KubeLibrary/version.py @@ -1,1 +1,1 @@ -version = "0.8.0" +version = "0.8.1"
devopsspiral/KubeLibrary
7f4037c283a38751f9a31160944a17e7b80ec97b
diff --git a/test/test_KubeLibrary.py b/test/test_KubeLibrary.py index b99291b..7cae67e 100644 --- a/test/test_KubeLibrary.py +++ b/test/test_KubeLibrary.py @@ -1,7 +1,6 @@ import json import mock import re -import ssl import unittest from KubeLibrary import KubeLibrary from KubeLibrary.exceptions import BearerTokenWithPrefixException @@ -306,7 +305,7 @@ class TestKubeLibrary(unittest.TestCase): kl = KubeLibrary(kube_config='test/resources/k3d', cert_validation=False) for api in TestKubeLibrary.apis: target = getattr(kl, api) - self.assertEqual(target.api_client.rest_client.pool_manager.connection_pool_kw['cert_reqs'], ssl.CERT_NONE) + self.assertEqual(target.api_client.configuration.verify_ssl, False) @responses.activate def test_KubeLibrary_inits_with_bearer_token(self):
certificate verify failed issue when using Get Namespaced Pod Exec When using the Get Namespaced Pod Exec keywork on a k8s cluster using a custom CA, the following error occurs : ``` ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get issuer certificate (_ssl.c:1129) ``` Other keywords (Read Namespaced Pod Status, List Namespaced Pod By Pattern ...) are working as expected. As a quick fix, I'm adding the following line in the _add_api method of the library : ``` def _add_api(self, reference, class_name): self.__dict__[reference] = class_name(self.api_client) if not self.cert_validation: self.__dict__[reference].api_client.rest_client.pool_manager.connection_pool_kw['cert_reqs'] = ssl.CERT_NONE self.__dict__[reference].api_client.configuration.verify_ssl = False ``` Am I missing something regarding the library configuration ? Versions : ``` KubeLibrary: 0.8.0 Python: 3.9.13 Kubernetes: 1.24 ``` KubeLibrary : ``` Library KubeLibrary kube_config=${KUBECONFIG_FILE} cert_validation=False KubeLibrary.Get Namespaced Pod Exec ... name=my-pod ... namespace=${namespace} ... argv_cmd=${command} ```
0.0
7f4037c283a38751f9a31160944a17e7b80ec97b
[ "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_deployment_by_pattern" ]
[ "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_dynamic_delete", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespace", "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_inits_with_bearer_token", "test/test_KubeLibrary.py::TestKubeLibrary::test_read_namespaced_endpoints", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_daemon_set", "test/test_KubeLibrary.py::TestKubeLibrary::test_inits_all_api_clients", "test/test_KubeLibrary.py::TestKubeLibrary::test_assert_pod_has_annotations", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_secret_by_pattern", "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_dynamic_create", "test/test_KubeLibrary.py::TestKubeLibrary::test_get_namespaced_exec_without_container", "test/test_KubeLibrary.py::TestKubeLibrary::test_read_namespaced_cron_job", "test/test_KubeLibrary.py::TestKubeLibrary::test_read_namespaced_ingress", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_service_account_by_pattern", "test/test_KubeLibrary.py::TestKubeLibrary::test_read_namespaced_horizontal_pod_autoscaler", "test/test_KubeLibrary.py::TestKubeLibrary::test_assert_container_has_env_vars", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_ingress", "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_dynamic_replace", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_job_by_pattern", "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_inits_with_context", "test/test_KubeLibrary.py::TestKubeLibrary::test_read_namespaced_daemon_set", "test/test_KubeLibrary.py::TestKubeLibrary::test_get_matching_pods_in_namespace", "test/test_KubeLibrary.py::TestKubeLibrary::test_get_namespaced_exec_not_argv_and_list", "test/test_KubeLibrary.py::TestKubeLibrary::test_get_configmaps_in_namespace", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_cluster_role_binding", "test/test_KubeLibrary.py::TestKubeLibrary::test_filter_containers_images", "test/test_KubeLibrary.py::TestKubeLibrary::test_filter_pods_containers_statuses_by_name", "test/test_KubeLibrary.py::TestKubeLibrary::test_evaluate_callable_from_k8s_client", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_persistent_volume_claim_by_pattern", "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_dynamic_init", "test/test_KubeLibrary.py::TestKubeLibrary::test_get_kubelet_version", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_role_binding", "test/test_KubeLibrary.py::TestKubeLibrary::test_generate_alphanumeric_str", "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_inits_from_kubeconfig", "test/test_KubeLibrary.py::TestKubeLibrary::test_assert_pod_has_labels", "test/test_KubeLibrary.py::TestKubeLibrary::test_filter_pods_containers_by_name", "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_dynamic_patch", "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_inits_with_bearer_token_with_ca_crt", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_role", "test/test_KubeLibrary.py::TestKubeLibrary::test_filter_containers_resources", "test/test_KubeLibrary.py::TestKubeLibrary::test_get_namespaced_exec_with_container", "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_fails_for_wrong_context", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_stateful_set_by_pattern", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_persistent_volume_claim", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_horizontal_pod_autoscaler", "test/test_KubeLibrary.py::TestKubeLibrary::test_KubeLibrary_dynamic_get", "test/test_KubeLibrary.py::TestKubeLibrary::test_read_namespaced_service", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_service", "test/test_KubeLibrary.py::TestKubeLibrary::test_inits_with_bearer_token_raises_BearerTokenWithPrefixException", "test/test_KubeLibrary.py::TestKubeLibrary::test_read_namespaced_pod_status", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_replica_set_by_pattern", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_cron_job", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_namespaced_pod_by_pattern", "test/test_KubeLibrary.py::TestKubeLibrary::test_list_cluster_role" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2022-12-16 14:17:09+00:00
mit
1,894
devsnd__tinytag-156
diff --git a/README.md b/README.md index 39bfda9..cec3e9d 100644 --- a/README.md +++ b/README.md @@ -66,7 +66,7 @@ List of possible attributes you can get with TinyTag: tag.title # title of the song tag.track # track number as string tag.track_total # total number of tracks as string - tag.year # year or data as string + tag.year # year or date as string For non-common fields and fields specific to single file formats use extra diff --git a/tinytag/tinytag.py b/tinytag/tinytag.py index 66fff62..a581e66 100644 --- a/tinytag/tinytag.py +++ b/tinytag/tinytag.py @@ -484,7 +484,7 @@ class ID3(TinyTag): FRAME_ID_TO_FIELD = { # Mapping from Frame ID to a field of the TinyTag 'COMM': 'comment', 'COM': 'comment', 'TRCK': 'track', 'TRK': 'track', - 'TYER': 'year', 'TYE': 'year', + 'TYER': 'year', 'TYE': 'year', 'TDRC': 'year', 'TALB': 'album', 'TAL': 'album', 'TPE1': 'artist', 'TP1': 'artist', 'TIT2': 'title', 'TT2': 'title',
devsnd/tinytag
5107f8611192a166dfea4f75619377ab2d5bda49
diff --git a/tinytag/tests/test_all.py b/tinytag/tests/test_all.py index abbb5dc..743e48b 100644 --- a/tinytag/tests/test_all.py +++ b/tinytag/tests/test_all.py @@ -73,7 +73,7 @@ testfiles = OrderedDict([ ('samples/utf-8-id3v2.mp3', {'extra': {}, 'genre': 'Acustico', 'track_total': '21', 'track': '01', 'filesize': 2119, 'title': 'Gran día', - 'artist': 'Paso a paso', 'album': 'S/T', 'disc': '', 'disc_total': '0'}), + 'artist': 'Paso a paso', 'album': 'S/T', 'disc': '', 'disc_total': '0', 'year': '2003'}), ('samples/empty_file.mp3', {'extra': {}, 'filesize': 0}), ('samples/silence-44khz-56k-mono-1s.mp3', @@ -88,10 +88,11 @@ testfiles = OrderedDict([ 'track_total': '12', 'genre': 'AlternRock', 'title': 'Out of the Woodwork', 'artist': 'Courtney Barnett', 'albumartist': 'Courtney Barnett', 'disc': '1', - 'comment': 'Amazon.com Song ID: 240853806', 'composer': 'Courtney Barnett'}), + 'comment': 'Amazon.com Song ID: 240853806', 'composer': 'Courtney Barnett', + 'year': '2013'}), ('samples/utf16be.mp3', {'extra': {}, 'title': '52-girls', 'filesize': 2048, 'track': '6', 'album': 'party mix', - 'artist': 'The B52s', 'genre': 'Rock'}), + 'artist': 'The B52s', 'genre': 'Rock', 'year': '1981'}), ('samples/id3v22_image.mp3', {'extra': {}, 'title': 'Kids (MGMT Cover) ', 'filesize': 35924, 'album': 'winniecooper.net ', 'artist': 'The Kooks', 'year': '2008', @@ -189,7 +190,7 @@ testfiles = OrderedDict([ ('samples/id3v24_genre_null_byte.mp3', {'extra': {}, 'filesize': 256, 'album': '\u79d8\u5bc6', 'albumartist': 'aiko', 'artist': 'aiko', 'disc': '1', 'genre': 'Pop', - 'title': '\u661f\u306e\u306a\u3044\u4e16\u754c', 'track': '10'}), + 'title': '\u661f\u306e\u306a\u3044\u4e16\u754c', 'track': '10', 'year': '2008'}), ('samples/vbr_xing_header_short.mp3', {'filesize': 432, 'audio_offset': 133, 'bitrate': 24.0, 'channels': 1, 'duration': 0.144, 'extra': {}, 'samplerate': 8000}), @@ -376,7 +377,7 @@ testfiles = OrderedDict([ {'extra': {}, 'channels': 2, 'duration': 0.2999546485260771, 'filesize': 6892, 'artist': 'Serhiy Storchaka', 'title': 'Pluck', 'album': 'Python Test Suite', 'bitrate': 176.4, 'samplerate': 11025, 'audio_offset': 116, - 'comment': 'Audacity Pluck + Wahwah'}), + 'comment': 'Audacity Pluck + Wahwah', 'year': '2013'}), ('samples/M1F1-mulawC-AFsp.afc', {'extra': {}, 'channels': 2, 'duration': 2.936625, 'filesize': 47148, 'bitrate': 256.0, 'samplerate': 8000, 'audio_offset': 154,
[BUG] Parsing mp3 file w/ valid TDRC tag does not populate year **Describe the bug** When parsing a mp3 file w/ valid v2.4 metadata and a TDRC frame, TinyTag does not populate the year attribute in the output. **To Reproduce** Steps to reproduce the behavior: 1. Open a valid mp3 file w/ TinyTag 2. See `Found id3 Frame TDRC` in the program output 3. Resulting dict still has `"year": null` **Expected behavior** Valid timestamps (yyyy, yyyy-MM, yyyy-MM-dd, yyyy-MM-ddTHH, yyyy-MM-ddTHH:mm and yyyy-MM-ddTHH:mm:ss) should result in year attribute populated. **Sample File** https://www.dropbox.com/s/lz6vlzhw18znqp8/cdwal5Kw3Fc.mp3?dl=0
0.0
5107f8611192a166dfea4f75619377ab2d5bda49
[ "tinytag/tests/test_all.py::test_file_reading[samples/utf-8-id3v2.mp3-expected8]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v24-long-title.mp3-expected12]", "tinytag/tests/test_all.py::test_file_reading[samples/utf16be.mp3-expected13]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v24_genre_null_byte.mp3-expected39]", "tinytag/tests/test_all.py::test_file_reading[samples/pluck-pcm8.aiff-expected77]" ]
[ "tinytag/tests/test_all.py::test_file_reading[samples/vbri.mp3-expected0]", "tinytag/tests/test_all.py::test_file_reading[samples/cbr.mp3-expected1]", "tinytag/tests/test_all.py::test_file_reading[samples/vbr_xing_header.mp3-expected2]", "tinytag/tests/test_all.py::test_file_reading[samples/vbr_xing_header_2channel.mp3-expected3]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v22-test.mp3-expected4]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-44-s-v1.mp3-expected5]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v1-latin1.mp3-expected6]", "tinytag/tests/test_all.py::test_file_reading[samples/UTF16.mp3-expected7]", "tinytag/tests/test_all.py::test_file_reading[samples/empty_file.mp3-expected9]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-44khz-56k-mono-1s.mp3-expected10]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-22khz-mono-1s.mp3-expected11]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v22_image.mp3-expected14]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v22.TCO.genre.mp3-expected15]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_comment_utf_16_with_bom.mp3-expected16]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_comment_utf_16_double_bom.mp3-expected17]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_genre_id_out_of_bounds.mp3-expected18]", "tinytag/tests/test_all.py::test_file_reading[samples/image-text-encoding.mp3-expected19]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v1_does_not_overwrite_id3v2.mp3-expected20]", "tinytag/tests/test_all.py::test_file_reading[samples/nicotinetestdata.mp3-expected21]", "tinytag/tests/test_all.py::test_file_reading[samples/chinese_id3.mp3-expected22]", "tinytag/tests/test_all.py::test_file_reading[samples/cut_off_titles.mp3-expected23]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_xxx_lang.mp3-expected24]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr8.mp3-expected25]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr8stereo.mp3-expected26]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr11.mp3-expected27]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr11stereo.mp3-expected28]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr16.mp3-expected29]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr16stereo.mp3-expected30]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr22.mp3-expected31]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr22stereo.mp3-expected32]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr32.mp3-expected33]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr32stereo.mp3-expected34]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr44.mp3-expected35]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr44stereo.mp3-expected36]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr48.mp3-expected37]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr48stereo.mp3-expected38]", "tinytag/tests/test_all.py::test_file_reading[samples/vbr_xing_header_short.mp3-expected40]", "tinytag/tests/test_all.py::test_file_reading[samples/empty.ogg-expected41]", "tinytag/tests/test_all.py::test_file_reading[samples/multipagecomment.ogg-expected42]", "tinytag/tests/test_all.py::test_file_reading[samples/multipage-setup.ogg-expected43]", "tinytag/tests/test_all.py::test_file_reading[samples/test.ogg-expected44]", "tinytag/tests/test_all.py::test_file_reading[samples/corrupt_metadata.ogg-expected45]", "tinytag/tests/test_all.py::test_file_reading[samples/composer.ogg-expected46]", "tinytag/tests/test_all.py::test_file_reading[samples/test.opus-expected47]", "tinytag/tests/test_all.py::test_file_reading[samples/8khz_5s.opus-expected48]", "tinytag/tests/test_all.py::test_file_reading[samples/test.wav-expected49]", "tinytag/tests/test_all.py::test_file_reading[samples/test3sMono.wav-expected50]", "tinytag/tests/test_all.py::test_file_reading[samples/test-tagged.wav-expected51]", "tinytag/tests/test_all.py::test_file_reading[samples/test-riff-tags.wav-expected52]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-22khz-mono-1s.wav-expected53]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_header_with_a_zero_byte.wav-expected54]", "tinytag/tests/test_all.py::test_file_reading[samples/adpcm.wav-expected55]", "tinytag/tests/test_all.py::test_file_reading[samples/riff_extra_zero.wav-expected56]", "tinytag/tests/test_all.py::test_file_reading[samples/riff_extra_zero_2.wav-expected57]", "tinytag/tests/test_all.py::test_file_reading[samples/flac1sMono.flac-expected58]", "tinytag/tests/test_all.py::test_file_reading[samples/flac453sStereo.flac-expected59]", "tinytag/tests/test_all.py::test_file_reading[samples/flac1.5sStereo.flac-expected60]", "tinytag/tests/test_all.py::test_file_reading[samples/flac_application.flac-expected61]", "tinytag/tests/test_all.py::test_file_reading[samples/no-tags.flac-expected62]", "tinytag/tests/test_all.py::test_file_reading[samples/variable-block.flac-expected63]", "tinytag/tests/test_all.py::test_file_reading[samples/106-invalid-streaminfo.flac-expected64]", "tinytag/tests/test_all.py::test_file_reading[samples/106-short-picture-block-size.flac-expected65]", "tinytag/tests/test_all.py::test_file_reading[samples/with_id3_header.flac-expected66]", "tinytag/tests/test_all.py::test_file_reading[samples/with_padded_id3_header.flac-expected67]", "tinytag/tests/test_all.py::test_file_reading[samples/with_padded_id3_header2.flac-expected68]", "tinytag/tests/test_all.py::test_file_reading[samples/flac_with_image.flac-expected69]", "tinytag/tests/test_all.py::test_file_reading[samples/test2.wma-expected70]", "tinytag/tests/test_all.py::test_file_reading[samples/test.m4a-expected71]", "tinytag/tests/test_all.py::test_file_reading[samples/test2.m4a-expected72]", "tinytag/tests/test_all.py::test_file_reading[samples/iso8859_with_image.m4a-expected73]", "tinytag/tests/test_all.py::test_file_reading[samples/alac_file.m4a-expected74]", "tinytag/tests/test_all.py::test_file_reading[samples/test-tagged.aiff-expected75]", "tinytag/tests/test_all.py::test_file_reading[samples/test.aiff-expected76]", "tinytag/tests/test_all.py::test_file_reading[samples/M1F1-mulawC-AFsp.afc-expected78]", "tinytag/tests/test_all.py::test_pathlib_compatibility", "tinytag/tests/test_all.py::test_binary_path_compatibility", "tinytag/tests/test_all.py::test_override_encoding", "tinytag/tests/test_all.py::test_mp3_length_estimation", "tinytag/tests/test_all.py::test_unpad", "tinytag/tests/test_all.py::test_mp3_image_loading", "tinytag/tests/test_all.py::test_mp3_id3v22_image_loading", "tinytag/tests/test_all.py::test_mp3_image_loading_without_description", "tinytag/tests/test_all.py::test_mp3_image_loading_with_utf8_description", "tinytag/tests/test_all.py::test_mp3_image_loading2", "tinytag/tests/test_all.py::test_mp3_utf_8_invalid_string_raises_exception", "tinytag/tests/test_all.py::test_mp3_utf_8_invalid_string_can_be_ignored", "tinytag/tests/test_all.py::test_mp4_image_loading", "tinytag/tests/test_all.py::test_flac_image_loading", "tinytag/tests/test_all.py::test_aiff_image_loading", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_mp3_id3.x-ID3]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_mp3_fffb.x-ID3]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_ogg.x-Ogg]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_wav.x-Wave]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_flac.x-Flac]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_wma.x-Wma]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_mp4_m4a.x-MP4]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_aiff.x-Aiff]", "tinytag/tests/test_all.py::test_show_hint_for_wrong_usage", "tinytag/tests/test_all.py::test_to_str" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2022-09-02 01:45:25+00:00
mit
1,895
devsnd__tinytag-171
diff --git a/tinytag/tinytag.py b/tinytag/tinytag.py index a7a8a21..8ba376d 100644 --- a/tinytag/tinytag.py +++ b/tinytag/tinytag.py @@ -924,8 +924,10 @@ class Ogg(TinyTag): 'artist': 'artist', 'date': 'year', 'tracknumber': 'track', + 'tracktotal': 'track_total', 'totaltracks': 'track_total', 'discnumber': 'disc', + 'disctotal': 'disc_total', 'totaldiscs': 'disc_total', 'genre': 'genre', 'description': 'comment',
devsnd/tinytag
85a16fa18bcc534d1d61f10ca539955823945d5d
diff --git a/tinytag/tests/test_all.py b/tinytag/tests/test_all.py index 8f4421c..0b70517 100644 --- a/tinytag/tests/test_all.py +++ b/tinytag/tests/test_all.py @@ -230,7 +230,7 @@ testfiles = OrderedDict([ 'track': '1', 'disc': '1', 'title': 'Bad Apple!!', 'duration': 2.0, 'year': '2008.05.25', 'filesize': 10000, 'artist': 'nomico', 'album': 'Exserens - A selection of Alstroemeria Records', - 'comment': 'ARCD0018 - Lovelight'}), + 'comment': 'ARCD0018 - Lovelight', 'disc_total': '1', 'track_total': '13'}), ('samples/8khz_5s.opus', {'extra': {}, 'filesize': 7251, 'channels': 1, 'samplerate': 48000, 'duration': 5.0}),
Fail to read track_total, but it is ok in foobar I got some tracks from qobuz. I have some problems in reading the track_total. It showed 'null' in track_total. The others is OK, such as artist, album etc.... But its track_total seems OK, when checked in foobar. Why? The attachment are an example flac file [19. I m Not The Man You Think I Am.zip](https://github.com/devsnd/tinytag/files/10875229/19.I.m.Not.The.Man.You.Think.I.Am.zip)
0.0
85a16fa18bcc534d1d61f10ca539955823945d5d
[ "tinytag/tests/test_all.py::test_file_reading[samples/test.opus-expected47]" ]
[ "tinytag/tests/test_all.py::test_file_reading[samples/vbri.mp3-expected0]", "tinytag/tests/test_all.py::test_file_reading[samples/cbr.mp3-expected1]", "tinytag/tests/test_all.py::test_file_reading[samples/vbr_xing_header.mp3-expected2]", "tinytag/tests/test_all.py::test_file_reading[samples/vbr_xing_header_2channel.mp3-expected3]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v22-test.mp3-expected4]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-44-s-v1.mp3-expected5]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v1-latin1.mp3-expected6]", "tinytag/tests/test_all.py::test_file_reading[samples/UTF16.mp3-expected7]", "tinytag/tests/test_all.py::test_file_reading[samples/utf-8-id3v2.mp3-expected8]", "tinytag/tests/test_all.py::test_file_reading[samples/empty_file.mp3-expected9]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-44khz-56k-mono-1s.mp3-expected10]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-22khz-mono-1s.mp3-expected11]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v24-long-title.mp3-expected12]", "tinytag/tests/test_all.py::test_file_reading[samples/utf16be.mp3-expected13]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v22_image.mp3-expected14]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v22.TCO.genre.mp3-expected15]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_comment_utf_16_with_bom.mp3-expected16]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_comment_utf_16_double_bom.mp3-expected17]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_genre_id_out_of_bounds.mp3-expected18]", "tinytag/tests/test_all.py::test_file_reading[samples/image-text-encoding.mp3-expected19]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v1_does_not_overwrite_id3v2.mp3-expected20]", "tinytag/tests/test_all.py::test_file_reading[samples/nicotinetestdata.mp3-expected21]", "tinytag/tests/test_all.py::test_file_reading[samples/chinese_id3.mp3-expected22]", "tinytag/tests/test_all.py::test_file_reading[samples/cut_off_titles.mp3-expected23]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_xxx_lang.mp3-expected24]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr8.mp3-expected25]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr8stereo.mp3-expected26]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr11.mp3-expected27]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr11stereo.mp3-expected28]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr16.mp3-expected29]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr16stereo.mp3-expected30]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr22.mp3-expected31]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr22stereo.mp3-expected32]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr32.mp3-expected33]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr32stereo.mp3-expected34]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr44.mp3-expected35]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr44stereo.mp3-expected36]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr48.mp3-expected37]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr48stereo.mp3-expected38]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v24_genre_null_byte.mp3-expected39]", "tinytag/tests/test_all.py::test_file_reading[samples/vbr_xing_header_short.mp3-expected40]", "tinytag/tests/test_all.py::test_file_reading[samples/empty.ogg-expected41]", "tinytag/tests/test_all.py::test_file_reading[samples/multipagecomment.ogg-expected42]", "tinytag/tests/test_all.py::test_file_reading[samples/multipage-setup.ogg-expected43]", "tinytag/tests/test_all.py::test_file_reading[samples/test.ogg-expected44]", "tinytag/tests/test_all.py::test_file_reading[samples/corrupt_metadata.ogg-expected45]", "tinytag/tests/test_all.py::test_file_reading[samples/composer.ogg-expected46]", "tinytag/tests/test_all.py::test_file_reading[samples/8khz_5s.opus-expected48]", "tinytag/tests/test_all.py::test_file_reading[samples/test.wav-expected49]", "tinytag/tests/test_all.py::test_file_reading[samples/test3sMono.wav-expected50]", "tinytag/tests/test_all.py::test_file_reading[samples/test-tagged.wav-expected51]", "tinytag/tests/test_all.py::test_file_reading[samples/test-riff-tags.wav-expected52]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-22khz-mono-1s.wav-expected53]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_header_with_a_zero_byte.wav-expected54]", "tinytag/tests/test_all.py::test_file_reading[samples/adpcm.wav-expected55]", "tinytag/tests/test_all.py::test_file_reading[samples/riff_extra_zero.wav-expected56]", "tinytag/tests/test_all.py::test_file_reading[samples/riff_extra_zero_2.wav-expected57]", "tinytag/tests/test_all.py::test_file_reading[samples/flac1sMono.flac-expected58]", "tinytag/tests/test_all.py::test_file_reading[samples/flac453sStereo.flac-expected59]", "tinytag/tests/test_all.py::test_file_reading[samples/flac1.5sStereo.flac-expected60]", "tinytag/tests/test_all.py::test_file_reading[samples/flac_application.flac-expected61]", "tinytag/tests/test_all.py::test_file_reading[samples/no-tags.flac-expected62]", "tinytag/tests/test_all.py::test_file_reading[samples/variable-block.flac-expected63]", "tinytag/tests/test_all.py::test_file_reading[samples/106-invalid-streaminfo.flac-expected64]", "tinytag/tests/test_all.py::test_file_reading[samples/106-short-picture-block-size.flac-expected65]", "tinytag/tests/test_all.py::test_file_reading[samples/with_id3_header.flac-expected66]", "tinytag/tests/test_all.py::test_file_reading[samples/with_padded_id3_header.flac-expected67]", "tinytag/tests/test_all.py::test_file_reading[samples/with_padded_id3_header2.flac-expected68]", "tinytag/tests/test_all.py::test_file_reading[samples/flac_with_image.flac-expected69]", "tinytag/tests/test_all.py::test_file_reading[samples/test2.wma-expected70]", "tinytag/tests/test_all.py::test_file_reading[samples/lossless.wma-expected71]", "tinytag/tests/test_all.py::test_file_reading[samples/test.m4a-expected72]", "tinytag/tests/test_all.py::test_file_reading[samples/test2.m4a-expected73]", "tinytag/tests/test_all.py::test_file_reading[samples/iso8859_with_image.m4a-expected74]", "tinytag/tests/test_all.py::test_file_reading[samples/alac_file.m4a-expected75]", "tinytag/tests/test_all.py::test_file_reading[samples/mpeg4_desc_cmt.m4a-expected76]", "tinytag/tests/test_all.py::test_file_reading[samples/mpeg4_xa9des.m4a-expected77]", "tinytag/tests/test_all.py::test_file_reading[samples/test-tagged.aiff-expected78]", "tinytag/tests/test_all.py::test_file_reading[samples/test.aiff-expected79]", "tinytag/tests/test_all.py::test_file_reading[samples/pluck-pcm8.aiff-expected80]", "tinytag/tests/test_all.py::test_file_reading[samples/M1F1-mulawC-AFsp.afc-expected81]", "tinytag/tests/test_all.py::test_file_reading[samples/invalid_sample_rate.aiff-expected82]", "tinytag/tests/test_all.py::test_pathlib_compatibility", "tinytag/tests/test_all.py::test_binary_path_compatibility", "tinytag/tests/test_all.py::test_override_encoding", "tinytag/tests/test_all.py::test_mp3_length_estimation", "tinytag/tests/test_all.py::test_unpad", "tinytag/tests/test_all.py::test_mp3_image_loading", "tinytag/tests/test_all.py::test_mp3_id3v22_image_loading", "tinytag/tests/test_all.py::test_mp3_image_loading_without_description", "tinytag/tests/test_all.py::test_mp3_image_loading_with_utf8_description", "tinytag/tests/test_all.py::test_mp3_image_loading2", "tinytag/tests/test_all.py::test_mp3_utf_8_invalid_string_raises_exception", "tinytag/tests/test_all.py::test_mp3_utf_8_invalid_string_can_be_ignored", "tinytag/tests/test_all.py::test_mp4_image_loading", "tinytag/tests/test_all.py::test_flac_image_loading", "tinytag/tests/test_all.py::test_ogg_image_loading", "tinytag/tests/test_all.py::test_aiff_image_loading", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_mp3_id3.x-ID3]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_mp3_fffb.x-ID3]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_ogg.x-Ogg]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_wav.x-Wave]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_flac.x-Flac]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_wma.x-Wma]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_mp4_m4a.x-MP4]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_aiff.x-Aiff]", "tinytag/tests/test_all.py::test_show_hint_for_wrong_usage", "tinytag/tests/test_all.py::test_to_str" ]
{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }
2023-03-20 22:28:45+00:00
mit
1,896
devsnd__tinytag-178
diff --git a/tinytag/tinytag.py b/tinytag/tinytag.py index a3f1305..595a101 100644 --- a/tinytag/tinytag.py +++ b/tinytag/tinytag.py @@ -170,40 +170,48 @@ class TinyTag(object): return parser @classmethod - def get_parser_class(cls, filename, filehandle): + def get_parser_class(cls, filename=None, filehandle=None): if cls != TinyTag: # if `get` is invoked on TinyTag, find parser by ext return cls # otherwise use the class on which `get` was invoked - parser_class = cls._get_parser_for_filename(filename) - if parser_class is not None: - return parser_class + if filename: + parser_class = cls._get_parser_for_filename(filename) + if parser_class is not None: + return parser_class # try determining the file type by magic byte header - parser_class = cls._get_parser_for_file_handle(filehandle) - if parser_class is not None: - return parser_class + if filehandle: + parser_class = cls._get_parser_for_file_handle(filehandle) + if parser_class is not None: + return parser_class raise TinyTagException('No tag reader found to support filetype! ') @classmethod - def get(cls, filename, tags=True, duration=True, image=False, ignore_errors=False, - encoding=None): - try: # cast pathlib.Path to str - import pathlib - if isinstance(filename, pathlib.Path): - filename = str(filename.absolute()) - except ImportError: - pass + def get(cls, filename=None, tags=True, duration=True, image=False, + ignore_errors=False, encoding=None, file_obj=None): + should_open_file = (file_obj is None) + if should_open_file: + try: + file_obj = io.open(filename, 'rb') + except TypeError: + file_obj = io.open(str(filename.absolute()), 'rb') # Python 3.4/3.5 pathlib support + filename = file_obj.name else: - filename = os.path.expanduser(filename) - size = os.path.getsize(filename) - if not size > 0: - return TinyTag(None, 0) - with io.open(filename, 'rb') as af: - parser_class = cls.get_parser_class(filename, af) - tag = parser_class(af, size, ignore_errors=ignore_errors) + file_obj = io.BufferedReader(file_obj) # buffered reader to support peeking + try: + file_obj.seek(0, os.SEEK_END) + filesize = file_obj.tell() + file_obj.seek(0) + if filesize <= 0: + return TinyTag(None, filesize) + parser_class = cls.get_parser_class(filename, file_obj) + tag = parser_class(file_obj, filesize, ignore_errors=ignore_errors) tag._filename = filename tag._default_encoding = encoding tag.load(tags=tags, duration=duration, image=image) tag.extra = dict(tag.extra) # turn default dict into dict so that it can throw KeyError return tag + finally: + if should_open_file: + file_obj.close() def __str__(self): return json.dumps(OrderedDict(sorted(self.as_dict().items())))
devsnd/tinytag
337c044ce51f9e707b8cd31d02896c9041a98afa
diff --git a/tinytag/tests/test_all.py b/tinytag/tests/test_all.py index 0b70517..aa3a38e 100644 --- a/tinytag/tests/test_all.py +++ b/tinytag/tests/test_all.py @@ -510,6 +510,13 @@ def test_pathlib_compatibility(): TinyTag.get(filename) +def test_bytesio_compatibility(): + testfile = next(iter(testfiles.keys())) + filename = os.path.join(testfolder, testfile) + with io.open(filename, 'rb') as file_handle: + TinyTag.get(file_obj=io.BytesIO(file_handle.read())) + + @pytest.mark.skipif(sys.platform == "win32", reason='Windows does not support binary paths') def test_binary_path_compatibility(): binary_file_path = os.path.join(os.path.dirname(__file__).encode('utf-8'), b'\x01.mp3')
Support BytesIo objects for tagging It would be awesome to support BytesIO or any other IO types with TinyTag. This way it can be used in some scenarios where files are packaged and do not have a normal path.
0.0
337c044ce51f9e707b8cd31d02896c9041a98afa
[ "tinytag/tests/test_all.py::test_bytesio_compatibility" ]
[ "tinytag/tests/test_all.py::test_file_reading[samples/vbri.mp3-expected0]", "tinytag/tests/test_all.py::test_file_reading[samples/cbr.mp3-expected1]", "tinytag/tests/test_all.py::test_file_reading[samples/vbr_xing_header.mp3-expected2]", "tinytag/tests/test_all.py::test_file_reading[samples/vbr_xing_header_2channel.mp3-expected3]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v22-test.mp3-expected4]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-44-s-v1.mp3-expected5]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v1-latin1.mp3-expected6]", "tinytag/tests/test_all.py::test_file_reading[samples/UTF16.mp3-expected7]", "tinytag/tests/test_all.py::test_file_reading[samples/utf-8-id3v2.mp3-expected8]", "tinytag/tests/test_all.py::test_file_reading[samples/empty_file.mp3-expected9]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-44khz-56k-mono-1s.mp3-expected10]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-22khz-mono-1s.mp3-expected11]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v24-long-title.mp3-expected12]", "tinytag/tests/test_all.py::test_file_reading[samples/utf16be.mp3-expected13]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v22_image.mp3-expected14]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v22.TCO.genre.mp3-expected15]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_comment_utf_16_with_bom.mp3-expected16]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_comment_utf_16_double_bom.mp3-expected17]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_genre_id_out_of_bounds.mp3-expected18]", "tinytag/tests/test_all.py::test_file_reading[samples/image-text-encoding.mp3-expected19]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v1_does_not_overwrite_id3v2.mp3-expected20]", "tinytag/tests/test_all.py::test_file_reading[samples/nicotinetestdata.mp3-expected21]", "tinytag/tests/test_all.py::test_file_reading[samples/chinese_id3.mp3-expected22]", "tinytag/tests/test_all.py::test_file_reading[samples/cut_off_titles.mp3-expected23]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_xxx_lang.mp3-expected24]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr8.mp3-expected25]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr8stereo.mp3-expected26]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr11.mp3-expected27]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr11stereo.mp3-expected28]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr16.mp3-expected29]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr16stereo.mp3-expected30]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr22.mp3-expected31]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr22stereo.mp3-expected32]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr32.mp3-expected33]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr32stereo.mp3-expected34]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr44.mp3-expected35]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr44stereo.mp3-expected36]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr48.mp3-expected37]", "tinytag/tests/test_all.py::test_file_reading[samples/mp3/vbr/vbr48stereo.mp3-expected38]", "tinytag/tests/test_all.py::test_file_reading[samples/id3v24_genre_null_byte.mp3-expected39]", "tinytag/tests/test_all.py::test_file_reading[samples/vbr_xing_header_short.mp3-expected40]", "tinytag/tests/test_all.py::test_file_reading[samples/empty.ogg-expected41]", "tinytag/tests/test_all.py::test_file_reading[samples/multipagecomment.ogg-expected42]", "tinytag/tests/test_all.py::test_file_reading[samples/multipage-setup.ogg-expected43]", "tinytag/tests/test_all.py::test_file_reading[samples/test.ogg-expected44]", "tinytag/tests/test_all.py::test_file_reading[samples/corrupt_metadata.ogg-expected45]", "tinytag/tests/test_all.py::test_file_reading[samples/composer.ogg-expected46]", "tinytag/tests/test_all.py::test_file_reading[samples/test.opus-expected47]", "tinytag/tests/test_all.py::test_file_reading[samples/8khz_5s.opus-expected48]", "tinytag/tests/test_all.py::test_file_reading[samples/test.wav-expected49]", "tinytag/tests/test_all.py::test_file_reading[samples/test3sMono.wav-expected50]", "tinytag/tests/test_all.py::test_file_reading[samples/test-tagged.wav-expected51]", "tinytag/tests/test_all.py::test_file_reading[samples/test-riff-tags.wav-expected52]", "tinytag/tests/test_all.py::test_file_reading[samples/silence-22khz-mono-1s.wav-expected53]", "tinytag/tests/test_all.py::test_file_reading[samples/id3_header_with_a_zero_byte.wav-expected54]", "tinytag/tests/test_all.py::test_file_reading[samples/adpcm.wav-expected55]", "tinytag/tests/test_all.py::test_file_reading[samples/riff_extra_zero.wav-expected56]", "tinytag/tests/test_all.py::test_file_reading[samples/riff_extra_zero_2.wav-expected57]", "tinytag/tests/test_all.py::test_file_reading[samples/flac1sMono.flac-expected58]", "tinytag/tests/test_all.py::test_file_reading[samples/flac453sStereo.flac-expected59]", "tinytag/tests/test_all.py::test_file_reading[samples/flac1.5sStereo.flac-expected60]", "tinytag/tests/test_all.py::test_file_reading[samples/flac_application.flac-expected61]", "tinytag/tests/test_all.py::test_file_reading[samples/no-tags.flac-expected62]", "tinytag/tests/test_all.py::test_file_reading[samples/variable-block.flac-expected63]", "tinytag/tests/test_all.py::test_file_reading[samples/106-invalid-streaminfo.flac-expected64]", "tinytag/tests/test_all.py::test_file_reading[samples/106-short-picture-block-size.flac-expected65]", "tinytag/tests/test_all.py::test_file_reading[samples/with_id3_header.flac-expected66]", "tinytag/tests/test_all.py::test_file_reading[samples/with_padded_id3_header.flac-expected67]", "tinytag/tests/test_all.py::test_file_reading[samples/with_padded_id3_header2.flac-expected68]", "tinytag/tests/test_all.py::test_file_reading[samples/flac_with_image.flac-expected69]", "tinytag/tests/test_all.py::test_file_reading[samples/test2.wma-expected70]", "tinytag/tests/test_all.py::test_file_reading[samples/lossless.wma-expected71]", "tinytag/tests/test_all.py::test_file_reading[samples/test.m4a-expected72]", "tinytag/tests/test_all.py::test_file_reading[samples/test2.m4a-expected73]", "tinytag/tests/test_all.py::test_file_reading[samples/iso8859_with_image.m4a-expected74]", "tinytag/tests/test_all.py::test_file_reading[samples/alac_file.m4a-expected75]", "tinytag/tests/test_all.py::test_file_reading[samples/mpeg4_desc_cmt.m4a-expected76]", "tinytag/tests/test_all.py::test_file_reading[samples/mpeg4_xa9des.m4a-expected77]", "tinytag/tests/test_all.py::test_file_reading[samples/test-tagged.aiff-expected78]", "tinytag/tests/test_all.py::test_file_reading[samples/test.aiff-expected79]", "tinytag/tests/test_all.py::test_file_reading[samples/pluck-pcm8.aiff-expected80]", "tinytag/tests/test_all.py::test_file_reading[samples/M1F1-mulawC-AFsp.afc-expected81]", "tinytag/tests/test_all.py::test_file_reading[samples/invalid_sample_rate.aiff-expected82]", "tinytag/tests/test_all.py::test_pathlib_compatibility", "tinytag/tests/test_all.py::test_binary_path_compatibility", "tinytag/tests/test_all.py::test_override_encoding", "tinytag/tests/test_all.py::test_mp3_length_estimation", "tinytag/tests/test_all.py::test_unpad", "tinytag/tests/test_all.py::test_mp3_image_loading", "tinytag/tests/test_all.py::test_mp3_id3v22_image_loading", "tinytag/tests/test_all.py::test_mp3_image_loading_without_description", "tinytag/tests/test_all.py::test_mp3_image_loading_with_utf8_description", "tinytag/tests/test_all.py::test_mp3_image_loading2", "tinytag/tests/test_all.py::test_mp3_utf_8_invalid_string_raises_exception", "tinytag/tests/test_all.py::test_mp3_utf_8_invalid_string_can_be_ignored", "tinytag/tests/test_all.py::test_mp4_image_loading", "tinytag/tests/test_all.py::test_flac_image_loading", "tinytag/tests/test_all.py::test_ogg_image_loading", "tinytag/tests/test_all.py::test_aiff_image_loading", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_mp3_id3.x-ID3]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_mp3_fffb.x-ID3]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_ogg.x-Ogg]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_wav.x-Wave]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_flac.x-Flac]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_wma.x-Wma]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_mp4_m4a.x-MP4]", "tinytag/tests/test_all.py::test_detect_magic_headers[samples/detect_aiff.x-Aiff]", "tinytag/tests/test_all.py::test_show_hint_for_wrong_usage", "tinytag/tests/test_all.py::test_to_str" ]
{ "failed_lite_validators": [ "has_short_problem_statement" ], "has_test_patch": true, "is_lite": false }
2023-06-02 19:58:04+00:00
mit
1,897
dfm__emcee-295
diff --git a/.travis.yml b/.travis.yml index fa02161..4aa919c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -23,7 +23,7 @@ install: - travis_retry python setup.py develop script: - - py.test -v emcee/tests --cov emcee + - pytest -v emcee/tests --cov emcee after_success: - coveralls diff --git a/emcee/ensemble.py b/emcee/ensemble.py index ae6a976..7d30afc 100644 --- a/emcee/ensemble.py +++ b/emcee/ensemble.py @@ -478,8 +478,8 @@ class EnsembleSampler(object): @property @deprecated("get_log_prob()") def lnprobability(self): # pragma: no cover - return self.get_log_prob() - + log_prob = self.get_log_prob() + return np.swapaxes(log_prob, 0, 1) @property @deprecated("get_log_prob(flat=True)") def flatlnprobability(self): # pragma: no cover
dfm/emcee
593a6b134170c47af6e31106244df78b6fb194db
diff --git a/emcee/tests/unit/test_sampler.py b/emcee/tests/unit/test_sampler.py index 48a351a..ca38a56 100644 --- a/emcee/tests/unit/test_sampler.py +++ b/emcee/tests/unit/test_sampler.py @@ -47,11 +47,15 @@ def test_shapes(backend, moves, nwalkers=32, ndim=3, nsteps=10, seed=1234): assert tau.shape == (ndim,) # Check the shapes. - assert sampler.chain.shape == (nwalkers, nsteps, ndim), \ - "incorrect coordinate dimensions" + with pytest.warns(DeprecationWarning): + assert sampler.chain.shape == (nwalkers, nsteps, ndim), \ + "incorrect coordinate dimensions" + with pytest.warns(DeprecationWarning): + assert sampler.lnprobability.shape == (nwalkers, nsteps), \ + "incorrect probability dimensions" assert sampler.get_chain().shape == (nsteps, nwalkers, ndim), \ "incorrect coordinate dimensions" - assert sampler.lnprobability.shape == (nsteps, nwalkers), \ + assert sampler.get_log_prob().shape == (nsteps, nwalkers), \ "incorrect probability dimensions" assert sampler.acceptance_fraction.shape == (nwalkers,), \ @@ -77,14 +81,14 @@ def test_errors(backend, nwalkers=32, ndim=3, nsteps=5, seed=1234): # Test for not running. with pytest.raises(AttributeError): - sampler.chain + sampler.get_chain() with pytest.raises(AttributeError): - sampler.lnprobability + sampler.get_log_prob() # What about not storing the chain. sampler.run_mcmc(coords, nsteps, store=False) with pytest.raises(AttributeError): - sampler.chain + sampler.get_chain() # Now what about if we try to continue using the sampler with an # ensemble of a different shape. @@ -121,12 +125,15 @@ def run_sampler(backend, nwalkers=32, ndim=3, nsteps=25, seed=1234, def test_thin(backend): with backend() as be: with pytest.raises(ValueError): - run_sampler(be, thin=-1) + with pytest.warns(DeprecationWarning): + run_sampler(be, thin=-1) with pytest.raises(ValueError): - run_sampler(be, thin=0.1) + with pytest.warns(DeprecationWarning): + run_sampler(be, thin=0.1) thinby = 3 sampler1 = run_sampler(None) - sampler2 = run_sampler(be, thin=thinby) + with pytest.warns(DeprecationWarning): + sampler2 = run_sampler(be, thin=thinby) for k in ["get_chain", "get_log_prob"]: a = getattr(sampler1, k)()[thinby-1::thinby] b = getattr(sampler2, k)()
sampler.lnprobability is transposed in emcee3? tl;dr it looks like `sampler.lnprobability` is transposed in emcee 3 from what I would expect from emcee 2. Sample code (copy pasta'd from the old docs): ```python import numpy as np import emcee def lnprob(x, ivar): return -0.5 * np.sum(ivar * x ** 2) ndim, nwalkers = 10, 100 ivar = 1. / np.random.rand(ndim) p0 = [np.random.rand(ndim) for i in range(nwalkers)] sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob, args=[ivar]) _ = sampler.run_mcmc(p0, 1000) print(emcee.__version__) print(sampler.chain.shape, sampler.lnprobability.shape) ``` ## Output from emcee 2.2.1 ``` 2.2.1 (100, 1000, 10) (100, 1000) ``` ## Output from emcee 3.0rc2 ``` 3.0rc2 (100, 1000, 10) (1000, 100) ```
0.0
593a6b134170c47af6e31106244df78b6fb194db
[ "emcee/tests/unit/test_sampler.py::test_shapes[Backend-None]", "emcee/tests/unit/test_sampler.py::test_shapes[Backend-moves1]", "emcee/tests/unit/test_sampler.py::test_shapes[Backend-moves2]", "emcee/tests/unit/test_sampler.py::test_shapes[Backend-moves3]" ]
[ "emcee/tests/unit/test_sampler.py::test_thin[Backend]", "emcee/tests/unit/test_sampler.py::test_thin_by[Backend-True]", "emcee/tests/unit/test_sampler.py::test_thin_by[Backend-False]", "emcee/tests/unit/test_sampler.py::test_restart[Backend]", "emcee/tests/unit/test_sampler.py::test_vectorize", "emcee/tests/unit/test_sampler.py::test_pickle[Backend]" ]
{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2019-04-11 00:18:44+00:00
mit
1,898
dfm__emcee-354
diff --git a/src/emcee/autocorr.py b/src/emcee/autocorr.py index 5156372..4a804ff 100644 --- a/src/emcee/autocorr.py +++ b/src/emcee/autocorr.py @@ -49,7 +49,7 @@ def integrated_time(x, c=5, tol=50, quiet=False): """Estimate the integrated autocorrelation time of a time series. This estimate uses the iterative procedure described on page 16 of - `Sokal's notes <http://www.stat.unc.edu/faculty/cji/Sokal.pdf>`_ to + `Sokal's notes <https://www.semanticscholar.org/paper/Monte-Carlo-Methods-in-Statistical-Mechanics%3A-and-Sokal/0bfe9e3db30605fe2d4d26e1a288a5e2997e7225>`_ to determine a reasonable window size. Args: diff --git a/src/emcee/backends/hdf.py b/src/emcee/backends/hdf.py index d4e6d6c..9503512 100644 --- a/src/emcee/backends/hdf.py +++ b/src/emcee/backends/hdf.py @@ -2,7 +2,7 @@ from __future__ import division, print_function -__all__ = ["HDFBackend", "TempHDFBackend"] +__all__ = ["HDFBackend", "TempHDFBackend", "does_hdf5_support_longdouble"] import os from tempfile import NamedTemporaryFile @@ -19,6 +19,25 @@ except ImportError: h5py = None +def does_hdf5_support_longdouble(): + if h5py is None: + return False + with NamedTemporaryFile(prefix="emcee-temporary-hdf5", + suffix=".hdf5", + delete=False) as f: + f.close() + + with h5py.File(f.name, "w") as hf: + g = hf.create_group("group") + g.create_dataset("data", data=np.ones(1, dtype=np.longdouble)) + if g["data"].dtype != np.longdouble: + return False + with h5py.File(f.name, "r") as hf: + if hf["group"]["data"].dtype != np.longdouble: + return False + return True + + class HDFBackend(Backend): """A backend that stores the chain in an HDF5 file using h5py diff --git a/tox.ini b/tox.ini index 6c09ae3..9f72a99 100644 --- a/tox.ini +++ b/tox.ini @@ -1,5 +1,5 @@ [tox] -envlist = py{36,37} +envlist = py{36,37,38} [testenv] description = Unit tests
dfm/emcee
c14b212964cfc1543c41f0bd186cafb399e847f7
diff --git a/src/emcee/tests/integration/test_longdouble.py b/src/emcee/tests/integration/test_longdouble.py index a2142d5..b8d2c7a 100644 --- a/src/emcee/tests/integration/test_longdouble.py +++ b/src/emcee/tests/integration/test_longdouble.py @@ -2,6 +2,7 @@ import numpy as np import pytest import emcee +from emcee.backends.hdf import does_hdf5_support_longdouble, TempHDFBackend def test_longdouble_doesnt_crash_bug_312(): @@ -17,9 +18,11 @@ def test_longdouble_doesnt_crash_bug_312(): sampler.run_mcmc(p0, 100) [email protected]("cls", [emcee.backends.Backend, - emcee.backends.TempHDFBackend]) [email protected]("cls", emcee.backends.get_test_backends()) def test_longdouble_actually_needed(cls): + if (issubclass(cls, TempHDFBackend) + and not does_hdf5_support_longdouble()): + pytest.xfail("HDF5 does not support long double on this platform") mjd = np.longdouble(58000.) sigma = 100*np.finfo(np.longdouble).eps*mjd diff --git a/src/emcee/tests/unit/test_backends.py b/src/emcee/tests/unit/test_backends.py index e5466ec..370008e 100644 --- a/src/emcee/tests/unit/test_backends.py +++ b/src/emcee/tests/unit/test_backends.py @@ -2,12 +2,18 @@ import os from itertools import product +from tempfile import NamedTemporaryFile -import h5py import numpy as np import pytest from emcee import EnsembleSampler, backends, State +from emcee.backends.hdf import does_hdf5_support_longdouble + +try: + import h5py +except ImportError: + h5py = None __all__ = ["test_backend", "test_reload"] @@ -55,6 +61,7 @@ def _custom_allclose(a, b): assert np.allclose(a[n], b[n]) [email protected](h5py is None, reason="HDF5 not available") def test_uninit(tmpdir): fn = str(tmpdir.join("EMCEE_TEST_FILE_DO_NOT_USE.h5")) if os.path.exists(fn): @@ -208,6 +215,7 @@ def test_restart(backend, dtype): assert np.allclose(a, b), "inconsistent acceptance fraction" [email protected](h5py is None, reason="HDF5 not available") def test_multi_hdf5(): with backends.TempHDFBackend() as backend1: run_sampler(backend1) @@ -227,6 +235,9 @@ def test_multi_hdf5(): @pytest.mark.parametrize("backend", all_backends) def test_longdouble_preserved(backend): + if (issubclass(backend, backends.TempHDFBackend) + and not does_hdf5_support_longdouble()): + pytest.xfail("HDF5 does not support long double on this platform") nwalkers = 10 ndim = 2 nsteps = 5 @@ -252,14 +263,3 @@ def test_longdouble_preserved(backend): assert s.log_prob.dtype == np.longdouble assert np.all(s.log_prob == lp) - - -def test_hdf5_dtypes(): - nwalkers = 10 - ndim = 2 - with backends.TempHDFBackend(dtype=np.longdouble) as b: - assert b.dtype == np.longdouble - b.reset(nwalkers, ndim) - with h5py.File(b.filename, "r") as f: - g = f["test"] - assert g["chain"].dtype == np.longdouble
long double tests fail on ppc64el **General information:** - emcee version: 3.0.2 - platform: ppc64el - installation method (pip/conda/source/other?): Ubuntu/Debian package **Problem description:** Version 3.0.2 of emcee is not migrating to the release pocket of Ubuntu because tests are failing on ppc64el: https://autopkgtest.ubuntu.com/packages/e/emcee/groovy/ppc64el ### Expected behavior tests pass ### Actual behavior: test_longdouble_actually_needed[TempHDFBackend] and test_longdouble_preserved[TempHDFBackend] fail: ``` _______________ test_longdouble_actually_needed[TempHDFBackend] ________________ cls = <class 'emcee.backends.hdf.TempHDFBackend'> @pytest.mark.parametrize("cls", [emcee.backends.Backend, emcee.backends.TempHDFBackend]) def test_longdouble_actually_needed(cls): mjd = np.longdouble(58000.) sigma = 100*np.finfo(np.longdouble).eps*mjd def log_prob(x): assert x.dtype == np.longdouble return -0.5 * np.sum(((x-mjd)/sigma) ** 2) ndim, nwalkers = 1, 20 steps = 1000 p0 = sigma*np.random.randn(nwalkers, ndim).astype(np.longdouble) + mjd assert not all(p0 == mjd) with cls(dtype=np.longdouble) as backend: sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob, backend=backend) sampler.run_mcmc(p0, steps) samples = sampler.get_chain().reshape((-1,)) > assert samples.dtype == np.longdouble E AssertionError: assert dtype('<f8') == <class 'numpy.float128'> E + where dtype('<f8') = array([ 5.80000000e+04, -4.60105223e-27, 5.80000000e+04, ...,\n -6.24580733e-26, 5.80000000e+04, -7.38930048e-27]).dtype E + and <class 'numpy.float128'> = np.longdouble ``` (the other failure is similar) ### What have you tried so far? Googling and getting a headache :) I know that "long double" on PowerPC / POWER is a strange pair-of-64-bit-doubles type so I'm not surprised that it's on POWER that I see the problem. I also see from searching that hd5/h5py/numpy have a history of problems in this area (e.g. https://github.com/h5py/h5py/issues/817) so I'm not sure what the resolution should be. Skipping these tests on ppc64el for now (maybe in an Ubuntu specific patch) might make sense -- it's not like the failure of these new tests indicates any kind of regression.
0.0
c14b212964cfc1543c41f0bd186cafb399e847f7
[ "src/emcee/tests/integration/test_longdouble.py::test_longdouble_actually_needed[Backend]", "src/emcee/tests/unit/test_backends.py::test_longdouble_preserved[Backend]" ]
[]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2020-08-18 14:48:36+00:00
mit
1,899
dfm__emcee-386
diff --git a/src/emcee/ensemble.py b/src/emcee/ensemble.py index 45cc4ba..24faba3 100644 --- a/src/emcee/ensemble.py +++ b/src/emcee/ensemble.py @@ -1,9 +1,10 @@ # -*- coding: utf-8 -*- import warnings +from itertools import count +from typing import Dict, List, Optional, Union import numpy as np -from itertools import count from .backends import Backend from .model import Model @@ -61,6 +62,10 @@ class EnsembleSampler(object): to accept a list of position vectors instead of just one. Note that ``pool`` will be ignored if this is ``True``. (default: ``False``) + parameter_names (Optional[Union[List[str], Dict[str, List[int]]]]): + names of individual parameters or groups of parameters. If + specified, the ``log_prob_fn`` will recieve a dictionary of + parameters, rather than a ``np.ndarray``. """ @@ -76,6 +81,7 @@ class EnsembleSampler(object): backend=None, vectorize=False, blobs_dtype=None, + parameter_names: Optional[Union[Dict[str, int], List[str]]] = None, # Deprecated... a=None, postargs=None, @@ -157,6 +163,49 @@ class EnsembleSampler(object): # ``args`` and ``kwargs`` pickleable. self.log_prob_fn = _FunctionWrapper(log_prob_fn, args, kwargs) + # Save the parameter names + self.params_are_named: bool = parameter_names is not None + if self.params_are_named: + assert isinstance(parameter_names, (list, dict)) + + # Don't support vectorizing yet + msg = "named parameters with vectorization unsupported for now" + assert not self.vectorize, msg + + # Check for duplicate names + dupes = set() + uniq = [] + for name in parameter_names: + if name not in dupes: + uniq.append(name) + dupes.add(name) + msg = f"duplicate paramters: {dupes}" + assert len(uniq) == len(parameter_names), msg + + if isinstance(parameter_names, list): + # Check for all named + msg = "name all parameters or set `parameter_names` to `None`" + assert len(parameter_names) == ndim, msg + # Convert a list to a dict + parameter_names: Dict[str, int] = { + name: i for i, name in enumerate(parameter_names) + } + + # Check not too many names + msg = "too many names" + assert len(parameter_names) <= ndim, msg + + # Check all indices appear + values = [ + v if isinstance(v, list) else [v] + for v in parameter_names.values() + ] + values = [item for sublist in values for item in sublist] + values = set(values) + msg = f"not all values appear -- set should be 0 to {ndim-1}" + assert values == set(np.arange(ndim)), msg + self.parameter_names = parameter_names + @property def random_state(self): """ @@ -251,8 +300,9 @@ class EnsembleSampler(object): raise ValueError("'store' must be False when 'iterations' is None") # Interpret the input as a walker state and check the dimensions. state = State(initial_state, copy=True) - if np.shape(state.coords) != (self.nwalkers, self.ndim): - raise ValueError("incompatible input dimensions") + state_shape = np.shape(state.coords) + if state_shape != (self.nwalkers, self.ndim): + raise ValueError(f"incompatible input dimensions {state_shape}") if (not skip_initial_state_check) and ( not walkers_independent(state.coords) ): @@ -416,6 +466,10 @@ class EnsembleSampler(object): if np.any(np.isnan(p)): raise ValueError("At least one parameter value was NaN") + # If the parmaeters are named, then switch to dictionaries + if self.params_are_named: + p = ndarray_to_list_of_dicts(p, self.parameter_names) + # Run the log-probability calculations (optionally in parallel). if self.vectorize: results = self.log_prob_fn(p) @@ -427,9 +481,7 @@ class EnsembleSampler(object): map_func = self.pool.map else: map_func = map - results = list( - map_func(self.log_prob_fn, (p[i] for i in range(len(p)))) - ) + results = list(map_func(self.log_prob_fn, p)) try: log_prob = np.array([float(l[0]) for l in results]) @@ -444,8 +496,9 @@ class EnsembleSampler(object): else: try: with warnings.catch_warnings(record=True): - warnings.simplefilter("error", - np.VisibleDeprecationWarning) + warnings.simplefilter( + "error", np.VisibleDeprecationWarning + ) try: dt = np.atleast_1d(blob[0]).dtype except Warning: @@ -455,7 +508,8 @@ class EnsembleSampler(object): "placed in an object array. Numpy has " "deprecated this automatic detection, so " "please specify " - "blobs_dtype=np.dtype('object')") + "blobs_dtype=np.dtype('object')" + ) dt = np.dtype("object") except ValueError: dt = np.dtype("object") @@ -557,8 +611,8 @@ class _FunctionWrapper(object): def __init__(self, f, args, kwargs): self.f = f - self.args = [] if args is None else args - self.kwargs = {} if kwargs is None else kwargs + self.args = args or [] + self.kwargs = kwargs or {} def __call__(self, x): try: @@ -605,3 +659,22 @@ def _scaled_cond(a): return np.inf c = b / bsum return np.linalg.cond(c.astype(float)) + + +def ndarray_to_list_of_dicts( + x: np.ndarray, + key_map: Dict[str, Union[int, List[int]]], +) -> List[Dict[str, Union[np.number, np.ndarray]]]: + """ + A helper function to convert a ``np.ndarray`` into a list + of dictionaries of parameters. Used when parameters are named. + + Args: + x (np.ndarray): parameter array of shape ``(N, n_dim)``, where + ``N`` is an integer + key_map (Dict[str, Union[int, List[int]]): + + Returns: + list of dictionaries of parameters + """ + return [{key: xi[val] for key, val in key_map.items()} for xi in x]
dfm/emcee
f0489d74250e2034d76c3a812b9afae74c9ca191
diff --git a/src/emcee/tests/unit/test_ensemble.py b/src/emcee/tests/unit/test_ensemble.py new file mode 100644 index 0000000..f6f5ad2 --- /dev/null +++ b/src/emcee/tests/unit/test_ensemble.py @@ -0,0 +1,184 @@ +""" +Unit tests of some functionality in ensemble.py when the parameters are named +""" +import string +from unittest import TestCase + +import numpy as np +import pytest + +from emcee.ensemble import EnsembleSampler, ndarray_to_list_of_dicts + + +class TestNP2ListOfDicts(TestCase): + def test_ndarray_to_list_of_dicts(self): + # Try different numbers of keys + for n_keys in [1, 2, 10, 26]: + keys = list(string.ascii_lowercase[:n_keys]) + key_set = set(keys) + key_dict = {key: i for i, key in enumerate(keys)} + # Try different number of walker/procs + for N in [1, 2, 3, 10, 100]: + x = np.random.rand(N, n_keys) + + LOD = ndarray_to_list_of_dicts(x, key_dict) + assert len(LOD) == N, "need 1 dict per row" + for i, dct in enumerate(LOD): + assert dct.keys() == key_set, "keys are missing" + for j, key in enumerate(keys): + assert dct[key] == x[i, j], f"wrong value at {(i, j)}" + + +class TestNamedParameters(TestCase): + """ + Test that a keyword-based log-probability function instead of + a positional. + """ + + # Keyword based lnpdf + def lnpdf(self, pars) -> np.float64: + mean = pars["mean"] + var = pars["var"] + if var <= 0: + return -np.inf + return ( + -0.5 * ((mean - self.x) ** 2 / var + np.log(2 * np.pi * var)).sum() + ) + + def lnpdf_mixture(self, pars) -> np.float64: + mean1 = pars["mean1"] + var1 = pars["var1"] + mean2 = pars["mean2"] + var2 = pars["var2"] + if var1 <= 0 or var2 <= 0: + return -np.inf + return ( + -0.5 + * ( + (mean1 - self.x) ** 2 / var1 + + np.log(2 * np.pi * var1) + + (mean2 - self.x - 3) ** 2 / var2 + + np.log(2 * np.pi * var2) + ).sum() + ) + + def lnpdf_mixture_grouped(self, pars) -> np.float64: + mean1, mean2 = pars["means"] + var1, var2 = pars["vars"] + const = pars["constant"] + if var1 <= 0 or var2 <= 0: + return -np.inf + return ( + -0.5 + * ( + (mean1 - self.x) ** 2 / var1 + + np.log(2 * np.pi * var1) + + (mean2 - self.x - 3) ** 2 / var2 + + np.log(2 * np.pi * var2) + ).sum() + + const + ) + + def setUp(self): + # Draw some data from a unit Gaussian + self.x = np.random.randn(100) + self.names = ["mean", "var"] + + def test_named_parameters(self): + sampler = EnsembleSampler( + nwalkers=10, + ndim=len(self.names), + log_prob_fn=self.lnpdf, + parameter_names=self.names, + ) + assert sampler.params_are_named + assert list(sampler.parameter_names.keys()) == self.names + + def test_asserts(self): + # ndim name mismatch + with pytest.raises(AssertionError): + _ = EnsembleSampler( + nwalkers=10, + ndim=len(self.names) - 1, + log_prob_fn=self.lnpdf, + parameter_names=self.names, + ) + + # duplicate names + with pytest.raises(AssertionError): + _ = EnsembleSampler( + nwalkers=10, + ndim=3, + log_prob_fn=self.lnpdf, + parameter_names=["a", "b", "a"], + ) + + # vectorize turned on + with pytest.raises(AssertionError): + _ = EnsembleSampler( + nwalkers=10, + ndim=len(self.names), + log_prob_fn=self.lnpdf, + parameter_names=self.names, + vectorize=True, + ) + + def test_compute_log_prob(self): + # Try different numbers of walkers + for N in [4, 8, 10]: + sampler = EnsembleSampler( + nwalkers=N, + ndim=len(self.names), + log_prob_fn=self.lnpdf, + parameter_names=self.names, + ) + coords = np.random.rand(N, len(self.names)) + lnps, _ = sampler.compute_log_prob(coords) + assert len(lnps) == N + assert lnps.dtype == np.float64 + + def test_compute_log_prob_mixture(self): + names = ["mean1", "var1", "mean2", "var2"] + # Try different numbers of walkers + for N in [8, 10, 20]: + sampler = EnsembleSampler( + nwalkers=N, + ndim=len(names), + log_prob_fn=self.lnpdf_mixture, + parameter_names=names, + ) + coords = np.random.rand(N, len(names)) + lnps, _ = sampler.compute_log_prob(coords) + assert len(lnps) == N + assert lnps.dtype == np.float64 + + def test_compute_log_prob_mixture_grouped(self): + names = {"means": [0, 1], "vars": [2, 3], "constant": 4} + # Try different numbers of walkers + for N in [8, 10, 20]: + sampler = EnsembleSampler( + nwalkers=N, + ndim=5, + log_prob_fn=self.lnpdf_mixture_grouped, + parameter_names=names, + ) + coords = np.random.rand(N, 5) + lnps, _ = sampler.compute_log_prob(coords) + assert len(lnps) == N + assert lnps.dtype == np.float64 + + def test_run_mcmc(self): + # Sort of an integration test + n_walkers = 4 + sampler = EnsembleSampler( + nwalkers=n_walkers, + ndim=len(self.names), + log_prob_fn=self.lnpdf, + parameter_names=self.names, + ) + guess = np.random.rand(n_walkers, len(self.names)) + n_steps = 50 + results = sampler.run_mcmc(guess, n_steps) + assert results.coords.shape == (n_walkers, len(self.names)) + chain = sampler.chain + assert chain.shape == (n_walkers, n_steps, len(self.names))
[ENH] support for dictionaries and/or namedtuples ## Proposal The sampler API shares a lot of features with `scipy.optimize.minimize` -- given a model that can be typed as `Callable(List,...)` keep proposing samples to improve the model. This is fine for many problems, but one can imagine a scenario where it would be useful for model developers to handle samples with more than just a `List`. Handling parameters in a `List` means that writing a posterior *requires defining parameters positionally*. In contrast, in packages like pytorch one can refer to model parameters by name (eg. a `torch.nn.Linear` has a `weight` and `bias` named parameters). This issue proposes enhancing the emcee API to allow for dictionary and/or namedtuple parameter constructs. Looking at the API for the `EnsembleSampler`, this would require an additional constructor argument, since the sampler does not inspect the state of the `log_prob_fn`. Here is a minimum proposed implementation for supporting a dictionary: ```python class EnsembleSampler(object): def __init__( self, nwalkers: int, ndim: int, log_prob_fn: Callable(Union[List, Dict]), parameter_names: Optional[List[str]] = None, ... ): ... # Save the names self.parameter_names = parameter_names self.name_parameters: bool = parameter_names is not None if self.name_parameters: assert len(parameter_names) == ndim, f"names must match dimensions" ... def sample(...): ... with get_progress_bar(progress, total) as pbar: i = 0 for _ in count() if iterations is None else range(iterations): for _ in range(yield_step): ... # If our parameters are named, return them in a named format if self.name_parameters: state = {key: value for key, value in zip(self.parameter_names, state)} yield state ``` This allows for a lot more flexibility downstream for model developers. As a simple example, consider a model composed of two parts, that each can be updated in a way that doesn't affect the higher level model: ```python class PartA: __slots__ = ["param_a"] param_a: float def __call__(self): ... class PartB: __slots__ = ["param_b"] param_b: float def __call__(self): ... class MyModel: def __init__(self, a = PartA(), b = PartB()): self.a = a self.b = b def log_likelihood_fn(self, params: Dict[str, float]): # Update the composed parts of the model for key in self.a.__slots__: setattr(self.a, params[key]) for key in self.b.__slots__: setattr(self.b, params[key]) # Final likelihood uses the results of A and B, but we don't # care how they are implemented return f(self.a(), self.b()) ``` If this sounds like an attractive feature I would be happy to work on a PR.
0.0
f0489d74250e2034d76c3a812b9afae74c9ca191
[ "src/emcee/tests/unit/test_ensemble.py::TestNP2ListOfDicts::test_ndarray_to_list_of_dicts", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_asserts", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_compute_log_prob", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_compute_log_prob_mixture", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_compute_log_prob_mixture_grouped", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_named_parameters", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_run_mcmc" ]
[]
{ "failed_lite_validators": [ "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }
2021-04-24 22:21:11+00:00
mit
1,900
dfm__emcee-510
diff --git a/src/emcee/ensemble.py b/src/emcee/ensemble.py index 3212099..cfef4a5 100644 --- a/src/emcee/ensemble.py +++ b/src/emcee/ensemble.py @@ -489,10 +489,19 @@ class EnsembleSampler(object): results = list(map_func(self.log_prob_fn, p)) try: - log_prob = np.array([float(l[0]) for l in results]) - blob = [l[1:] for l in results] + # perhaps log_prob_fn returns blobs? + + # deal with the blobs first + # if l does not have a len attribute (i.e. not a sequence, no blob) + # then a TypeError is raised. However, no error will be raised if + # l is a length-1 array, np.array([1.234]). In that case blob + # will become an empty list. + blob = [l[1:] for l in results if len(l) > 1] + if not len(blob): + raise IndexError + log_prob = np.array([_scalar(l[0]) for l in results]) except (IndexError, TypeError): - log_prob = np.array([float(l) for l in results]) + log_prob = np.array([_scalar(l) for l in results]) blob = None else: # Get the blobs dtype @@ -502,7 +511,7 @@ class EnsembleSampler(object): try: with warnings.catch_warnings(record=True): warnings.simplefilter( - "error", np.VisibleDeprecationWarning + "error", np.exceptions.VisibleDeprecationWarning ) try: dt = np.atleast_1d(blob[0]).dtype @@ -682,3 +691,16 @@ def ndarray_to_list_of_dicts( list of dictionaries of parameters """ return [{key: xi[val] for key, val in key_map.items()} for xi in x] + + +def _scalar(fx): + # Make sure a value is a true scalar + # 1.0, np.float64(1.0), np.array([1.0]), np.array(1.0) + if not np.isscalar(fx): + try: + fx = np.asarray(fx).item() + except (TypeError, ValueError) as e: + raise ValueError("log_prob_fn should return scalar") from e + return float(fx) + else: + return float(fx) diff --git a/tox.ini b/tox.ini index d759fa6..c566174 100644 --- a/tox.ini +++ b/tox.ini @@ -1,12 +1,12 @@ [tox] -envlist = py{37,38,39,310}{,-extras},lint +envlist = py{39,310,311,312}{,-extras},lint [gh-actions] python = - 3.7: py37 - 3.8: py38 - 3.9: py39-extras + 3.9: py39 3.10: py310 + 3.11: py311-extras + 3.12: py312 [testenv] deps = coverage[toml]
dfm/emcee
b68933df3df80634cf133cab7e92db0458fffe13
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 3a3dc22..063f0c0 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -16,7 +16,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - python-version: ["3.7", "3.8", "3.9", "3.10"] + python-version: ["3.9", "3.10", "3.11", "3.12"] os: ["ubuntu-latest"] include: - python-version: "3.9" @@ -49,6 +49,30 @@ jobs: COVERALLS_PARALLEL: true COVERALLS_FLAG_NAME: ${{ matrix.python-version }}-${{ matrix.os }} + leading_edge: + runs-on: ${{ matrix.os }} + strategy: + matrix: + python-version: ["3.12"] + os: ["ubuntu-latest"] + + steps: + - name: Checkout + uses: actions/checkout@v4 + with: + fetch-depth: 0 + - name: Setup Python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install -U pip + python -m pip install pip install pytest "numpy>=2.0.0rc1" + python -m pip install -e. + - name: Run tests + run: pytest + coverage: needs: tests runs-on: ubuntu-latest diff --git a/src/emcee/tests/unit/test_ensemble.py b/src/emcee/tests/unit/test_ensemble.py index f0568b2..e7981c8 100644 --- a/src/emcee/tests/unit/test_ensemble.py +++ b/src/emcee/tests/unit/test_ensemble.py @@ -183,3 +183,37 @@ class TestNamedParameters(TestCase): assert results.coords.shape == (n_walkers, len(self.names)) chain = sampler.chain assert chain.shape == (n_walkers, n_steps, len(self.names)) + + +class TestLnProbFn(TestCase): + # checks that the log_prob_fn can deal with a variety of 'scalar-likes' + def lnpdf(self, x): + v = np.log(np.sqrt(np.pi) * np.exp(-((x / 2.0) ** 2))) + v = float(v[0]) + assert np.isscalar(v) + return v + + def lnpdf_arr1(self, x): + v = self.lnpdf(x) + return np.array([v]) + + def lnpdf_float64(self, x): + v = self.lnpdf(x) + return np.float64(v) + + def lnpdf_arr0D(self, x): + v = self.lnpdf(x) + return np.array(v) + + def test_deal_with_scalar_likes(self): + rng = np.random.default_rng() + fns = [ + self.lnpdf, + self.lnpdf_arr1, + self.lnpdf_float64, + self.lnpdf_arr0D, + ] + for fn in fns: + init = rng.random((50, 1)) + sampler = EnsembleSampler(50, 1, fn) + _ = sampler.run_mcmc(initial_state=init, nsteps=20)
Incompatible with numpy 2.0.0rc1 Numpy 2 is around the corner with having its first release candidate: https://pypi.org/project/numpy/2.0.0rc1 `emcee` at least uses `VisibleDeprecationWarning` from numpy that will be removed with numpy 2: https://numpy.org/devdocs/release/2.0.0-notes.html > Warnings and exceptions present in [numpy.exceptions](https://numpy.org/devdocs/reference/routines.exceptions.html#module-numpy.exceptions) (e.g, [ComplexWarning](https://numpy.org/devdocs/reference/generated/numpy.exceptions.ComplexWarning.html#numpy.exceptions.ComplexWarning), [VisibleDeprecationWarning](https://numpy.org/devdocs/reference/generated/numpy.exceptions.VisibleDeprecationWarning.html#numpy.exceptions.VisibleDeprecationWarning)) are no longer exposed in the main namespace. So with the release of numpy 2, emcee will run into some troubles.
0.0
b68933df3df80634cf133cab7e92db0458fffe13
[ "src/emcee/tests/unit/test_ensemble.py::TestLnProbFn::test_deal_with_scalar_likes" ]
[ "src/emcee/tests/unit/test_ensemble.py::TestNP2ListOfDicts::test_ndarray_to_list_of_dicts", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_asserts", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_compute_log_prob", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_compute_log_prob_mixture", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_compute_log_prob_mixture_grouped", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_named_parameters", "src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_run_mcmc" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2024-04-04 22:01:34+00:00
mit
1,901
dfm__tess-atlas-108
diff --git a/setup.py b/setup.py index 0a7c68b..dabe2f7 100644 --- a/setup.py +++ b/setup.py @@ -31,15 +31,17 @@ INSTALL_REQUIRES = [ "lightkurve>=2.0.11", "plotly>=4.9.0", "arviz>=0.10.0", - "corner", + "corner>=2.2.1", "pandas", "jupyter", "ipykernel", - "jupytext", + "jupytext<1.11,>=1.8", # pinned for jypyter-book "kaleido", "aesara-theano-fallback", "theano-pymc>=1.1.2", "jupyter-book", + "seaborn", + "jupyter_client==6.1.12", # pinned beacuse of nbconvert bug https://github.com/jupyter/nbconvert/pull/1549#issuecomment-818734169 ] EXTRA_REQUIRE = {"test": ["pytest>=3.6", "testbook>=0.2.3"]} EXTRA_REQUIRE["dev"] = EXTRA_REQUIRE["test"] + [ @@ -101,6 +103,7 @@ if __name__ == "__main__": "run_tois=tess_atlas.notebook_preprocessors.run_tois:main", "runs_stats_plotter=tess_atlas.analysis.stats_plotter:main", "make_webpages=tess_atlas.webbuilder.build_pages:main", + "make_slurm_job=tess_atlas.batch_job_generator.slurm_job_generator:main", ] }, ) diff --git a/src/tess_atlas/batch_job_generator/__init__.py b/src/tess_atlas/batch_job_generator/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/tess_atlas/batch_job_generator/slurm_job_generator.py b/src/tess_atlas/batch_job_generator/slurm_job_generator.py new file mode 100644 index 0000000..a1ed5a4 --- /dev/null +++ b/src/tess_atlas/batch_job_generator/slurm_job_generator.py @@ -0,0 +1,67 @@ +import argparse +import os +import shutil +from typing import List + +import pandas as pd + +TEMPLATE_FILE = os.path.join(os.path.dirname(__file__), "slurm_template.sh") + + +def make_slurm_file(outdir: str, toi_numbers: List[int], module_loads: str): + with open(TEMPLATE_FILE, "r") as f: + file_contents = f.read() + outdir = os.path.abspath(outdir) + logfile_name = os.path.join(outdir, "toi_slurm_jobs.log") + jobfile_name = os.path.join(outdir, "slurm_job.sh") + path_to_python = shutil.which("python") + path_to_env_activate = path_to_python.replace("python", "activate") + file_contents = file_contents.replace( + "{{{TOTAL NUM}}}", str(len(toi_numbers) - 1) + ) + file_contents = file_contents.replace("{{{MODULE LOADS}}}", module_loads) + file_contents = file_contents.replace("{{{OUTDIR}}}", outdir) + file_contents = file_contents.replace( + "{{{LOAD ENV}}}", f"source {path_to_env_activate}" + ) + file_contents = file_contents.replace("{{{LOG FILE}}}", logfile_name) + toi_str = " ".join([str(toi) for toi in toi_numbers]) + file_contents = file_contents.replace("{{{TOI NUMBERS}}}", toi_str) + with open(jobfile_name, "w") as f: + f.write(file_contents) + print(f"Jobfile created, to run job: \nsbatch {jobfile_name}") + + +def get_toi_numbers(toi_csv: str): + df = pd.read_csv(toi_csv) + return list(df.toi_numbers.values) + + +def get_cli_args(): + parser = argparse.ArgumentParser( + description="Create slurm job for analysing TOIs" + ) + parser.add_argument( + "--toi_csv", + help="CSV with the toi numbers to analyse (csv needs a column with `toi_numbers`)", + ) + parser.add_argument( + "--outdir", help="outdir for jobs", default="notebooks" + ) + parser.add_argument( + "--module_loads", + help="String containing all module loads in one line (each module separated by a space)", + ) + args = parser.parse_args() + return args.toi_csv, args.outdir, args.module_loads + + +def main(): + toi_csv, outdir, module_loads = get_cli_args() + os.makedirs(outdir, exist_ok=True) + toi_numbers = get_toi_numbers(toi_csv) + make_slurm_file(outdir, toi_numbers, module_loads) + + +if __name__ == "__main__": + main() diff --git a/src/tess_atlas/batch_job_generator/slurm_template.sh b/src/tess_atlas/batch_job_generator/slurm_template.sh new file mode 100644 index 0000000..250c930 --- /dev/null +++ b/src/tess_atlas/batch_job_generator/slurm_template.sh @@ -0,0 +1,18 @@ +#!/bin/bash +# +#SBATCH --job-name=run_tois +#SBATCH --output={{{LOG FILE}}} +# +#SBATCH --ntasks=1 +#SBATCH --time=300:00 +#SBATCH --mem-per-cpu=500MB +# +#SBATCH --array=0-{{{TOTAL NUM}}} + +module load {{{MODULE LOADS}}} +{{{LOAD ENV}}} + + +TOI_NUMBERS=({{{TOI NUMBERS}}}) + +srun run_toi ${TOI_NUMBERS[$SLURM_ARRAY_TASK_ID]} --outdir {{{OUTDIR}}} diff --git a/src/tess_atlas/notebook_preprocessors/run_toi.py b/src/tess_atlas/notebook_preprocessors/run_toi.py index 1f17ba7..a76c4f5 100644 --- a/src/tess_atlas/notebook_preprocessors/run_toi.py +++ b/src/tess_atlas/notebook_preprocessors/run_toi.py @@ -87,7 +87,7 @@ def execute_toi_notebook(notebook_filename): def get_cli_args(): """Get the TOI number from the CLI and return it""" - parser = argparse.ArgumentParser(prog="run_toi_in_pool") + parser = argparse.ArgumentParser(prog="run_toi") default_outdir = os.path.join(os.getcwd(), "notebooks") parser.add_argument( "toi_number", type=int, help="The TOI number to be analysed (e.g. 103)"
dfm/tess-atlas
6274de545082661de3677fb609fa7274f26afb47
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d45d0c3..ca420da 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -26,7 +26,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install --use-feature=2020-resolver -U -e ".[dev]" + pip install -U -e ".[dev]" # Test the py:light -> ipynb -> py:light round trip conversion - name: roundtrip conversion test diff --git a/tests/test_slurm_job_generator.py b/tests/test_slurm_job_generator.py new file mode 100644 index 0000000..59a582a --- /dev/null +++ b/tests/test_slurm_job_generator.py @@ -0,0 +1,24 @@ +import os +import unittest + +from tess_atlas.batch_job_generator.slurm_job_generator import make_slurm_file + + +class JobgenTest(unittest.TestCase): + def setUp(self): + self.start_dir = os.getcwd() + self.outdir = f"test_jobgen" + os.makedirs(self.outdir, exist_ok=True) + + def tearDown(self): + import shutil + + if os.path.exists(self.outdir): + shutil.rmtree(self.outdir) + + def test_slurmfile(self): + make_slurm_file(self.outdir, [100, 101, 102], "module load 1") + + +if __name__ == "__main__": + unittest.main()
Cluster jobs failing to pre-process notebooks: TypeError: 'coroutine' object is not subscriptable
0.0
6274de545082661de3677fb609fa7274f26afb47
[ "tests/test_slurm_job_generator.py::JobgenTest::test_slurmfile" ]
[]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2021-10-06 02:54:35+00:00
mit
1,902
dgasmith__opt_einsum-11
diff --git a/README.md b/README.md index a792df7..9e4ed20 100644 --- a/README.md +++ b/README.md @@ -131,6 +131,35 @@ True By contracting terms in the correct order we can see that this expression can be computed with N^4 scaling. Even with the overhead of finding the best order or 'path' and small dimensions, opt_einsum is roughly 900 times faster than pure einsum for this expression. + +## Reusing paths using ``contract_expression`` + +If you expect to repeatedly use a particular contraction it can make things simpler and more efficient to not compute the path each time. Instead, supplying ``contract_expression`` with the contraction string and the shapes of the tensors generates a ``ContractExpression`` which can then be repeatedly called with any matching set of arrays. For example: + +```python +>>> my_expr = oe.contract_expression("abc,cd,dbe->ea", (2, 3, 4), (4, 5), (5, 3, 6)) +>>> print(my_expr) +<ContractExpression> for 'abc,cd,dbe->ea': + 1. 'dbe,cd->bce' [GEMM] + 2. 'bce,abc->ea' [GEMM] +``` + +Now we can call this expression with 3 arrays that match the original shapes without having to compute the path again: + +```python +>>> x, y, z = (np.random.rand(*s) for s in [(2, 3, 4), (4, 5), (5, 3, 6)]) +>>> my_expr(x, y, z) +array([[ 3.08331541, 4.13708916], + [ 2.92793729, 4.57945185], + [ 3.55679457, 5.56304115], + [ 2.6208398 , 4.39024187], + [ 3.66736543, 5.41450334], + [ 3.67772272, 5.46727192]]) +``` + +Note that few checks are performed when calling the expression, and while it will work for a set of arrays with the same ranks as the original shapes but differing sizes, it might no longer be optimal. + + ## More details on paths Finding the optimal order of contraction is not an easy problem and formally scales factorially with respect to the number of terms in the expression. First, lets discuss what a path looks like in opt_einsum: diff --git a/opt_einsum/__init__.py b/opt_einsum/__init__.py index 2b3430f..16c844a 100644 --- a/opt_einsum/__init__.py +++ b/opt_einsum/__init__.py @@ -1,4 +1,4 @@ -from .contract import contract, contract_path +from .contract import contract, contract_path, contract_expression from . import paths from . import blas from . import helpers diff --git a/opt_einsum/contract.py b/opt_einsum/contract.py index 43b78e9..4efb1a9 100644 --- a/opt_einsum/contract.py +++ b/opt_einsum/contract.py @@ -259,7 +259,7 @@ def contract_path(*operands, **kwargs): def contract(*operands, **kwargs): """ contract(subscripts, *operands, out=None, dtype=None, order='K', - casting='safe', use_blas=False, optimize=True, memory_limit=None) + casting='safe', use_blas=True, optimize=True, memory_limit=None) Evaluates the Einstein summation convention on the operands. A drop in replacment for NumPy's einsum function that optimizes the order of contraction @@ -323,14 +323,10 @@ def contract(*operands, **kwargs): See opt_einsum.contract_path or numpy.einsum """ - - # Grab non-einsum kwargs optimize_arg = kwargs.pop('optimize', True) if optimize_arg is True: optimize_arg = 'greedy' - use_blas = kwargs.pop('use_blas', True) - valid_einsum_kwargs = ['out', 'dtype', 'order', 'casting'] einsum_kwargs = {k: v for (k, v) in kwargs.items() if k in valid_einsum_kwargs} @@ -338,25 +334,38 @@ def contract(*operands, **kwargs): if optimize_arg is False: return np.einsum(*operands, **einsum_kwargs) - # Make sure all keywords are valid - valid_contract_kwargs = ['memory_limit', 'use_blas'] + valid_einsum_kwargs - unknown_kwargs = [k for (k, v) in kwargs.items() if k not in valid_contract_kwargs] + # Grab non-einsum kwargs + use_blas = kwargs.pop('use_blas', True) + memory_limit = kwargs.pop('memory_limit', None) + gen_expression = kwargs.pop('gen_expression', False) + + # Make sure remaining keywords are valid for einsum + unknown_kwargs = [k for (k, v) in kwargs.items() if k not in valid_einsum_kwargs] if len(unknown_kwargs): raise TypeError("Did not understand the following kwargs: %s" % unknown_kwargs) - # Special handeling if out is specified - specified_out = False - out_array = einsum_kwargs.pop('out', None) - if out_array is not None: - specified_out = True + if gen_expression: + full_str = operands[0] # Build the contraction list and operand - memory_limit = kwargs.pop('memory_limit', None) - operands, contraction_list = contract_path( *operands, path=optimize_arg, memory_limit=memory_limit, einsum_call=True, use_blas=use_blas) - handle_out = False + # check if performing contraction or just building expression + if gen_expression: + return ContractExpression(full_str, contraction_list, **einsum_kwargs) + + return _core_contract(operands, contraction_list, **einsum_kwargs) + + +def _core_contract(operands, contraction_list, **einsum_kwargs): + """Inner loop used to perform an actual contraction given the output + from a ``contract_path(..., einsum_call=True)`` call. + """ + + # Special handeling if out is specified + out_array = einsum_kwargs.pop('out', None) + specified_out = out_array is not None # Start contraction loop for num, contraction in enumerate(contraction_list): @@ -366,8 +375,7 @@ def contract(*operands, **kwargs): tmp_operands.append(operands.pop(x)) # Do we need to deal with the output? - if specified_out and ((num + 1) == len(contraction_list)): - handle_out = True + handle_out = specified_out and ((num + 1) == len(contraction_list)) # Call tensordot if blas: @@ -412,3 +420,104 @@ def contract(*operands, **kwargs): return out_array else: return operands[0] + + +class ContractExpression: + """Helper class for storing an explicit ``contraction_list`` which can + then be repeatedly called solely with the array arguments. + """ + + def __init__(self, contraction, contraction_list, **einsum_kwargs): + self.contraction = contraction + self.contraction_list = contraction_list + self.einsum_kwargs = einsum_kwargs + self.num_args = len(contraction.split('->')[0].split(',')) + + def __call__(self, *arrays, **kwargs): + if len(arrays) != self.num_args: + raise ValueError("This `ContractExpression` takes exactly %s array arguments " + "but received %s." % (self.num_args, len(arrays))) + + out = kwargs.pop('out', None) + if kwargs: + raise ValueError("The only valid keyword argument to a `ContractExpression` " + "call is `out=`. Got: %s." % kwargs) + + try: + return _core_contract(list(arrays), self.contraction_list, out=out, **self.einsum_kwargs) + except ValueError as err: + original_msg = "".join(err.args) if err.args else "" + msg = ("Internal error while evaluating `ContractExpression`. Note that few checks are performed" + " - the number and rank of the array arguments must match the original expression. " + "The internal error was: '%s'" % original_msg, ) + err.args = msg + raise + + def __repr__(self): + return "ContractExpression('%s')" % self.contraction + + def __str__(self): + s = "<ContractExpression> for '%s':" % self.contraction + for i, c in enumerate(self.contraction_list): + s += "\n %i. " % (i + 1) + s += "'%s'" % c[2] + (" [%s]" % c[-1] if c[-1] else "") + if self.einsum_kwargs: + s += "\neinsum_kwargs=%s" % self.einsum_kwargs + return s + + +class _ShapeOnly(np.ndarray): + """Dummy ``numpy.ndarray`` which has a shape only - for generating + contract expressions. + """ + + def __init__(self, shape): + self.shape = shape + + +def contract_expression(subscripts, *shapes, **kwargs): + """Generate an reusable expression for a given contraction with + specific shapes, which can for example be cached. + + Parameters + ---------- + subscripts : str + Specifies the subscripts for summation. + shapes : sequence of integer tuples + Shapes of the arrays to optimize the contraction for. + kwargs : + Passed on to ``contract_path`` or ``einsum``. See ``contract``. + + Returns + ------- + expr : ContractExpression + Callable with signature ``expr(*arrays)`` where the array's shapes + should match ``shapes``. + + Notes + ----- + - The `out` keyword argument should be supplied to the generated expression + rather than this function. + - The generated expression will work with any arrays which have + the same rank (number of dimensions) as the original shapes, however, if + the actual sizes are different, the expression may no longer be optimal. + + Examples + -------- + + >>> expr = contract_expression("ab,bc->ac", (3, 4), (4, 5)) + >>> a, b = np.random.rand(3, 4), np.random.rand(4, 5) + >>> c = expr(a, b) + >>> np.allclose(c, a @ b) + True + + """ + if not kwargs.get('optimize', True): + raise ValueError("Can only generate expressions for optimized contractions.") + + if kwargs.get('out', None) is not None: + raise ValueError("`out` should only be specified when calling a `ContractExpression`, not when building it.") + + dummy_arrays = [_ShapeOnly(s) for s in shapes] + + return contract(subscripts, *dummy_arrays, gen_expression=True, **kwargs)
dgasmith/opt_einsum
fd612f0966a555f8a9783669ad3842f2dbfd1462
diff --git a/tests/test_contract.py b/tests/test_contract.py index 016d784..6885522 100644 --- a/tests/test_contract.py +++ b/tests/test_contract.py @@ -5,7 +5,7 @@ Tets a series of opt_einsum contraction paths to ensure the results are the same from __future__ import division, absolute_import, print_function import numpy as np -from opt_einsum import contract, contract_path, helpers +from opt_einsum import contract, contract_path, helpers, contract_expression import pytest tests = [ @@ -127,3 +127,73 @@ def test_printing(): ein = contract_path(string, *views) assert len(ein[1]) == 729 + + [email protected]("string", tests) [email protected]("optimize", ['greedy', 'optimal']) [email protected]("use_blas", [False, True]) [email protected]("out_spec", [False, True]) +def test_contract_expressions(string, optimize, use_blas, out_spec): + views = helpers.build_views(string) + shapes = [view.shape for view in views] + expected = contract(string, *views, optimize=False, use_blas=False) + + expr = contract_expression( + string, *shapes, optimize=optimize, use_blas=use_blas) + + if out_spec and ("->" in string) and (string[-2:] != "->"): + out, = helpers.build_views(string.split('->')[1]) + expr(*views, out=out) + else: + out = expr(*views) + + assert np.allclose(out, expected) + + # check representations + assert string in expr.__repr__() + assert string in expr.__str__() + + +def test_contract_expression_checks(): + # check optimize needed + with pytest.raises(ValueError): + contract_expression("ab,bc->ac", (2, 3), (3, 4), optimize=False) + + # check sizes are still checked + with pytest.raises(ValueError): + contract_expression("ab,bc->ac", (2, 3), (3, 4), (42, 42)) + + # check if out given + out = np.empty((2, 4)) + with pytest.raises(ValueError): + contract_expression("ab,bc->ac", (2, 3), (3, 4), out=out) + + # check still get errors when wrong ranks supplied to expression + expr = contract_expression("ab,bc->ac", (2, 3), (3, 4)) + + # too few arguments + with pytest.raises(ValueError) as err: + expr(np.random.rand(2, 3)) + assert "`ContractExpression` takes exactly 2" in str(err) + + # too many arguments + with pytest.raises(ValueError) as err: + expr(np.random.rand(2, 3), np.random.rand(2, 3), np.random.rand(2, 3)) + assert "`ContractExpression` takes exactly 2" in str(err) + + # wrong shapes + with pytest.raises(ValueError) as err: + expr(np.random.rand(2, 3, 4), np.random.rand(3, 4)) + assert "Internal error while evaluating `ContractExpression`" in str(err) + with pytest.raises(ValueError) as err: + expr(np.random.rand(2, 4), np.random.rand(3, 4, 5)) + assert "Internal error while evaluating `ContractExpression`" in str(err) + with pytest.raises(ValueError) as err: + expr(np.random.rand(2, 3), np.random.rand(3, 4), + out=np.random.rand(2, 4, 6)) + assert "Internal error while evaluating `ContractExpression`" in str(err) + + # should only be able to specify out + with pytest.raises(ValueError) as err: + expr(np.random.rand(2, 3), np.random.rand(3, 4), order='F') + assert "only valid keyword argument to a `ContractExpression`" in str(err)
reusable einsum expressions Essentially, I'm using ``opt_einsum`` for some tensor network calculations, and a significant proportion of time is spent in ``contract_path``, even for relatively large sized tensors and pre-calculated paths. Specifically, a huge number of contractions with the same indices and shapes are performed over and over again and I already cache these using the path from ``contract_path``. However, it seems even with the path supplied, a large amount of time is spent parsing the input, in ``can_blas``, ``parse_einsum_input`` etc. My suggestion would be something like: ```python shapes = [(2, 3), (3, 4), (4, 5)] my_expr = einsum_expression("ab,bc,cd->ad", *shapes) for _ in many_repeats: ... x, y, z = (rand(s) for s in shapes) out = my_expr(x, y, z) ... ``` I.e. it would only accept arrays of the same dimensions (and probably an ``out`` argument) and would otherwise skip all parsing, using a ``contraction_list`` stored within the function. Anyway, I'm about to knock something up to test for myself, but thought it might be of more general interest.
0.0
fd612f0966a555f8a9783669ad3842f2dbfd1462
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[]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2017-12-04 01:27:21+00:00
mit
1,903
dgasmith__opt_einsum-141
diff --git a/opt_einsum/contract.py b/opt_einsum/contract.py index b837b21..6e7550a 100644 --- a/opt_einsum/contract.py +++ b/opt_einsum/contract.py @@ -214,7 +214,7 @@ def contract_path(*operands, **kwargs): indices = set(input_subscripts.replace(',', '')) # Get length of each unique dimension and ensure all dimensions are correct - dimension_dict = {} + size_dict = {} for tnum, term in enumerate(input_list): sh = input_shps[tnum] @@ -224,18 +224,18 @@ def contract_path(*operands, **kwargs): for cnum, char in enumerate(term): dim = int(sh[cnum]) - if char in dimension_dict: + if char in size_dict: # For broadcasting cases we always want the largest dim size - if dimension_dict[char] == 1: - dimension_dict[char] = dim - elif dim not in (1, dimension_dict[char]): + if size_dict[char] == 1: + size_dict[char] = dim + elif dim not in (1, size_dict[char]): raise ValueError("Size of label '{}' for operand {} ({}) does not match previous " - "terms ({}).".format(char, tnum, dimension_dict[char], dim)) + "terms ({}).".format(char, tnum, size_dict[char], dim)) else: - dimension_dict[char] = dim + size_dict[char] = dim # Compute size of each input array plus the output array - size_list = [helpers.compute_size_by_dict(term, dimension_dict) for term in input_list + [output_subscript]] + size_list = [helpers.compute_size_by_dict(term, size_dict) for term in input_list + [output_subscript]] memory_arg = _choose_memory_arg(memory_limit, size_list) num_ops = len(input_list) @@ -245,7 +245,7 @@ def contract_path(*operands, **kwargs): # indices_in_input = input_subscripts.replace(',', '') inner_product = (sum(len(x) for x in input_sets) - len(indices)) > 0 - naive_cost = helpers.flop_count(indices, inner_product, num_ops, dimension_dict) + naive_cost = helpers.flop_count(indices, inner_product, num_ops, size_dict) # Compute the path if not isinstance(path_type, (str, paths.PathOptimizer)): @@ -256,10 +256,10 @@ def contract_path(*operands, **kwargs): path = [tuple(range(num_ops))] elif isinstance(path_type, paths.PathOptimizer): # Custom path optimizer supplied - path = path_type(input_sets, output_set, dimension_dict, memory_arg) + path = path_type(input_sets, output_set, size_dict, memory_arg) else: path_optimizer = paths.get_path_fn(path_type) - path = path_optimizer(input_sets, output_set, dimension_dict, memory_arg) + path = path_optimizer(input_sets, output_set, size_dict, memory_arg) cost_list = [] scale_list = [] @@ -275,10 +275,10 @@ def contract_path(*operands, **kwargs): out_inds, input_sets, idx_removed, idx_contract = contract_tuple # Compute cost, scale, and size - cost = helpers.flop_count(idx_contract, idx_removed, len(contract_inds), dimension_dict) + cost = helpers.flop_count(idx_contract, idx_removed, len(contract_inds), size_dict) cost_list.append(cost) scale_list.append(len(idx_contract)) - size_list.append(helpers.compute_size_by_dict(out_inds, dimension_dict)) + size_list.append(helpers.compute_size_by_dict(out_inds, size_dict)) tmp_inputs = [input_list.pop(x) for x in contract_inds] tmp_shapes = [input_shps.pop(x) for x in contract_inds] @@ -312,7 +312,7 @@ def contract_path(*operands, **kwargs): return operands, contraction_list path_print = PathInfo(contraction_list, input_subscripts, output_subscript, indices, path, scale_list, naive_cost, - opt_cost, size_list, dimension_dict) + opt_cost, size_list, size_dict) return path, path_print @@ -393,15 +393,26 @@ def contract(*operands, **kwargs): - ``'optimal'`` An algorithm that explores all possible ways of contracting the listed tensors. Scales factorially with the number of terms in the contraction. + - ``'dp'`` A faster (but essentially optimal) algorithm that uses + dynamic programming to exhaustively search all contraction paths + without outer-products. + - ``'greedy'`` An cheap algorithm that heuristically chooses the best + pairwise contraction at each step. Scales linearly in the number of + terms in the contraction. + - ``'random-greedy'`` Run a randomized version of the greedy algorithm + 32 times and pick the best path. + - ``'random-greedy-128'`` Run a randomized version of the greedy + algorithm 128 times and pick the best path. - ``'branch-all'`` An algorithm like optimal but that restricts itself to searching 'likely' paths. Still scales factorially. - ``'branch-2'`` An even more restricted version of 'branch-all' that only searches the best two options at each step. Scales exponentially with the number of terms in the contraction. - - ``'greedy'`` An algorithm that heuristically chooses the best pair - contraction at each step. - ``'auto'`` Choose the best of the above algorithms whilst aiming to keep the path finding time below 1ms. + - ``'auto-hq'`` Aim for a high quality contraction, choosing the best + of the above algorithms whilst aiming to keep the path finding time + below 1sec. memory_limit : {None, int, 'max_input'} (default: None) Give the upper bound of the largest intermediate tensor contract will build. @@ -412,7 +423,7 @@ def contract(*operands, **kwargs): The default is None. Note that imposing a limit can make contractions exponentially slower to perform. - backend : str, optional (default: ``numpy``) + backend : str, optional (default: ``auto``) Which library to use to perform the required ``tensordot``, ``transpose`` and ``einsum`` calls. Should match the types of arrays supplied, See :func:`contract_expression` for generating expressions which convert diff --git a/opt_einsum/path_random.py b/opt_einsum/path_random.py index a49c06c..94b29a8 100644 --- a/opt_einsum/path_random.py +++ b/opt_einsum/path_random.py @@ -163,6 +163,8 @@ class RandomOptimizer(paths.PathOptimizer): raise NotImplementedError def __call__(self, inputs, output, size_dict, memory_limit): + self._check_args_against_first_call(inputs, output, size_dict) + # start a timer? if self.max_time is not None: t0 = time.time() diff --git a/opt_einsum/paths.py b/opt_einsum/paths.py index 4103224..b952bc2 100644 --- a/opt_einsum/paths.py +++ b/opt_einsum/paths.py @@ -43,6 +43,19 @@ class PathOptimizer(object): where ``path`` is a list of int-tuples specifiying a contraction order. """ + + def _check_args_against_first_call(self, inputs, output, size_dict): + """Utility that stateful optimizers can use to ensure they are not + called with different contractions across separate runs. + """ + args = (inputs, output, size_dict) + if not hasattr(self, '_first_call_args'): + # simply set the attribute as currently there is no global PathOptimizer init + self._first_call_args = args + elif args != self._first_call_args: + raise ValueError("The arguments specifiying the contraction that this path optimizer " + "instance was called with have changed - try creating a new instance.") + def __call__(self, inputs, output, size_dict, memory_limit=None): raise NotImplementedError @@ -336,6 +349,7 @@ class BranchBound(PathOptimizer): >>> optimal(isets, oset, idx_sizes, 5000) [(0, 2), (0, 1)] """ + self._check_args_against_first_call(inputs, output, size_dict) inputs = tuple(map(frozenset, inputs)) output = frozenset(output)
dgasmith/opt_einsum
95c1c80b081cce3f50b55422511d362e6fe1f0cd
diff --git a/opt_einsum/tests/test_paths.py b/opt_einsum/tests/test_paths.py index 5105bbe..04769f6 100644 --- a/opt_einsum/tests/test_paths.py +++ b/opt_einsum/tests/test_paths.py @@ -299,6 +299,12 @@ def test_custom_random_greedy(): assert path_info.largest_intermediate == optimizer.best['size'] assert path_info.opt_cost == optimizer.best['flops'] + # check error if we try and reuse the optimizer on a different expression + eq, shapes = oe.helpers.rand_equation(10, 4, seed=41) + views = list(map(np.ones, shapes)) + with pytest.raises(ValueError): + path, path_info = oe.contract_path(eq, *views, optimize=optimizer) + def test_custom_branchbound(): eq, shapes = oe.helpers.rand_equation(8, 4, seed=42) @@ -320,6 +326,12 @@ def test_custom_branchbound(): assert path_info.largest_intermediate == optimizer.best['size'] assert path_info.opt_cost == optimizer.best['flops'] + # check error if we try and reuse the optimizer on a different expression + eq, shapes = oe.helpers.rand_equation(8, 4, seed=41) + views = list(map(np.ones, shapes)) + with pytest.raises(ValueError): + path, path_info = oe.contract_path(eq, *views, optimize=optimizer) + @pytest.mark.skipif(sys.version_info < (3, 2), reason="requires python3.2 or higher") def test_parallel_random_greedy():
Possible bug in RandomGreedy path I have found an interesting quirk of the RandomGreedy optimizer that may not have been intended. In my application, I need to repeat two contractions several times. I use the same optimizer to compute the paths in advance and cache the result. If I use RandomGreedy, then I get the wrong shape for the second contraction, which leads me to believe that there's some internal state of RandomGreedy that persists into computing the second path. Below is a MWE. ```python import torch import opt_einsum as oe eqn1 = 'abc,bef,ahi,ehk,uvc,vwf,uxi,wxk->' eqn2 = 'abd,beg,ahj,ehl,mndo,npgq,mrjs,prlt,uvo,vwq,uxs,wxt->' shapes1 = [(1, 1, 2), (1, 1, 2), (1, 1, 2), (1, 1, 2), (1, 1, 2), (1, 1, 2), (1, 1, 2), (1, 1, 2)] shapes2 = [(1, 1, 2), (1, 1, 2), (1, 1, 2), (1, 1, 2), (1, 1, 2, 2), (1, 1, 2, 2), (1, 1, 2, 2), (1, 1, 2, 2), (1, 1, 2), (1, 1, 2), (1, 1, 2), (1, 1, 2)] tens1 = [torch.randn(*sh) for sh in shapes1] tens2 = [torch.randn(*sh) for sh in shapes2] for Opt in [oe.DynamicProgramming, oe.RandomGreedy]: opt = Opt(minimize='flops') expr1 = oe.contract_expression(eqn1, *[ten.shape for ten in tens1], optimize=opt) expr2 = oe.contract_expression(eqn2, *[ten.shape for ten in tens2], optimize=opt) print(expr1(*tens1)) print(expr2(*tens2)) ``` The output of this program, using the latest PyPI release, is: ``` tensor(-0.0187) tensor(0.4303) tensor(-0.0187) tensor([[[[[-0.4418]], [[ 1.2737]]]]]) ``` Lines 1 and 3 should match (and do), but so should 2 and 4 (and don't).
0.0
95c1c80b081cce3f50b55422511d362e6fe1f0cd
[ "opt_einsum/tests/test_paths.py::test_custom_random_greedy", "opt_einsum/tests/test_paths.py::test_custom_branchbound" ]
[ "opt_einsum/tests/test_paths.py::test_size_by_dict", "opt_einsum/tests/test_paths.py::test_flop_cost", "opt_einsum/tests/test_paths.py::test_bad_path_option", "opt_einsum/tests/test_paths.py::test_explicit_path", "opt_einsum/tests/test_paths.py::test_path_optimal", "opt_einsum/tests/test_paths.py::test_path_greedy", "opt_einsum/tests/test_paths.py::test_memory_paths", "opt_einsum/tests/test_paths.py::test_path_edge_cases[greedy-eb,cb,fb->cef-order0]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[branch-all-eb,cb,fb->cef-order1]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[branch-2-eb,cb,fb->cef-order2]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[optimal-eb,cb,fb->cef-order3]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[dp-eb,cb,fb->cef-order4]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[greedy-dd,fb,be,cdb->cef-order5]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[branch-all-dd,fb,be,cdb->cef-order6]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[branch-2-dd,fb,be,cdb->cef-order7]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[optimal-dd,fb,be,cdb->cef-order8]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[optimal-dd,fb,be,cdb->cef-order9]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[dp-dd,fb,be,cdb->cef-order10]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[greedy-bca,cdb,dbf,afc->-order11]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[branch-all-bca,cdb,dbf,afc->-order12]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[branch-2-bca,cdb,dbf,afc->-order13]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[optimal-bca,cdb,dbf,afc->-order14]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[dp-bca,cdb,dbf,afc->-order15]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[greedy-dcc,fce,ea,dbf->ab-order16]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[branch-all-dcc,fce,ea,dbf->ab-order17]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[branch-2-dcc,fce,ea,dbf->ab-order18]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[optimal-dcc,fce,ea,dbf->ab-order19]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[dp-dcc,fce,ea,dbf->ab-order20]", "opt_einsum/tests/test_paths.py::test_optimal_edge_cases", "opt_einsum/tests/test_paths.py::test_greedy_edge_cases", "opt_einsum/tests/test_paths.py::test_dp_edge_cases_dimension_1", "opt_einsum/tests/test_paths.py::test_dp_edge_cases_all_singlet_indices", "opt_einsum/tests/test_paths.py::test_custom_dp_can_optimize_for_outer_products", "opt_einsum/tests/test_paths.py::test_custom_dp_can_optimize_for_size", "opt_einsum/tests/test_paths.py::test_custom_dp_can_set_cost_cap", "opt_einsum/tests/test_paths.py::test_can_optimize_outer_products[greedy]", "opt_einsum/tests/test_paths.py::test_can_optimize_outer_products[branch-2]", "opt_einsum/tests/test_paths.py::test_can_optimize_outer_products[branch-all]", "opt_einsum/tests/test_paths.py::test_can_optimize_outer_products[optimal]", "opt_einsum/tests/test_paths.py::test_can_optimize_outer_products[dp]", "opt_einsum/tests/test_paths.py::test_large_path[2]", "opt_einsum/tests/test_paths.py::test_large_path[3]", "opt_einsum/tests/test_paths.py::test_large_path[26]", "opt_einsum/tests/test_paths.py::test_large_path[52]", "opt_einsum/tests/test_paths.py::test_large_path[116]", "opt_einsum/tests/test_paths.py::test_large_path[300]", "opt_einsum/tests/test_paths.py::test_parallel_random_greedy", "opt_einsum/tests/test_paths.py::test_custom_path_optimizer", "opt_einsum/tests/test_paths.py::test_custom_random_optimizer", "opt_einsum/tests/test_paths.py::test_optimizer_registration" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2020-05-12 21:47:13+00:00
mit
1,904
dgasmith__opt_einsum-145
diff --git a/docs/source/backends.rst b/docs/source/backends.rst index d297b19..7e48678 100644 --- a/docs/source/backends.rst +++ b/docs/source/backends.rst @@ -325,3 +325,47 @@ so again just the ``backend`` keyword needs to be supplied: [-462.52362 , -121.12659 , -67.84769 , 624.5455 ], [ 5.2839584, 36.44155 , 81.62852 , 703.15784 ]], dtype=float32) + + +Contracting arbitrary objects +============================= + +There is one more explicit backend that can handle arbitrary arrays of objects, +so long the *objects themselves* just support multiplication and addition ( +``__mul__`` and ``__add__`` dunder methods respectively). Use it by supplying +``backend='object'``. + +For example, imagine we want to perform a contraction of arrays made up of +`sympy <www.sympy.org>`_ symbols: + +.. code-block:: python + + >>> import opt_einsum as oe + >>> import numpy as np + >>> import sympy + + >>> # define the symbols + >>> a, b, c, d, e, f, g, h, i, j, k, l = [sympy.symbols(oe.get_symbol(i)) for i in range(12)] + >>> a * b + c * d + 𝑎𝑏+𝑐𝑑 + + >>> # define the tensors (you might explicitly specify ``dtype=object``) + >>> X = np.array([[a, b], [c, d]]) + >>> Y = np.array([[e, f], [g, h]]) + >>> Z = np.array([[i, j], [k, l]]) + + >>> # contract the tensors! + >>> oe.contract('uv,vw,wu->u', X, Y, Z, backend='object') + array([i*(a*e + b*g) + k*(a*f + b*h), j*(c*e + d*g) + l*(c*f + d*h)], + dtype=object) + +There are a few things to note here: + +* The returned array is a ``numpy.ndarray`` but since it has ``dtype=object`` + it can really hold *any* python objects +* We had to explicitly use ``backend='object'``, since :func:`numpy.einsum` + would have otherwise been dispatched to, which can't handle ``dtype=object`` + (though :func:`numpy.tensordot` in fact can) +* Although an optimized pairwise contraction order is used, the looping in each + single contraction is **performed in python so performance will be + drastically lower than for numeric dtypes!** diff --git a/opt_einsum/backends/dispatch.py b/opt_einsum/backends/dispatch.py index 85a6ceb..f5777ae 100644 --- a/opt_einsum/backends/dispatch.py +++ b/opt_einsum/backends/dispatch.py @@ -8,6 +8,7 @@ import importlib import numpy +from . import object_arrays from . import cupy as _cupy from . import jax as _jax from . import tensorflow as _tensorflow @@ -49,6 +50,10 @@ _cached_funcs = { ('tensordot', 'numpy'): numpy.tensordot, ('transpose', 'numpy'): numpy.transpose, ('einsum', 'numpy'): numpy.einsum, + # also pre-populate with the arbitrary object backend + ('tensordot', 'object'): numpy.tensordot, + ('transpose', 'object'): numpy.transpose, + ('einsum', 'object'): object_arrays.object_einsum, } diff --git a/opt_einsum/backends/object_arrays.py b/opt_einsum/backends/object_arrays.py new file mode 100644 index 0000000..3b394e1 --- /dev/null +++ b/opt_einsum/backends/object_arrays.py @@ -0,0 +1,60 @@ +""" +Functions for performing contractions with array elements which are objects. +""" + +import numpy as np +import functools +import operator + + +def object_einsum(eq, *arrays): + """A ``einsum`` implementation for ``numpy`` arrays with object dtype. + The loop is performed in python, meaning the objects themselves need + only to implement ``__mul__`` and ``__add__`` for the contraction to be + computed. This may be useful when, for example, computing expressions of + tensors with symbolic elements, but note it will be very slow when compared + to ``numpy.einsum`` and numeric data types! + + Parameters + ---------- + eq : str + The contraction string, should specify output. + arrays : sequence of arrays + These can be any indexable arrays as long as addition and + multiplication is defined on the elements. + + Returns + ------- + out : numpy.ndarray + The output tensor, with ``dtype=object``. + """ + + # when called by ``opt_einsum`` we will always be given a full eq + lhs, output = eq.split('->') + inputs = lhs.split(',') + + sizes = {} + for term, array in zip(inputs, arrays): + for k, d in zip(term, array.shape): + sizes[k] = d + + out_size = tuple(sizes[k] for k in output) + out = np.empty(out_size, dtype=object) + + inner = tuple(k for k in sizes if k not in output) + inner_size = tuple(sizes[k] for k in inner) + + for coo_o in np.ndindex(*out_size): + + coord = dict(zip(output, coo_o)) + + def gen_inner_sum(): + for coo_i in np.ndindex(*inner_size): + coord.update(dict(zip(inner, coo_i))) + locs = (tuple(coord[k] for k in term) for term in inputs) + elements = (array[loc] for array, loc in zip(arrays, locs)) + yield functools.reduce(operator.mul, elements) + + out[coo_o] = functools.reduce(operator.add, gen_inner_sum()) + + return out
dgasmith/opt_einsum
e88983faeb1221cc802ca8cefe2b425cfebe4880
diff --git a/opt_einsum/tests/test_backends.py b/opt_einsum/tests/test_backends.py index 905d2ba..2c05f35 100644 --- a/opt_einsum/tests/test_backends.py +++ b/opt_einsum/tests/test_backends.py @@ -431,3 +431,25 @@ def test_auto_backend_custom_array_no_tensordot(): # Shaped is an array-like object defined by opt_einsum - which has no TDOT assert infer_backend(x) == 'opt_einsum' assert parse_backend([x], 'auto') == 'numpy' + + [email protected]("string", tests) +def test_object_arrays_backend(string): + views = helpers.build_views(string) + ein = contract(string, *views, optimize=False, use_blas=False) + assert ein.dtype != object + + shps = [v.shape for v in views] + expr = contract_expression(string, *shps, optimize=True) + + obj_views = [view.astype(object) for view in views] + + # try raw contract + obj_opt = contract(string, *obj_views, backend='object') + assert obj_opt.dtype == object + assert np.allclose(ein, obj_opt.astype(float)) + + # test expression + obj_opt = expr(*obj_views, backend='object') + assert obj_opt.dtype == object + assert np.allclose(ein, obj_opt.astype(float))
Potential bug (outer tensor product) This works...: ```python >>> import mpmath >>> import numpy >>> m0 = numpy.eye(2) >>> opt_einsum.contract('bc,ad->abcd', m0, m0) array([[[[1., 0.], ...) ``` ...but this breaks: ```python >>> m1 = m0 + mpmath.mpc(0) >>> opt_einsum.contract('bc,ad->abcd', m1, m1) Traceback (most recent call last): (...) TypeError: invalid data type for einsum ``` However, using opt_einsum with mpmath is otherwise OK in principle: ```python >>> opt_einsum.contract('bc,cd->bd', m1, m1) array([[mpc(real='1.0', imag='0.0'), mpc(real='0.0', imag='0.0')], [mpc(real='0.0', imag='0.0'), mpc(real='1.0', imag='0.0')]], dtype=object) ```
0.0
e88983faeb1221cc802ca8cefe2b425cfebe4880
[ "opt_einsum/tests/test_backends.py::test_object_arrays_backend[ab,bc->ca]", "opt_einsum/tests/test_backends.py::test_object_arrays_backend[abc,bcd,dea]", "opt_einsum/tests/test_backends.py::test_object_arrays_backend[abc,def->fedcba]", "opt_einsum/tests/test_backends.py::test_object_arrays_backend[abc,bcd,df->fa]", "opt_einsum/tests/test_backends.py::test_object_arrays_backend[ijk,ikj]", "opt_einsum/tests/test_backends.py::test_object_arrays_backend[i,j->ij]", "opt_einsum/tests/test_backends.py::test_object_arrays_backend[ijk,k->ij]", "opt_einsum/tests/test_backends.py::test_object_arrays_backend[AB,BC->CA]" ]
[ "opt_einsum/tests/test_backends.py::test_auto_backend_custom_array_no_tensordot" ]
{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2020-07-02 04:12:10+00:00
mit
1,905
dgasmith__opt_einsum-149
diff --git a/opt_einsum/backends/jax.py b/opt_einsum/backends/jax.py index 6bc1a1f..aefd941 100644 --- a/opt_einsum/backends/jax.py +++ b/opt_einsum/backends/jax.py @@ -13,18 +13,18 @@ _JAX = None def _get_jax_and_to_jax(): - global _JAX - if _JAX is None: - import jax + global _JAX + if _JAX is None: + import jax - @to_backend_cache_wrap - @jax.jit - def to_jax(x): - return x + @to_backend_cache_wrap + @jax.jit + def to_jax(x): + return x - _JAX = jax, to_jax + _JAX = jax, to_jax - return _JAX + return _JAX def build_expression(_, expr): # pragma: no cover diff --git a/opt_einsum/contract.py b/opt_einsum/contract.py index 6e7550a..1403f98 100644 --- a/opt_einsum/contract.py +++ b/opt_einsum/contract.py @@ -51,16 +51,22 @@ class PathInfo(object): " Complete contraction: {}\n".format(self.eq), " Naive scaling: {}\n".format(len(self.indices)), " Optimized scaling: {}\n".format(max(self.scale_list)), " Naive FLOP count: {:.3e}\n".format( self.naive_cost), " Optimized FLOP count: {:.3e}\n".format(self.opt_cost), - " Theoretical speedup: {:3.3f}\n".format(self.speedup), + " Theoretical speedup: {:.3e}\n".format(self.speedup), " Largest intermediate: {:.3e} elements\n".format(self.largest_intermediate), "-" * 80 + "\n", "{:>6} {:>11} {:>22} {:>37}\n".format(*header), "-" * 80 ] for n, contraction in enumerate(self.contraction_list): inds, idx_rm, einsum_str, remaining, do_blas = contraction - remaining_str = ",".join(remaining) + "->" + self.output_subscript - path_run = (self.scale_list[n], do_blas, einsum_str, remaining_str) - path_print.append("\n{:>4} {:>14} {:>22} {:>37}".format(*path_run)) + + if remaining is not None: + remaining_str = ",".join(remaining) + "->" + self.output_subscript + else: + remaining_str = "..." + size_remaining = max(0, 56 - max(22, len(einsum_str))) + + path_run = (self.scale_list[n], do_blas, einsum_str, remaining_str, size_remaining) + path_print.append("\n{:>4} {:>14} {:>22} {:>{}}".format(*path_run)) return "".join(path_print) @@ -303,7 +309,14 @@ def contract_path(*operands, **kwargs): einsum_str = ",".join(tmp_inputs) + "->" + idx_result - contraction = (contract_inds, idx_removed, einsum_str, input_list[:], do_blas) + # for large expressions saving the remaining terms at each step can + # incur a large memory footprint - and also be messy to print + if len(input_list) <= 20: + remaining = tuple(input_list) + else: + remaining = None + + contraction = (contract_inds, idx_removed, einsum_str, remaining, do_blas) contraction_list.append(contraction) opt_cost = sum(cost_list) @@ -529,7 +542,7 @@ def _core_contract(operands, contraction_list, backend='auto', evaluate_constant # Start contraction loop for num, contraction in enumerate(contraction_list): - inds, idx_rm, einsum_str, remaining, blas_flag = contraction + inds, idx_rm, einsum_str, _, blas_flag = contraction # check if we are performing the pre-pass of an expression with constants, # if so, break out upon finding first non-constant (None) operand
dgasmith/opt_einsum
2cbd28e612ff0af54656c34d7f6c239efe524b12
diff --git a/opt_einsum/tests/test_contract.py b/opt_einsum/tests/test_contract.py index e6dfb04..8268e88 100644 --- a/opt_einsum/tests/test_contract.py +++ b/opt_einsum/tests/test_contract.py @@ -171,7 +171,7 @@ def test_printing(): views = helpers.build_views(string) ein = contract_path(string, *views) - assert len(str(ein[1])) == 726 + assert len(str(ein[1])) == 728 @pytest.mark.parametrize("string", tests) diff --git a/opt_einsum/tests/test_input.py b/opt_einsum/tests/test_input.py index e5c1677..f3b6c06 100644 --- a/opt_einsum/tests/test_input.py +++ b/opt_einsum/tests/test_input.py @@ -34,7 +34,8 @@ def test_type_errors(): contract("", 0, out='test') # order parameter must be a valid order - with pytest.raises(TypeError): + # changed in Numpy 1.19, see https://github.com/numpy/numpy/commit/35b0a051c19265f5643f6011ee11e31d30c8bc4c + with pytest.raises((TypeError, ValueError)): contract("", 0, order='W') # casting parameter must be a valid casting
Remove 'remaining' from PathInfo? (incurs n^2 memory overhead) When building the ``contraction_list``, ``opt_einsum`` handles a list of 'remaining' terms, and at each new step these are copied (``input_list`` below): https://github.com/dgasmith/opt_einsum/blob/2cbd28e612ff0af54656c34d7f6c239efe524b12/opt_einsum/contract.py#L306 A single, consumed version of this list is needed for constructing the items in the contraction list. However all the copies at each stage are not needed in the actual contraction (``_core_contract``) function - they are just for printing in the ``PathInfo`` object. The problem is that each copied list of remaining terms is of average length `n / 2` and there are generally `n - 1` of them, incurring a `n^2` memory overhead, which caused problems for us (10s of gigabytes of problems!) in some large contractions. Here's an extreme sample of such a gigantic ``PathInfo``: ![Screenshot from 2020-07-15 19-11-55](https://user-images.githubusercontent.com/8982598/87640894-486a1400-c73f-11ea-98a1-dab04d3e02f8.png) With 50 contractions each of several thousand tensors there was a total of nearly 100,000,000 'remaining' lists of strings. I'd suggest either: * a) *Easiest* - we just remove the 'remaining' terms from the ``PathInfo`` object, I'd be fine with this but possibly its useful information for others? * b) *Medium* - the 'remaining' terms are only accumulated below a certain threshold size * c) *Hardest* - they are generated lazily (and maybe optionally) by the ``PathInfo`` object upon request only (e.g. printing)
0.0
2cbd28e612ff0af54656c34d7f6c239efe524b12
[ "opt_einsum/tests/test_contract.py::test_printing" ]
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{ "failed_lite_validators": [ "has_hyperlinks", "has_media", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2020-07-16 19:23:46+00:00
mit
1,906
dgasmith__opt_einsum-196
diff --git a/opt_einsum/contract.py b/opt_einsum/contract.py index 0df94d0..0f70379 100644 --- a/opt_einsum/contract.py +++ b/opt_einsum/contract.py @@ -4,6 +4,7 @@ Contains the primary optimization and contraction routines. from collections import namedtuple from decimal import Decimal +from functools import lru_cache from typing import Any, Dict, Iterable, List, Optional, Sequence, Tuple from . import backends, blas, helpers, parser, paths, sharing @@ -542,15 +543,20 @@ def contract(*operands_: Any, **kwargs: Any) -> ArrayType: return _core_contract(operands, contraction_list, backend=backend, **einsum_kwargs) +@lru_cache(None) +def _infer_backend_class_cached(cls: type) -> str: + return cls.__module__.split(".")[0] + + def infer_backend(x: Any) -> str: - return x.__class__.__module__.split(".")[0] + return _infer_backend_class_cached(x.__class__) -def parse_backend(arrays: Sequence[ArrayType], backend: str) -> str: +def parse_backend(arrays: Sequence[ArrayType], backend: Optional[str]) -> str: """Find out what backend we should use, dipatching based on the first array if ``backend='auto'`` is specified. """ - if backend != "auto": + if (backend != "auto") and (backend is not None): return backend backend = infer_backend(arrays[0]) @@ -565,7 +571,7 @@ def parse_backend(arrays: Sequence[ArrayType], backend: str) -> str: def _core_contract( operands_: Sequence[ArrayType], contraction_list: ContractionListType, - backend: str = "auto", + backend: Optional[str] = "auto", evaluate_constants: bool = False, **einsum_kwargs: Any, ) -> ArrayType: @@ -703,7 +709,7 @@ class ContractExpression: self._evaluated_constants: Dict[str, Any] = {} self._backend_expressions: Dict[str, Any] = {} - def evaluate_constants(self, backend: str = "auto") -> None: + def evaluate_constants(self, backend: Optional[str] = "auto") -> None: """Convert any constant operands to the correct backend form, and perform as many contractions as possible to create a new list of operands, stored in ``self._evaluated_constants[backend]``. This also @@ -746,7 +752,7 @@ class ContractExpression: self, arrays: Sequence[ArrayType], out: Optional[ArrayType] = None, - backend: str = "auto", + backend: Optional[str] = "auto", evaluate_constants: bool = False, ) -> ArrayType: """The normal, core contraction.""" diff --git a/opt_einsum/paths.py b/opt_einsum/paths.py index eac3630..ac8ccd5 100644 --- a/opt_einsum/paths.py +++ b/opt_einsum/paths.py @@ -1217,7 +1217,7 @@ class DynamicProgramming(PathOptimizer): output = frozenset(symbol2int[c] for c in output_) size_dict_canonical = {symbol2int[c]: v for c, v in size_dict_.items() if c in symbol2int} size_dict = [size_dict_canonical[j] for j in range(len(size_dict_canonical))] - naive_cost = naive_scale * len(inputs) * functools.reduce(operator.mul, size_dict) + naive_cost = naive_scale * len(inputs) * functools.reduce(operator.mul, size_dict, 1) inputs, inputs_done, inputs_contractions = _dp_parse_out_single_term_ops(inputs, all_inds, ind_counts)
dgasmith/opt_einsum
a274599c87c6224382e2ce328c7439b7b713e363
diff --git a/opt_einsum/tests/test_backends.py b/opt_einsum/tests/test_backends.py index 87d2ba2..7c81c67 100644 --- a/opt_einsum/tests/test_backends.py +++ b/opt_einsum/tests/test_backends.py @@ -443,6 +443,7 @@ def test_auto_backend_custom_array_no_tensordot(): # Shaped is an array-like object defined by opt_einsum - which has no TDOT assert infer_backend(x) == "opt_einsum" assert parse_backend([x], "auto") == "numpy" + assert parse_backend([x], None) == "numpy" @pytest.mark.parametrize("string", tests) diff --git a/opt_einsum/tests/test_contract.py b/opt_einsum/tests/test_contract.py index 453a779..ef3ee5d 100644 --- a/opt_einsum/tests/test_contract.py +++ b/opt_einsum/tests/test_contract.py @@ -13,6 +13,7 @@ tests = [ "a,->a", "ab,->ab", ",ab,->ab", + ",,->", # Test hadamard-like products "a,ab,abc->abc", "a,b,ab->ab", diff --git a/opt_einsum/tests/test_paths.py b/opt_einsum/tests/test_paths.py index c6fef4f..eb4b18b 100644 --- a/opt_einsum/tests/test_paths.py +++ b/opt_einsum/tests/test_paths.py @@ -58,6 +58,7 @@ path_scalar_tests = [ ["ab,->ab", 1], [",a,->a", 2], [",,a,->a", 3], + [",,->", 2], ]
allow `backend=None` as shorthand for 'auto' A couple of times I've be caught out (e.g. https://github.com/jcmgray/quimb/issues/130) that the special value for inferring the backend is not `backend=None`. Might be nice to allow both? If so would just require a simple: ```python if backend not in ("auto", None): return backend ``` in `parse_backend` of `contract.py`.
0.0
a274599c87c6224382e2ce328c7439b7b713e363
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"opt_einsum/tests/test_paths.py::test_custom_random_optimizer", "opt_einsum/tests/test_paths.py::test_optimizer_registration" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2022-07-06 09:27:11+00:00
mit
1,907
dgasmith__opt_einsum-48
diff --git a/opt_einsum/compat.py b/opt_einsum/compat.py new file mode 100644 index 0000000..38cf55d --- /dev/null +++ b/opt_einsum/compat.py @@ -0,0 +1,10 @@ +# Python 2/3 compatability shim + +try: + # Python 2 + get_chr = unichr + strings = (str, type(get_chr(300))) +except NameError: + # Python 3 + get_chr = chr + strings = str diff --git a/opt_einsum/contract.py b/opt_einsum/contract.py index a7932f0..01998dd 100644 --- a/opt_einsum/contract.py +++ b/opt_einsum/contract.py @@ -6,6 +6,7 @@ import numpy as np from . import backends from . import blas +from . import compat from . import helpers from . import parser from . import paths @@ -176,7 +177,7 @@ def contract_path(*operands, **kwargs): naive_cost = helpers.flop_count(indices, inner_product, num_ops, dimension_dict) # Compute the path - if not isinstance(path_type, str): + if not isinstance(path_type, compat.strings): path = path_type elif num_ops == 1: # Nothing to be optimized @@ -274,7 +275,7 @@ def _einsum(*operands, **kwargs): """ fn = backends.get_func('einsum', kwargs.pop('backend', 'numpy')) - if not isinstance(operands[0], str): + if not isinstance(operands[0], compat.strings): return fn(*operands, **kwargs) einsum_str, operands = operands[0], operands[1:] diff --git a/opt_einsum/parser.py b/opt_einsum/parser.py index c5370b1..adfc19f 100644 --- a/opt_einsum/parser.py +++ b/opt_einsum/parser.py @@ -8,6 +8,8 @@ from collections import OrderedDict import numpy as np +from . import compat + einsum_symbols_base = 'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' @@ -40,7 +42,7 @@ def get_symbol(i): """ if i < 52: return einsum_symbols_base[i] - return chr(i + 140) + return compat.get_chr(i + 140) def gen_unused_symbols(used, n): @@ -133,7 +135,7 @@ def parse_einsum_input(operands): if len(operands) == 0: raise ValueError("No input operands") - if isinstance(operands[0], str): + if isinstance(operands[0], compat.strings): subscripts = operands[0].replace(" ", "") operands = [possibly_convert_to_numpy(x) for x in operands[1:]] diff --git a/opt_einsum/sharing.py b/opt_einsum/sharing.py index 504ba05..54c94bd 100644 --- a/opt_einsum/sharing.py +++ b/opt_einsum/sharing.py @@ -129,7 +129,7 @@ def einsum_cache_wrap(einsum): canonical = sorted(zip(inputs, map(id, operands)), key=lambda x: x[1]) canonical_ids = tuple(id_ for _, id_ in canonical) canonical_inputs = ','.join(input_ for input_, _ in canonical) - canonical_equation = alpha_canonicalize('{}->{}'.format(canonical_inputs, output)) + canonical_equation = alpha_canonicalize(canonical_inputs + "->" + output) key = 'einsum', backend, canonical_equation, canonical_ids return _memoize(key, einsum, equation, *operands, backend=backend)
dgasmith/opt_einsum
9e646be16b0a7be8ee88becefc1bba267956bc3b
diff --git a/opt_einsum/tests/test_contract.py b/opt_einsum/tests/test_contract.py index 43b5061..fdfacc7 100644 --- a/opt_einsum/tests/test_contract.py +++ b/opt_einsum/tests/test_contract.py @@ -7,7 +7,7 @@ import sys import numpy as np import pytest -from opt_einsum import contract, contract_path, helpers, contract_expression +from opt_einsum import compat, contract, contract_path, helpers, contract_expression tests = [ # Test hadamard-like products @@ -117,7 +117,6 @@ def test_drop_in_replacement(string): assert np.allclose(opt, np.einsum(string, *views)) [email protected](sys.version_info[0] < 3, reason='requires python3') @pytest.mark.parametrize("string", tests) def test_compare_greek(string): views = helpers.build_views(string) @@ -125,7 +124,7 @@ def test_compare_greek(string): ein = contract(string, *views, optimize=False, use_blas=False) # convert to greek - string = ''.join(chr(ord(c) + 848) if c not in ',->.' else c for c in string) + string = ''.join(compat.get_chr(ord(c) + 848) if c not in ',->.' else c for c in string) opt = contract(string, *views, optimize='greedy', use_blas=False) assert np.allclose(ein, opt) @@ -146,7 +145,6 @@ def test_compare_blas(string): assert np.allclose(ein, opt) [email protected](sys.version_info[0] < 3, reason='requires python3') @pytest.mark.parametrize("string", tests) def test_compare_blas_greek(string): views = helpers.build_views(string) @@ -154,7 +152,7 @@ def test_compare_blas_greek(string): ein = contract(string, *views, optimize=False) # convert to greek - string = ''.join(chr(ord(c) + 848) if c not in ',->.' else c for c in string) + string = ''.join(compat.get_chr(ord(c) + 848) if c not in ',->.' else c for c in string) opt = contract(string, *views, optimize='greedy') assert np.allclose(ein, opt) @@ -163,10 +161,9 @@ def test_compare_blas_greek(string): assert np.allclose(ein, opt) [email protected](sys.version_info[0] < 3, reason='requires python3') def test_some_non_alphabet_maintains_order(): # 'c beta a' should automatically go to -> 'a c beta' - string = 'c' + chr(ord('b') + 848) + 'a' + string = 'c' + compat.get_chr(ord('b') + 848) + 'a' # but beta will be temporarily replaced with 'b' for which 'cba->abc' # so check manual output kicks in: x = np.random.rand(2, 3, 4) diff --git a/opt_einsum/tests/test_input.py b/opt_einsum/tests/test_input.py index 022a078..311356e 100644 --- a/opt_einsum/tests/test_input.py +++ b/opt_einsum/tests/test_input.py @@ -230,7 +230,6 @@ def test_singleton_dimension_broadcast(): assert np.allclose(res2, np.full((1, 5), 5)) [email protected](sys.version_info.major == 2, reason="Requires python 3.") def test_large_int_input_format(): string = 'ab,bc,cd' x, y, z = build_views(string) diff --git a/opt_einsum/tests/test_paths.py b/opt_einsum/tests/test_paths.py index 8087dd2..da39e23 100644 --- a/opt_einsum/tests/test_paths.py +++ b/opt_einsum/tests/test_paths.py @@ -3,6 +3,8 @@ Tests the accuracy of the opt_einsum paths in addition to unit tests for the various path helper functions. """ +import itertools + import numpy as np import pytest @@ -174,3 +176,14 @@ def test_can_optimize_outer_products(): a, b, c = [np.random.randn(10, 10) for _ in range(3)] d = np.random.randn(10, 2) assert oe.contract_path("ab,cd,ef,fg", a, b, c, d, path='greedy')[0] == [(2, 3), (0, 2), (0, 1)] + + [email protected]('num_symbols', [2, 3, 26, 26 + 26, 256 - 140, 300]) +def test_large_path(num_symbols): + symbols = ''.join(oe.get_symbol(i) for i in range(num_symbols)) + dimension_dict = dict(zip(symbols, itertools.cycle([2, 3, 4]))) + expression = ','.join(symbols[t:t+2] for t in range(num_symbols - 1)) + tensors = oe.helpers.build_views(expression, dimension_dict=dimension_dict) + + # Check that path construction does not crash + oe.contract_path(expression, *tensors, path='greedy')
Support for get_symbol(116) in Python 2 `get_symbol(x)` currently fails in Python 2 for any `x >= 116`: ``` i = 116 def get_symbol(i): """Get the symbol corresponding to int ``i`` - runs through the usual 52 letters before resorting to unicode characters, starting at ``chr(192)``. Examples -------- >>> get_symbol(2) 'c' >>> oe.get_symbol(200) 'Ŕ' >>> oe.get_symbol(20000) '京' """ if i < 52: return einsum_symbols_base[i] > return chr(i + 140) E ValueError: chr() arg not in range(256) ``` Can we fix this by use `unichr()` and unicode strings in Python 2?
0.0
9e646be16b0a7be8ee88becefc1bba267956bc3b
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"opt_einsum/tests/test_contract.py::test_contract_expression_with_constants[ab,bc,cd-constants6]", "opt_einsum/tests/test_input.py::test_value_errors", "opt_einsum/tests/test_input.py::test_compare[...a->...]", "opt_einsum/tests/test_input.py::test_compare[a...->...]", "opt_einsum/tests/test_input.py::test_compare[a...a->...a]", "opt_einsum/tests/test_input.py::test_compare[...,...]", "opt_einsum/tests/test_input.py::test_compare[a,b]", "opt_einsum/tests/test_input.py::test_compare[...a,...b]", "opt_einsum/tests/test_input.py::test_ellipse_input1", "opt_einsum/tests/test_input.py::test_ellipse_input2", "opt_einsum/tests/test_input.py::test_ellipse_input3", "opt_einsum/tests/test_input.py::test_ellipse_input4", "opt_einsum/tests/test_input.py::test_singleton_dimension_broadcast", "opt_einsum/tests/test_input.py::test_large_int_input_format", "opt_einsum/tests/test_paths.py::test_size_by_dict", "opt_einsum/tests/test_paths.py::test_flop_cost", "opt_einsum/tests/test_paths.py::test_path_optimal", "opt_einsum/tests/test_paths.py::test_path_greedy", "opt_einsum/tests/test_paths.py::test_memory_paths", "opt_einsum/tests/test_paths.py::test_path_edge_cases[greedy-eb,cb,fb->cef-order0]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[optimal-eb,cb,fb->cef-order1]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[greedy-dd,fb,be,cdb->cef-order2]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[optimal-dd,fb,be,cdb->cef-order3]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[greedy-bca,cdb,dbf,afc->-order4]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[optimal-bca,cdb,dbf,afc->-order5]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[greedy-dcc,fce,ea,dbf->ab-order6]", "opt_einsum/tests/test_paths.py::test_path_edge_cases[optimal-dcc,fce,ea,dbf->ab-order7]", "opt_einsum/tests/test_paths.py::test_optimal_edge_cases", "opt_einsum/tests/test_paths.py::test_greedy_edge_cases", "opt_einsum/tests/test_paths.py::test_can_optimize_outer_products", "opt_einsum/tests/test_paths.py::test_large_path[2]", "opt_einsum/tests/test_paths.py::test_large_path[3]", "opt_einsum/tests/test_paths.py::test_large_path[26]", "opt_einsum/tests/test_paths.py::test_large_path[52]", "opt_einsum/tests/test_paths.py::test_large_path[116]", "opt_einsum/tests/test_paths.py::test_large_path[300]" ]
[]
{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2018-08-23 19:50:31+00:00
mit
1,908
dgasmith__opt_einsum-53
diff --git a/opt_einsum/sharing.py b/opt_einsum/sharing.py index 54c94bd..038309f 100644 --- a/opt_einsum/sharing.py +++ b/opt_einsum/sharing.py @@ -3,11 +3,43 @@ import contextlib import functools import numbers -from collections import Counter +from collections import Counter, defaultdict +import threading from .parser import alpha_canonicalize, parse_einsum_input -_SHARING_STACK = [] + +_SHARING_STACK = defaultdict(list) + + +try: + get_thread_id = threading.get_ident +except AttributeError: + def get_thread_id(): + return threading.current_thread().ident + + +def currently_sharing(): + """Check if we are currently sharing a cache -- thread specific. + """ + return get_thread_id() in _SHARING_STACK + + +def get_sharing_cache(): + """Return the most recent sharing cache -- thread specific. + """ + return _SHARING_STACK[get_thread_id()][-1] + + +def _add_sharing_cache(cache): + _SHARING_STACK[get_thread_id()].append(cache) + + +def _remove_sharing_cache(): + tid = get_thread_id() + _SHARING_STACK[tid].pop() + if not _SHARING_STACK[tid]: + del _SHARING_STACK[tid] @contextlib.contextmanager @@ -34,11 +66,11 @@ def shared_intermediates(cache=None): """ if cache is None: cache = {} + _add_sharing_cache(cache) try: - _SHARING_STACK.append(cache) yield cache finally: - _SHARING_STACK.pop() + _remove_sharing_cache() def count_cached_ops(cache): @@ -52,7 +84,7 @@ def _save_tensors(*tensors): """Save tensors in the cache to prevent their ids from being recycled. This is needed to prevent false cache lookups. """ - cache = _SHARING_STACK[-1] + cache = get_sharing_cache() for tensor in tensors: cache['tensor', id(tensor)] = tensor @@ -62,7 +94,7 @@ def _memoize(key, fn, *args, **kwargs): Results will be stored in the innermost ``cache`` yielded by :func:`shared_intermediates`. """ - cache = _SHARING_STACK[-1] + cache = get_sharing_cache() if key in cache: return cache[key] result = fn(*args, **kwargs) @@ -77,7 +109,7 @@ def transpose_cache_wrap(transpose): @functools.wraps(transpose) def cached_transpose(a, axes, backend='numpy'): - if not _SHARING_STACK: + if not currently_sharing(): return transpose(a, axes, backend=backend) # hash by axes @@ -96,7 +128,7 @@ def tensordot_cache_wrap(tensordot): @functools.wraps(tensordot) def cached_tensordot(x, y, axes=2, backend='numpy'): - if not _SHARING_STACK: + if not currently_sharing(): return tensordot(x, y, axes, backend=backend) # hash based on the (axes_x,axes_y) form of axes @@ -117,7 +149,7 @@ def einsum_cache_wrap(einsum): @functools.wraps(einsum) def cached_einsum(*args, **kwargs): - if not _SHARING_STACK: + if not currently_sharing(): return einsum(*args, **kwargs) # hash modulo commutativity by computing a canonical ordering and names @@ -143,7 +175,7 @@ def to_backend_cache_wrap(to_backend): @functools.wraps(to_backend) def cached_to_backend(array): - if not _SHARING_STACK: + if not currently_sharing(): return to_backend(array) # hash by id
dgasmith/opt_einsum
284f233a4057e57ba8a3c1eef28e6bb6b8bfe2b1
diff --git a/opt_einsum/tests/test_sharing.py b/opt_einsum/tests/test_sharing.py index b0b860a..ea7f00e 100644 --- a/opt_einsum/tests/test_sharing.py +++ b/opt_einsum/tests/test_sharing.py @@ -6,11 +6,11 @@ import numpy as np import pytest from opt_einsum import (contract_expression, contract_path, get_symbol, - helpers, shared_intermediates) + contract, helpers, shared_intermediates) from opt_einsum.backends import to_cupy, to_torch from opt_einsum.contract import _einsum from opt_einsum.parser import parse_einsum_input -from opt_einsum.sharing import count_cached_ops +from opt_einsum.sharing import count_cached_ops, currently_sharing, get_sharing_cache try: import cupy @@ -362,3 +362,23 @@ def test_chain_sharing(size, backend): print('Without sharing: {} expressions'.format(num_exprs_nosharing)) print('With sharing: {} expressions'.format(num_exprs_sharing)) assert num_exprs_nosharing > num_exprs_sharing + + +def test_multithreaded_sharing(): + from multiprocessing.pool import ThreadPool + + def fn(): + X, Y, Z = helpers.build_views('ab,bc,cd') + + with shared_intermediates(): + contract('ab,bc,cd->a', X, Y, Z) + contract('ab,bc,cd->b', X, Y, Z) + + return len(get_sharing_cache()) + + expected = fn() + pool = ThreadPool(8) + fs = [pool.apply_async(fn) for _ in range(16)] + assert not currently_sharing() + assert [f.get() for f in fs] == [expected] * 16 + pool.close()
Support multi-threading in shared_intermediates Following up on https://github.com/dgasmith/opt_einsum/pull/43#issuecomment-414661988, the `shared_intermediates` cache is currently not locked. One option would be to assign the thread id of a unique owner of the cache, such that at least thread conflicts could be detected and reported, rather than mere silent performance degradation.
0.0
284f233a4057e57ba8a3c1eef28e6bb6b8bfe2b1
[ "opt_einsum/tests/test_sharing.py::test_sharing_value[numpy-ab,bc->ca]", "opt_einsum/tests/test_sharing.py::test_sharing_value[numpy-abc,bcd,dea]", "opt_einsum/tests/test_sharing.py::test_sharing_value[numpy-abc,def->fedcba]", "opt_einsum/tests/test_sharing.py::test_sharing_value[numpy-abc,bcd,df->fa]", "opt_einsum/tests/test_sharing.py::test_sharing_value[numpy-ijk,ikj]", "opt_einsum/tests/test_sharing.py::test_sharing_value[numpy-i,j->ij]", "opt_einsum/tests/test_sharing.py::test_sharing_value[numpy-ijk,k->ij]", "opt_einsum/tests/test_sharing.py::test_sharing_value[numpy-AB,BC->CA]", "opt_einsum/tests/test_sharing.py::test_complete_sharing[numpy]", "opt_einsum/tests/test_sharing.py::test_sharing_reused_cache[numpy]", "opt_einsum/tests/test_sharing.py::test_no_sharing_separate_cache[numpy]", "opt_einsum/tests/test_sharing.py::test_sharing_nesting[numpy]", "opt_einsum/tests/test_sharing.py::test_sharing_modulo_commutativity[numpy-ab,bc->ca]", "opt_einsum/tests/test_sharing.py::test_sharing_modulo_commutativity[numpy-abc,bcd,dea]", "opt_einsum/tests/test_sharing.py::test_sharing_modulo_commutativity[numpy-abc,def->fedcba]", "opt_einsum/tests/test_sharing.py::test_sharing_modulo_commutativity[numpy-abc,bcd,df->fa]", "opt_einsum/tests/test_sharing.py::test_sharing_modulo_commutativity[numpy-ijk,ikj]", "opt_einsum/tests/test_sharing.py::test_sharing_modulo_commutativity[numpy-i,j->ij]", "opt_einsum/tests/test_sharing.py::test_sharing_modulo_commutativity[numpy-ijk,k->ij]", "opt_einsum/tests/test_sharing.py::test_sharing_modulo_commutativity[numpy-AB,BC->CA]", "opt_einsum/tests/test_sharing.py::test_partial_sharing[numpy]", "opt_einsum/tests/test_sharing.py::test_sharing_with_constants[numpy]", "opt_einsum/tests/test_sharing.py::test_chain[numpy-3]", "opt_einsum/tests/test_sharing.py::test_chain[numpy-4]", "opt_einsum/tests/test_sharing.py::test_chain[numpy-5]", "opt_einsum/tests/test_sharing.py::test_chain_2[numpy-3]", "opt_einsum/tests/test_sharing.py::test_chain_2[numpy-4]", "opt_einsum/tests/test_sharing.py::test_chain_2[numpy-5]", "opt_einsum/tests/test_sharing.py::test_chain_2[numpy-10]", "opt_einsum/tests/test_sharing.py::test_chain_2_growth[numpy]", "opt_einsum/tests/test_sharing.py::test_chain_sharing[numpy-3]", "opt_einsum/tests/test_sharing.py::test_chain_sharing[numpy-4]", "opt_einsum/tests/test_sharing.py::test_chain_sharing[numpy-5]", "opt_einsum/tests/test_sharing.py::test_multithreaded_sharing" ]
[]
{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2018-08-24 18:55:58+00:00
mit
1,909
dgasmith__opt_einsum-84
diff --git a/opt_einsum/__init__.py b/opt_einsum/__init__.py index 3d8b47b..0ec9eb6 100644 --- a/opt_einsum/__init__.py +++ b/opt_einsum/__init__.py @@ -6,15 +6,18 @@ from . import blas from . import helpers from . import paths from . import path_random -# Handle versioneer -from ._version import get_versions from .contract import contract, contract_path, contract_expression from .parser import get_symbol from .sharing import shared_intermediates from .paths import BranchBound from .path_random import RandomGreedy +# Handle versioneer +from ._version import get_versions versions = get_versions() __version__ = versions['version'] __git_revision__ = versions['full-revisionid'] del get_versions, versions + + +paths.register_path_fn('random-greedy', path_random.random_greedy) diff --git a/opt_einsum/contract.py b/opt_einsum/contract.py index 2f2d262..f7d2d91 100644 --- a/opt_einsum/contract.py +++ b/opt_einsum/contract.py @@ -13,10 +13,9 @@ from . import compat from . import helpers from . import parser from . import paths -from . import path_random from . import sharing -__all__ = ["contract_path", "contract", "format_const_einsum_str", "ContractExpression", "shape_only", "shape_only"] +__all__ = ["contract_path", "contract", "format_const_einsum_str", "ContractExpression", "shape_only"] class PathInfo(object): @@ -93,6 +92,9 @@ def _choose_memory_arg(memory_limit, size_list): return int(memory_limit) +_VALID_CONTRACT_KWARGS = {'optimize', 'path', 'memory_limit', 'einsum_call', 'use_blas', 'shapes'} + + def contract_path(*operands, **kwargs): """ Find a contraction order 'path', without performing the contraction. @@ -124,6 +126,9 @@ def contract_path(*operands, **kwargs): Use BLAS functions or not memory_limit : int, optional (default: None) Maximum number of elements allowed in intermediate arrays. + shapes : bool, optional + Whether ``contract_path`` should assume arrays (the default) or array + shapes have been supplied. Returns ------- @@ -193,8 +198,7 @@ def contract_path(*operands, **kwargs): """ # Make sure all keywords are valid - valid_contract_kwargs = ['optimize', 'path', 'memory_limit', 'einsum_call', 'use_blas'] - unknown_kwargs = [k for (k, v) in kwargs.items() if k not in valid_contract_kwargs] + unknown_kwargs = set(kwargs) - _VALID_CONTRACT_KWARGS if len(unknown_kwargs): raise TypeError("einsum_path: Did not understand the following kwargs: {}".format(unknown_kwargs)) @@ -206,6 +210,7 @@ def contract_path(*operands, **kwargs): path_type = kwargs.pop('optimize', 'auto') memory_limit = kwargs.pop('memory_limit', None) + shapes = kwargs.pop('shapes', False) # Hidden option, only einsum should call this einsum_call_arg = kwargs.pop("einsum_call", False) @@ -217,7 +222,10 @@ def contract_path(*operands, **kwargs): # Build a few useful list and sets input_list = input_subscripts.split(',') input_sets = [set(x) for x in input_list] - input_shps = [x.shape for x in operands] + if shapes: + input_shps = operands + else: + input_shps = [x.shape for x in operands] output_set = set(output_subscript) indices = set(input_subscripts.replace(',', '')) @@ -257,29 +265,17 @@ def contract_path(*operands, **kwargs): # Compute the path if not isinstance(path_type, (compat.strings, paths.PathOptimizer)): + # Custom path supplied path = path_type - elif num_ops == 1: - # Nothing to be optimized - path = [(0, )] - elif num_ops == 2: + elif num_ops <= 2: # Nothing to be optimized - path = [(0, 1)] + path = [tuple(range(num_ops))] elif isinstance(path_type, paths.PathOptimizer): + # Custom path optimizer supplied path = path_type(input_sets, output_set, dimension_dict, memory_arg) - elif path_type == "optimal" or (path_type == "auto" and num_ops <= 4): - path = paths.optimal(input_sets, output_set, dimension_dict, memory_arg) - elif path_type == 'branch-all' or (path_type == "auto" and num_ops <= 6): - path = paths.branch(input_sets, output_set, dimension_dict, memory_arg, nbranch=None) - elif path_type == 'branch-2' or (path_type == "auto" and num_ops <= 8): - path = paths.branch(input_sets, output_set, dimension_dict, memory_arg, nbranch=2) - elif path_type == 'branch-1' or (path_type == "auto" and num_ops <= 14): - path = paths.branch(input_sets, output_set, dimension_dict, memory_arg, nbranch=1) - elif path_type == 'random-greedy': - path = path_random.random_greedy(input_sets, output_set, dimension_dict, memory_arg) - elif path_type in ("auto", "greedy", "eager", "opportunistic"): - path = paths.greedy(input_sets, output_set, dimension_dict, memory_arg) else: - raise KeyError("Path name '{}' not found".format(path_type)) + path_optimizer = paths.get_path_fn(path_type) + path = path_optimizer(input_sets, output_set, dimension_dict, memory_arg) cost_list = [] scale_list = [] diff --git a/opt_einsum/path_random.py b/opt_einsum/path_random.py index 5f40cc8..49bf95e 100644 --- a/opt_einsum/path_random.py +++ b/opt_einsum/path_random.py @@ -11,13 +11,13 @@ import functools from collections import deque from . import helpers -from .paths import PathOptimizer, ssa_greedy_optimize, get_better_fn, ssa_to_linear, calc_k12_flops +from . import paths __all__ = ["RandomGreedy", "random_greedy"] -class RandomOptimizer(PathOptimizer): +class RandomOptimizer(paths.PathOptimizer): """Base class for running any random path finder that benefits from repeated calling, possibly in a parallel fashion. Custom random optimizers should subclass this, and the ``setup`` method should be @@ -81,7 +81,7 @@ class RandomOptimizer(PathOptimizer): self.max_repeats = max_repeats self.max_time = max_time self.minimize = minimize - self.better = get_better_fn(minimize) + self.better = paths.get_better_fn(minimize) self.parallel = parallel self.pre_dispatch = pre_dispatch @@ -95,7 +95,7 @@ class RandomOptimizer(PathOptimizer): def path(self): """The best path found so far. """ - return ssa_to_linear(self.best['ssa_path']) + return paths.ssa_to_linear(self.best['ssa_path']) @property def parallel(self): @@ -256,7 +256,7 @@ def thermal_chooser(queue, remaining, nbranch=8, temperature=1, rel_temperature= # compute relative probability for each potential contraction if temperature == 0.0: - energies = [1 if cost == cmin else 0 for cost in costs] + energies = [1 if c == cmin else 0 for c in costs] else: # shift by cmin for numerical reasons energies = [math.exp(-(c - cmin) / temperature) for c in costs] @@ -282,7 +282,7 @@ def ssa_path_compute_cost(ssa_path, inputs, output, size_dict): max_size = 0 for i, j in ssa_path: - k12, flops12 = calc_k12_flops(inputs, output, remaining, i, j, size_dict) + k12, flops12 = paths.calc_k12_flops(inputs, output, remaining, i, j, size_dict) remaining.discard(i) remaining.discard(j) remaining.add(len(inputs)) @@ -302,7 +302,7 @@ def _trial_greedy_ssa_path_and_cost(r, inputs, output, size_dict, choose_fn, cos else: random.seed(r) - ssa_path = ssa_greedy_optimize(inputs, output, size_dict, choose_fn, cost_fn) + ssa_path = paths.ssa_greedy_optimize(inputs, output, size_dict, choose_fn, cost_fn) cost, size = ssa_path_compute_cost(ssa_path, inputs, output, size_dict) return ssa_path, cost, size diff --git a/opt_einsum/paths.py b/opt_einsum/paths.py index df800bf..8ce6a67 100644 --- a/opt_einsum/paths.py +++ b/opt_einsum/paths.py @@ -5,6 +5,7 @@ from __future__ import absolute_import, division, print_function import heapq import random +import functools import itertools from collections import defaultdict @@ -12,7 +13,8 @@ import numpy as np from . import helpers -__all__ = ["optimal", "BranchBound", "branch", "greedy"] + +__all__ = ["optimal", "BranchBound", "branch", "greedy", "auto", "get_path_fn"] _UNLIMITED_MEM = {-1, None, float('inf')} @@ -444,6 +446,11 @@ def branch(inputs, output, size_dict, memory_limit=None, **optimizer_kwargs): return optimizer(inputs, output, size_dict, memory_limit) +branch_all = functools.partial(branch, nbranch=None) +branch_2 = functools.partial(branch, nbranch=2) +branch_1 = functools.partial(branch, nbranch=1) + + def _get_candidate(output, sizes, remaining, footprints, dim_ref_counts, k1, k2, cost_fn): either = k1 | k2 two = k1 & k2 @@ -645,3 +652,53 @@ def greedy(inputs, output, size_dict, memory_limit=None, choose_fn=None, cost_fn ssa_path = ssa_greedy_optimize(inputs, output, size_dict, cost_fn=cost_fn, choose_fn=choose_fn) return ssa_to_linear(ssa_path) + + +_AUTO_CHOICES = {} +for i in range(1, 5): + _AUTO_CHOICES[i] = optimal +for i in range(5, 7): + _AUTO_CHOICES[i] = branch_all +for i in range(7, 9): + _AUTO_CHOICES[i] = branch_2 +for i in range(9, 15): + _AUTO_CHOICES[i] = branch_1 + + +def auto(inputs, output, size_dict, memory_limit=None): + """Finds the contraction path by automatically choosing the method based on + how many input arguments there are. + """ + N = len(inputs) + return _AUTO_CHOICES.get(N, greedy)(inputs, output, size_dict, memory_limit) + + +_PATH_OPTIONS = { + 'auto': auto, + 'optimal': optimal, + 'branch-all': branch_all, + 'branch-2': branch_2, + 'branch-1': branch_1, + 'greedy': greedy, + 'eager': greedy, + 'opportunistic': greedy, +} + + +def register_path_fn(name, fn): + """Add path finding function ``fn`` as an option with ``name``. + """ + if name in _PATH_OPTIONS: + raise KeyError("Path optimizer '{}' already exists.".format(name)) + + _PATH_OPTIONS[name.lower()] = fn + + +def get_path_fn(path_type): + """Get the correct path finding function from str ``path_type``. + """ + if path_type not in _PATH_OPTIONS: + raise KeyError("Path optimizer '{}' not found, valid options are {}." + .format(path_type, set(_PATH_OPTIONS.keys()))) + + return _PATH_OPTIONS[path_type]
dgasmith/opt_einsum
ff86c2c9d2bb51d9816b2a92c08787379d512eb2
diff --git a/opt_einsum/tests/test_backends.py b/opt_einsum/tests/test_backends.py index ca046e4..b596cf1 100644 --- a/opt_einsum/tests/test_backends.py +++ b/opt_einsum/tests/test_backends.py @@ -2,6 +2,7 @@ import numpy as np import pytest from opt_einsum import contract, helpers, contract_expression, backends, sharing +from opt_einsum.contract import infer_backend, parse_backend, Shaped try: import cupy @@ -337,3 +338,10 @@ def test_torch_with_constants(): assert isinstance(res_got3, torch.Tensor) res_got3 = res_got3.numpy() if res_got3.device.type == 'cpu' else res_got3.cpu().numpy() assert np.allclose(res_exp, res_got3) + + +def test_auto_backend_custom_array_no_tensordot(): + x = Shaped((1, 2, 3)) + # Shaped is an array-like object defined by opt_einsum - which has no TDOT + assert infer_backend(x) == 'opt_einsum' + assert parse_backend([x], 'auto') == 'numpy' diff --git a/opt_einsum/tests/test_contract.py b/opt_einsum/tests/test_contract.py index 7227e2d..775aac0 100644 --- a/opt_einsum/tests/test_contract.py +++ b/opt_einsum/tests/test_contract.py @@ -257,3 +257,9 @@ def test_linear_vs_ssa(equation): ssa_path = linear_to_ssa(linear_path) linear_path2 = ssa_to_linear(ssa_path) assert linear_path2 == linear_path + + +def test_contract_path_supply_shapes(): + eq = 'ab,bc,cd' + shps = [(2, 3), (3, 4), (4, 5)] + contract_path(eq, *shps, shapes=True) diff --git a/opt_einsum/tests/test_paths.py b/opt_einsum/tests/test_paths.py index a860ee7..33b876b 100644 --- a/opt_einsum/tests/test_paths.py +++ b/opt_einsum/tests/test_paths.py @@ -108,6 +108,16 @@ def test_flop_cost(): assert 2000 == oe.helpers.flop_count("abc", True, 2, size_dict) +def test_bad_path_option(): + with pytest.raises(KeyError): + oe.contract("a,b,c", [1], [2], [3], optimize='optimall') + + +def test_explicit_path(): + x = oe.contract("a,b,c", [1], [2], [3], optimize=[(1, 2), (0, 1)]) + assert x.item() == 6 + + def test_path_optimal(): test_func = oe.paths.optimal @@ -353,3 +363,22 @@ def test_custom_random_optimizer(): assert optimizer.was_used assert len(optimizer.costs) == 16 + + +def test_optimizer_registration(): + + def custom_optimizer(inputs, output, size_dict, memory_limit): + return [(0, 1)] * (len(inputs) - 1) + + with pytest.raises(KeyError): + oe.paths.register_path_fn('optimal', custom_optimizer) + + oe.paths.register_path_fn('custom', custom_optimizer) + assert 'custom' in oe.paths._PATH_OPTIONS + + eq = 'ab,bc,cd' + shapes = [(2, 3), (3, 4), (4, 5)] + path, path_info = oe.contract_path(eq, *shapes, shapes=True, + optimize='custom') + assert path == [(0, 1), (0, 1)] + del oe.paths._PATH_OPTIONS['custom']
FR: separate 'auto' strategy out of contract_path The 'auto' strategy is really nice, but it requires actual arrays because it is based into `contract_path`. Sometimes I want to get a path based merely on shapes. It should be easy to factor out the logic from `contract_path` to a new `paths.auto` that conforms to the standard shape-based path interface.
0.0
ff86c2c9d2bb51d9816b2a92c08787379d512eb2
[ "opt_einsum/tests/test_contract.py::test_contract_path_supply_shapes", "opt_einsum/tests/test_paths.py::test_optimizer_registration" ]
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{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2019-02-20 14:10:04+00:00
mit
1,910
dgilland__pydash-164
diff --git a/AUTHORS.rst b/AUTHORS.rst index a1843ad..d167ec9 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -24,3 +24,4 @@ Contributors - Gonzalo Naveira, `gonzalonaveira@github <https://github.com/gonzalonaveira>`_ - Wenbo Zhao, [email protected], `zhaowb@github <https://github.com/zhaowb>`_ - Mervyn Lee, `mervynlee94@github <https://github.com/mervynlee94>`_ +- Weineel Lee, `weineel@github <https://github.com/weineel>`_ diff --git a/src/pydash/objects.py b/src/pydash/objects.py index f3bed2b..6949e8e 100644 --- a/src/pydash/objects.py +++ b/src/pydash/objects.py @@ -934,7 +934,7 @@ def _merge_with(obj, *sources, **kwargs): if _result is not None: result = _result elif all_sequences or all_mappings: - result = _merge_with(obj_value, src_value, _setter=setter) + result = _merge_with(obj_value, src_value, iteratee=iteratee, _setter=setter) else: result = src_value
dgilland/pydash
fa61732c01b39cec0de66f958cef27e7f31bcac2
diff --git a/tests/test_objects.py b/tests/test_objects.py index 2217438..b218043 100644 --- a/tests/test_objects.py +++ b/tests/test_objects.py @@ -573,11 +573,11 @@ def test_merge_no_link_list(): [ ( ( - {"fruits": ["apple"], "vegetables": ["beet"]}, - {"fruits": ["banana"], "vegetables": ["carrot"]}, - lambda a, b: a + b if isinstance(a, list) else b, + {"fruits": ["apple"], "others": {"vegetables": ["beet"]}}, + {"fruits": ["banana"], "others": {"vegetables": ["carrot"]}}, + lambda a, b: a + b if isinstance(a, list) else None, ), - {"fruits": ["apple", "banana"], "vegetables": ["beet", "carrot"]}, + {"fruits": ["apple", "banana"], "others": {"vegetables": ["beet", "carrot"]}}, ), ], )
merge_with: iteratee is lost when _merge_with is recursing. ```python def merge_array(obj_val, src_val): if isinstance(obj_val, list) and isinstance(src_val, list): return difference(obj_val + src_val) merge_with({ 'd': { 'x': [2] } }, { 'd': { 'x': [5] } }, merge_array) ``` ### expect ``` { 'd': { 'x': [2, 5] } } ``` ### actual ``` { 'd': { 'x': [5] } } ```
0.0
fa61732c01b39cec0de66f958cef27e7f31bcac2
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{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2021-06-26 09:07:43+00:00
mit
1,911
dgilland__pydash-222
diff --git a/src/pydash/arrays.py b/src/pydash/arrays.py index d9540a5..03b1847 100644 --- a/src/pydash/arrays.py +++ b/src/pydash/arrays.py @@ -98,6 +98,9 @@ __all__ = ( T = t.TypeVar("T") T2 = t.TypeVar("T2") +T3 = t.TypeVar("T3") +T4 = t.TypeVar("T4") +T5 = t.TypeVar("T5") SequenceT = t.TypeVar("SequenceT", bound=t.Sequence) MutableSequenceT = t.TypeVar("MutableSequenceT", bound=t.MutableSequence) @@ -2387,9 +2390,34 @@ def unshift(array: t.List[T], *items: T2) -> t.List[t.Union[T, T2]]: return array # type: ignore -def unzip(array: t.Iterable[t.Iterable[T]]) -> t.List[t.List[T]]: [email protected] +def unzip(array: t.Iterable[t.Tuple[T, T2]]) -> t.List[t.Tuple[T, T2]]: + ... + + [email protected] +def unzip(array: t.Iterable[t.Tuple[T, T2, T3]]) -> t.List[t.Tuple[T, T2, T3]]: + ... + + [email protected] +def unzip(array: t.Iterable[t.Tuple[T, T2, T3, T4]]) -> t.List[t.Tuple[T, T2, T3, T4]]: + ... + + [email protected] +def unzip(array: t.Iterable[t.Tuple[T, T2, T3, T4, T5]]) -> t.List[t.Tuple[T, T2, T3, T4, T5]]: + ... + + [email protected] +def unzip(array: t.Iterable[t.Iterable[t.Any]]) -> t.List[t.Tuple[t.Any, ...]]: + ... + + +def unzip(array): """ - The inverse of :func:`zip_`, this method splits groups of elements into lists composed of + The inverse of :func:`zip_`, this method splits groups of elements into tuples composed of elements from each group at their corresponding indexes. Args: @@ -2400,24 +2428,38 @@ def unzip(array: t.Iterable[t.Iterable[T]]) -> t.List[t.List[T]]: Example: - >>> unzip([[1, 4, 7], [2, 5, 8], [3, 6, 9]]) - [[1, 2, 3], [4, 5, 6], [7, 8, 9]] + >>> unzip([(1, 4, 7), (2, 5, 8), (3, 6, 9)]) + [(1, 2, 3), (4, 5, 6), (7, 8, 9)] .. versionadded:: 1.0.0 + + .. versionchanged:: 8.0.0 + Support list of tuples instead. """ return zip_(*array) @t.overload def unzip_with( - array: t.Iterable[t.Iterable[T]], + array: t.Iterable[t.Tuple[T, T2]], iteratee: t.Union[ - t.Callable[[T, T, int, t.List[T]], T2], - t.Callable[[T, T, int], T2], - t.Callable[[T, T], T2], - t.Callable[[T], T2], + t.Callable[[t.Union[T, T2, T3], t.Union[T, T2], int], T3], + t.Callable[[t.Union[T, T2, T3], t.Union[T, T2]], T3], + t.Callable[[t.Union[T, T2, T3]], T3], ], -) -> t.List[T2]: +) -> t.List[T3]: + ... + + [email protected] +def unzip_with( + array: t.Iterable[t.Iterable[t.Any]], + iteratee: t.Union[ + t.Callable[[t.Any, t.Any, int], T3], + t.Callable[[t.Any, t.Any], T3], + t.Callable[[t.Any], T3], + ], +) -> t.List[T3]: ... @@ -2425,15 +2467,15 @@ def unzip_with( def unzip_with( array: t.Iterable[t.Iterable[T]], iteratee: None = None, -) -> t.List[t.List[T]]: +) -> t.List[t.Tuple[T]]: ... def unzip_with(array, iteratee=None): """ This method is like :func:`unzip` except that it accepts an iteratee to specify how regrouped - values should be combined. The iteratee is invoked with four arguments: ``(accumulator, value, - index, group)``. + values should be combined. The iteratee is invoked with three arguments: ``(accumulator, value, + index)``. Args: array: List to process. @@ -2445,7 +2487,7 @@ def unzip_with(array, iteratee=None): Example: >>> from pydash import add - >>> unzip_with([[1, 10, 100], [2, 20, 200]], add) + >>> unzip_with([(1, 10, 100), (2, 20, 200)], add) [3, 30, 300] .. versionadded:: 3.3.0 @@ -2624,7 +2666,43 @@ def xor_with(array, *lists, **kwargs): ) -def zip_(*arrays: t.Iterable[T]) -> t.List[t.List[T]]: [email protected] +def zip_(array1: t.Iterable[T], array2: t.Iterable[T2], /) -> t.List[t.Tuple[T, T2]]: + ... + + [email protected] +def zip_( + array1: t.Iterable[T], array2: t.Iterable[T2], array3: t.Iterable[T3], / +) -> t.List[t.Tuple[T, T2, T3]]: + ... + + [email protected] +def zip_( + array1: t.Iterable[T], array2: t.Iterable[T2], array3: t.Iterable[T3], array4: t.Iterable[T4], / +) -> t.List[t.Tuple[T, T2, T3, T4]]: + ... + + [email protected] +def zip_( + array1: t.Iterable[T], + array2: t.Iterable[T2], + array3: t.Iterable[T3], + array4: t.Iterable[T4], + array5: t.Iterable[T5], + /, +) -> t.List[t.Tuple[T, T2, T3, T4, T5]]: + ... + + [email protected] +def zip_(*arrays: t.Iterable[t.Any]) -> t.List[t.Tuple[t.Any, ...]]: + ... + + +def zip_(*arrays): """ Groups the elements of each array at their corresponding indexes. Useful for separate data sources that are coordinated through matching array indexes. @@ -2638,12 +2716,14 @@ def zip_(*arrays: t.Iterable[T]) -> t.List[t.List[T]]: Example: >>> zip_([1, 2, 3], [4, 5, 6], [7, 8, 9]) - [[1, 4, 7], [2, 5, 8], [3, 6, 9]] + [(1, 4, 7), (2, 5, 8), (3, 6, 9)] .. versionadded:: 1.0.0 + + .. versionchanged:: 8.0.0 + Return list of tuples instead of list of lists. """ - # zip returns as a list of tuples so convert to list of lists - return [list(item) for item in zip(*arrays)] + return list(zip(*arrays)) @t.overload @@ -2724,40 +2804,47 @@ def zip_object_deep(keys: t.Iterable[t.Any], values: t.Union[t.List[t.Any], None @t.overload def zip_with( - *arrays: t.Iterable[T], + array1: t.Iterable[T], + array2: t.Iterable[T2], + *, iteratee: t.Union[ - t.Callable[[T, T, int, t.List[T]], T2], - t.Callable[[T, T, int], T2], - t.Callable[[T, T], T2], - t.Callable[[T], T2], + t.Callable[[T, T2, int], T3], + t.Callable[[T, T2], T3], + t.Callable[[T], T3], ], -) -> t.List[T2]: +) -> t.List[T3]: ... @t.overload -def zip_with(*arrays: t.Iterable[T]) -> t.List[t.List[T]]: +def zip_with( + *arrays: t.Iterable[t.Any], + iteratee: t.Union[ + t.Callable[[t.Any, t.Any, int], T2], + t.Callable[[t.Any, t.Any], T2], + t.Callable[[t.Any], T2], + ], +) -> t.List[T2]: ... @t.overload def zip_with( *arrays: t.Union[ - t.Iterable[T], - t.Callable[[T, T, int, t.List[T]], T2], - t.Callable[[T, T, int], T2], - t.Callable[[T, T], T2], - t.Callable[[T], T2], + t.Iterable[t.Any], + t.Callable[[t.Any, t.Any, int], T2], + t.Callable[[t.Any, t.Any], T2], + t.Callable[[t.Any], T2], ], -) -> t.List[t.Union[t.List[T], T2]]: +) -> t.List[T2]: ... def zip_with(*arrays, **kwargs): """ This method is like :func:`zip` except that it accepts an iteratee to specify how grouped values - should be combined. The iteratee is invoked with four arguments: ``(accumulator, value, index, - group)``. + should be combined. The iteratee is invoked with three arguments: + ``(accumulator, value, index)``. Args: *arrays: Lists to process. diff --git a/src/pydash/chaining/all_funcs.pyi b/src/pydash/chaining/all_funcs.pyi index c1e3145..3d7f90a 100644 --- a/src/pydash/chaining/all_funcs.pyi +++ b/src/pydash/chaining/all_funcs.pyi @@ -562,23 +562,49 @@ class AllFuncs: def unshift(self: "Chain[t.List[T]]", *items: T2) -> "Chain[t.List[t.Union[T, T2]]]": return self._wrap(pyd.unshift)(*items) - def unzip(self: "Chain[t.Iterable[t.Iterable[T]]]") -> "Chain[t.List[t.List[T]]]": + @t.overload + def unzip(self: "Chain[t.Iterable[t.Tuple[T, T2]]]") -> "Chain[t.List[t.Tuple[T, T2]]]": ... + @t.overload + def unzip( + self: "Chain[t.Iterable[t.Tuple[T, T2, T3]]]", + ) -> "Chain[t.List[t.Tuple[T, T2, T3]]]": ... + @t.overload + def unzip( + self: "Chain[t.Iterable[t.Tuple[T, T2, T3, T4]]]", + ) -> "Chain[t.List[t.Tuple[T, T2, T3, T4]]]": ... + @t.overload + def unzip( + self: "Chain[t.Iterable[t.Tuple[T, T2, T3, T4, T5]]]", + ) -> "Chain[t.List[t.Tuple[T, T2, T3, T4, T5]]]": ... + @t.overload + def unzip( + self: "Chain[t.Iterable[t.Iterable[t.Any]]]", + ) -> "Chain[t.List[t.Tuple[t.Any, ...]]]": ... + def unzip(self): return self._wrap(pyd.unzip)() @t.overload def unzip_with( - self: "Chain[t.Iterable[t.Iterable[T]]]", + self: "Chain[t.Iterable[t.Tuple[T, T2]]]", iteratee: t.Union[ - t.Callable[[T, T, int, t.List[T]], T2], - t.Callable[[T, T, int], T2], - t.Callable[[T, T], T2], - t.Callable[[T], T2], + t.Callable[[t.Union[T, T2, T3], t.Union[T, T2], int], T3], + t.Callable[[t.Union[T, T2, T3], t.Union[T, T2]], T3], + t.Callable[[t.Union[T, T2, T3]], T3], ], - ) -> "Chain[t.List[T2]]": ... + ) -> "Chain[t.List[T3]]": ... + @t.overload + def unzip_with( + self: "Chain[t.Iterable[t.Iterable[t.Any]]]", + iteratee: t.Union[ + t.Callable[[t.Any, t.Any, int], T3], + t.Callable[[t.Any, t.Any], T3], + t.Callable[[t.Any], T3], + ], + ) -> "Chain[t.List[T3]]": ... @t.overload def unzip_with( self: "Chain[t.Iterable[t.Iterable[T]]]", iteratee: None = None - ) -> "Chain[t.List[t.List[T]]]": ... + ) -> "Chain[t.List[t.Tuple[T]]]": ... def unzip_with(self, iteratee=None): return self._wrap(pyd.unzip_with)(iteratee) @@ -612,7 +638,11 @@ class AllFuncs: def xor_with(self, *lists, **kwargs): return self._wrap(pyd.xor_with)(*lists, **kwargs) - def zip_(self: "Chain[t.Iterable[T]]", *arrays: t.Iterable[T]) -> "Chain[t.List[t.List[T]]]": + @t.overload + def zip_( + self: "Chain[t.Iterable[t.Any]]", *arrays: t.Iterable[t.Any] + ) -> "Chain[t.List[t.Tuple[t.Any, ...]]]": ... + def zip_(self, *arrays): return self._wrap(pyd.zip_)(*arrays) zip = zip_ @@ -638,29 +668,32 @@ class AllFuncs: @t.overload def zip_with( self: "Chain[t.Iterable[T]]", - *arrays: t.Iterable[T], + array2: t.Iterable[T2], + *, iteratee: t.Union[ - t.Callable[[T, T, int, t.List[T]], T2], - t.Callable[[T, T, int], T2], - t.Callable[[T, T], T2], - t.Callable[[T], T2], + t.Callable[[T, T2, int], T3], t.Callable[[T, T2], T3], t.Callable[[T], T3] ], - ) -> "Chain[t.List[T2]]": ... + ) -> "Chain[t.List[T3]]": ... @t.overload def zip_with( - self: "Chain[t.Iterable[T]]", *arrays: t.Iterable[T] - ) -> "Chain[t.List[t.List[T]]]": ... + self: "Chain[t.Iterable[t.Any]]", + *arrays: t.Iterable[t.Any], + iteratee: t.Union[ + t.Callable[[t.Any, t.Any, int], T2], + t.Callable[[t.Any, t.Any], T2], + t.Callable[[t.Any], T2], + ], + ) -> "Chain[t.List[T2]]": ... @t.overload def zip_with( - self: "Chain[t.Union[t.Iterable[T], t.Callable[[T, T, int, t.List[T]], T2], t.Callable[[T, T, int], T2], t.Callable[[T, T], T2], t.Callable[[T], T2]]]", + self: "Chain[t.Union[t.Iterable[t.Any], t.Callable[[t.Any, t.Any, int], T2], t.Callable[[t.Any, t.Any], T2], t.Callable[[t.Any], T2]]]", *arrays: t.Union[ - t.Iterable[T], - t.Callable[[T, T, int, t.List[T]], T2], - t.Callable[[T, T, int], T2], - t.Callable[[T, T], T2], - t.Callable[[T], T2], + t.Iterable[t.Any], + t.Callable[[t.Any, t.Any, int], T2], + t.Callable[[t.Any, t.Any], T2], + t.Callable[[t.Any], T2], ], - ) -> "Chain[t.List[t.Union[t.List[T], T2]]]": ... + ) -> "Chain[t.List[T2]]": ... def zip_with(self, *arrays, **kwargs): return self._wrap(pyd.zip_with)(*arrays, **kwargs) @@ -2689,9 +2722,9 @@ class AllFuncs: return self._wrap(pyd.to_number)(precision) @t.overload - def to_pairs(self: "Chain[t.Mapping[T, T2]]") -> "Chain[t.List[t.List[t.Union[T, T2]]]]": ... + def to_pairs(self: "Chain[t.Mapping[T, T2]]") -> "Chain[t.List[t.Tuple[T, T2]]]": ... @t.overload - def to_pairs(self: "Chain[t.Iterable[T]]") -> "Chain[t.List[t.List[t.Union[int, T]]]]": ... + def to_pairs(self: "Chain[t.Iterable[T]]") -> "Chain[t.List[t.Tuple[int, T]]]": ... @t.overload def to_pairs(self: "Chain[t.Any]") -> "Chain[t.List]": ... def to_pairs(self): diff --git a/src/pydash/objects.py b/src/pydash/objects.py index d5a7c66..c325cb9 100644 --- a/src/pydash/objects.py +++ b/src/pydash/objects.py @@ -2114,12 +2114,12 @@ def to_number(obj: t.Any, precision: int = 0) -> t.Union[float, None]: @t.overload -def to_pairs(obj: t.Mapping[T, T2]) -> t.List[t.List[t.Union[T, T2]]]: +def to_pairs(obj: t.Mapping[T, T2]) -> t.List[t.Tuple[T, T2]]: ... @t.overload -def to_pairs(obj: t.Iterable[T]) -> t.List[t.List[t.Union[int, T]]]: +def to_pairs(obj: t.Iterable[T]) -> t.List[t.Tuple[int, T]]: ... @@ -2130,28 +2130,31 @@ def to_pairs(obj: t.Any) -> t.List: def to_pairs(obj): """ - Creates a two-dimensional list of an object's key-value pairs, i.e., ``[[key1, value1], [key2, - value2]]``. + Creates a list of tuples of an object's key-value pairs, i.e., + ``[(key1, value1), (key2, value2)]``. Args: obj: Object to process. Returns: - Two dimensional list of object's key-value pairs. + List of tuples of the object's key-value pairs. Example: >>> to_pairs([1, 2, 3, 4]) - [[0, 1], [1, 2], [2, 3], [3, 4]] + [(0, 1), (1, 2), (2, 3), (3, 4)] >>> to_pairs({"a": 1}) - [['a', 1]] + [('a', 1)] .. versionadded:: 1.0.0 .. versionchanged:: 4.0.0 Renamed from ``pairs`` to ``to_pairs``. + + .. versionchanged:: 8.0.0 + Returning list of tuples instead of list of lists. """ - return [[key, value] for key, value in iterator(obj)] + return [(key, value) for key, value in iterator(obj)] def to_string(obj: t.Any) -> str:
dgilland/pydash
ef48d55fb5eecf5d3da3a69cab337e6345b1fc29
diff --git a/tests/pytest_mypy_testing/test_arrays.py b/tests/pytest_mypy_testing/test_arrays.py index 2e30951..d7d6cb3 100644 --- a/tests/pytest_mypy_testing/test_arrays.py +++ b/tests/pytest_mypy_testing/test_arrays.py @@ -408,8 +408,7 @@ def test_mypy_unshift() -> None: @pytest.mark.mypy_testing def test_mypy_unzip() -> None: - reveal_type(_.unzip([[1, 4, 7], [2, 5, 8], [3, 6, 9]])) # R: builtins.list[builtins.list[builtins.int]] - reveal_type(_.unzip([(1, 4, 7), (2, 5, 8), (3, 6, 9)])) # R: builtins.list[builtins.list[builtins.int]] + reveal_type(_.unzip([(1, 4, 7), (2, 5, 8), (3, 6, 9)])) # R: builtins.list[Tuple[builtins.int, builtins.int, builtins.int]] @pytest.mark.mypy_testing @@ -447,7 +446,8 @@ def test_mypy_xor_with() -> None: @pytest.mark.mypy_testing def test_mypy_zip_() -> None: - reveal_type(_.zip_([1, 2, 3], [4, 5, 6], [7, 8, 9])) # R: builtins.list[builtins.list[builtins.int]] + reveal_type(_.zip_([1, 2, 3], [4, 5, 6], [7, 8, 9])) # R: builtins.list[Tuple[builtins.int, builtins.int, builtins.int]] + reveal_type(_.zip_([1, 2, 3], ["one", "two", "three"])) # R: builtins.list[Tuple[builtins.int, builtins.str]] @pytest.mark.mypy_testing @@ -469,5 +469,10 @@ def test_mypy_zip_with() -> None: def add(x: int, y: int) -> int: return x + y - reveal_type(_.zip_with([1, 2], [10, 20], [100, 200], add)) # R: builtins.list[Union[builtins.list[builtins.int], builtins.int]] + reveal_type(_.zip_with([1, 2], [10, 20], add)) # R: builtins.list[builtins.int] reveal_type(_.zip_with([1, 2], [10, 20], [100, 200], iteratee=add)) # R: builtins.list[builtins.int] + + def more_hello(s: str, n: int) -> str: + return s * n + + reveal_type(_.zip_with(["hello", "hello", "hello"], [1, 2, 3], iteratee=more_hello)) # R: builtins.list[builtins.str] diff --git a/tests/pytest_mypy_testing/test_objects.py b/tests/pytest_mypy_testing/test_objects.py index b4df527..28645e0 100644 --- a/tests/pytest_mypy_testing/test_objects.py +++ b/tests/pytest_mypy_testing/test_objects.py @@ -298,8 +298,8 @@ def test_mypy_to_number() -> None: @pytest.mark.mypy_testing def test_mypy_to_pairs() -> None: - reveal_type(_.to_pairs([1, 2, 3, 4])) # R: builtins.list[builtins.list[builtins.int]] - reveal_type(_.to_pairs({'a': 1})) # R: builtins.list[builtins.list[Union[builtins.str, builtins.int]]] + reveal_type(_.to_pairs([1, 2, 3, 4])) # R: builtins.list[Tuple[builtins.int, builtins.int]] + reveal_type(_.to_pairs({'a': 1})) # R: builtins.list[Tuple[builtins.str, builtins.int]] reveal_type(_.to_pairs(MyClass())) # R: builtins.list[Any] diff --git a/tests/test_arrays.py b/tests/test_arrays.py index cdf6217..a0070cf 100644 --- a/tests/test_arrays.py +++ b/tests/test_arrays.py @@ -853,8 +853,8 @@ def test_unshift(case, expected): "case,expected", [ ( - [["moe", 30, True], ["larry", 40, False], ["curly", 35, True]], - [["moe", "larry", "curly"], [30, 40, 35], [True, False, True]], + [("moe", 30, True), ("larry", 40, False), ("curly", 35, True)], + [("moe", "larry", "curly"), (30, 40, 35), (True, False, True)], ) ], ) @@ -866,7 +866,7 @@ def test_unzip(case, expected): "case,expected", [ (([],), []), - (([[1, 10, 100], [2, 20, 200]],), [[1, 2], [10, 20], [100, 200]]), + (([[1, 10, 100], [2, 20, 200]],), [(1, 2), (10, 20), (100, 200)]), (([[2, 4, 6], [2, 2, 2]], _.power), [4, 16, 36]), ], ) @@ -902,7 +902,7 @@ def test_xor_with(case, expected): [ ( (["moe", "larry", "curly"], [30, 40, 35], [True, False, True]), - [["moe", 30, True], ["larry", 40, False], ["curly", 35, True]], + [("moe", 30, True), ("larry", 40, False), ("curly", 35, True)], ) ], ) @@ -935,7 +935,7 @@ def test_zip_object_deep(case, expected): @parametrize( "case,expected", [ - (([1, 2],), [[1], [2]]), + (([1, 2],), [(1,), (2,)]), (([1, 2], [3, 4], _.add), [4, 6]), ], ) diff --git a/tests/test_objects.py b/tests/test_objects.py index d3328cf..d0f0ea4 100644 --- a/tests/test_objects.py +++ b/tests/test_objects.py @@ -847,8 +847,8 @@ def test_to_number(case, expected): @parametrize( "case,expected", [ - ({"a": 1, "b": 2, "c": 3}, [["a", 1], ["b", 2], ["c", 3]]), - ([1, 2, 3], [[0, 1], [1, 2], [2, 3]]), + ({"a": 1, "b": 2, "c": 3}, [("a", 1), ("b", 2), ("c", 3)]), + ([1, 2, 3], [(0, 1), (1, 2), (2, 3)]), ], ) def test_to_pairs(case, expected):
Embrace the tuple Would you be open to PR that switches `zip_`, `zip_with` and `to_pairs` to return list of tuples instead? Using a list in python is very similar to using a tuple but in static typing having lists is a bit annoying. For example: ```py import pydash d: dict[str, int] = {"key1": 1, "key2": 2} pairs = pydash.to_pairs(d) # this is list[list[str | int]] first_key, first_value = pairs[0] # first_key is `str | int` and first_value is `str | int` ``` This doesn't make much sense, we know `first_key` should be `str` and `first_value` should be `int`. If `to_pairs` returned list of tuples instead we could type it better and not have this problem. Same with `zip_`: ```py import pydash zipped = pydash.zip_([1, 2, 3], ["hello", "hello", "hello"]) ``` `zipped` is a list of lists of `str | int`, we lost the order on the type level, int and str are blend in the lists. And I think the hardest to work with might be `zip_with` ```py import pydash def more_hello(s: str, time: int) -> str: return s.upper() * time zipped = pydash.zip_with( ["hello", "hello", "hello"], [1, 2, 3], iteratee=more_hello # type error here: cannot assign `str | int` to `str` and `str | int` to `int` ) ``` while this is valid at runtime, the type checker doesn't know that the first argument is `str` and second is `int` because it is all blend into the `list[str | int]` This makes them really hard to use in a type checked context. Chaining functions with the result of these functions is very impractical. I think it would make a lot more sense for these functions to return tuples.
0.0
ef48d55fb5eecf5d3da3a69cab337e6345b1fc29
[ "tests/pytest_mypy_testing/test_arrays.py::[mypy]test_mypy_unzip", "tests/pytest_mypy_testing/test_arrays.py::[mypy]test_mypy_zip_", "tests/pytest_mypy_testing/test_arrays.py::[mypy]test_mypy_zip_with", "tests/pytest_mypy_testing/test_objects.py::[mypy]test_mypy_to_pairs", "tests/test_arrays.py::test_unzip[case0-expected0]", "tests/test_arrays.py::test_unzip_with[case1-expected1]", "tests/test_arrays.py::test_zip_[case0-expected0]", "tests/test_arrays.py::test_zip_with[case0-expected0]" ]
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"tests/test_objects.py::test_get__does_not_raise_for_objects_when_path_is_unrestricted[obj1-foo.__dict__]", "tests/test_objects.py::test_get__does_not_raise_for_objects_when_path_is_unrestricted[obj2-__len__]", "tests/test_objects.py::test_has[case0-True]", "tests/test_objects.py::test_has[case1-True]", "tests/test_objects.py::test_has[case2-True]", "tests/test_objects.py::test_has[case3-False]", "tests/test_objects.py::test_has[case4-True]", "tests/test_objects.py::test_has[case5-True]", "tests/test_objects.py::test_has[case6-True]", "tests/test_objects.py::test_has[case7-False]", "tests/test_objects.py::test_has[case8-True]", "tests/test_objects.py::test_has[case9-True]", "tests/test_objects.py::test_has[case10-True]", "tests/test_objects.py::test_has[case11-True]", "tests/test_objects.py::test_has[case12-False]", "tests/test_objects.py::test_has[case13-False]", "tests/test_objects.py::test_has[case14-False]", "tests/test_objects.py::test_has[case15-False]", 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"tests/test_objects.py::test_rename_keys[case1-expected1]", "tests/test_objects.py::test_rename_keys[case2-expected2]", "tests/test_objects.py::test_set_[case0-expected0]", "tests/test_objects.py::test_set_[case1-expected1]", "tests/test_objects.py::test_set_[case2-expected2]", "tests/test_objects.py::test_set_[case3-expected3]", "tests/test_objects.py::test_set_[case4-expected4]", "tests/test_objects.py::test_set_[case5-expected5]", "tests/test_objects.py::test_set_[case6-expected6]", "tests/test_objects.py::test_set_[case7-expected7]", "tests/test_objects.py::test_set_[case8-expected8]", "tests/test_objects.py::test_set_[case9-expected9]", "tests/test_objects.py::test_set_[case10-expected10]", "tests/test_objects.py::test_set_[case11-expected11]", "tests/test_objects.py::test_set_[case12-expected12]", "tests/test_objects.py::test_set_[case13-expected13]", "tests/test_objects.py::test_set_[case14-expected14]", "tests/test_objects.py::test_set_on_class_works_the_same_with_string_and_list", "tests/test_objects.py::test_set_with[case0-expected0]", "tests/test_objects.py::test_set_with[case1-expected1]", "tests/test_objects.py::test_set_with[case2-expected2]", "tests/test_objects.py::test_set_with[case3-expected3]", "tests/test_objects.py::test_to_boolean[case0-True]", "tests/test_objects.py::test_to_boolean[case1-False]", "tests/test_objects.py::test_to_boolean[case2-True]", "tests/test_objects.py::test_to_boolean[case3-True]", "tests/test_objects.py::test_to_boolean[case4-False]", "tests/test_objects.py::test_to_boolean[case5-False]", "tests/test_objects.py::test_to_boolean[case6-None]", "tests/test_objects.py::test_to_boolean[case7-None]", "tests/test_objects.py::test_to_boolean[case8-False]", "tests/test_objects.py::test_to_boolean[case9-True]", "tests/test_objects.py::test_to_boolean[case10-False]", "tests/test_objects.py::test_to_boolean[case11-True]", 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"tests/test_objects.py::test_to_integer[case10-0]", "tests/test_objects.py::test_to_number[case0-3.0]", "tests/test_objects.py::test_to_number[case1-2.6]", "tests/test_objects.py::test_to_number[case2-990.0]", "tests/test_objects.py::test_to_number[case3-None]", "tests/test_objects.py::test_to_pairs[case0-expected0]", "tests/test_objects.py::test_to_pairs[case1-expected1]", "tests/test_objects.py::test_to_string[1-1]", "tests/test_objects.py::test_to_string[1.25-1.25]", "tests/test_objects.py::test_to_string[True-True]", "tests/test_objects.py::test_to_string[case3-[1]]", "tests/test_objects.py::test_to_string[d\\xc3\\xa9j\\xc3\\xa0", "tests/test_objects.py::test_to_string[-]", "tests/test_objects.py::test_to_string[None-]", "tests/test_objects.py::test_to_string[case7-2024-08-08]", "tests/test_objects.py::test_transform[case0-expected0]", "tests/test_objects.py::test_transform[case1-expected1]", "tests/test_objects.py::test_transform[case2-expected2]", "tests/test_objects.py::test_update[case0-expected0]", "tests/test_objects.py::test_update[case1-expected1]", "tests/test_objects.py::test_update[case2-expected2]", "tests/test_objects.py::test_update_with[case0-expected0]", "tests/test_objects.py::test_update_with[case1-expected1]", "tests/test_objects.py::test_update_with[case2-expected2]", "tests/test_objects.py::test_unset[obj0-a.0.b.c-True-new_obj0]", "tests/test_objects.py::test_unset[obj1-1-True-new_obj1]", "tests/test_objects.py::test_unset[obj2-1-True-new_obj2]", "tests/test_objects.py::test_unset[obj3-path3-True-new_obj3]", "tests/test_objects.py::test_unset[obj4-[0][0]-False-new_obj4]", "tests/test_objects.py::test_unset[obj5-[0][0][0]-False-new_obj5]", "tests/test_objects.py::test_values[case0-expected0]", "tests/test_objects.py::test_values[case1-expected1]" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2024-02-20 03:09:03+00:00
mit
1,912
dhatim__python-license-check-75
diff --git a/liccheck/requirements.py b/liccheck/requirements.py index 8bfc446..8c8e106 100644 --- a/liccheck/requirements.py +++ b/liccheck/requirements.py @@ -25,6 +25,10 @@ def parse_requirements(requirement_file): for req in pip_parse_requirements(requirement_file, session=PipSession()): install_req = install_req_from_parsed_requirement(req) if install_req.markers and not pkg_resources.evaluate_marker(str(install_req.markers)): + # req should not installed due to env markers + continue + elif install_req.editable: + # skip editable req as they are failing in the resolve phase continue requirements.append(pkg_resources.Requirement.parse(str(install_req.req))) return requirements
dhatim/python-license-check
6f804d1314997075883a57ce24baa5a8ee4afe98
diff --git a/tests/test_get_packages_info.py b/tests/test_get_packages_info.py index 1ec99b0..8daadbe 100644 --- a/tests/test_get_packages_info.py +++ b/tests/test_get_packages_info.py @@ -11,6 +11,7 @@ def test_license_strip(tmpfile): tmpfh.close() assert get_packages_info(tmppath)[0]["licenses"] == ["MIT"] + def test_requirements_markers(tmpfile): tmpfh, tmppath = tmpfile tmpfh.write( @@ -24,6 +25,19 @@ def test_requirements_markers(tmpfile): assert len(get_packages_info(tmppath)) == 1 +def test_editable_requirements_get_ignored(tmpfile): + tmpfh, tmppath = tmpfile + tmpfh.write( + "-e file:some_editable_req\n" + "pip\n" + ) + tmpfh.close() + + packages_info = get_packages_info(tmppath) + assert len(packages_info) == 1 + assert packages_info[0]["name"] == "pip" + + @pytest.mark.parametrize( ('no_deps', 'expected_packages'), ( pytest.param(
Editable requirements (-e) raises "DistributionNotFound: The 'None' distribution was not found" Editable requirements, i.e: rows like this one `-e file:some_internal_package # via -r requirements.in` Are currently making this library fail with `pkg_resources.DistributionNotFound: The 'None' distribution was not found and is required by the application` This is kind of related to https://github.com/dhatim/python-license-check/issues/33 but although error message is the same, it is actually a different problem as that one relates to `git+https://` construct, and this one, to the `-e` construct
0.0
6f804d1314997075883a57ce24baa5a8ee4afe98
[ "tests/test_get_packages_info.py::test_editable_requirements_get_ignored" ]
[ "tests/test_get_packages_info.py::test_license_strip", "tests/test_get_packages_info.py::test_deps[with", "tests/test_get_packages_info.py::test_deps[without" ]
{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }
2021-07-12 08:57:27+00:00
apache-2.0
1,913
dicompyler__dicompyler-core-96
diff --git a/.travis.yml b/.travis.yml index 8de7b4f..d399453 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,7 +1,6 @@ language: python python: - 2.7 - - 3.4 - 3.5 - 3.6 install: diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst index e37af2c..048bc4b 100644 --- a/CONTRIBUTING.rst +++ b/CONTRIBUTING.rst @@ -101,7 +101,7 @@ Before you submit a pull request, check that it meets these guidelines: 2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst. -3. The pull request should work for Python 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check +3. The pull request should work for Python 2.7, 3.5, and 3.6. Check https://travis-ci.org/dicompyler/dicompyler-core/pull_requests and make sure that the tests pass for all supported Python versions. diff --git a/README.rst b/README.rst index cf7c59f..c24a703 100644 --- a/README.rst +++ b/README.rst @@ -15,7 +15,7 @@ Other information - Free software: `BSD license <https://github.com/dicompyler/dicompyler-core/blob/master/LICENSE>`__ - Documentation: `Read the docs <https://dicompyler-core.readthedocs.io>`__ -- Tested on Python 2.7, 3.4, 3.5, 3.6 +- Tested on Python 2.7, 3.5, 3.6 Dependencies ------------ diff --git a/dicompylercore/dicomparser.py b/dicompylercore/dicomparser.py index 3be8daa..2aa8346 100755 --- a/dicompylercore/dicomparser.py +++ b/dicompylercore/dicomparser.py @@ -410,7 +410,7 @@ class DicomParser: if (pixel_array.min() < wmin): wmin = pixel_array.min() # Default window is the range of the data array - window = int(abs(wmax) + abs(wmin)) + window = int(wmax - wmin) # Default level is the range midpoint minus the window minimum level = int(window / 2 - abs(wmin)) return window, level diff --git a/dicompylercore/dvh.py b/dicompylercore/dvh.py index 24155a4..14c2777 100644 --- a/dicompylercore/dvh.py +++ b/dicompylercore/dvh.py @@ -262,7 +262,7 @@ class DVH(object): @property def max(self): """Return the maximum dose.""" - if self.counts.size == 1: + if self.counts.size <= 1 or max(self.counts) == 0: return 0 diff = self.differential # Find the the maximum non-zero dose bin @@ -271,7 +271,7 @@ class DVH(object): @property def min(self): """Return the minimum dose.""" - if self.counts.size == 1: + if self.counts.size <= 1 or max(self.counts) == 0: return 0 diff = self.differential # Find the the minimum non-zero dose bin @@ -280,7 +280,7 @@ class DVH(object): @property def mean(self): """Return the mean dose.""" - if self.counts.size == 1: + if self.counts.size <= 1 or max(self.counts) == 0: return 0 diff = self.differential # Find the area under the differential histogram @@ -462,7 +462,7 @@ class DVH(object): else: volume_counts = self.absolute_volume(self.volume).counts - if volume > volume_counts.max(): + if volume_counts.size == 0 or volume > volume_counts.max(): return DVHValue(0.0, self.dose_units) # D100 case diff --git a/requirements_dev.txt b/requirements_dev.txt index 8193cbd..7af08f4 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -1,8 +1,8 @@ bumpversion==0.5.3 -wheel==0.32.3 -flake8==3.6.0 -tox==3.6.1 +wheel==0.33.1 +flake8==3.7.7 +tox==3.7.0 coverage==4.5.2 -Sphinx==1.8.3 -sphinx-rtd-theme==0.4.2 -cryptography==2.4.2 +Sphinx==1.8.4 +sphinx-rtd-theme==0.4.3 +cryptography==2.6.1 diff --git a/setup.py b/setup.py index 59ad242..82124af 100644 --- a/setup.py +++ b/setup.py @@ -62,8 +62,6 @@ setup( "Programming Language :: Python :: 2", 'Programming Language :: Python :: 2.7', 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.3', - 'Programming Language :: Python :: 3.4', 'Programming Language :: Python :: 3.5', 'Programming Language :: Python :: 3.6', 'Topic :: Scientific/Engineering :: Medical Science Apps.',
dicompyler/dicompyler-core
f5f9fa770d0573373510135863fa2933919cdba7
diff --git a/tests/test_dvh.py b/tests/test_dvh.py index 6c9d403..3e64782 100644 --- a/tests/test_dvh.py +++ b/tests/test_dvh.py @@ -204,6 +204,27 @@ class TestDVH(unittest.TestCase): self.dvh.name = "test" self.assertEqual(self.dvh.plot(), self.dvh) + def test_dvh_statistics_with_no_counts(self): + subject = dvh.DVH(array([]), array([0])) + self.assertEqual(subject.max, 0) + self.assertEqual(subject.min, 0) + self.assertEqual(subject.mean, 0) + + def test_dose_constraint_with_no_counts(self): + subject = dvh.DVH(array([]), array([0])) + subject.dose_constraint(1) + + def test_dvh_statistics_with_zero_volume(self): + subject = dvh.DVH(array([0, 0]), array([0, 1])) + self.assertEqual(subject.max, 0) + self.assertEqual(subject.min, 0) + self.assertEqual(subject.mean, 0) + + def test_dose_constraint_with_zero_volume(self): + subject = dvh.DVH(array([0, 0]), array([0, 1])) + subject.dose_constraint(1) + + if __name__ == '__main__': import sys sys.exit(unittest.main())
dvh.max gives IndexError Hello and thank you for the project. I am using dicompyler-core 0.5.4 to extract statistics and I have been running into an exception with certain DCM files. When calculating `dvh.max`, the following error is thrown: ``` File "/home/nico/.local/share/virtualenvs/dcm-extractor-8Y6EYVZw/lib/python3.7/site-packages/dicompylercore/dvh.py", line 269, in max return diff.bins[1:][diff.counts > 0][-1] IndexError: boolean index did not match indexed array along dimension 0; dimension is 0 but corresponding boolean dimension is 1 ``` This seems to happen whenever dvh.counts is either empty, or has all same values (such that dvh.diff.counts is all 0s). Please let me know if I can assist in troubleshooting.
0.0
f5f9fa770d0573373510135863fa2933919cdba7
[ "tests/test_dvh.py::TestDVH::test_dose_constraint_with_no_counts", "tests/test_dvh.py::TestDVH::test_dose_constraint_with_zero_volume", "tests/test_dvh.py::TestDVH::test_dvh_statistics_with_no_counts", "tests/test_dvh.py::TestDVH::test_dvh_statistics_with_zero_volume" ]
[ "tests/test_dvh.py::TestDVH::test_absolute_relative_dose_dvh", "tests/test_dvh.py::TestDVH::test_absolute_relative_full_conversion", "tests/test_dvh.py::TestDVH::test_absolute_relative_volume_dvh", "tests/test_dvh.py::TestDVH::test_cumulative_dvh", "tests/test_dvh.py::TestDVH::test_differential_dvh", "tests/test_dvh.py::TestDVH::test_dvh_compare", "tests/test_dvh.py::TestDVH::test_dvh_describe", "tests/test_dvh.py::TestDVH::test_dvh_properties", "tests/test_dvh.py::TestDVH::test_dvh_statistics", "tests/test_dvh.py::TestDVH::test_dvh_statistics_shorthand", "tests/test_dvh.py::TestDVH::test_dvh_statistics_shorthand_fail", "tests/test_dvh.py::TestDVH::test_dvh_value", "tests/test_dvh.py::TestDVH::test_plotting", "tests/test_dvh.py::TestDVH::test_raw_data_dvh_max_bins" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2019-02-25 13:56:03+00:00
bsd-3-clause
1,914
differint__differint-12
diff --git a/differint/differint.py b/differint/differint.py index b503322..f001e13 100644 --- a/differint/differint.py +++ b/differint/differint.py @@ -145,6 +145,49 @@ def Beta(x,y): return Gamma(x)*Gamma(y)/Gamma(x+y) +def MittagLeffler(a, b, x, num_terms=50, *, ignore_special_cases=False): + ''' Calculate the Mittag-Leffler function by checking for special cases, and trying to + reduce the parameters. If neither of those work, it just brute forces it. + + Parameters + ========== + a : float + The first parameter of the Mittag-Leffler function. + b : float + The second parameter of the Mittag-Leffler function + x : float or 1D-array of floats + The value or values to be evaluated at. + num_terms : int + The number of terms to calculate in the sum. Ignored if + a special case can be used instead. Default value is 100. + ignore_special_cases : bool + Don't use the special cases, use the series definition. + Probably only useful for testing. Default value is False. + ''' + # check for quick special cases + if not ignore_special_cases: + if a == 0: + if (np.abs(x) < 1).all(): + return 1 / Gamma(b) * 1 / (1 - x) + return x * np.inf + elif a == 0.5 and b == 1: + # requires calculation of the complementary error function + pass + elif a == 1 and b == 1: + return np.exp(x) + elif a == 2 and b == 1: + return np.cosh(np.sqrt(x)) + elif a == 1 and b == 2: + return (np.exp(x) - 1) / x + elif a == 2 and b == 2: + return np.sinh(np.sqrt(x)) / np.sqrt(x) + # manually calculate with series definition + exponents = np.arange(num_terms) + exp_vals = np.array([x]).T ** exponents + gamma_vals = np.array([Gamma(exponent * a + b) for exponent in exponents]) + return np.sum(exp_vals / gamma_vals, axis=1) + + def GLcoeffs(alpha,n): """ Computes the GL coefficient array of size n. @@ -489,3 +532,93 @@ class GLIinterpolat: self.nxt = alpha*(2+alpha)/8 self.crr = (4-alpha*alpha)/4 self.prv = alpha*(alpha-2)/8 + +def PCcoeffs(alpha, j, n): + if 1 < alpha: + if j == 0: + return (n+1)**alpha * (alpha - n) + n**alpha * (2 * n - alpha - 1) - (n - 1)**(alpha + 1) + elif j == n: + return 2 ** (alpha + 1) - alpha - 3 + return (n - j + 2) ** (alpha + 1) + 3 * (n - j) ** (alpha + 1) - 3 * (n - j + 1) ** (alpha + 1) - (n - j - 1) ** (alpha + 1) + +def PCsolver(initial_values, alpha, f_name, domain_start=0, domain_end=1, num_points=100): + """ Solve an equation of the form D[y(x)]=f(x, y(x)) using the predictor-corrector + method, modified to be compatible with fractional derivatives. + + see Deng, W. (2007) Short memory principle and a predictor–corrector approach for + fractional differential equations. Journal of Computational and Applied + Mathematics. + + test examples from + Baskonus, H.M., Bulut, H. (2015) On the numerical solutions of some fractional + ordinary differential equations by fractional Adams-Bashforth-Moulton method. + De Gruyter. + Weilbeer, M. (2005) Efficient Numerical Methods for Fractional Differential + Equations and their Analytical Background. + + + + Parameters + ========== + initial_values : float 1d-array + A list of initial values for the IVP. There should be as many IVs + as ceil(alpha). + alpha : float + The order of the differintegral in the equation to be computed. + f_name : function handle or lambda function + This is the function on the right side of the equation, and should + accept two variables; first the independant variable, and second + the equation to be solved. + domain_start : float + The left-endpoint of the function domain. Default value is 0. + domain_end : float + The right-endpoint of the function domain; the point at which the + differintegral is being evaluated. Default value is 1. + num_points : integer + The number of points in the domain. Default value is 100. + + Output + ====== + y_correction : float 1d-array + The calculated solution to the IVP at each of the points + between the left and right endpoint. + + Examples: + >>> f_name = lambda x, y : y - x - 1 + >>> initial_values = [1, 1] + >>> y_solved = PCsolver(initial_values, 1.5, f_name) + >>> theoretical = np.linspace(0, 1, 100) + 1 + >>> np.allclose(y_solved, theoretical) + True + """ + x_points = np.linspace(domain_start, domain_end, num_points) + step_size = x_points[1] - x_points[0] + y_correction = np.zeros(num_points, dtype='complex_') + y_prediction = np.zeros(num_points, dtype='complex_') + + y_prediction[0] = initial_values[0] + y_correction[0] = initial_values[0] + for x_index in range(num_points - 1): + initial_value_contribution = 0 + if 1 < alpha and alpha < 2: + initial_value_contribution = initial_values[1] * step_size + elif 2 < alpha: + for k in range(1, int(np.ceil(alpha))): + initial_value_contribution += initial_values[k] / np.math.factorial(k) * (x_points[x_index + 1] ** k - x_points[x_index] ** k) + elif alpha < 1: + raise ValueError('Not yet supported!') + y_prediction[x_index + 1] += initial_value_contribution + y_prediction[x_index + 1] += y_correction[x_index] + y_prediction[x_index + 1] += step_size ** alpha / Gamma(alpha + 1) * f_name(x_points[x_index], y_correction[x_index]) + subsum = 0 + for j in range(x_index + 1): + subsum += PCcoeffs(alpha, j, x_index) * f_name(x_points[j], y_correction[j]) + y_prediction[x_index + 1] += step_size ** alpha / Gamma(alpha + 2) * subsum + + y_correction[x_index + 1] += initial_value_contribution + y_correction[x_index + 1] += y_correction[x_index] + y_correction[x_index + 1] += step_size ** alpha / Gamma(alpha + 2) * alpha * f_name(x_points[x_index], y_correction[x_index]) + y_correction[x_index + 1] += step_size ** alpha / Gamma(alpha + 2) * f_name(x_points[x_index + 1], y_prediction[x_index + 1]) + y_correction[x_index + 1] += step_size ** alpha / Gamma(alpha + 2) * subsum + + return y_correction
differint/differint
6b0a4813a37b6734fb9733dd769f340ecb74aa27
diff --git a/tests/test.py b/tests/test.py index d663249..af03cbd 100644 --- a/tests/test.py +++ b/tests/test.py @@ -12,6 +12,7 @@ size_coefficient_array = 20 test_N = 512 sqrtpi2 = 0.88622692545275794 truevaluepoly = 0.94031597258 +PC_x_power = np.linspace(0, 1, 100) ** 5.5 INTER = GLIinterpolat(1) @@ -33,6 +34,10 @@ RL_r = RL(0.5, lambda x: np.sqrt(x), 0, 1, test_N) RL_result = RL_r[-1] RL_length = len(RL_r) +# Get FODE function for solving. +PC_func_power = lambda x, y : 1/24 * Gamma(5 + 1.5) * x**4 + x**(8 + 2 * 1.5) - y**2 +PC_func_ML = lambda x,y : y + class HelperTestCases(unittest.TestCase): """ Tests for helper functions. """ @@ -89,6 +94,23 @@ class HelperTestCases(unittest.TestCase): def testComplexValue(self): self.assertEqual(np.round(Gamma(1j), 4), -0.1549-0.498j) + + """ Unit tests for Mittag-Leffler function. """ + + def test_ML_cosh_root(self): + xs = np.arange(10, 0.1) + self.assertTrue((np.abs(MittagLeffler(2, 1, xs, ignore_special_cases=True)\ + - np.cosh(np.sqrt(xs))) <= 1e-3).all()) + + def test_ML_exp(self): + xs = np.arange(10, 0.1) + self.assertTrue((np.abs(MittagLeffler(1, 1, xs, ignore_special_cases=True)\ + - np.exp(xs)) <= 1e-3).all()) + + def test_ML_geometric(self): + xs = np.arange(1, 0.05) + self.assertTrue((np.abs(MittagLeffler(0, 1, xs, ignore_special_cases=True)\ + - 1 / (1 - xs)) <= 1e-3).all()) class TestInterpolantCoefficients(unittest.TestCase): """ Test the correctness of the interpolant coefficients. """ @@ -131,7 +153,21 @@ class TestAlgorithms(unittest.TestCase): def test_RL_accuracy_sqrt(self): self.assertTrue(abs(RL_result - sqrtpi2) <= 1e-4) - + +class TestSolvers(unittest.TestCase): + """ Tests for the correct solution to the equations. """ + def test_PC_solution_three_halves(self): + self.assertTrue((np.abs(PCsolver([0, 0], 1.5, PC_func_power, 0, 1, 100)-PC_x_power) <= 1e-2).all()) + + def test_PC_solution_ML(self): + xs = np.linspace(0, 1, 100) + ML_alpha = MittagLeffler(5.5, 1, xs ** 5.5) + self.assertTrue((np.abs(PCsolver([1, 0, 0, 0, 0, 0], 5.5, PC_func_ML)-ML_alpha) <= 1e-2).all()) + + def test_PC_solution_linear(self): + xs = np.linspace(0, 1, 100) + self.assertTrue((np.abs(PCsolver([1, 1], 1.5, lambda x,y : y-x-1)-(xs+1)) <= 1e-2).all()) + if __name__ == '__main__': unittest.main(argv=['first-arg-is-ignored'], exit=False)
Caputo Fractional Derivative - reg HI! Good Morning! Is it applicable for caputo derivative? In specific, predictor-corrector algorithm.
0.0
6b0a4813a37b6734fb9733dd769f340ecb74aa27
[ "tests/test.py::HelperTestCases::test_ML_cosh_root", "tests/test.py::HelperTestCases::test_ML_exp", "tests/test.py::HelperTestCases::test_ML_geometric" ]
[ "tests/test.py::HelperTestCases::testComplexValue", "tests/test.py::HelperTestCases::testFiveFactorial", "tests/test.py::HelperTestCases::testNegativePoles", "tests/test.py::HelperTestCases::testRealValue", "tests/test.py::HelperTestCases::test_GL_binomial_coefficient_array_size", "tests/test.py::HelperTestCases::test_checkValues", "tests/test.py::HelperTestCases::test_functionCheck", "tests/test.py::HelperTestCases::test_isInteger", "tests/test.py::HelperTestCases::test_isPositiveInteger", "tests/test.py::HelperTestCases::test_pochhammer", "tests/test.py::TestAlgorithms::test_GLI_accuracy_sqrt", "tests/test.py::TestAlgorithms::test_GLI_result_length", "tests/test.py::TestAlgorithms::test_GL_accuracy_sqrt", "tests/test.py::TestAlgorithms::test_GLpoint_accuracy_polynomial", "tests/test.py::TestAlgorithms::test_GLpoint_sqrt_accuracy", "tests/test.py::TestAlgorithms::test_RL_accuracy_sqrt", "tests/test.py::TestAlgorithms::test_RL_matrix_shape", "tests/test.py::TestAlgorithms::test_RL_result_length", "tests/test.py::TestAlgorithms::test_RLpoint_accuracy_polynomial", "tests/test.py::TestAlgorithms::test_RLpoint_sqrt_accuracy" ]
{ "failed_lite_validators": [ "has_short_problem_statement" ], "has_test_patch": true, "is_lite": false }
2022-11-16 05:58:58+00:00
mit
1,915
diogommartins__simple_json_logger-14
diff --git a/setup.py b/setup.py index a1dddaa..db14acc 100644 --- a/setup.py +++ b/setup.py @@ -1,7 +1,7 @@ from setuptools import setup, find_packages -VERSION = '0.2.2' +VERSION = '0.2.3' setup(name='simple_json_logger', diff --git a/simple_json_logger/formatter.py b/simple_json_logger/formatter.py index b4eb58a..629eecb 100644 --- a/simple_json_logger/formatter.py +++ b/simple_json_logger/formatter.py @@ -1,7 +1,7 @@ import logging try: from logging import _levelToName -except ImportError: +except ImportError: # pragma: no cover from logging import _levelNames as _levelToName import traceback @@ -32,7 +32,7 @@ class JsonFormatter(logging.Formatter): return obj.strftime(DATETIME_FORMAT) elif istraceback(obj): tb = ''.join(traceback.format_tb(obj)) - return tb.strip() + return tb.strip().split('\n') elif isinstance(obj, Exception): return "Exception: %s" % str(obj) elif callable(obj):
diogommartins/simple_json_logger
1bc3c8d12784d55417e8d46b4fe9b44bd8cd1f99
diff --git a/tests/test_logger.py b/tests/test_logger.py index a98e7f4..8094814 100644 --- a/tests/test_logger.py +++ b/tests/test_logger.py @@ -78,12 +78,11 @@ class LoggerTests(unittest.TestCase): json_log = json.loads(logged_content) exc_class, exc_message, exc_traceback = json_log['exc_info'] - self.assertIn(member=exception_message, - container=exc_message) + self.assertEqual('Exception: {}'.format(exception_message), exc_message) current_func_name = inspect.currentframe().f_code.co_name - self.assertIn(member=current_func_name, - container=exc_traceback) + self.assertIn(current_func_name, exc_traceback[0]) + self.assertIn('raise Exception(exception_message)', exc_traceback[1]) def test_it_logs_datetime_objects(self): message = {
Fix multiline log for stacktraces Multiline stack traces must be formatted as a list of strings
0.0
1bc3c8d12784d55417e8d46b4fe9b44bd8cd1f99
[ "tests/test_logger.py::LoggerTests::test_it_logs_exceptions_tracebacks" ]
[ "tests/test_logger.py::LoggerTests::test_flatten_method_parameter_does_nothing_is_message_isnt_a_dict", "tests/test_logger.py::LoggerTests::test_extra_param_adds_content_to_document_root", "tests/test_logger.py::LoggerTests::test_it_escapes_strings", "tests/test_logger.py::LoggerTests::test_extra_parameter_on_log_method_function_call_updates_extra_parameter_on_init", "tests/test_logger.py::LoggerTests::test_flatten_instance_attr_adds_messages_to_document_root", "tests/test_logger.py::LoggerTests::test_flatten_param_adds_message_to_document_root", "tests/test_logger.py::LoggerTests::test_it_forwards_serializer_kwargs_parameter_to_serializer", "tests/test_logger.py::LoggerTests::test_it_logs_valid_json_string_if_message_is_json_serializeable", "tests/test_logger.py::LoggerTests::test_flatten_instance_attr_overwrites_default_attributes", "tests/test_logger.py::LoggerTests::test_callable_values_are_called_before_serialization", "tests/test_logger.py::LoggerTests::test_it_logs_valid_json_string_if_message_isnt_json_serializeable", "tests/test_logger.py::LoggerTests::test_extra_parameter_adds_content_to_root_of_all_messages", "tests/test_logger.py::LoggerTests::test_it_forwards_serializer_kwargs_instance_attr_to_serializer", "tests/test_logger.py::LoggerTests::test_it_logs_datetime_objects", "tests/test_logger.py::LoggerTests::test_flatten_method_parameter_overwrites_default_attributes", "tests/test_logger.py::LoggerTests::test_it_logs_current_log_time" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2018-05-31 14:58:34+00:00
mit
1,916
dirty-cat__dirty_cat-197
diff --git a/dirty_cat/super_vectorizer.py b/dirty_cat/super_vectorizer.py index 84b39c9..420d00b 100644 --- a/dirty_cat/super_vectorizer.py +++ b/dirty_cat/super_vectorizer.py @@ -106,10 +106,9 @@ class SuperVectorizer(ColumnTransformer): None to apply `remainder`, 'drop' for dropping the columns, or 'passthrough' to return the unencoded columns. - auto_cast: bool, default=False + auto_cast: bool, default=True If set to `True`, will try to convert each column to the best possible data type (dtype). - Experimental. It is advised to cast them beforehand, and leave this false. handle_missing: str, default='' One of the following values: 'error' or '' (empty). @@ -144,7 +143,7 @@ class SuperVectorizer(ColumnTransformer): high_card_cat_transformer: Optional[Union[BaseEstimator, str]] = GapEncoder(), numerical_transformer: Optional[Union[BaseEstimator, str]] = None, datetime_transformer: Optional[Union[BaseEstimator, str]] = None, - auto_cast: bool = False, + auto_cast: bool = True, # Following parameters are inherited from ColumnTransformer handle_missing: str = '', remainder='passthrough', @@ -171,8 +170,6 @@ class SuperVectorizer(ColumnTransformer): self.transformer_weights = transformer_weights self.verbose = verbose - self.columns_ = [] - def _auto_cast_array(self, X): """ Takes an array and tries to convert its columns to the best possible diff --git a/examples/03_automatic_preprocessing_with_the_supervectorizer.py b/examples/03_automatic_preprocessing_with_the_supervectorizer.py index 69ed18a..b9f6d88 100644 --- a/examples/03_automatic_preprocessing_with_the_supervectorizer.py +++ b/examples/03_automatic_preprocessing_with_the_supervectorizer.py @@ -82,7 +82,7 @@ from sklearn.pipeline import Pipeline from dirty_cat import SuperVectorizer pipeline = Pipeline([ - ('vectorizer', SuperVectorizer(auto_cast=True)), + ('vectorizer', SuperVectorizer()), ('clf', HistGradientBoostingRegressor(random_state=42)) ]) @@ -111,7 +111,6 @@ print(f'std={np.std(scores)}') # Let us perform the same workflow, but without the `Pipeline`, so we can # analyze its mechanisms along the way. sup_vec = SuperVectorizer( - auto_cast=True, high_card_str_transformer=GapEncoder(n_components=50), high_card_cat_transformer=GapEncoder(n_components=50) )
dirty-cat/dirty_cat
766aa5c905a737d0a90e8432bed84aac6101754a
diff --git a/dirty_cat/test/test_super_vectorizer.py b/dirty_cat/test/test_super_vectorizer.py index 2f34d8e..b70a26b 100644 --- a/dirty_cat/test/test_super_vectorizer.py +++ b/dirty_cat/test/test_super_vectorizer.py @@ -3,6 +3,8 @@ import sklearn import pandas as pd from sklearn.preprocessing import StandardScaler +from sklearn.utils.validation import check_is_fitted +from sklearn.exceptions import NotFittedError from distutils.version import LooseVersion @@ -79,7 +81,6 @@ def test_super_vectorizer(): # Test casting values vectorizer_cast = SuperVectorizer( cardinality_threshold=3, - auto_cast=True, # we must have n_samples = 5 >= n_components high_card_str_transformer=GapEncoder(n_components=2), high_card_cat_transformer=GapEncoder(n_components=2), @@ -130,6 +131,18 @@ def test_get_feature_names(): assert vectorizer_w_drop.get_feature_names() == expected_feature_names_drop +def test_fit(): + # Simply checks sklearn's `check_is_fitted` function raises an error if + # the SuperVectorizer is instantiated but not fitted. + # See GH#193 + sup_vec = SuperVectorizer() + with pytest.raises(NotFittedError): + if LooseVersion(sklearn.__version__) >= LooseVersion('0.22'): + assert check_is_fitted(sup_vec) + else: + assert check_is_fitted(sup_vec, attributes=dir(sup_vec)) + + if __name__ == '__main__': print('start test_super_vectorizer') test_super_vectorizer() @@ -137,5 +150,8 @@ if __name__ == '__main__': print('start test_get_feature_names') test_get_feature_names() print('test_get_feature_names passed') + print('start test_fit') + test_fit() + print('test_fit passed') print('Done')
Better error message when SuperVectorizer's transform method is called before fit Scikit-learn has a mechanism to check that an estimator is fitted, and if not raise a good error message. We should use it.
0.0
766aa5c905a737d0a90e8432bed84aac6101754a
[ "dirty_cat/test/test_super_vectorizer.py::test_fit" ]
[]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2021-07-21 13:30:28+00:00
bsd-3-clause
1,917
dirty-cat__dirty_cat-261
diff --git a/CHANGES.rst b/CHANGES.rst index 3b92fa9..027a15b 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -30,6 +30,7 @@ Release 0.2.1 Major changes ------------- + * Improvements to the :class:`SuperVectorizer` - Type detection works better: handles dates, numerics columns encoded as strings, @@ -51,6 +52,8 @@ Bug-fixes * GapEncoder's `get_feature_names_out` now accepts all iterators, not just lists. +* Fixed `DeprecationWarning` raised by the usage of `distutils.version.LooseVersion` + Notes ----- diff --git a/build_tools/circle/list_versions.py b/build_tools/circle/list_versions.py index 19fa8aa..0322cda 100755 --- a/build_tools/circle/list_versions.py +++ b/build_tools/circle/list_versions.py @@ -5,9 +5,10 @@ import json import re import sys -from distutils.version import LooseVersion +from dirty_cat.utils import Version from urllib.request import urlopen + def json_urlread(url): try: return json.loads(urlopen(url).read().decode('utf8')) @@ -80,7 +81,7 @@ for src, dst in symlinks.items(): seen = set() for name in (NAMED_DIRS + sorted((k for k in dirs if k[:1].isdigit()), - key=LooseVersion, reverse=True)): + key=Version, reverse=True)): version_num, pdf_size = dirs[name] if version_num in seen: # symlink came first diff --git a/dirty_cat/datasets/fetching.py b/dirty_cat/datasets/fetching.py index f42dd59..8b28c93 100644 --- a/dirty_cat/datasets/fetching.py +++ b/dirty_cat/datasets/fetching.py @@ -24,8 +24,8 @@ import pandas as pd from pathlib import Path from collections import namedtuple from typing import Union, Dict, Any -from distutils.version import LooseVersion +from dirty_cat.utils import Version from dirty_cat.datasets.utils import get_data_dir @@ -165,7 +165,7 @@ def _download_and_write_openml_dataset(dataset_id: int, from sklearn.datasets import fetch_openml fetch_kwargs = {} - if LooseVersion(sklearn.__version__) >= LooseVersion('0.22'): + if Version(sklearn.__version__) >= Version('0.22'): fetch_kwargs.update({'as_frame': True}) # The ``fetch_openml()`` function returns a Scikit-Learn ``Bunch`` object, diff --git a/dirty_cat/gap_encoder.py b/dirty_cat/gap_encoder.py index dea1cdc..772c6d2 100644 --- a/dirty_cat/gap_encoder.py +++ b/dirty_cat/gap_encoder.py @@ -16,7 +16,6 @@ The principle is as follows: """ import warnings import numpy as np -from distutils.version import LooseVersion from scipy import sparse from sklearn import __version__ as sklearn_version from sklearn.utils import check_random_state, gen_batches @@ -28,15 +27,16 @@ from sklearn.neighbors import NearestNeighbors from sklearn.utils.fixes import _object_dtype_isnan import pandas as pd from .utils import check_input +from dirty_cat.utils import Version -if LooseVersion(sklearn_version) <= LooseVersion('0.22'): +if Version(sklearn_version) <= Version('0.22'): from sklearn.cluster.k_means_ import _k_init -elif LooseVersion(sklearn_version) < LooseVersion('0.24'): +elif Version(sklearn_version) < Version('0.24'): from sklearn.cluster._kmeans import _k_init else: from sklearn.cluster import kmeans_plusplus -if LooseVersion(sklearn_version) <= LooseVersion('0.22'): +if Version(sklearn_version) <= Version('0.22'): from sklearn.decomposition.nmf import _beta_divergence else: from sklearn.decomposition._nmf import _beta_divergence @@ -106,12 +106,12 @@ class GapEncoderColumn(BaseEstimator, TransformerMixin): unq_V = sparse.hstack((unq_V, unq_V2), format='csr') if not self.hashing: # Build n-grams/word vocabulary - if LooseVersion(sklearn_version) < LooseVersion('1.0'): + if Version(sklearn_version) < Version('1.0'): self.vocabulary = self.ngrams_count_.get_feature_names() else: self.vocabulary = self.ngrams_count_.get_feature_names_out() if self.add_words: - if LooseVersion(sklearn_version) < LooseVersion('1.0'): + if Version(sklearn_version) < Version('1.0'): self.vocabulary = np.concatenate(( self.vocabulary, self.word_count_.get_feature_names() @@ -153,7 +153,7 @@ class GapEncoderColumn(BaseEstimator, TransformerMixin): n-grams counts. """ if self.init == 'k-means++': - if LooseVersion(sklearn_version) < LooseVersion('0.24'): + if Version(sklearn_version) < Version('0.24'): W = _k_init( V, self.n_components, x_squared_norms=row_norms(V, squared=True), @@ -179,7 +179,7 @@ class GapEncoderColumn(BaseEstimator, TransformerMixin): W = np.hstack((W, W2)) # if k-means doesn't find the exact number of prototypes if W.shape[0] < self.n_components: - if LooseVersion(sklearn_version) < LooseVersion('0.24'): + if Version(sklearn_version) < Version('0.24'): W2 = _k_init( V, self.n_components - W.shape[0], x_squared_norms=row_norms(V, squared=True), @@ -284,7 +284,7 @@ class GapEncoderColumn(BaseEstimator, TransformerMixin): """ vectorizer = CountVectorizer() vectorizer.fit(list(self.H_dict_.keys())) - if LooseVersion(sklearn_version) < LooseVersion('1.0'): + if Version(sklearn_version) < Version('1.0'): vocabulary = np.array(vectorizer.get_feature_names()) else: vocabulary = np.array(vectorizer.get_feature_names_out()) diff --git a/dirty_cat/similarity_encoder.py b/dirty_cat/similarity_encoder.py index c0cfe8b..18b9f4e 100644 --- a/dirty_cat/similarity_encoder.py +++ b/dirty_cat/similarity_encoder.py @@ -15,7 +15,6 @@ The principle is as follows: import warnings import numpy as np -from distutils.version import LooseVersion from joblib import Parallel, delayed from scipy import sparse import sklearn @@ -26,6 +25,7 @@ from sklearn.preprocessing import OneHotEncoder from sklearn.utils import check_random_state from sklearn.utils.fixes import _object_dtype_isnan +from dirty_cat.utils import Version from . import string_distances from .string_distances import get_ngram_count, preprocess @@ -400,7 +400,7 @@ class SimilarityEncoder(OneHotEncoder): self.vocabulary_ngram_counts_.append(vocabulary_ngram_count) self.drop_idx_ = self._compute_drop_idx() - if LooseVersion(sklearn.__version__) >= LooseVersion('1.1.0'): + if Version(sklearn.__version__) >= Version('1.1.0'): self._infrequent_enabled = False return self diff --git a/dirty_cat/super_vectorizer.py b/dirty_cat/super_vectorizer.py index e31e00a..219d117 100644 --- a/dirty_cat/super_vectorizer.py +++ b/dirty_cat/super_vectorizer.py @@ -15,15 +15,15 @@ import pandas as pd from warnings import warn from typing import Union, Optional, List -from distutils.version import LooseVersion from sklearn.base import BaseEstimator from sklearn.compose import ColumnTransformer from sklearn.preprocessing import OneHotEncoder from dirty_cat import GapEncoder, DatetimeEncoder +from dirty_cat.utils import Version -_sklearn_loose_version = LooseVersion(sklearn.__version__) +_sklearn_loose_version = Version(sklearn.__version__) def _has_missing_values(df: Union[pd.DataFrame, pd.Series]) -> bool: @@ -402,7 +402,7 @@ class SuperVectorizer(ColumnTransformer): impute: bool = False if isinstance(trans, OneHotEncoder) \ - and _sklearn_loose_version < LooseVersion('0.24'): + and _sklearn_loose_version < Version('0.24'): impute = True if impute: @@ -446,9 +446,9 @@ class SuperVectorizer(ColumnTransformer): e.g. "job_title_Police officer", or "<column_name>" if not encoded. """ - if _sklearn_loose_version < LooseVersion('0.23'): + if _sklearn_loose_version < Version('0.23'): try: - if _sklearn_loose_version < LooseVersion('1.0'): + if _sklearn_loose_version < Version('1.0'): ct_feature_names = super().get_feature_names() else: ct_feature_names = super().get_feature_names_out() @@ -460,7 +460,7 @@ class SuperVectorizer(ColumnTransformer): 'transformers, or update your copy of scikit-learn.' ) else: - if _sklearn_loose_version < LooseVersion('1.0'): + if _sklearn_loose_version < Version('1.0'): ct_feature_names = super().get_feature_names() else: ct_feature_names = super().get_feature_names_out() @@ -478,7 +478,7 @@ class SuperVectorizer(ColumnTransformer): if not hasattr(trans, 'get_feature_names'): all_trans_feature_names.extend(cols) else: - if _sklearn_loose_version < LooseVersion('1.0'): + if _sklearn_loose_version < Version('1.0'): trans_feature_names = trans.get_feature_names(cols) else: trans_feature_names = trans.get_feature_names_out(cols) diff --git a/dirty_cat/utils.py b/dirty_cat/utils.py index 4891f7a..920e0ad 100644 --- a/dirty_cat/utils.py +++ b/dirty_cat/utils.py @@ -2,6 +2,8 @@ import collections import numpy as np +from typing import Tuple, Union + class LRUDict: """ dict with limited capacity @@ -44,3 +46,81 @@ def check_input(X): 'array.reshape(1, -1) if it contains a single sample.' ) return X + + +class Version: + """ + Replacement for `distutil.version.LooseVersion` and `packaging.version.Version`. + Implemented to avoid `DeprecationWarning`s raised by the former, + and avoid adding a dependency for the latter. + + It is therefore very bare-bones, so its code shouldn't be too + hard to understand. + It currently only supports major and minor versions. + + Inspired from https://stackoverflow.com/a/11887825/9084059 + Should eventually dissapear. + + Examples: + >>> # Standard usage + >>> Version(sklearn.__version__) > Version('0.22') + >>> Version(sklearn.__version__) > '0.22' + >>> # In general, pass the version as numbers separated by dots. + >>> Version('1.5') <= Version('1.6.5') + >>> Version('1.5') <= '1.6.5' + >>> # You can also pass the separator for specific cases + >>> Version('1-5', separator='-') == Version('1-6-5', separator='-') + >>> Version('1-5', separator='-') == '1-6-5' + >>> Version('1-5', separator='-') == '1.6.5' # Won't work ! + """ + + def __init__(self, value: str, separator: str = '.'): + self.separator = separator + self.major, self.minor = self._parse_version(value) + + def __repr__(self): + return f'Version({self.major}.{self.minor})' + + def _parse_version(self, value: str) -> Tuple[int, int]: + raw_parts = value.split(self.separator) + if len(raw_parts) == 0: + raise ValueError(f'Could not extract version from {value!r} ' + f'(separator: {self.separator!r})') + elif len(raw_parts) == 1: + major = int(raw_parts[0]) + minor = 0 + else: + major = int(raw_parts[0]) + minor = int(raw_parts[1]) + # Ditch the rest + return major, minor + + def _cast_to_version(self, other: Union["Version", str]) -> "Version": + if isinstance(other, str): + # We pass our separator, as we expect they are the same + other = Version(other, self.separator) + return other + + def __eq__(self, other: Union["Version", str]): + other = self._cast_to_version(other) + return (self.major, self.minor) == (other.major, other.minor) + + def __ne__(self, other: Union["Version", str]): + other = self._cast_to_version(other) + return (self.major, self.minor) != (other.major, other.minor) + + def __lt__(self, other: Union["Version", str]): + other = self._cast_to_version(other) + return (self.major, self.minor) < (other.major, other.minor) + + def __le__(self, other: Union["Version", str]): + other = self._cast_to_version(other) + return (self.major, self.minor) <= (other.major, other.minor) + + def __gt__(self, other: Union["Version", str]): + other = self._cast_to_version(other) + return (self.major, self.minor) > (other.major, other.minor) + + def __ge__(self, other: Union["Version", str]): + other = self._cast_to_version(other) + return (self.major, self.minor) >= (other.major, other.minor)
dirty-cat/dirty_cat
4c5b7892f5be9bf070690bba302dbc9a60164349
diff --git a/dirty_cat/datasets/tests/test_fetching.py b/dirty_cat/datasets/tests/test_fetching.py index b0056c4..a85f425 100644 --- a/dirty_cat/datasets/tests/test_fetching.py +++ b/dirty_cat/datasets/tests/test_fetching.py @@ -15,7 +15,7 @@ import warnings import pandas as pd from pathlib import Path -from distutils.version import LooseVersion +from dirty_cat.utils import Version from unittest import mock from unittest.mock import mock_open @@ -152,7 +152,7 @@ def test__download_and_write_openml_dataset(mock_fetch_openml): test_data_dir = get_test_data_dir() _download_and_write_openml_dataset(1, test_data_dir) - if LooseVersion(sklearn.__version__) >= LooseVersion('0.22'): + if Version(sklearn.__version__) >= Version('0.22'): mock_fetch_openml.assert_called_once_with(data_id=1, data_home=str(test_data_dir), as_frame=True) diff --git a/dirty_cat/test/test_super_vectorizer.py b/dirty_cat/test/test_super_vectorizer.py index d299f19..a836dcc 100644 --- a/dirty_cat/test/test_super_vectorizer.py +++ b/dirty_cat/test/test_super_vectorizer.py @@ -7,10 +7,10 @@ from sklearn.preprocessing import StandardScaler from sklearn.utils.validation import check_is_fitted from sklearn.exceptions import NotFittedError -from distutils.version import LooseVersion from dirty_cat import SuperVectorizer from dirty_cat import GapEncoder +from dirty_cat.utils import Version def check_same_transformers(expected_transformers: dict, actual_transformers: list): @@ -336,7 +336,7 @@ def test_get_feature_names_out(): vectorizer_w_pass = SuperVectorizer(remainder='passthrough') vectorizer_w_pass.fit(X) - if LooseVersion(sklearn.__version__) < LooseVersion('0.23'): + if Version(sklearn.__version__) < Version('0.23'): with pytest.raises(NotImplementedError): # Prior to sklearn 0.23, ColumnTransformer.get_feature_names # with "passthrough" transformer(s) raises a NotImplementedError @@ -370,7 +370,7 @@ def test_fit(): # See GH#193 sup_vec = SuperVectorizer() with pytest.raises(NotFittedError): - if LooseVersion(sklearn.__version__) >= LooseVersion('0.22'): + if Version(sklearn.__version__) >= Version('0.22'): assert check_is_fitted(sup_vec) else: assert check_is_fitted(sup_vec, attributes=dir(sup_vec)) diff --git a/dirty_cat/test/test_utils.py b/dirty_cat/test/test_utils.py index 70caf4a..a339c34 100644 --- a/dirty_cat/test/test_utils.py +++ b/dirty_cat/test/test_utils.py @@ -1,4 +1,6 @@ -from dirty_cat.utils import LRUDict +import pytest + +from dirty_cat.utils import LRUDict, Version def test_lrudict(): @@ -13,3 +15,28 @@ def test_lrudict(): for x in range(5): assert (x not in dict_) + + +def test_version(): + # Test those specified in its docstring + assert Version('1.5') <= Version('1.6.5') + assert Version('1.5') <= '1.6.5' + + assert (Version('1-5', separator='-') == Version('1-6-5', separator='-')) is False + assert (Version('1-5', separator='-') == '1-6-5') is False + with pytest.raises(ValueError): + assert not (Version('1-5', separator='-') == '1.6.5') + + # Test all comparison methods + assert Version('1.0') == Version('1.0') + assert (Version('1.0') != Version('1.0')) is False + + assert Version('1.0') < Version('1.1') + assert Version('1.1') <= Version('1.5') + assert Version('1.1') <= Version('1.1') + assert (Version('1.1') < Version('1.1')) is False + + assert Version('1.1') > Version('0.5') + assert Version('1.1') >= Version('0.9') + assert Version('1.1') >= Version('1.1') + assert (Version('1.1') >= Version('1.9')) is False
DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. <!--Provide a brief description of the bug.--> Since december 2021, `distutils.version.Version` (and thus `LooseVersion`) [is deprecated](https://github.com/pypa/setuptools/commit/1701579e0827317d8888c2254a17b5786b6b5246). We use it in [several components](https://github.com/dirty-cat/dirty_cat/search?q=LooseVersion), and therefore we have a number of warnings in the CI logs ([for example](https://github.com/dirty-cat/dirty_cat/runs/6667648188?check_suite_focus=true), under "Run tests") Sample: ``` dirty_cat/test/test_similarity_encoder.py: 118 warnings /Users/runner/work/dirty_cat/dirty_cat/dirty_cat/similarity_encoder.py:328: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if LooseVersion(sklearn.__version__) > LooseVersion('0.21'): ``` as suggested by the warning, we could use `packaging.version.Version` instead.
0.0
4c5b7892f5be9bf070690bba302dbc9a60164349
[ "dirty_cat/datasets/tests/test_fetching.py::test_fetch_openml_dataset", "dirty_cat/datasets/tests/test_fetching.py::test_fetch_openml_dataset_mocked", "dirty_cat/datasets/tests/test_fetching.py::test__download_and_write_openml_dataset", "dirty_cat/datasets/tests/test_fetching.py::test__read_json_from_gz", "dirty_cat/datasets/tests/test_fetching.py::test__get_details", "dirty_cat/datasets/tests/test_fetching.py::test__get_features", "dirty_cat/datasets/tests/test_fetching.py::test__export_gz_data_to_csv", "dirty_cat/datasets/tests/test_fetching.py::test__features_to_csv_format", "dirty_cat/datasets/tests/test_fetching.py::test_import_all_datasets", "dirty_cat/test/test_super_vectorizer.py::test_with_clean_data", "dirty_cat/test/test_super_vectorizer.py::test_with_dirty_data", "dirty_cat/test/test_super_vectorizer.py::test_with_arrays", "dirty_cat/test/test_super_vectorizer.py::test_fit", "dirty_cat/test/test_super_vectorizer.py::test_transform", "dirty_cat/test/test_super_vectorizer.py::test_fit_transform_equiv", "dirty_cat/test/test_utils.py::test_lrudict", "dirty_cat/test/test_utils.py::test_version" ]
[]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2022-06-07 13:06:50+00:00
bsd-3-clause
1,918
dirty-cat__dirty_cat-300
diff --git a/CHANGES.rst b/CHANGES.rst index a1f7651..da2fc09 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -7,14 +7,21 @@ Major changes * New encoder: :class:`DatetimeEncoder` can transform a datetime column into several numerical columns (year, month, day, hour, minute, second, ...). It is now the default transformer used in the :class:`SuperVectorizer` for datetime columns. -* The :class:`SuperVectorizer` has seen some major improvements and bug fixes. +* The :class:`SuperVectorizer` has seen some major improvements and bug fixes + - Fixes the automatic casting logic in ``transform``. + - **Behavior change** To avoid dimensionality explosion when a feature has two unique values, + the default encoder (:class:`OneHotEncoder`) now drops one of the two + vectors (see parameter `drop="if_binary"`). + - ``fit_transform`` and ``transform`` can now return unencoded features, + like the :class:`ColumnTransformer`'s behavior. + Previously, a ``RuntimeError`` was raised. * **Backward-incompatible change in the SuperVectorizer**: to apply ``remainder`` to features (with the ``*_transformer`` parameters), the value ``'remainder'`` must be passed, instead of ``None`` in previous versions. ``None`` now indicates that we want to use the default transformer. * Support for Python 3.6 and 3.7 has been dropped. Python >= 3.8 is now required. * Bumped minimum dependencies: - - sklearn>=0.22 + - sklearn>=0.23 - scipy>=1.4.0 - numpy>=1.17.3 - pandas>=1.2.0 diff --git a/README.rst b/README.rst index e0e232c..26a7a14 100644 --- a/README.rst +++ b/README.rst @@ -38,7 +38,7 @@ dirty_cat requires: - Python (>= 3.8) - NumPy (>= 1.17.3) - SciPy (>= 1.4.0) -- scikit-learn (>= 0.22.0) +- scikit-learn (>= 0.23.0) - pandas (>= 1.2.0) User installation diff --git a/dirty_cat/gap_encoder.py b/dirty_cat/gap_encoder.py index a0471af..b06d622 100644 --- a/dirty_cat/gap_encoder.py +++ b/dirty_cat/gap_encoder.py @@ -35,21 +35,12 @@ from dirty_cat.utils import Version from .utils import check_input -if Version(sklearn_version) == Version("0.22"): - with warnings.catch_warnings(): - warnings.simplefilter("ignore") - from sklearn.cluster.k_means_ import _k_init -elif Version(sklearn_version) < Version("0.24"): +if Version(sklearn_version) < Version("0.24"): from sklearn.cluster._kmeans import _k_init else: from sklearn.cluster import kmeans_plusplus -if Version(sklearn_version) == Version("0.22"): - with warnings.catch_warnings(): - warnings.simplefilter("ignore") - from sklearn.decomposition.nmf import _beta_divergence -else: - from sklearn.decomposition._nmf import _beta_divergence +from sklearn.decomposition._nmf import _beta_divergence class GapEncoderColumn(BaseEstimator, TransformerMixin): diff --git a/dirty_cat/super_vectorizer.py b/dirty_cat/super_vectorizer.py index 6643dc7..6c4e8b4 100644 --- a/dirty_cat/super_vectorizer.py +++ b/dirty_cat/super_vectorizer.py @@ -96,16 +96,18 @@ class SuperVectorizer(ColumnTransformer): cardinality_threshold : int, default=40 Two lists of features will be created depending on this value: strictly - under this value, the low cardinality categorical values, and above or - equal, the high cardinality categorical values. + under this value, the low cardinality categorical features, and above or + equal, the high cardinality categorical features. Different transformers will be applied to these two groups, defined by the parameters `low_card_cat_transformer` and `high_card_cat_transformer` respectively. + Note: currently, missing values are counted as a single unique value + (so they count in the cardinality). low_card_cat_transformer : typing.Optional[typing.Union[sklearn.base.TransformerMixin, typing.Literal["drop", "remainder", "passthrough"]]], default=None # noqa Transformer used on categorical/string features with low cardinality (threshold is defined by `cardinality_threshold`). - Can either be a transformer object instance (e.g. `OneHotEncoder()`), + Can either be a transformer object instance (e.g. `OneHotEncoder(drop="if_binary")`), a `Pipeline` containing the preprocessing steps, 'drop' for dropping the columns, 'remainder' for applying `remainder`, @@ -226,6 +228,16 @@ class SuperVectorizer(ColumnTransformer): imputed_columns_: typing.List[str] The list of columns in which we imputed the missing values. + Notes + ----- + The column order of the input data is not guaranteed to be the same + as the output data (returned by `transform`). + This is a due to the way the ColumnTransformer works. + However, the output column order will always be the same for different + calls to `transform` on a same fitted SuperVectorizer instance. + For example, if input data has columns ['name', 'job', 'year], then output + columns might be shuffled, e.g., ['job', 'year', 'name'], but every call + to `transform` will return this order. """ transformers_: List[Tuple[str, Union[str, TransformerMixin], List[str]]] @@ -290,7 +302,7 @@ class SuperVectorizer(ColumnTransformer): if isinstance(self.low_card_cat_transformer, sklearn.base.TransformerMixin): self.low_card_cat_transformer_ = clone(self.low_card_cat_transformer) elif self.low_card_cat_transformer is None: - self.low_card_cat_transformer_ = OneHotEncoder() + self.low_card_cat_transformer_ = OneHotEncoder(drop="if_binary") elif self.low_card_cat_transformer == "remainder": self.low_card_cat_transformer_ = self.remainder else: @@ -406,6 +418,11 @@ class SuperVectorizer(ColumnTransformer): def fit_transform(self, X, y=None): """ Fit all transformers, transform the data, and concatenate the results. + In practice, it (1) converts features to their best possible types + if `auto_cast=True`, (2) classify columns based on their data type, + (3) replaces "false missing" (see function `_replace_false_missing`), + and imputes categorical columns depending on `impute_missing`, and + finally, transforms X. Parameters ---------- @@ -470,16 +487,21 @@ class SuperVectorizer(ColumnTransformer): ).columns.to_list() # Classify categorical columns by cardinality + _nunique_values = { # Cache results + col: X[col].nunique() for col in categorical_columns + } low_card_cat_columns = [ col for col in categorical_columns - if X[col].nunique() < self.cardinality_threshold + if _nunique_values[col] < self.cardinality_threshold ] high_card_cat_columns = [ col for col in categorical_columns - if X[col].nunique() >= self.cardinality_threshold + if _nunique_values[col] >= self.cardinality_threshold ] + # Clear cache + del _nunique_values # Next part: construct the transformers # Create the list of all the transformers. @@ -603,24 +625,10 @@ class SuperVectorizer(ColumnTransformer): typing.List[str] Feature names. """ - if Version(sklearn_version) < Version("0.23"): - try: - if Version(sklearn_version) < Version("1.0"): - ct_feature_names = super().get_feature_names() - else: - ct_feature_names = super().get_feature_names_out() - except NotImplementedError: - raise NotImplementedError( - "Prior to sklearn 0.23, get_feature_names with " - '"passthrough" is unsupported. To use the method, ' - 'either make sure there is no "passthrough" in the ' - "transformers, or update your copy of scikit-learn. " - ) + if Version(sklearn_version) < Version("1.0"): + ct_feature_names = super().get_feature_names() else: - if Version(sklearn_version) < Version("1.0"): - ct_feature_names = super().get_feature_names() - else: - ct_feature_names = super().get_feature_names_out() + ct_feature_names = super().get_feature_names_out() all_trans_feature_names = [] for name, trans, cols, _ in self._iter(fitted=True): diff --git a/dirty_cat/utils.py b/dirty_cat/utils.py index c5b8442..d7f780f 100644 --- a/dirty_cat/utils.py +++ b/dirty_cat/utils.py @@ -77,8 +77,8 @@ class Version: Examples: >>> # Standard usage - >>> Version(sklearn.__version__) > Version('0.22') - >>> Version(sklearn.__version__) > '0.22' + >>> Version(sklearn.__version__) > Version('0.23') + >>> Version(sklearn.__version__) > '0.23' >>> # In general, pass the version as numbers separated by dots. >>> Version('1.5') <= Version('1.6.5') >>> Version('1.5') <= '1.6.5' diff --git a/requirements-min.txt b/requirements-min.txt index eff1e8c..75702d6 100644 --- a/requirements-min.txt +++ b/requirements-min.txt @@ -1,6 +1,6 @@ numpy==1.17.3 scipy==1.4.0 -scikit-learn==0.22.0 +scikit-learn==0.23.0 pytest pytest-cov coverage diff --git a/setup.py b/setup.py index 73bf659..a015caa 100755 --- a/setup.py +++ b/setup.py @@ -39,7 +39,7 @@ if __name__ == "__main__": packages=find_packages(), package_data={"dirty_cat": ["VERSION.txt"]}, install_requires=[ - "scikit-learn>=0.21", + "scikit-learn>=0.23", "numpy>=1.16", "scipy>=1.2", "pandas>=1.2.0",
dirty-cat/dirty_cat
9e59a1ae72abfb453768d6cd41daca9cbb4cc942
diff --git a/dirty_cat/test/test_super_vectorizer.py b/dirty_cat/test/test_super_vectorizer.py index 4b04c77..c97e826 100644 --- a/dirty_cat/test/test_super_vectorizer.py +++ b/dirty_cat/test/test_super_vectorizer.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, List, Tuple +from typing import Any, Tuple import numpy as np import pandas as pd @@ -145,15 +145,7 @@ def _get_datetimes_dataframe() -> pd.DataFrame: ) -def _test_possibilities( - X, - expected_transformers_df: Dict[str, List[str]], - expected_transformers_2: Dict[str, List[str]], - expected_transformers_np_no_cast: Dict[str, List[int]], - expected_transformers_series: Dict[str, List[str]], - expected_transformers_plain: Dict[str, List[str]], - expected_transformers_np_cast: Dict[str, List[int]], -): +def _test_possibilities(X): """ Do a bunch of tests with the SuperVectorizer. We take some expected transformers results as argument. They're usually @@ -167,10 +159,18 @@ def _test_possibilities( numerical_transformer=StandardScaler(), ) # Warning: order-dependant + expected_transformers_df = { + "numeric": ["int", "float"], + "low_card_cat": ["str1", "cat1"], + "high_card_cat": ["str2", "cat2"], + } vectorizer_base.fit_transform(X) check_same_transformers(expected_transformers_df, vectorizer_base.transformers) # Test with higher cardinality threshold and no numeric transformer + expected_transformers_2 = { + "low_card_cat": ["str1", "str2", "cat1", "cat2"], + } vectorizer_default = SuperVectorizer() # Using default values vectorizer_default.fit_transform(X) check_same_transformers(expected_transformers_2, vectorizer_default.transformers) @@ -178,12 +178,20 @@ def _test_possibilities( # Test with a numpy array arr = X.to_numpy() # Instead of the columns names, we'll have the column indices. + expected_transformers_np_no_cast = { + "low_card_cat": [2, 4], + "high_card_cat": [3, 5], + "numeric": [0, 1], + } vectorizer_base.fit_transform(arr) check_same_transformers( expected_transformers_np_no_cast, vectorizer_base.transformers ) # Test with pandas series + expected_transformers_series = { + "low_card_cat": ["cat1"], + } vectorizer_base.fit_transform(X["cat1"]) check_same_transformers(expected_transformers_series, vectorizer_base.transformers) @@ -196,9 +204,19 @@ def _test_possibilities( ) X_str = X.astype("object") # With pandas + expected_transformers_plain = { + "high_card_cat": ["str2", "cat2"], + "low_card_cat": ["str1", "cat1"], + "numeric": ["int", "float"], + } vectorizer_cast.fit_transform(X_str) check_same_transformers(expected_transformers_plain, vectorizer_cast.transformers) # With numpy + expected_transformers_np_cast = { + "numeric": [0, 1], + "low_card_cat": [2, 4], + "high_card_cat": [3, 5], + } vectorizer_cast.fit_transform(X_str.to_numpy()) check_same_transformers(expected_transformers_np_cast, vectorizer_cast.transformers) @@ -208,43 +226,7 @@ def test_with_clean_data(): Defines the expected returns of the vectorizer in different settings, and runs the tests with a clean dataset. """ - X = _get_clean_dataframe() - # Define the transformers we'll use throughout the test. - expected_transformers_df = { - "numeric": ["int", "float"], - "low_card_cat": ["str1", "cat1"], - "high_card_cat": ["str2", "cat2"], - } - expected_transformers_2 = { - "low_card_cat": ["str1", "str2", "cat1", "cat2"], - } - expected_transformers_np_no_cast = { - "low_card_cat": [2, 4], - "high_card_cat": [3, 5], - "numeric": [0, 1], - } - expected_transformers_series = { - "low_card_cat": ["cat1"], - } - expected_transformers_plain = { - "high_card_cat": ["str2", "cat2"], - "low_card_cat": ["str1", "cat1"], - "numeric": ["int", "float"], - } - expected_transformers_np_cast = { - "numeric": [0, 1], - "low_card_cat": [2, 4], - "high_card_cat": [3, 5], - } - _test_possibilities( - X, - expected_transformers_df, - expected_transformers_2, - expected_transformers_np_no_cast, - expected_transformers_series, - expected_transformers_plain, - expected_transformers_np_cast, - ) + _test_possibilities(_get_clean_dataframe()) def test_with_dirty_data() -> None: @@ -252,44 +234,7 @@ def test_with_dirty_data() -> None: Defines the expected returns of the vectorizer in different settings, and runs the tests with a dataset containing missing values. """ - X = _get_dirty_dataframe() - # Define the transformers we'll use throughout the test. - expected_transformers_df = { - "numeric": ["int", "float"], - "low_card_cat": ["str1", "cat1"], - "high_card_cat": ["str2", "cat2"], - } - expected_transformers_2 = { - "low_card_cat": ["str1", "str2", "cat1", "cat2"], - } - expected_transformers_np_no_cast = { - "low_card_cat": [2, 4], - "high_card_cat": [3, 5], - "numeric": [0, 1], - } - expected_transformers_series = { - "low_card_cat": ["cat1"], - } - expected_transformers_plain = { - "high_card_cat": ["str2", "cat2"], - "low_card_cat": ["str1", "cat1"], - "numeric": ["int", "float"], - } - expected_transformers_np_cast = { - "numeric": [0, 1], - "low_card_cat": [2, 4], - "high_card_cat": [3, 5], - } - - _test_possibilities( - X, - expected_transformers_df, - expected_transformers_2, - expected_transformers_np_no_cast, - expected_transformers_series, - expected_transformers_plain, - expected_transformers_np_cast, - ) + _test_possibilities(_get_dirty_dataframe()) def test_auto_cast() -> None: @@ -376,49 +321,39 @@ def test_get_feature_names_out() -> None: vec_w_pass = SuperVectorizer(remainder="passthrough") vec_w_pass.fit(X) - if Version(sklearn.__version__) < Version("0.23"): - with pytest.raises(NotImplementedError): - # Prior to sklearn 0.23, ColumnTransformer.get_feature_names - # with "passthrough" transformer(s) raises a NotImplementedError - assert vec_w_pass.get_feature_names_out() + # In this test, order matters. If it doesn't, convert to set. + expected_feature_names_pass = [ + "str1_public", + "str2_chef", + "str2_lawyer", + "str2_manager", + "str2_officer", + "str2_teacher", + "cat1_yes", + "cat2_20K+", + "cat2_30K+", + "cat2_40K+", + "cat2_50K+", + "cat2_60K+", + "int", + "float", + ] + if Version(sklearn.__version__) < Version("1.0"): + assert vec_w_pass.get_feature_names() == expected_feature_names_pass else: - # In this test, order matters. If it doesn't, convert to set. - expected_feature_names_pass = [ - "str1_private", - "str1_public", - "str2_chef", - "str2_lawyer", - "str2_manager", - "str2_officer", - "str2_teacher", - "cat1_no", - "cat1_yes", - "cat2_20K+", - "cat2_30K+", - "cat2_40K+", - "cat2_50K+", - "cat2_60K+", - "int", - "float", - ] - if Version(sklearn.__version__) < Version("1.0"): - assert vec_w_pass.get_feature_names() == expected_feature_names_pass - else: - assert vec_w_pass.get_feature_names_out() == expected_feature_names_pass + assert vec_w_pass.get_feature_names_out() == expected_feature_names_pass vec_w_drop = SuperVectorizer(remainder="drop") vec_w_drop.fit(X) # In this test, order matters. If it doesn't, convert to set. expected_feature_names_drop = [ - "str1_private", "str1_public", "str2_chef", "str2_lawyer", "str2_manager", "str2_officer", "str2_teacher", - "cat1_no", "cat1_yes", "cat2_20K+", "cat2_30K+", @@ -448,7 +383,11 @@ def test_transform() -> None: s = [34, 5.5, "private", "manager", "yes", "60K+"] x = np.array(s).reshape(1, -1) x_trans = sup_vec.transform(x) - assert (x_trans == [[1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 34, 5.5]]).all() + assert x_trans.tolist() == [ + [0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 34.0, 5.5] + ] + # To understand the list above: + # print(dict(zip(sup_vec.get_feature_names_out(), x_trans.tolist()[0]))) def test_fit_transform_equiv() -> None: @@ -492,13 +431,20 @@ def test_passthrough(): auto_cast=False, ) - X_enc_dirty = sv.fit_transform(X_dirty) - X_enc_clean = sv.fit_transform(X_clean) + X_enc_dirty = pd.DataFrame( + sv.fit_transform(X_dirty), columns=sv.get_feature_names_out() + ) + X_enc_clean = pd.DataFrame( + sv.fit_transform(X_clean), columns=sv.get_feature_names_out() + ) + # Reorder encoded arrays' columns (see SV's doc "Notes" section as to why) + X_enc_dirty = X_enc_dirty[X_dirty.columns] + X_enc_clean = X_enc_clean[X_clean.columns] dirty_flat_df = X_dirty.to_numpy().ravel().tolist() - dirty_flat_trans_df = X_enc_dirty.ravel().tolist() + dirty_flat_trans_df = X_enc_dirty.to_numpy().ravel().tolist() assert all(map(_is_equal, zip(dirty_flat_df, dirty_flat_trans_df))) - assert (X_clean.to_numpy() == X_enc_clean).all() + assert (X_clean.to_numpy() == X_enc_clean.to_numpy()).all() if __name__ == "__main__":
One hot encoding of Supervectorizer for columns with 2 values Just something I observed using SuperVectorizer, on a dataset with columns having mostly 2 categorical values. As documented, it runs one hot encoding on them, and this blows up the feature space. This is probably an edge case, and the example I have here is maybe an extreme one. For just two values it seemed excessive to do one-hot encoding. ``` from dirty_cat import SuperVectorizer from sklearn.datasets import fetch_openml X, y = fetch_openml("kr-vs-kp", return_X_y=True) X.shape (3196, 36) X.describe() bkblk bknwy bkon8 bkona bkspr bkxbq bkxcr bkxwp blxwp bxqsq cntxt dsopp dwipd ... simpl skach skewr skrxp spcop stlmt thrsk wkcti wkna8 wknck wkovl wkpos wtoeg count 3196 3196 3196 3196 3196 3196 3196 3196 3196 3196 3196 3196 3196 ... 3196 3196 3196 3196 3196 3196 3196 3196 3196 3196 3196 3196 3196 unique 2 2 2 2 2 2 2 2 2 2 2 2 2 ... 2 2 2 2 2 2 2 2 2 2 2 2 2 top f f f f f f f f f f f f l ... f f t f f f f f f f t t n freq 2839 2971 3076 2874 2129 1722 2026 2500 1980 2225 1817 2860 2205 ... 1975 3185 2216 3021 3195 3149 3060 2631 3021 1984 2007 2345 2407 [4 rows x 36 columns] sv = SuperVectorizer() X_tx = sv.fit_transform(X) X_tx.shape (3196, 73) ```
0.0
9e59a1ae72abfb453768d6cd41daca9cbb4cc942
[ "dirty_cat/test/test_super_vectorizer.py::test_transform" ]
[ "dirty_cat/test/test_super_vectorizer.py::test_with_clean_data", "dirty_cat/test/test_super_vectorizer.py::test_fit", "dirty_cat/test/test_super_vectorizer.py::test_with_dirty_data" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2022-08-08 12:14:01+00:00
bsd-3-clause
1,919
dirty-cat__dirty_cat-378
diff --git a/CHANGES.rst b/CHANGES.rst index f774809..49769fe 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -3,12 +3,21 @@ Release 0.4.0 ============= -Minor changes +Major changes ------------- * Unnecessary API has been made private: everything (files, functions, classes) starting with an underscore shouldn't be imported in your code. +Minor changes +------------- + +Bug fixes +--------- + +* :class:`MinHashEncoder` now considers `None` as missing values, rather + than raising an error. + Release 0.3.0 ============= @@ -55,7 +64,7 @@ Notes Release 0.2.2 ============= -Bug-fixes +Bug fixes --------- * Fixed a bug in the :class:`SuperVectorizer` causing a `FutureWarning` diff --git a/dirty_cat/_minhash_encoder.py b/dirty_cat/_minhash_encoder.py index 96a9a6e..8c6c86c 100644 --- a/dirty_cat/_minhash_encoder.py +++ b/dirty_cat/_minhash_encoder.py @@ -26,6 +26,7 @@ from ._fast_hash import ngram_min_hash from ._string_distances import get_unique_ngrams from ._utils import LRUDict, check_input +NoneType = type(None) class MinHashEncoder(BaseEstimator, TransformerMixin): """ @@ -208,7 +209,8 @@ class MinHashEncoder(BaseEstimator, TransformerMixin): for k in range(X.shape[1]): X_in = X[:, k].reshape(-1) for i, x in enumerate(X_in): - if isinstance(x, float): # true if x is a missing value + if (isinstance(x, float) # true if x is a missing value + or x is None): is_nan_idx = True elif x not in self.hash_dict_: X_out[i, k * self.n_components : counter] = self.hash_dict_[
dirty-cat/dirty_cat
9eb591250ab9dfd756ab08ef764278f256bf9d3c
diff --git a/dirty_cat/tests/test_minhash_encoder.py b/dirty_cat/tests/test_minhash_encoder.py index b55f56d..c640fb0 100644 --- a/dirty_cat/tests/test_minhash_encoder.py +++ b/dirty_cat/tests/test_minhash_encoder.py @@ -133,6 +133,15 @@ def test_missing_values(input_type: str, missing: str, hashing: str) -> None: return +def test_missing_values_none(): + # Test that "None" is also understood as a missing value + a = np.array([['a', 'b', None, 'c']], dtype=object).T + + enc = MinHashEncoder() + d = enc.fit_transform(a) + np.testing.assert_array_equal(d[2], 0) + + def test_cache_overflow() -> None: # Regression test for cache overflow resulting in -1s in encoding def get_random_string(length):
MinHashEncoder does not understand "None" as missing value The following raises an error because the None is not captured as a NaN: ```python import numpy as np a = np.array([['a', 'b', None, 'c']], dtype=object).T from dirty_cat import MinHashEncoder enc = MinHashEncoder() enc.fit_transform(a) ```
0.0
9eb591250ab9dfd756ab08ef764278f256bf9d3c
[ "dirty_cat/tests/test_minhash_encoder.py::test_missing_values_none" ]
[ "dirty_cat/tests/test_minhash_encoder.py::test_multiple_columns", "dirty_cat/tests/test_minhash_encoder.py::test_input_type", "dirty_cat/tests/test_minhash_encoder.py::test_missing_values[numpy-error-fast]", "dirty_cat/tests/test_minhash_encoder.py::test_missing_values[numpy-zero_impute-fast]", "dirty_cat/tests/test_minhash_encoder.py::test_cache_overflow", "dirty_cat/tests/test_minhash_encoder.py::test_min_hash_encoder_hashing_fast_minmax_hash[0]", "dirty_cat/tests/test_minhash_encoder.py::test_min_hash_encoder_hashing_fast_minmax_hash[1]", "dirty_cat/tests/test_minhash_encoder.py::test_min_hash_encoder_hashing_fast_minmax_hash[2]", "dirty_cat/tests/test_minhash_encoder.py::test_min_hash_encoder_hashing_fast[0]", "dirty_cat/tests/test_minhash_encoder.py::test_min_hash_encoder_hashing_fast[1]", "dirty_cat/tests/test_minhash_encoder.py::test_min_hash_encoder_hashing_fast[2]" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2022-10-06 09:24:23+00:00
bsd-3-clause
1,920
dirty-cat__dirty_cat-401
diff --git a/dirty_cat/_super_vectorizer.py b/dirty_cat/_super_vectorizer.py index db8f862..d5bac42 100644 --- a/dirty_cat/_super_vectorizer.py +++ b/dirty_cat/_super_vectorizer.py @@ -4,7 +4,6 @@ transformers/encoders to different types of data, without the need to manually categorize them beforehand, or construct complex Pipelines. """ - from typing import Dict, List, Literal, Optional, Tuple, Union from warnings import warn @@ -20,6 +19,9 @@ from sklearn.preprocessing import OneHotEncoder from dirty_cat import DatetimeEncoder, GapEncoder from dirty_cat._utils import Version +# Required for ignoring lines too long in the docstrings +# flake8: noqa: E501 + def _has_missing_values(df: Union[pd.DataFrame, pd.Series]) -> bool: """ @@ -82,19 +84,21 @@ OptionalTransformer = Optional[ class SuperVectorizer(ColumnTransformer): - """ - Easily transforms a heterogeneous data table (such as a dataframe) to - a numerical array for machine learning. For this it transforms each - column depending on its data type. - It provides a simplified interface for the :class:`sklearn.compose.ColumnTransformer` ; - more documentation of attributes and functions are available in its doc. + """Easily transform a heterogeneous array to a numerical one. + + Easily transforms a heterogeneous data table + (such as a :class:`pandas.DataFrame`) to a numerical array for machine + learning. For this it transforms each column depending on its data type. + It provides a simplified interface for the + :class:`sklearn.compose.ColumnTransformer`; more documentation of + attributes and functions are available in its doc. .. versionadded:: 0.2.0 Parameters ---------- - cardinality_threshold : int, default=40 + cardinality_threshold : int, optional, default=40 Two lists of features will be created depending on this value: strictly under this value, the low cardinality categorical features, and above or equal, the high cardinality categorical features. @@ -104,19 +108,19 @@ class SuperVectorizer(ColumnTransformer): Note: currently, missing values are counted as a single unique value (so they count in the cardinality). - low_card_cat_transformer : typing.Optional[typing.Union[sklearn.base.TransformerMixin, typing.Literal["drop", "remainder", "passthrough"]]], default=None # noqa + low_card_cat_transformer : {"drop", "remainder", "passthrough"} or Transformer, optional Transformer used on categorical/string features with low cardinality (threshold is defined by `cardinality_threshold`). - Can either be a transformer object instance (e.g. `OneHotEncoder(drop="if_binary")`), + Can either be a transformer object instance (e.g. `OneHotEncoder()`), a `Pipeline` containing the preprocessing steps, 'drop' for dropping the columns, 'remainder' for applying `remainder`, 'passthrough' to return the unencoded columns, - or None to use the default transformer (`OneHotEncoder()`). + or None to use the default transformer (`OneHotEncoder(drop="if_binary")`). Features classified under this category are imputed based on the strategy defined with `impute_missing`. - high_card_cat_transformer : typing.Optional[typing.Union[sklearn.base.TransformerMixin, typing.Literal["drop", "remainder", "passthrough"]]], default=None # noqa + high_card_cat_transformer : {"drop", "remainder", "passthrough"} or Transformer, optional Transformer used on categorical/string features with high cardinality (threshold is defined by `cardinality_threshold`). Can either be a transformer object instance (e.g. `GapEncoder()`), @@ -128,7 +132,7 @@ class SuperVectorizer(ColumnTransformer): Features classified under this category are imputed based on the strategy defined with `impute_missing`. - numerical_transformer : typing.Optional[typing.Union[sklearn.base.TransformerMixin, typing.Literal["drop", "remainder", "passthrough"]]], default=None # noqa + numerical_transformer : {"drop", "remainder", "passthrough"} or Transformer, optional Transformer used on numerical features. Can either be a transformer object instance (e.g. `StandardScaler()`), a `Pipeline` containing the preprocessing steps, @@ -139,7 +143,7 @@ class SuperVectorizer(ColumnTransformer): Features classified under this category are not imputed at all (regardless of `impute_missing`). - datetime_transformer : typing.Optional[typing.Union[sklearn.base.TransformerMixin, typing.Literal["drop", "remainder", "passthrough"]]], default=None + datetime_transformer : {"drop", "remainder", "passthrough"} or Transformer, optional Transformer used on datetime features. Can either be a transformer object instance (e.g. `DatetimeEncoder()`), a `Pipeline` containing the preprocessing steps, @@ -150,11 +154,11 @@ class SuperVectorizer(ColumnTransformer): Features classified under this category are not imputed at all (regardless of `impute_missing`). - auto_cast : bool, default=True + auto_cast : bool, optional, default=True If set to `True`, will try to convert each column to the best possible data type (dtype). - impute_missing : str, default='auto' + impute_missing : {"auto", "force", "skip"}, optional, default='auto' When to impute missing values in categorical (textual) columns. 'auto' will impute missing values if it is considered appropriate (we are using an encoder that does not support missing values and/or @@ -166,7 +170,7 @@ class SuperVectorizer(ColumnTransformer): it is left to the user to manage. See also attribute `imputed_columns_`. - remainder : typing.Union[typing.Literal["drop", "passthrough"], sklearn.base.TransformerMixin], default='drop' # noqa + remainder : {"drop", "passthrough"} or Transformer, optional, default='drop' By default, only the specified columns in `transformers` are transformed and combined in the output, and the non-specified columns are dropped. (default ``'drop'``). @@ -180,31 +184,32 @@ class SuperVectorizer(ColumnTransformer): Note that using this feature requires that the DataFrame columns input at :term:`fit` and :term:`transform` have identical order. - sparse_threshold: float, default=0.3 + sparse_threshold : float, optional, default=0.3 If the output of the different transformers contains sparse matrices, these will be stacked as a sparse matrix if the overall density is lower than this value. Use sparse_threshold=0 to always return dense. When the transformed output consists of all dense data, the stacked result will be dense, and this keyword will be ignored. - n_jobs : int, default=None + n_jobs : int, optional Number of jobs to run in parallel. - ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``None`` (the default) means 1 unless in a + :obj:`joblib.parallel_backend` context. ``-1`` means using all processors. - transformer_weights : dict, default=None + transformer_weights : dict, optional Multiplicative weights for features per transformer. The output of the transformer is multiplied by these weights. Keys are transformer names, values the weights. - verbose : bool, default=False + verbose : bool, optional, default=False If True, the time elapsed while fitting each transformer will be - printed as it is completed + printed as it is completed. Attributes ---------- - transformers_: typing.List[typing.Tuple[str, typing.Union[str, sklearn.base.TransformerMixin], typing.List[str]]] # noqa + transformers_: list of 3-tuples (str, Transformer or str, list of str) The collection of fitted transformers as tuples of (name, fitted_transformer, column). `fitted_transformer` can be an estimator, 'drop', or 'passthrough'. In case there were no columns @@ -220,24 +225,27 @@ class SuperVectorizer(ColumnTransformer): The fitted array's columns. They are applied to the data passed to the `transform` method. - types_: typing.Dict[str, type] + types_: dict mapping str to type A mapping of inferred types per column. Key is the column name, value is the inferred dtype. Exists only if `auto_cast=True`. - imputed_columns_: typing.List[str] + imputed_columns_: list of str The list of columns in which we imputed the missing values. Notes ----- The column order of the input data is not guaranteed to be the same - as the output data (returned by `transform`). - This is a due to the way the ColumnTransformer works. + as the output data (returned by :func:`SuperVectorizer.transform`). + This is a due to the way the :class:`sklearn.compose.ColumnTransformer` + works. However, the output column order will always be the same for different - calls to `transform` on a same fitted SuperVectorizer instance. - For example, if input data has columns ['name', 'job', 'year], then output + calls to :func:`SuperVectorizer.transform` on a same fitted + :class:`SuperVectorizer` instance. + For example, if input data has columns ['name', 'job', 'year'], then output columns might be shuffled, e.g., ['job', 'year', 'name'], but every call - to `transform` will return this order. + to :func:`SuperVectorizer.transform` on this instance will return this + order. """ transformers_: List[Tuple[str, Union[str, TransformerMixin], List[str]]] @@ -257,7 +265,7 @@ class SuperVectorizer(ColumnTransformer): numerical_transformer: OptionalTransformer = None, datetime_transformer: OptionalTransformer = None, auto_cast: bool = True, - impute_missing: str = "auto", + impute_missing: Literal["auto", "force", "skip"] = "auto", # The next parameters are inherited from ColumnTransformer remainder: Union[ Literal["drop", "passthrough"], TransformerMixin
dirty-cat/dirty_cat
9bc0f1fa93a151fc599f6198960ba6d1fabdf5a3
diff --git a/dirty_cat/tests/test_docstrings.py b/dirty_cat/tests/test_docstrings.py index 7177f69..c8772bb 100644 --- a/dirty_cat/tests/test_docstrings.py +++ b/dirty_cat/tests/test_docstrings.py @@ -35,7 +35,6 @@ DOCSTRING_TEMP_IGNORE_SET = { "dirty_cat._similarity_encoder.SimilarityEncoder.fit", "dirty_cat._similarity_encoder.SimilarityEncoder.transform", "dirty_cat._similarity_encoder.SimilarityEncoder.fit_transform", - "dirty_cat._super_vectorizer.SuperVectorizer", "dirty_cat._super_vectorizer.SuperVectorizer.fit_transform", "dirty_cat._super_vectorizer.SuperVectorizer.transform", "dirty_cat._super_vectorizer.SuperVectorizer._auto_cast", @@ -148,17 +147,18 @@ def filter_errors(errors, method, Estimator=None): # - GL02: If there's a blank line, it should be before the # first line of the Returns section, not after (it allows to have # short docstrings for properties). + # - SA01: See Also section not found + # - EX01: No examples section found; FIXME: remove when #373 resolved - if code in ["RT02", "GL01", "GL02"]: + if code in ["RT02", "GL01", "GL02", "SA01", "EX01"]: continue # Following codes are only taken into account for the # top level class docstrings: # - ES01: No extended summary found - # - SA01: See Also section not found # - EX01: No examples section found - if method is not None and code in ["EX01", "SA01", "ES01"]: + if method is not None and code in ["EX01", "ES01"]: continue yield code, message diff --git a/dirty_cat/tests/test_gap_encoder.py b/dirty_cat/tests/test_gap_encoder.py index 3c4ecc0..f891508 100644 --- a/dirty_cat/tests/test_gap_encoder.py +++ b/dirty_cat/tests/test_gap_encoder.py @@ -2,10 +2,10 @@ import numpy as np import pandas as pd import pytest from sklearn import __version__ as sklearn_version -from sklearn.datasets import fetch_20newsgroups from dirty_cat import GapEncoder from dirty_cat._utils import Version +from dirty_cat.tests.utils import generate_data def test_analyzer(): @@ -15,8 +15,7 @@ def test_analyzer(): """ add_words = False n_samples = 70 - X_txt = fetch_20newsgroups(subset="train")["data"][:n_samples] - X = np.array([X_txt, X_txt]).T + X = generate_data(n_samples) n_components = 10 # Test first analyzer output: encoder = GapEncoder( @@ -56,8 +55,7 @@ def test_analyzer(): def test_gap_encoder( hashing: bool, init: str, analyzer: str, add_words: bool, n_samples: int = 70 ) -> None: - X_txt = fetch_20newsgroups(subset="train")["data"][:n_samples] - X = np.array([X_txt, X_txt]).T + X = generate_data(n_samples) n_components = 10 # Test output shape encoder = GapEncoder( @@ -117,8 +115,7 @@ def test_input_type() -> None: def test_partial_fit(n_samples=70) -> None: - X_txt = fetch_20newsgroups(subset="train")["data"][:n_samples] - X = np.array([X_txt, X_txt]).T + X = generate_data(n_samples) # Gap encoder with fit on one batch enc = GapEncoder(random_state=42, batch_size=n_samples, max_iter=1) X_enc = enc.fit_transform(X) @@ -131,8 +128,7 @@ def test_partial_fit(n_samples=70) -> None: def test_get_feature_names_out(n_samples=70) -> None: - X_txt = fetch_20newsgroups(subset="train")["data"][:n_samples] - X = np.array([X_txt, X_txt]).T + X = generate_data(n_samples) enc = GapEncoder(random_state=42) enc.fit(X) # Expect a warning if sklearn >= 1.0 @@ -164,8 +160,7 @@ def test_overflow_error() -> None: def test_score(n_samples: int = 70) -> None: - X_txt = fetch_20newsgroups(subset="train")["data"][:n_samples] - X1 = np.array(X_txt)[:, None] + X1 = generate_data(n_samples) X2 = np.hstack([X1, X1]) enc = GapEncoder(random_state=42) enc.fit(X1) diff --git a/dirty_cat/tests/utils.py b/dirty_cat/tests/utils.py index b710d5b..15da3e1 100644 --- a/dirty_cat/tests/utils.py +++ b/dirty_cat/tests/utils.py @@ -5,7 +5,6 @@ import numpy as np def generate_data(n_samples, as_list=False): MAX_LIMIT = 255 # extended ASCII Character set - i = 0 str_list = [] for i in range(n_samples): random_string = "category " @@ -14,7 +13,6 @@ def generate_data(n_samples, as_list=False): random_string += chr(random_integer) if random_integer < 50: random_string += " " - i += 1 str_list += [random_string] if as_list is True: X = str_list
Make our tests more robust to flawky downloads Some tests use data downloaded from internet: https://github.com/dirty-cat/dirty_cat/blob/master/dirty_cat/tests/test_minhash_encoder.py As a result, the tests are fragile (see https://github.com/dirty-cat/dirty_cat/actions/runs/3175021096/jobs/5176906979#step:6:907 for instance). It seems to me that some of these tests could be rewritten on generated data. ### Tests with flawky downloads - [X] `test_fast_hash.py` #402 - [X] `test_gap_encoder.py` #401 - [X] `test_minhash_encoder.py` #379
0.0
9bc0f1fa93a151fc599f6198960ba6d1fabdf5a3
[ "dirty_cat/tests/test_docstrings.py::test_docstring[SuperVectorizer-None]" ]
[ "dirty_cat/tests/test_docstrings.py::test_docstring[DatetimeEncoder-fit]", "dirty_cat/tests/test_docstrings.py::test_docstring[DatetimeEncoder-fit_transform]", "dirty_cat/tests/test_docstrings.py::test_docstring[DatetimeEncoder-get_metadata_routing]", "dirty_cat/tests/test_docstrings.py::test_docstring[DatetimeEncoder-get_params]", "dirty_cat/tests/test_docstrings.py::test_docstring[DatetimeEncoder-set_output]", "dirty_cat/tests/test_docstrings.py::test_docstring[DatetimeEncoder-set_params]", "dirty_cat/tests/test_docstrings.py::test_docstring[DatetimeEncoder-transform]", "dirty_cat/tests/test_docstrings.py::test_docstring[GapEncoder-fit_transform]", "dirty_cat/tests/test_docstrings.py::test_docstring[GapEncoder-get_metadata_routing]", "dirty_cat/tests/test_docstrings.py::test_docstring[GapEncoder-get_params]", "dirty_cat/tests/test_docstrings.py::test_docstring[GapEncoder-set_output]", "dirty_cat/tests/test_docstrings.py::test_docstring[GapEncoder-set_params]", "dirty_cat/tests/test_docstrings.py::test_docstring[MinHashEncoder-fit_transform]", "dirty_cat/tests/test_docstrings.py::test_docstring[MinHashEncoder-get_metadata_routing]", "dirty_cat/tests/test_docstrings.py::test_docstring[MinHashEncoder-get_params]", "dirty_cat/tests/test_docstrings.py::test_docstring[MinHashEncoder-set_output]", "dirty_cat/tests/test_docstrings.py::test_docstring[MinHashEncoder-set_params]", "dirty_cat/tests/test_docstrings.py::test_docstring[SimilarityEncoder-get_feature_names_out]", "dirty_cat/tests/test_docstrings.py::test_docstring[SimilarityEncoder-get_metadata_routing]", "dirty_cat/tests/test_docstrings.py::test_docstring[SimilarityEncoder-get_most_frequent]", "dirty_cat/tests/test_docstrings.py::test_docstring[SimilarityEncoder-get_params]", "dirty_cat/tests/test_docstrings.py::test_docstring[SimilarityEncoder-infrequent_categories_]", "dirty_cat/tests/test_docstrings.py::test_docstring[SimilarityEncoder-inverse_transform]", "dirty_cat/tests/test_docstrings.py::test_docstring[SimilarityEncoder-set_output]", "dirty_cat/tests/test_docstrings.py::test_docstring[SimilarityEncoder-set_params]", "dirty_cat/tests/test_docstrings.py::test_docstring[SimilarityEncoder-set_transform_request]", "dirty_cat/tests/test_docstrings.py::test_docstring[SuperVectorizer-get_metadata_routing]", "dirty_cat/tests/test_docstrings.py::test_docstring[SuperVectorizer-get_params]", "dirty_cat/tests/test_docstrings.py::test_docstring[SuperVectorizer-set_output]", "dirty_cat/tests/test_docstrings.py::test_docstring[TargetEncoder-fit_transform]", "dirty_cat/tests/test_docstrings.py::test_docstring[TargetEncoder-get_metadata_routing]", "dirty_cat/tests/test_docstrings.py::test_docstring[TargetEncoder-get_params]", "dirty_cat/tests/test_docstrings.py::test_docstring[TargetEncoder-set_output]", "dirty_cat/tests/test_docstrings.py::test_docstring[TargetEncoder-set_params]", "dirty_cat/tests/test_gap_encoder.py::test_analyzer", "dirty_cat/tests/test_gap_encoder.py::test_gap_encoder[False-k-means++-word-True]", "dirty_cat/tests/test_gap_encoder.py::test_gap_encoder[True-random-char-False]", "dirty_cat/tests/test_gap_encoder.py::test_gap_encoder[True-k-means-char_wb-True]", "dirty_cat/tests/test_gap_encoder.py::test_input_type", "dirty_cat/tests/test_gap_encoder.py::test_partial_fit", "dirty_cat/tests/test_gap_encoder.py::test_get_feature_names_out", "dirty_cat/tests/test_gap_encoder.py::test_overflow_error", "dirty_cat/tests/test_gap_encoder.py::test_score", "dirty_cat/tests/test_gap_encoder.py::test_missing_values[zero_impute]", "dirty_cat/tests/test_gap_encoder.py::test_missing_values[error]", "dirty_cat/tests/test_gap_encoder.py::test_missing_values[aaa]" ]
{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2022-10-28 09:16:09+00:00
bsd-3-clause
1,921
disqus__python-phabricator-64
diff --git a/CHANGES b/CHANGES index 2fd4c34..64c95a0 100644 --- a/CHANGES +++ b/CHANGES @@ -1,3 +1,7 @@ +0.8.1 + +* Fixed bug where built-in interface dict overwrote `interface` methods from Almanac (`interface.search`, `interface.edit`). The `Resource` attribute `interface` is renamed `_interface`. + 0.8.0 * Switch to using requests diff --git a/phabricator/__init__.py b/phabricator/__init__.py index b01d167..6d53748 100644 --- a/phabricator/__init__.py +++ b/phabricator/__init__.py @@ -224,7 +224,7 @@ class Result(MutableMapping): class Resource(object): def __init__(self, api, interface=None, endpoint=None, method=None, nested=False): self.api = api - self.interface = interface or copy.deepcopy(parse_interfaces(INTERFACES)) + self._interface = interface or copy.deepcopy(parse_interfaces(INTERFACES)) self.endpoint = endpoint self.method = method self.nested = nested @@ -232,7 +232,7 @@ class Resource(object): def __getattr__(self, attr): if attr in getattr(self, '__dict__'): return getattr(self, attr) - interface = self.interface + interface = self._interface if self.nested: attr = "%s.%s" % (self.endpoint, attr) submethod_exists = False @@ -254,7 +254,7 @@ class Resource(object): def _request(self, **kwargs): # Check for missing variables - resource = self.interface + resource = self._interface def validate_kwarg(key, target): # Always allow list @@ -391,4 +391,4 @@ class Phabricator(Resource): interfaces = query() - self.interface = parse_interfaces(interfaces) + self._interface = parse_interfaces(interfaces) diff --git a/setup.py b/setup.py index c7586bc..ec3f0e5 100644 --- a/setup.py +++ b/setup.py @@ -14,7 +14,7 @@ if sys.version_info[:2] <= (3, 3): setup( name='phabricator', - version='0.8.0', + version='0.8.1', author='Disqus', author_email='[email protected]', url='http://github.com/disqus/python-phabricator',
disqus/python-phabricator
a922ba404a4578f9f909e241539b1fb5a99585b2
diff --git a/phabricator/tests/test_phabricator.py b/phabricator/tests/test_phabricator.py index cad5a8e..e12b285 100644 --- a/phabricator/tests/test_phabricator.py +++ b/phabricator/tests/test_phabricator.py @@ -163,7 +163,7 @@ class PhabricatorTest(unittest.TestCase): def test_endpoint_shadowing(self): - shadowed_endpoints = [e for e in self.api.interface.keys() if e in self.api.__dict__] + shadowed_endpoints = [e for e in self.api._interface.keys() if e in self.api.__dict__] self.assertEqual( shadowed_endpoints, [],
Conflict between Resource class attribute and new almanac interface endpoints With [rPe502df509d5f](https://secure.phabricator.com/rPe502df509d5f8dd3106be50d7d83ac244ff96cb4), upstream phab implements almanac conduit endpoints: `almanc.interface.search` and `almanc.interface.edit`. This now conflicts with the existing Resource class attribute `self.interface`. If you reproduce this against a Phab instance with the new `almanac.interface.*` conduit endpoints: ``` from phabricator import Phabricator phab = Phabricator() phab.almanac.interface.search Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'dict' object has no attribute 'search' ``` it throws an error because it is using the Resource class attribute `self.interface` instead of treating it like a normal method. This does not occur when the method name does not conflict with the Resource attributes: ``` phab.almanac.device.search <phabricator.Resource object at 0x7f760699cf60> ``` The Resource class should not rely on certain keywords *not* becoming conduit methods.
0.0
a922ba404a4578f9f909e241539b1fb5a99585b2
[ "phabricator/tests/test_phabricator.py::PhabricatorTest::test_endpoint_shadowing" ]
[ "phabricator/tests/test_phabricator.py::PhabricatorTest::test_bad_status", "phabricator/tests/test_phabricator.py::PhabricatorTest::test_classic_resources", "phabricator/tests/test_phabricator.py::PhabricatorTest::test_connect", "phabricator/tests/test_phabricator.py::PhabricatorTest::test_generate_hash", "phabricator/tests/test_phabricator.py::PhabricatorTest::test_maniphest_find", "phabricator/tests/test_phabricator.py::PhabricatorTest::test_map_param_type", "phabricator/tests/test_phabricator.py::PhabricatorTest::test_nested_resources", "phabricator/tests/test_phabricator.py::PhabricatorTest::test_user_whoami", "phabricator/tests/test_phabricator.py::PhabricatorTest::test_validation" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2021-02-09 01:47:25+00:00
apache-2.0
1,922
dixudx__rtcclient-184
diff --git a/examples/how_to/workitem/get_workitem.py b/examples/how_to/workitem/get_workitem.py index ef095f8..7064f40 100644 --- a/examples/how_to/workitem/get_workitem.py +++ b/examples/how_to/workitem/get_workitem.py @@ -9,7 +9,7 @@ if __name__ == "__main__": url = "https://your_domain:9443/jazz" username = "your_username" password = "your_password" - myclient = RTCClient(url, username, password) + myclient = RTCClient(url, username, password) # ends_with_jazz , old_rtc_authentication kwargs # get all workitems # If both projectarea_id and projectarea_name are None, all the workitems diff --git a/poetry.lock b/poetry.lock index 739b595..7f9ad3d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -747,6 +747,18 @@ files = [ {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"}, ] +[[package]] +name = "toml" +version = "0.10.2" +description = "Python Library for Tom's Obvious, Minimal Language" +category = "dev" +optional = false +python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +files = [ + {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"}, + {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"}, +] + [[package]] name = "tomli" version = "2.0.1" @@ -932,4 +944,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "2.0" python-versions = ">=3.7.0,<4.0" -content-hash = "e34c2dbb238bb43211cc83b01a6fef54cfed2547b3f034dd4c7e47940cc84f95" +content-hash = "d1b93aabe50ca296f8324af41db0ba3b97b09444730854b7ebc3497f6e70fbdb" diff --git a/pyproject.toml b/pyproject.toml index bd2a89d..7fe23fe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,6 +53,7 @@ ] yapf = "*" tox = "*" + toml = "*" [build-system] diff --git a/rtcclient/client.py b/rtcclient/client.py index aba7afb..5d2be51 100644 --- a/rtcclient/client.py +++ b/rtcclient/client.py @@ -8,7 +8,7 @@ import six import xmltodict from rtcclient import exception -from rtcclient import urlparse, urlquote, OrderedDict +from rtcclient import urlencode, urlparse, urlquote, OrderedDict from rtcclient.base import RTCBase from rtcclient.models import FiledAgainst, FoundIn, Comment, Action, State # noqa: F401 from rtcclient.models import IncludedInBuild, ChangeSet, Attachment # noqa: F401 @@ -58,7 +58,8 @@ class RTCClient(RTCBase): proxies=None, searchpath=None, ends_with_jazz=True, - verify: Union[bool, str] = False): + verify: Union[bool, str] = False, + old_rtc_authentication=False): """Initialization See params above @@ -68,6 +69,7 @@ class RTCClient(RTCBase): self.password = password self.proxies = proxies self.verify = verify + self.old_rtc_authentication = old_rtc_authentication RTCBase.__init__(self, url) if not isinstance(ends_with_jazz, bool): @@ -99,6 +101,24 @@ class RTCClient(RTCBase): proxies=self.proxies, allow_redirects=_allow_redirects) + if self.old_rtc_authentication: + # works with server that needs 0.6.0 version + _headers["Content-Type"] = self.CONTENT_URL_ENCODED + if resp.headers.get("set-cookie") is not None: + _headers["Cookie"] = resp.headers.get("set-cookie") + + credentials = urlencode({ + "j_username": self.username, + "j_password": self.password + }) + + resp = self.post(self.url + "/authenticated/j_security_check", + data=credentials, + verify=False, + headers=_headers, + proxies=self.proxies, + allow_redirects=_allow_redirects) + # authfailed authfailed = resp.headers.get("x-com-ibm-team-repository-web-auth-msg") if authfailed == "authfailed":
dixudx/rtcclient
da253d2d1eedb8e9e88c98cfba2828daa2a81f60
diff --git a/tests/test_client.py b/tests/test_client.py index ad6309f..49e7fd5 100644 --- a/tests/test_client.py +++ b/tests/test_client.py @@ -2,6 +2,8 @@ from rtcclient import RTCClient import requests import pytest import utils_test +from unittest.mock import call + from rtcclient.project_area import ProjectArea from rtcclient.models import Severity, Priority, FoundIn, FiledAgainst from rtcclient.models import TeamArea, Member, PlannedFor @@ -42,6 +44,254 @@ def test_headers(mocker): assert client.headers == expected_headers +def test_client_rest_calls_new_auth(mocker): + mocked_get = mocker.patch("requests.get") + mocked_post = mocker.patch("requests.post") + + mock_rsp = mocker.MagicMock(spec=requests.Response) + mock_rsp.status_code = 200 + + mocked_get.return_value = mock_rsp + mocked_post.return_value = mock_rsp + + mock_rsp.headers = {"set-cookie": "cookie-id"} + _ = RTCClient(url="http://test.url:9443/jazz", + username="user", + password="password") + + # assert GET calls + assert mocked_get.call_count == 2 + mocked_get.assert_has_calls([ + call('http://test.url:9443/jazz/authenticated/identity', + verify=False, + headers={ + 'Content-Type': 'text/xml', + 'Cookie': 'cookie-id', + 'Accept': 'text/xml' + }, + proxies=None, + timeout=60, + auth=('user', 'password'), + allow_redirects=True), + call('http://test.url:9443/jazz/authenticated/identity', + verify=False, + headers={ + 'Content-Type': 'text/xml', + 'Cookie': 'cookie-id', + 'Accept': 'text/xml' + }, + proxies=None, + timeout=60, + auth=('user', 'password'), + allow_redirects=True) + ]) + + # assert POST calls + assert mocked_post.call_count == 0 + + +def test_client_rest_calls_old_auth(mocker): + mocked_get = mocker.patch("requests.get") + mocked_post = mocker.patch("requests.post") + + mock_rsp = mocker.MagicMock(spec=requests.Response) + mock_rsp.status_code = 200 + + mocked_get.return_value = mock_rsp + mocked_post.return_value = mock_rsp + + mock_rsp.headers = {"set-cookie": "cookie-id"} + _ = RTCClient(url="http://test.url:9443/jazz", + username="user", + password="password", + old_rtc_authentication=True) + + # assert GET calls + assert mocked_get.call_count == 2 + mocked_get.assert_has_calls([ + call('http://test.url:9443/jazz/authenticated/identity', + verify=False, + headers={ + 'Content-Type': 'application/x-www-form-urlencoded', + 'Cookie': 'cookie-id', + 'Accept': 'text/xml' + }, + proxies=None, + timeout=60, + auth=('user', 'password'), + allow_redirects=True), + call('http://test.url:9443/jazz/authenticated/identity', + verify=False, + headers={ + 'Content-Type': 'application/x-www-form-urlencoded', + 'Cookie': 'cookie-id', + 'Accept': 'text/xml' + }, + proxies=None, + timeout=60, + auth=('user', 'password'), + allow_redirects=True) + ]) + + # assert POST calls + assert mocked_post.call_count == 1 + mocked_post.assert_has_calls([ + call('http://test.url:9443/jazz/authenticated/j_security_check', + data='j_username=user&j_password=password', + json=None, + verify=False, + headers={ + 'Content-Type': 'application/x-www-form-urlencoded', + 'Cookie': 'cookie-id', + 'Accept': 'text/xml' + }, + proxies=None, + timeout=60, + allow_redirects=True) + ]) + + +def test_headers_auth_required_new_auth(mocker): + mocked_get = mocker.patch("requests.get") + mocked_post = mocker.patch("requests.post") + + mock_rsp = mocker.MagicMock(spec=requests.Response) + mock_rsp.status_code = 200 + + # auth required + mock_rsp.headers = { + "set-cookie": "cookie-id", + "X-com-ibm-team-repository-web-auth-msg": "authrequired" + } + + mocked_get.return_value = mock_rsp + mocked_post.return_value = mock_rsp + + _ = RTCClient(url="http://test.url:9443/jazz", + username="user", + password="password") + + # assert GET calls + assert mocked_get.call_count == 2 + mocked_get.assert_has_calls([ + call('http://test.url:9443/jazz/authenticated/identity', + verify=False, + headers={ + 'Content-Type': 'text/xml', + 'Cookie': 'cookie-id', + 'Accept': 'text/xml' + }, + proxies=None, + timeout=60, + auth=('user', 'password'), + allow_redirects=True), + call('http://test.url:9443/jazz/authenticated/identity', + verify=False, + headers={ + 'Content-Type': 'text/xml', + 'Cookie': 'cookie-id', + 'Accept': 'text/xml' + }, + proxies=None, + timeout=60, + auth=('user', 'password'), + allow_redirects=True) + ]) + + # assert POST calls + assert mocked_post.call_count == 1 + mocked_post.assert_has_calls([ + call('http://test.url:9443/jazz/authenticated/j_security_check', + data={ + 'j_username': 'user', + 'j_password': 'password' + }, + json=None, + verify=False, + headers={'Content-Type': 'application/x-www-form-urlencoded'}, + proxies=None, + timeout=60, + allow_redirects=True) + ]) + + +def test_headers_auth_required_old_auth(mocker): + mocked_get = mocker.patch("requests.get") + mocked_post = mocker.patch("requests.post") + + mock_rsp = mocker.MagicMock(spec=requests.Response) + mock_rsp.status_code = 200 + + # auth required + mock_rsp.headers = { + "set-cookie": "cookie-id", + "X-com-ibm-team-repository-web-auth-msg": "authrequired" + } + + mocked_get.return_value = mock_rsp + mocked_post.return_value = mock_rsp + + _ = RTCClient(url="http://test.url:9443/jazz", + username="user", + password="password", + old_rtc_authentication=True) + + # assert GET calls + assert mocked_get.call_count == 2 + mocked_get.assert_has_calls([ + call('http://test.url:9443/jazz/authenticated/identity', + verify=False, + headers={ + 'Content-Type': 'application/x-www-form-urlencoded', + 'Cookie': 'cookie-id', + 'Accept': 'text/xml' + }, + proxies=None, + timeout=60, + auth=('user', 'password'), + allow_redirects=True), + call('http://test.url:9443/jazz/authenticated/identity', + verify=False, + headers={ + 'Content-Type': 'application/x-www-form-urlencoded', + 'Cookie': 'cookie-id', + 'Accept': 'text/xml' + }, + proxies=None, + timeout=60, + auth=('user', 'password'), + allow_redirects=True) + ]) + + # assert POST calls + assert mocked_post.call_count == 2 + mocked_post.assert_has_calls([ + call('http://test.url:9443/jazz/authenticated/j_security_check', + data='j_username=user&j_password=password', + json=None, + verify=False, + headers={ + 'Content-Type': 'application/x-www-form-urlencoded', + 'Cookie': 'cookie-id', + 'Accept': 'text/xml' + }, + proxies=None, + timeout=60, + allow_redirects=True), + call('http://test.url:9443/jazz/authenticated/j_security_check', + data={ + 'j_username': 'user', + 'j_password': 'password' + }, + json=None, + verify=False, + headers={'Content-Type': 'application/x-www-form-urlencoded'}, + proxies=None, + timeout=60, + allow_redirects=True) + ]) + + class TestRTCClient: @pytest.fixture(autouse=True)
url not found: jazz/authenticated Hi, I was trying to use your plugin to, at least, connect to a jazz server using your `get_workitem.py` script into `examples/how_to/workitem` folder. I've changed the file with : ```python url = "https://__the_url__:443/ccm/jazz" username = "my_username" password = "my_password" myclient = RTCClient(url, username, password, ends_with_jazz=True) ``` Adding also `ends_with_jazz=True` that I saw from docs/other issues. This is the trace I get: ```python 2023-03-22 14:49:42,753 DEBUG client.RTCClient: Get response from https://__the_url__:443/ccm/jazz/authenticated/identity 2023-03-22 14:49:42,764 DEBUG urllib3.connectionpool: Starting new HTTPS connection (1): __the_url__:443 2023-03-22 14:49:42,979 DEBUG urllib3.connectionpool: https://__the_url__:443 "GET /ccm/jazz/authenticated/identity HTTP/1.1" 302 0 2023-03-22 14:49:43,000 DEBUG urllib3.connectionpool: Resetting dropped connection: __the_url__ 2023-03-22 14:49:43,153 DEBUG urllib3.connectionpool: https://__the_url__:443 "GET /ccm/secure/authenticated/identity?redirectPath=%2Fccm%2Fjazz%2Fauthenticated%2Fidentity HTTP/1.1" 302 0 2023-03-22 14:49:43,167 DEBUG urllib3.connectionpool: Resetting dropped connection: __the_url__ 2023-03-22 14:49:43,325 DEBUG urllib3.connectionpool: https://__the_url__:443 "GET /ccm/auth/authrequired HTTP/1.1" 200 1072 2023-03-22 14:49:48,130 DEBUG client.RTCClient: Get response from https://__the_url__:443/ccm/jazz/authenticated/identity 2023-03-22 14:49:48,141 DEBUG urllib3.connectionpool: Starting new HTTPS connection (1): __the_url__:443 2023-03-22 14:49:48,368 DEBUG urllib3.connectionpool: https://__the_url__:443 "GET /ccm/jazz/authenticated/identity HTTP/1.1" 302 0 2023-03-22 14:49:48,381 DEBUG urllib3.connectionpool: Resetting dropped connection: __the_url__ 2023-03-22 14:49:48,543 DEBUG urllib3.connectionpool: https://__the_url__:443 "GET /ccm/secure/authenticated/identity?redirectPath=%2Fccm%2Fjazz%2Fauthenticated%2Fidentity HTTP/1.1" 302 0 2023-03-22 14:49:48,583 DEBUG urllib3.connectionpool: Resetting dropped connection: __the_url__ 2023-03-22 14:49:48,837 DEBUG urllib3.connectionpool: https://__the_url__:443 "GET /ccm/auth/authrequired HTTP/1.1" 200 1072 2023-03-22 14:49:56,708 DEBUG client.RTCClient: Post a request to https://__the_url__:443/ccm/jazz/authenticated/j_security_check with data: {'j_username': 'my_username', 'j_password': 'my_password'} and json: None 2023-03-22 14:49:56,717 DEBUG urllib3.connectionpool: Starting new HTTPS connection (1): __the_url__:443 2023-03-22 14:49:57,598 DEBUG urllib3.connectionpool: https://__the_url__:443 "POST /ccm/jazz/authenticated/j_security_check HTTP/1.1" 302 0 2023-03-22 14:49:57,610 DEBUG urllib3.connectionpool: Resetting dropped connection: __the_url__ 2023-03-22 14:49:57,768 DEBUG urllib3.connectionpool: https://__the_url__:443 "GET /ccm/jazz/authenticated/ HTTP/1.1" 404 None 2023-03-22 14:49:57,773 ERROR client.RTCClient: Failed POST request at <https://__the_url__:443/ccm/jazz/authenticated/j_security_check> with response: b'Error 404: Not Found\n' 2023-03-22 14:49:57,773 INFO client.RTCClient: 404 Traceback (most recent call last): File "...\rtcclient\examples\how_to\workitem\get_workitem.py", line 13, in <module> myclient = RTCClient(url, username, password, ends_with_jazz=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "...\rtcclient\rtcclient\client.py", line 77, in __init__ self.headers = self._get_headers() ^^^^^^^^^^^^^^^^^^^ File "...\rtcclient\rtcclient\client.py", line 155, in _get_headers resp = self.post(self.url + "/authenticated/j_security_check", ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "...\rtcclient\rtcclient\utils.py", line 27, in wrapper return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "...\rtcclient\rtcclient\base.py", line 144, in post response.raise_for_status() File "...\rtcclient\venv\Lib\site-packages\requests\models.py", line 1021, in raise_for_status raise HTTPError(http_error_msg, response=self) requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://__the_url__/ccm/jazz/authenticated/ python-BaseException ``` So the point that raises exception is [this line](https://github.com/dixudx/rtcclient/blob/master/rtcclient/client.py#L136), the line number differs because of some tests I made related to cookies (from a fork), but those changes are commented. Some information on my environment: - Python3.11 - rtcclient checkout of main branch - IBM Jazz 7.0.2 Thank you!
0.0
da253d2d1eedb8e9e88c98cfba2828daa2a81f60
[ "tests/test_client.py::test_client_rest_calls_old_auth", "tests/test_client.py::test_headers_auth_required_old_auth" ]
[ "tests/test_client.py::test_headers", "tests/test_client.py::test_client_rest_calls_new_auth", "tests/test_client.py::test_headers_auth_required_new_auth", "tests/test_client.py::TestRTCClient::test_get_projectareas_unarchived", "tests/test_client.py::TestRTCClient::test_get_projectareas_archived", "tests/test_client.py::TestRTCClient::test_get_projectarea_unarchived", "tests/test_client.py::TestRTCClient::test_get_projectarea_exception", "tests/test_client.py::TestRTCClient::test_get_projectarea_archived", "tests/test_client.py::TestRTCClient::test_get_projectarea_byid", "tests/test_client.py::TestRTCClient::test_get_projectarea_id", "tests/test_client.py::TestRTCClient::test_get_projectarea_id_exception", "tests/test_client.py::TestRTCClient::test_get_projectarea_byid_exception", "tests/test_client.py::TestRTCClient::test_get_projectarea_ids", "tests/test_client.py::TestRTCClient::test_get_projectarea_ids_exception", "tests/test_client.py::TestRTCClient::test_check_projectarea_id", "tests/test_client.py::TestRTCClient::test_get_teamareas_unarchived", "tests/test_client.py::TestRTCClient::test_get_teamareas_archived", "tests/test_client.py::TestRTCClient::test_get_teamarea_unarchived", "tests/test_client.py::TestRTCClient::test_get_teamarea_archived", "tests/test_client.py::TestRTCClient::test_get_owned_by", "tests/test_client.py::TestRTCClient::test_get_plannedfors_unarchived", "tests/test_client.py::TestRTCClient::test_get_plannedfors_archived", "tests/test_client.py::TestRTCClient::test_get_plannedfor_unarchived", "tests/test_client.py::TestRTCClient::test_get_plannedfor_archived", "tests/test_client.py::TestRTCClient::test_get_severities", "tests/test_client.py::TestRTCClient::test_get_severity", "tests/test_client.py::TestRTCClient::test_get_priorities", "tests/test_client.py::TestRTCClient::test_get_priority", "tests/test_client.py::TestRTCClient::test_get_foundins_unarchived", "tests/test_client.py::TestRTCClient::test_get_foundins_archived", "tests/test_client.py::TestRTCClient::test_get_foundin_unarchived", "tests/test_client.py::TestRTCClient::test_get_foundin_archived", "tests/test_client.py::TestRTCClient::test_get_filedagainsts_unarchived", "tests/test_client.py::TestRTCClient::test_get_filedagainsts_archived", "tests/test_client.py::TestRTCClient::test_get_filedagainst_unarchived", "tests/test_client.py::TestRTCClient::test_get_filedagainst_archived", "tests/test_client.py::TestRTCClient::test_get_workitem", "tests/test_client.py::TestRTCClient::test_get_workitems_unarchived", "tests/test_client.py::TestRTCClient::test_get_workitems_archived", "tests/test_client.py::TestRTCClient::test_list_fields", "tests/test_client.py::TestRTCClient::test_list_fields_from_workitem", "tests/test_client.py::TestRTCClient::test_create_workitem", "tests/test_client.py::TestRTCClient::test_copy_workitem", "tests/test_client.py::TestRTCClient::test_update_workitem", "tests/test_client.py::TestRTCClient::test_check_itemtype" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-03-28 16:13:18+00:00
apache-2.0
1,923
django-json-api__django-rest-framework-json-api-1074
diff --git a/CHANGELOG.md b/CHANGELOG.md index 91faffd..91551dc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ any parts of the framework not mentioned in the documentation should generally b * Fixed invalid relationship pointer in error objects when field naming formatting is used. * Properly resolved related resource type when nested source field is defined. +* Prevented overwriting of pointer in custom error object ### Added diff --git a/docs/usage.md b/docs/usage.md index 939e4e6..952fe80 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -237,7 +237,7 @@ class MyViewset(ModelViewSet): ``` -### Exception handling +### Error objects / Exception handling For the `exception_handler` class, if the optional `JSON_API_UNIFORM_EXCEPTIONS` is set to True, all exceptions will respond with the JSON:API [error format](https://jsonapi.org/format/#error-objects). @@ -245,6 +245,21 @@ all exceptions will respond with the JSON:API [error format](https://jsonapi.org When `JSON_API_UNIFORM_EXCEPTIONS` is False (the default), non-JSON:API views will respond with the normal DRF error format. +In case you need a custom error object you can simply raise an `rest_framework.serializers.ValidationError` like the following: + +```python +raise serializers.ValidationError( + { + "id": "your-id", + "detail": "your detail message", + "source": { + "pointer": "/data/attributes/your-pointer", + } + + } +) +``` + ### Performance Testing If you are trying to see if your viewsets are configured properly to optimize performance, diff --git a/rest_framework_json_api/utils.py b/rest_framework_json_api/utils.py index 8317c10..2e86e76 100644 --- a/rest_framework_json_api/utils.py +++ b/rest_framework_json_api/utils.py @@ -417,21 +417,20 @@ def format_error_object(message, pointer, response): if isinstance(message, dict): # as there is no required field in error object we check that all fields are string - # except links and source which might be a dict + # except links, source or meta which might be a dict is_custom_error = all( [ isinstance(value, str) for key, value in message.items() - if key not in ["links", "source"] + if key not in ["links", "source", "meta"] ] ) if is_custom_error: if "source" not in message: message["source"] = {} - message["source"] = { - "pointer": pointer, - } + if "pointer" not in message["source"]: + message["source"]["pointer"] = pointer errors.append(message) else: for k, v in message.items():
django-json-api/django-rest-framework-json-api
46551a9aada19c503e363b20b47765009038d996
diff --git a/tests/test_utils.py b/tests/test_utils.py index 9b47e9f..038e8ce 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -7,6 +7,7 @@ from rest_framework.views import APIView from rest_framework_json_api import serializers from rest_framework_json_api.utils import ( + format_error_object, format_field_name, format_field_names, format_link_segment, @@ -389,3 +390,45 @@ def test_get_resource_type_from_serializer_without_resource_name_raises_error(): "can not detect 'resource_name' on serializer " "'SerializerWithoutResourceName' in module 'tests.test_utils'" ) + + [email protected]( + "message,pointer,response,result", + [ + # Test that pointer does not get overridden in custom error + ( + { + "status": "400", + "source": { + "pointer": "/data/custom-pointer", + }, + "meta": {"key": "value"}, + }, + "/data/default-pointer", + Response(status.HTTP_400_BAD_REQUEST), + [ + { + "status": "400", + "source": {"pointer": "/data/custom-pointer"}, + "meta": {"key": "value"}, + } + ], + ), + # Test that pointer gets added to custom error + ( + { + "detail": "custom message", + }, + "/data/default-pointer", + Response(status.HTTP_400_BAD_REQUEST), + [ + { + "detail": "custom message", + "source": {"pointer": "/data/default-pointer"}, + } + ], + ), + ], +) +def test_format_error_object(message, pointer, response, result): + assert result == format_error_object(message, pointer, response)
Avoid overwriting of pointer when using custom errors The code that produces JSON:API error objects assumes that all fields being validated are under `/data/attributes`: https://github.com/django-json-api/django-rest-framework-json-api/blob/b0257c065ac2439036ac0543139e7f5913755177/rest_framework_json_api/utils.py#L339 and there doesn't appear to be a way to override the `pointer` value when specifying the field on a serializer. Use case: I would like to be able to specify a serializer for the top-level `"meta"` field and have any validation errors on that data generate responses properly populated with `"source": {"pointer": "/meta/foo"}`.
0.0
46551a9aada19c503e363b20b47765009038d996
[ "tests/test_utils.py::test_format_error_object[message0-/data/default-pointer-response0-result0]" ]
[ "tests/test_utils.py::test_get_related_resource_type_from_nested_source[m2m_source.targets-ManyToManyTarget-related_field_kwargs0]", "tests/test_utils.py::test_get_related_resource_type_from_nested_source[m2m_target.sources.-ManyToManySource-related_field_kwargs1]", "tests/test_utils.py::test_get_related_resource_type_from_nested_source[fk_source.target-ForeignKeyTarget-related_field_kwargs2]", "tests/test_utils.py::test_get_related_resource_type_from_nested_source[fk_target.source-ForeignKeySource-related_field_kwargs3]", "tests/test_utils.py::test_get_resource_name_no_view", "tests/test_utils.py::test_get_resource_name_from_view[False-False-APIView]", "tests/test_utils.py::test_get_resource_name_from_view[False-True-APIViews]", "tests/test_utils.py::test_get_resource_name_from_view[dasherize-False-api-view]", "tests/test_utils.py::test_get_resource_name_from_view[dasherize-True-api-views]", "tests/test_utils.py::test_get_resource_name_from_view_custom_resource_name[False-False]", "tests/test_utils.py::test_get_resource_name_from_view_custom_resource_name[False-True]", "tests/test_utils.py::test_get_resource_name_from_view_custom_resource_name[dasherize-False]", "tests/test_utils.py::test_get_resource_name_from_view_custom_resource_name[dasherize-True]", "tests/test_utils.py::test_get_resource_name_from_model[False-False-BasicModel]", "tests/test_utils.py::test_get_resource_name_from_model[False-True-BasicModels]", "tests/test_utils.py::test_get_resource_name_from_model[dasherize-False-basic-model]", "tests/test_utils.py::test_get_resource_name_from_model[dasherize-True-basic-models]", "tests/test_utils.py::test_get_resource_name_from_model_serializer_class[False-False-BasicModel]", "tests/test_utils.py::test_get_resource_name_from_model_serializer_class[False-True-BasicModels]", "tests/test_utils.py::test_get_resource_name_from_model_serializer_class[dasherize-False-basic-model]", "tests/test_utils.py::test_get_resource_name_from_model_serializer_class[dasherize-True-basic-models]", "tests/test_utils.py::test_get_resource_name_from_model_serializer_class_custom_resource_name[False-False]", "tests/test_utils.py::test_get_resource_name_from_model_serializer_class_custom_resource_name[False-True]", "tests/test_utils.py::test_get_resource_name_from_model_serializer_class_custom_resource_name[dasherize-False]", "tests/test_utils.py::test_get_resource_name_from_model_serializer_class_custom_resource_name[dasherize-True]", "tests/test_utils.py::test_get_resource_name_from_plain_serializer_class[False-False]", "tests/test_utils.py::test_get_resource_name_from_plain_serializer_class[False-True]", "tests/test_utils.py::test_get_resource_name_from_plain_serializer_class[dasherize-False]", "tests/test_utils.py::test_get_resource_name_from_plain_serializer_class[dasherize-True]", "tests/test_utils.py::test_get_resource_name_with_errors[400]", "tests/test_utils.py::test_get_resource_name_with_errors[403]", "tests/test_utils.py::test_get_resource_name_with_errors[500]", "tests/test_utils.py::test_format_field_names[False-output0]", "tests/test_utils.py::test_format_field_names[camelize-output1]", "tests/test_utils.py::test_format_field_names[capitalize-output2]", "tests/test_utils.py::test_format_field_names[dasherize-output3]", "tests/test_utils.py::test_format_field_names[underscore-output4]", "tests/test_utils.py::test_undo_format_field_names[False-output0]", "tests/test_utils.py::test_undo_format_field_names[camelize-output1]", "tests/test_utils.py::test_format_field_name[False-full_name]", "tests/test_utils.py::test_format_field_name[camelize-fullName]", "tests/test_utils.py::test_format_field_name[capitalize-FullName]", "tests/test_utils.py::test_format_field_name[dasherize-full-name]", "tests/test_utils.py::test_format_field_name[underscore-full_name]", "tests/test_utils.py::test_undo_format_field_name[False-fullName]", "tests/test_utils.py::test_undo_format_field_name[camelize-full_name]", "tests/test_utils.py::test_format_link_segment[False-first_Name]", "tests/test_utils.py::test_format_link_segment[camelize-firstName]", "tests/test_utils.py::test_format_link_segment[capitalize-FirstName]", "tests/test_utils.py::test_format_link_segment[dasherize-first-name]", "tests/test_utils.py::test_format_link_segment[underscore-first_name]", "tests/test_utils.py::test_undo_format_link_segment[False-fullName]", "tests/test_utils.py::test_undo_format_link_segment[camelize-full_name]", "tests/test_utils.py::test_format_value[False-first_name]", "tests/test_utils.py::test_format_value[camelize-firstName]", "tests/test_utils.py::test_format_value[capitalize-FirstName]", "tests/test_utils.py::test_format_value[dasherize-first-name]", "tests/test_utils.py::test_format_value[underscore-first_name]", "tests/test_utils.py::test_format_resource_type[None-None-ResourceType]", "tests/test_utils.py::test_format_resource_type[camelize-False-resourceType]", "tests/test_utils.py::test_format_resource_type[camelize-True-resourceTypes]", "tests/test_utils.py::test_get_related_resource_type[ManyToManySource-targets-ManyToManyTarget]", "tests/test_utils.py::test_get_related_resource_type[ManyToManyTarget-sources-ManyToManySource]", "tests/test_utils.py::test_get_related_resource_type[ForeignKeySource-target-ForeignKeyTarget]", "tests/test_utils.py::test_get_related_resource_type[ForeignKeyTarget-sources-ForeignKeySource]", "tests/test_utils.py::test_get_related_resource_type_from_plain_serializer_class[related_field_kwargs0-BasicModel]", "tests/test_utils.py::test_get_related_resource_type_from_plain_serializer_class[related_field_kwargs1-BasicModel]", "tests/test_utils.py::test_get_related_resource_type_from_plain_serializer_class[related_field_kwargs2-BasicModel]", "tests/test_utils.py::test_get_resource_type_from_serializer_without_resource_name_raises_error", "tests/test_utils.py::test_format_error_object[message1-/data/default-pointer-response1-result1]" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2022-07-20 11:13:20+00:00
bsd-2-clause
1,924
django-json-api__django-rest-framework-json-api-1137
diff --git a/AUTHORS b/AUTHORS index e27ba5f..797ab52 100644 --- a/AUTHORS +++ b/AUTHORS @@ -3,6 +3,7 @@ Adam Ziolkowski <[email protected]> Alan Crosswell <[email protected]> Alex Seidmann <[email protected]> Anton Shutik <[email protected]> +Arttu Perälä <[email protected]> Ashley Loewen <[email protected]> Asif Saif Uddin <[email protected]> Beni Keller <[email protected]> diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a1c344..3f9c175 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ any parts of the framework not mentioned in the documentation should generally b ### Fixed * Refactored handling of the `sort` query parameter to fix duplicate declaration in the generated schema definition +* Non-field serializer errors are given a source.pointer value of "/data". ## [6.0.0] - 2022-09-24 diff --git a/example/api/serializers/identity.py b/example/api/serializers/identity.py index 069259d..5e2a42e 100644 --- a/example/api/serializers/identity.py +++ b/example/api/serializers/identity.py @@ -23,6 +23,13 @@ class IdentitySerializer(serializers.ModelSerializer): ) return data + def validate(self, data): + if data["first_name"] == data["last_name"]: + raise serializers.ValidationError( + "First name cannot be the same as last name!" + ) + return data + class Meta: model = auth_models.User fields = ( diff --git a/rest_framework_json_api/serializers.py b/rest_framework_json_api/serializers.py index a288471..4b619ac 100644 --- a/rest_framework_json_api/serializers.py +++ b/rest_framework_json_api/serializers.py @@ -155,7 +155,12 @@ class IncludedResourcesValidationMixin: class ReservedFieldNamesMixin: """Ensures that reserved field names are not used and an error raised instead.""" - _reserved_field_names = {"meta", "results", "type"} + _reserved_field_names = { + "meta", + "results", + "type", + api_settings.NON_FIELD_ERRORS_KEY, + } def get_fields(self): fields = super().get_fields() diff --git a/rest_framework_json_api/utils.py b/rest_framework_json_api/utils.py index 3d374ee..dab8a3b 100644 --- a/rest_framework_json_api/utils.py +++ b/rest_framework_json_api/utils.py @@ -13,6 +13,7 @@ from django.utils import encoding from django.utils.translation import gettext_lazy as _ from rest_framework import exceptions, relations from rest_framework.exceptions import APIException +from rest_framework.settings import api_settings from .settings import json_api_settings @@ -381,10 +382,14 @@ def format_drf_errors(response, context, exc): ] for field, error in response.data.items(): + non_field_error = field == api_settings.NON_FIELD_ERRORS_KEY field = format_field_name(field) pointer = None - # pointer can be determined only if there's a serializer. - if has_serializer: + if non_field_error: + # Serializer error does not refer to a specific field. + pointer = "/data" + elif has_serializer: + # pointer can be determined only if there's a serializer. rel = "relationships" if field in relationship_fields else "attributes" pointer = f"/data/{rel}/{field}" if isinstance(exc, Http404) and isinstance(error, str):
django-json-api/django-rest-framework-json-api
ad5a793b54ca2922223352a58830515d25fa4807
diff --git a/example/tests/test_generic_viewset.py b/example/tests/test_generic_viewset.py index c8a28f2..40812d6 100644 --- a/example/tests/test_generic_viewset.py +++ b/example/tests/test_generic_viewset.py @@ -129,3 +129,35 @@ class GenericViewSet(TestBase): ) assert expected == response.json() + + def test_nonfield_validation_exceptions(self): + """ + Non-field errors should be attributed to /data source.pointer. + """ + expected = { + "errors": [ + { + "status": "400", + "source": { + "pointer": "/data", + }, + "detail": "First name cannot be the same as last name!", + "code": "invalid", + }, + ] + } + response = self.client.post( + "/identities", + { + "data": { + "type": "users", + "attributes": { + "email": "[email protected]", + "first_name": "Miles", + "last_name": "Miles", + }, + } + }, + ) + + assert expected == response.json()
Object-level validation errors given an incorrect source.pointer ## Description of the Bug Report When raising a non-field `ValidationError` in a serializer [in accordance with the DRF documentation](https://www.django-rest-framework.org/api-guide/serializers/#object-level-validation), the error is attributed to a non-existing `/data/attributes/non_field_errors` path instead of `/data`. ```python from rest_framework_json_api import serializers class ProductSerializer(serializers.ModelSerializer): def validate(self, data): if data.get("best_before_date") and data.get("expiry_date"): raise serializers.ValidationError( "Specify either a best before date or an expiry date." ) return data ``` ```json { "errors": [ { "detail": "Specify either a best before date or an expiry date.", "status": "400", "source": { "pointer": "/data/attributes/non_field_errors" }, "code": "invalid" } ] } ``` Complete minimal example available [here](https://github.com/arttuperala/jsonapi_non_field_errors). ### Discussed in https://github.com/django-json-api/django-rest-framework-json-api/discussions/1135 ## Checklist - [x] Certain that this is a bug (if unsure or you have a question use [discussions](https://github.com/django-json-api/django-rest-framework-json-api/discussions) instead) - [x] Code snippet or unit test added to reproduce bug
0.0
ad5a793b54ca2922223352a58830515d25fa4807
[ "example/tests/test_generic_viewset.py::GenericViewSet::test_nonfield_validation_exceptions" ]
[ "example/tests/test_generic_viewset.py::GenericViewSet::test_ember_expected_renderer", "example/tests/test_generic_viewset.py::GenericViewSet::test_default_validation_exceptions", "example/tests/test_generic_viewset.py::GenericViewSet::test_default_rest_framework_behavior", "example/tests/test_generic_viewset.py::GenericViewSet::test_custom_validation_exceptions" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2023-03-07 08:33:04+00:00
bsd-2-clause
1,925
django-json-api__django-rest-framework-json-api-1162
diff --git a/CHANGELOG.md b/CHANGELOG.md index d494fc2..a9dc65d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,6 +40,8 @@ any parts of the framework not mentioned in the documentation should generally b return value.name ``` +* `SerializerMethodResourceRelatedField(many=True)` relationship data now includes a meta section. + ### Fixed * Refactored handling of the `sort` query parameter to fix duplicate declaration in the generated schema definition diff --git a/rest_framework_json_api/renderers.py b/rest_framework_json_api/renderers.py index f766020..9a0d9c0 100644 --- a/rest_framework_json_api/renderers.py +++ b/rest_framework_json_api/renderers.py @@ -19,6 +19,7 @@ import rest_framework_json_api from rest_framework_json_api import utils from rest_framework_json_api.relations import ( HyperlinkedMixin, + ManySerializerMethodResourceRelatedField, ResourceRelatedField, SkipDataMixin, ) @@ -152,6 +153,11 @@ class JSONRenderer(renderers.JSONRenderer): if not isinstance(field, SkipDataMixin): relation_data.update({"data": resource.get(field_name)}) + if isinstance(field, ManySerializerMethodResourceRelatedField): + relation_data.update( + {"meta": {"count": len(resource.get(field_name))}} + ) + data.update({field_name: relation_data}) continue
django-json-api/django-rest-framework-json-api
71508efa3fee8ff75c9cfcd092844801aeb407e1
diff --git a/example/tests/integration/test_non_paginated_responses.py b/example/tests/integration/test_non_paginated_responses.py index 60376a8..92d26de 100644 --- a/example/tests/integration/test_non_paginated_responses.py +++ b/example/tests/integration/test_non_paginated_responses.py @@ -51,6 +51,7 @@ def test_multiple_entries_no_pagination(multiple_entries, client): "related": "http://testserver/entries/1/suggested/", "self": "http://testserver/entries/1/relationships/suggested", }, + "meta": {"count": 1}, }, "suggestedHyperlinked": { "links": { @@ -106,6 +107,7 @@ def test_multiple_entries_no_pagination(multiple_entries, client): "related": "http://testserver/entries/2/suggested/", "self": "http://testserver/entries/2/relationships/suggested", }, + "meta": {"count": 1}, }, "suggestedHyperlinked": { "links": { diff --git a/example/tests/integration/test_pagination.py b/example/tests/integration/test_pagination.py index 4c60e96..1a4bd05 100644 --- a/example/tests/integration/test_pagination.py +++ b/example/tests/integration/test_pagination.py @@ -51,6 +51,7 @@ def test_pagination_with_single_entry(single_entry, client): "related": "http://testserver/entries/1/suggested/", "self": "http://testserver/entries/1/relationships/suggested", }, + "meta": {"count": 0}, }, "suggestedHyperlinked": { "links": { diff --git a/example/tests/test_filters.py b/example/tests/test_filters.py index ab74dd0..87f9d05 100644 --- a/example/tests/test_filters.py +++ b/example/tests/test_filters.py @@ -512,6 +512,7 @@ class DJATestFilters(APITestCase): {"type": "entries", "id": "11"}, {"type": "entries", "id": "12"}, ], + "meta": {"count": 11}, }, "suggestedHyperlinked": { "links": {
SerializerMethodResourceRelatedField does not include meta section in relationship response. `SerializerMethodResourceRelatedField` does not include a meta section in the relationship response like `ResourceRelatedField` does. This doesn't make sense, because `SerializerMethodResourceRelatedField` extends `ResourceRelatedField` and both seem to return every related record in the response (for the record I've only tried with a little over a thousand related records). So for example if you had an ObjectA with a has many relationship with ObjectB: ```python objectbs = SerializerMethodResourceRelatedField( source='get_objectbs', many=True, model=ObjectB, read_only=True ) def get_objectbs(self, obj): return ObjectB.objects.filter(objecta=obj) ``` then your response would look like: ```json "relationships": { "objectb": { "data": [...] } } ``` instead of: ```json "relationships": { "objectb": { "meta": { "count": 2 }, "data": [...] } } ```
0.0
71508efa3fee8ff75c9cfcd092844801aeb407e1
[ "example/tests/integration/test_non_paginated_responses.py::test_multiple_entries_no_pagination", "example/tests/integration/test_pagination.py::test_pagination_with_single_entry", "example/tests/test_filters.py::DJATestFilters::test_search_keywords" ]
[ "example/tests/test_filters.py::DJATestFilters::test_filter_empty_association_name", "example/tests/test_filters.py::DJATestFilters::test_filter_exact", "example/tests/test_filters.py::DJATestFilters::test_filter_exact_fail", "example/tests/test_filters.py::DJATestFilters::test_filter_fields_intersection", "example/tests/test_filters.py::DJATestFilters::test_filter_fields_union_list", "example/tests/test_filters.py::DJATestFilters::test_filter_in", "example/tests/test_filters.py::DJATestFilters::test_filter_invalid_association_name", "example/tests/test_filters.py::DJATestFilters::test_filter_isempty", "example/tests/test_filters.py::DJATestFilters::test_filter_isnull", "example/tests/test_filters.py::DJATestFilters::test_filter_malformed_left_bracket", "example/tests/test_filters.py::DJATestFilters::test_filter_missing_right_bracket", "example/tests/test_filters.py::DJATestFilters::test_filter_missing_rvalue", "example/tests/test_filters.py::DJATestFilters::test_filter_missing_rvalue_equal", "example/tests/test_filters.py::DJATestFilters::test_filter_no_brackets", "example/tests/test_filters.py::DJATestFilters::test_filter_no_brackets_equal", "example/tests/test_filters.py::DJATestFilters::test_filter_no_brackets_rvalue", "example/tests/test_filters.py::DJATestFilters::test_filter_not_null", "example/tests/test_filters.py::DJATestFilters::test_filter_related", "example/tests/test_filters.py::DJATestFilters::test_filter_related_fieldset_class", "example/tests/test_filters.py::DJATestFilters::test_filter_related_missing_fieldset_class", "example/tests/test_filters.py::DJATestFilters::test_filter_repeated_relations", "example/tests/test_filters.py::DJATestFilters::test_filter_single_relation", "example/tests/test_filters.py::DJATestFilters::test_many_params", "example/tests/test_filters.py::DJATestFilters::test_param_duplicate_page", "example/tests/test_filters.py::DJATestFilters::test_param_duplicate_sort", "example/tests/test_filters.py::DJATestFilters::test_param_invalid", "example/tests/test_filters.py::DJATestFilters::test_search_multiple_keywords", "example/tests/test_filters.py::DJATestFilters::test_sort", "example/tests/test_filters.py::DJATestFilters::test_sort_camelcase", "example/tests/test_filters.py::DJATestFilters::test_sort_double_negative", "example/tests/test_filters.py::DJATestFilters::test_sort_invalid", "example/tests/test_filters.py::DJATestFilters::test_sort_related", "example/tests/test_filters.py::DJATestFilters::test_sort_reverse", "example/tests/test_filters.py::DJATestFilters::test_sort_underscore" ]
{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2023-06-28 06:04:41+00:00
bsd-2-clause
1,926
django-json-api__django-rest-framework-json-api-1220
diff --git a/CHANGELOG.md b/CHANGELOG.md index 964f6b1..0b05600 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ any parts of the framework not mentioned in the documentation should generally b * `ModelSerializer` fields are now returned in the same order than DRF * Avoided that an empty attributes dict is rendered in case serializer does not provide any attribute fields. +* Avoided shadowing of exception when rendering errors (regression since 4.3.0). ### Removed diff --git a/rest_framework_json_api/utils.py b/rest_framework_json_api/utils.py index 2e57fbb..e12080a 100644 --- a/rest_framework_json_api/utils.py +++ b/rest_framework_json_api/utils.py @@ -381,11 +381,7 @@ def format_drf_errors(response, context, exc): errors.extend(format_error_object(message, "/data", response)) # handle all errors thrown from serializers else: - # Avoid circular deps - from rest_framework import generics - - has_serializer = isinstance(context["view"], generics.GenericAPIView) - if has_serializer: + try: serializer = context["view"].get_serializer() fields = get_serializer_fields(serializer) or dict() relationship_fields = [ @@ -393,6 +389,11 @@ def format_drf_errors(response, context, exc): for name, field in fields.items() if is_relationship_field(field) ] + except Exception: + # ignore potential errors when retrieving serializer + # as it might shadow error which is currently being + # formatted + serializer = None for field, error in response.data.items(): non_field_error = field == api_settings.NON_FIELD_ERRORS_KEY @@ -401,7 +402,7 @@ def format_drf_errors(response, context, exc): if non_field_error: # Serializer error does not refer to a specific field. pointer = "/data" - elif has_serializer: + elif serializer: # pointer can be determined only if there's a serializer. rel = "relationships" if field in relationship_fields else "attributes" pointer = f"/data/{rel}/{field}"
django-json-api/django-rest-framework-json-api
2568417f1940834c058ccf8319cf3e4bc0913bee
diff --git a/tests/test_views.py b/tests/test_views.py index de5d1b7..acba7e6 100644 --- a/tests/test_views.py +++ b/tests/test_views.py @@ -154,6 +154,17 @@ class TestModelViewSet: "included" ] + @pytest.mark.urls(__name__) + def test_list_with_invalid_include(self, client, foreign_key_source): + url = reverse("foreign-key-source-list") + response = client.get(url, data={"include": "invalid"}) + assert response.status_code == status.HTTP_400_BAD_REQUEST + result = response.json() + assert ( + result["errors"][0]["detail"] + == "This endpoint does not support the include parameter for path invalid" + ) + @pytest.mark.urls(__name__) def test_list_with_default_included_resources(self, client, foreign_key_source): url = reverse("default-included-resources-list")
Validation of include parameter causes unhandled exception ## Description of the Bug Report When requesting an API endpoint with the `include` query param, specifying an unsupported value results in an uncaught exception and traceback (below). Note: this only seems to happen when querying using the browseable API. When I use [Insomnia](https://insomnia.rest/), I get a 400 response as I'd expect. Versions: - Python: 3.6.15 - Django: 3.1.8 - DRF: 3.12.4 - DRF-JA: 3.1.0 <details><summary>Stack trace (browseable API)</summary> <pre><code> Traceback (most recent call last): File "/opt/python/django/core/handlers/exception.py", line 47, in inner response = get_response(request) File "/opt/python/django/core/handlers/base.py", line 204, in _get_response response = response.render() File "/opt/python/django/template/response.py", line 105, in render self.content = self.rendered_content File "/opt/python/rest_framework/response.py", line 70, in rendered_content ret = renderer.render(self.data, accepted_media_type, context) File "/opt/python/rest_framework/renderers.py", line 724, in render context = self.get_context(data, accepted_media_type, renderer_context) File "/opt/python/rest_framework/renderers.py", line 655, in get_context raw_data_post_form = self.get_raw_data_form(data, view, 'POST', request) File "/opt/python/rest_framework/renderers.py", line 554, in get_raw_data_form serializer = view.get_serializer() File "/opt/python/rest_framework/generics.py", line 110, in get_serializer return serializer_class(*args, **kwargs) File "/opt/python/rest_framework_json_api/serializers.py", line 113, in __init__ validate_path(this_serializer_class, included_field_path, included_field_name) File "/opt/python/rest_framework_json_api/serializers.py", line 99, in validate_path path </code></pre> </details> <details><summary>400 response (Insomnia)</summary> <pre><code> { "errors": [ { "detail": "This endpoint does not support the include parameter for path foo", "status": "400", "source": { "pointer": "/data" }, "code": "parse_error" } ], "meta": { "version": "unversioned" } } </code></pre> </details> ## Checklist - [x] Certain that this is a bug (if unsure or you have a question use [discussions](https://github.com/django-json-api/django-rest-framework-json-api/discussions) instead) - [ ] Code snippet or unit test added to reproduce bug - Should be reproducible in any minimal app with no include serializers configured
0.0
2568417f1940834c058ccf8319cf3e4bc0913bee
[ "tests/test_views.py::TestModelViewSet::test_list_with_invalid_include" ]
[ "tests/test_views.py::TestModelViewSet::test_list", "tests/test_views.py::TestModelViewSet::test_list_with_include_foreign_key", "tests/test_views.py::TestModelViewSet::test_list_with_include_many_to_many_field", "tests/test_views.py::TestModelViewSet::test_list_with_include_nested_related_field", "tests/test_views.py::TestModelViewSet::test_list_with_default_included_resources", "tests/test_views.py::TestModelViewSet::test_retrieve", "tests/test_views.py::TestModelViewSet::test_retrieve_with_include_foreign_key", "tests/test_views.py::TestModelViewSet::test_patch", "tests/test_views.py::TestModelViewSet::test_delete", "tests/test_views.py::TestModelViewSet::test_get_related_field_name_handles_formatted_link_segments[False]", "tests/test_views.py::TestModelViewSet::test_get_related_field_name_handles_formatted_link_segments[dasherize]", "tests/test_views.py::TestModelViewSet::test_get_related_field_name_handles_formatted_link_segments[camelize]", "tests/test_views.py::TestModelViewSet::test_get_related_field_name_handles_formatted_link_segments[capitalize]", "tests/test_views.py::TestModelViewSet::test_get_related_field_name_handles_formatted_link_segments[underscore]", "tests/test_views.py::TestReadonlyModelViewSet::test_custom_action_allows_all_methods[list_action-action_kwargs0-get]", "tests/test_views.py::TestReadonlyModelViewSet::test_custom_action_allows_all_methods[list_action-action_kwargs0-post]", "tests/test_views.py::TestReadonlyModelViewSet::test_custom_action_allows_all_methods[list_action-action_kwargs0-patch]", "tests/test_views.py::TestReadonlyModelViewSet::test_custom_action_allows_all_methods[list_action-action_kwargs0-delete]", "tests/test_views.py::TestReadonlyModelViewSet::test_custom_action_allows_all_methods[detail_action-action_kwargs1-get]", "tests/test_views.py::TestReadonlyModelViewSet::test_custom_action_allows_all_methods[detail_action-action_kwargs1-post]", "tests/test_views.py::TestReadonlyModelViewSet::test_custom_action_allows_all_methods[detail_action-action_kwargs1-patch]", "tests/test_views.py::TestReadonlyModelViewSet::test_custom_action_allows_all_methods[detail_action-action_kwargs1-delete]", "tests/test_views.py::TestAPIView::test_patch", "tests/test_views.py::TestAPIView::test_post_with_missing_id", "tests/test_views.py::TestAPIView::test_patch_with_custom_id" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2024-04-18 19:46:32+00:00
bsd-2-clause
1,927
django-money__django-money-594
diff --git a/djmoney/money.py b/djmoney/money.py index 70bea0b..b744c66 100644 --- a/djmoney/money.py +++ b/djmoney/money.py @@ -106,7 +106,6 @@ class Money(DefaultMoney): # we overwrite the 'targets' so the wrong synonyms are called # Example: we overwrite __add__; __radd__ calls __add__ on DefaultMoney... __radd__ = __add__ - __rsub__ = __sub__ __rmul__ = __mul__ diff --git a/docs/changes.rst b/docs/changes.rst index 2643b4d..8c0b272 100644 --- a/docs/changes.rst +++ b/docs/changes.rst @@ -15,6 +15,7 @@ Changelog **Fixed** - Pin ``pymoneyed<1.0`` as it changed the ``repr`` output of the ``Money`` class. +- Subtracting ``Money`` from ``moneyed.Money``. Regression, introduced in ``1.2``. `#593`_ `1.2.2`_ - 2020-12-29 --------------------- @@ -694,6 +695,7 @@ wrapping with ``money_manager``. .. _0.3: https://github.com/django-money/django-money/compare/0.2...0.3 .. _0.2: https://github.com/django-money/django-money/compare/0.2...a6d90348085332a393abb40b86b5dd9505489b04 +.. _#593: https://github.com/django-money/django-money/issues/593 .. _#586: https://github.com/django-money/django-money/issues/586 .. _#585: https://github.com/django-money/django-money/pull/585 .. _#583: https://github.com/django-money/django-money/issues/583
django-money/django-money
bb222ed619f72a0112aef8c0fd9a4823b1e6e388
diff --git a/tests/test_money.py b/tests/test_money.py index 65199c4..bb7ea79 100644 --- a/tests/test_money.py +++ b/tests/test_money.py @@ -2,7 +2,7 @@ from django.utils.translation import override import pytest -from djmoney.money import Money, get_current_locale +from djmoney.money import DefaultMoney, Money, get_current_locale def test_repr(): @@ -114,3 +114,12 @@ def test_decimal_places_display_overwrite(): assert str(number) == "$1.23457" number.decimal_places_display = None assert str(number) == "$1.23" + + +def test_sub_negative(): + # See GH-593 + total = DefaultMoney(0, "EUR") + bills = (Money(8, "EUR"), Money(25, "EUR")) + for bill in bills: + total -= bill + assert total == Money(-33, "EUR")
Money should not override `__rsub__` method As [reported](https://github.com/py-moneyed/py-moneyed/issues/144) in pymoneyed the following test case fails: ```python from moneyed import Money as PyMoney from djmoney.money import Money def test_sub_negative(): total = PyMoney(0, "EUR") bills = (Money(8, "EUR"), Money(25, "EUR")) for bill in bills: total -= bill assert total == Money(-33, "EUR") # AssertionError: assert <Money: -17 EUR> == <Money: -33 EUR> ``` This is caused by `djmoney.money.Money` overriding `__rsub__`.
0.0
bb222ed619f72a0112aef8c0fd9a4823b1e6e388
[ "tests/test_money.py::test_sub_negative" ]
[ "tests/test_money.py::test_repr", "tests/test_money.py::test_html_safe", "tests/test_money.py::test_html_unsafe", "tests/test_money.py::test_default_mul", "tests/test_money.py::test_default_truediv", "tests/test_money.py::test_reverse_truediv_fails", "tests/test_money.py::test_get_current_locale[pl-PL_PL]", "tests/test_money.py::test_get_current_locale[pl_PL-pl_PL]", "tests/test_money.py::test_round", "tests/test_money.py::test_configurable_decimal_number", "tests/test_money.py::test_localize_decimal_places_default", "tests/test_money.py::test_localize_decimal_places_overwrite", "tests/test_money.py::test_localize_decimal_places_both", "tests/test_money.py::test_add_decimal_places", "tests/test_money.py::test_add_decimal_places_zero", "tests/test_money.py::test_mul_decimal_places", "tests/test_money.py::test_fix_decimal_places", "tests/test_money.py::test_fix_decimal_places_none", "tests/test_money.py::test_fix_decimal_places_multiple", "tests/test_money.py::test_decimal_places_display_overwrite" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }
2021-01-10 12:54:57+00:00
bsd-3-clause
1,928
django-money__django-money-596
diff --git a/djmoney/money.py b/djmoney/money.py index b744c66..f109fdc 100644 --- a/djmoney/money.py +++ b/djmoney/money.py @@ -39,17 +39,27 @@ class Money(DefaultMoney): """ Set number of digits being displayed - `None` resets to `DECIMAL_PLACES_DISPLAY` setting """ self._decimal_places_display = value - def _fix_decimal_places(self, *args): - """ Make sure to user 'biggest' number of decimal places of all given money instances """ - candidates = (getattr(candidate, "decimal_places", 0) for candidate in args) - return max([self.decimal_places, *candidates]) + def _copy_attributes(self, source, target): + """Copy attributes to the new `Money` instance. + + This class stores extra bits of information about string formatting that the parent class doesn't have. + The problem is that the parent class creates new instances of `Money` without in some of its methods and + it does so without knowing about `django-money`-level attributes. + For this reason, when this class uses some methods of the parent class that have this behavior, the resulting + instances lose those attribute values. + + When it comes to what number of decimal places to choose, we take the maximum number. + """ + for attribute_name in ("decimal_places", "decimal_places_display"): + value = max([getattr(candidate, attribute_name, 0) for candidate in (self, source)]) + setattr(target, attribute_name, value) def __add__(self, other): if isinstance(other, F): return other.__radd__(self) other = maybe_convert(other, self.currency) result = super().__add__(other) - result.decimal_places = self._fix_decimal_places(other) + self._copy_attributes(other, result) return result def __sub__(self, other): @@ -57,14 +67,14 @@ class Money(DefaultMoney): return other.__rsub__(self) other = maybe_convert(other, self.currency) result = super().__sub__(other) - result.decimal_places = self._fix_decimal_places(other) + self._copy_attributes(other, result) return result def __mul__(self, other): if isinstance(other, F): return other.__rmul__(self) result = super().__mul__(other) - result.decimal_places = self._fix_decimal_places(other) + self._copy_attributes(other, result) return result def __truediv__(self, other): @@ -72,11 +82,11 @@ class Money(DefaultMoney): return other.__rtruediv__(self) result = super().__truediv__(other) if isinstance(result, self.__class__): - result.decimal_places = self._fix_decimal_places(other) + self._copy_attributes(other, result) return result def __rtruediv__(self, other): - # Backported from py-moneyd, non released bug-fix + # Backported from py-moneyed, non released bug-fix # https://github.com/py-moneyed/py-moneyed/blob/c518745dd9d7902781409daec1a05699799474dd/moneyed/classes.py#L217-L218 raise TypeError("Cannot divide non-Money by a Money instance.") @@ -100,7 +110,34 @@ class Money(DefaultMoney): def __round__(self, n=None): amount = round(self.amount, n) - return self.__class__(amount, self.currency) + new = self.__class__(amount, self.currency) + self._copy_attributes(self, new) + return new + + def round(self, ndigits=0): + new = super().round(ndigits) + self._copy_attributes(self, new) + return new + + def __pos__(self): + new = super().__pos__() + self._copy_attributes(self, new) + return new + + def __neg__(self): + new = super().__neg__() + self._copy_attributes(self, new) + return new + + def __abs__(self): + new = super().__abs__() + self._copy_attributes(self, new) + return new + + def __rmod__(self, other): + new = super().__rmod__(other) + self._copy_attributes(self, new) + return new # DefaultMoney sets those synonym functions # we overwrite the 'targets' so the wrong synonyms are called diff --git a/docs/changes.rst b/docs/changes.rst index 8c0b272..f526c12 100644 --- a/docs/changes.rst +++ b/docs/changes.rst @@ -16,6 +16,7 @@ Changelog - Pin ``pymoneyed<1.0`` as it changed the ``repr`` output of the ``Money`` class. - Subtracting ``Money`` from ``moneyed.Money``. Regression, introduced in ``1.2``. `#593`_ +- Missing the right ``Money.decimal_places`` and ``Money.decimal_places_display`` values after some arithmetic operations. `#595`_ `1.2.2`_ - 2020-12-29 --------------------- @@ -695,6 +696,7 @@ wrapping with ``money_manager``. .. _0.3: https://github.com/django-money/django-money/compare/0.2...0.3 .. _0.2: https://github.com/django-money/django-money/compare/0.2...a6d90348085332a393abb40b86b5dd9505489b04 +.. _#595: https://github.com/django-money/django-money/issues/595 .. _#593: https://github.com/django-money/django-money/issues/593 .. _#586: https://github.com/django-money/django-money/issues/586 .. _#585: https://github.com/django-money/django-money/pull/585
django-money/django-money
9ac8d8b1f7060437bfb1912c4182cb0b553c1519
diff --git a/tests/test_money.py b/tests/test_money.py index bb7ea79..e736854 100644 --- a/tests/test_money.py +++ b/tests/test_money.py @@ -80,31 +80,31 @@ def test_add_decimal_places_zero(): assert result.decimal_places == 3 -def test_mul_decimal_places(): - """ Test __mul__ and __rmul__ """ - two = Money("1.0000", "USD", decimal_places=4) - - result = 2 * two - assert result.decimal_places == 4 - - result = two * 2 - assert result.decimal_places == 4 - - -def test_fix_decimal_places(): - one = Money(1, "USD", decimal_places=7) - assert one._fix_decimal_places(Money(2, "USD", decimal_places=3)) == 7 - assert one._fix_decimal_places(Money(2, "USD", decimal_places=30)) == 30 - - -def test_fix_decimal_places_none(): - one = Money(1, "USD", decimal_places=7) - assert one._fix_decimal_places(None) == 7 - - -def test_fix_decimal_places_multiple(): - one = Money(1, "USD", decimal_places=7) - assert one._fix_decimal_places(None, Money(3, "USD", decimal_places=8)) == 8 [email protected]("decimal_places", (1, 4)) [email protected]( + "operation", + ( + lambda a, d: a * 2, + lambda a, d: 2 * a, + lambda a, d: a / 5, + lambda a, d: a - Money("2", "USD", decimal_places=d, decimal_places_display=d), + lambda a, d: Money("2", "USD", decimal_places=d, decimal_places_display=d) - a, + lambda a, d: a + Money("2", "USD", decimal_places=d, decimal_places_display=d), + lambda a, d: Money("2", "USD", decimal_places=d, decimal_places_display=d) + a, + lambda a, d: -a, + lambda a, d: +a, + lambda a, d: abs(a), + lambda a, d: 5 % a, + lambda a, d: round(a), + lambda a, d: a.round(), + ), +) +def test_keep_decimal_places(operation, decimal_places): + # Arithmetic operations should keep the `decimal_places` value + amount = Money("1.0000", "USD", decimal_places=decimal_places, decimal_places_display=decimal_places) + new = operation(amount, decimal_places) + assert new.decimal_places == decimal_places + assert new.decimal_places_display == decimal_places def test_decimal_places_display_overwrite():
`Money.decimal_places` are not always the same after arithmetic operations `djmoney.money.Money` uses some methods from `moneyed.Money`. In these methods (e.g. `__neg__`) new instances are created with only `amount` and `currency`. For this reason, our `django-money` specific attributes are not copied. Example: ```python amount = -Money(1, "USD", decimal_places=7) amount.decimal_places # 2 ```
0.0
9ac8d8b1f7060437bfb1912c4182cb0b553c1519
[ "tests/test_money.py::test_keep_decimal_places[<lambda>0-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>0-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>1-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>1-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>2-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>2-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>3-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>3-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>4-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>4-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>5-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>5-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>6-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>6-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>7-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>7-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>8-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>8-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>9-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>9-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>10-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>10-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>11-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>11-4]", "tests/test_money.py::test_keep_decimal_places[<lambda>12-1]", "tests/test_money.py::test_keep_decimal_places[<lambda>12-4]" ]
[ "tests/test_money.py::test_repr", "tests/test_money.py::test_html_safe", "tests/test_money.py::test_html_unsafe", "tests/test_money.py::test_default_mul", "tests/test_money.py::test_default_truediv", "tests/test_money.py::test_reverse_truediv_fails", "tests/test_money.py::test_get_current_locale[pl-PL_PL]", "tests/test_money.py::test_get_current_locale[pl_PL-pl_PL]", "tests/test_money.py::test_round", "tests/test_money.py::test_configurable_decimal_number", "tests/test_money.py::test_localize_decimal_places_default", "tests/test_money.py::test_localize_decimal_places_overwrite", "tests/test_money.py::test_localize_decimal_places_both", "tests/test_money.py::test_add_decimal_places", "tests/test_money.py::test_add_decimal_places_zero", "tests/test_money.py::test_decimal_places_display_overwrite", "tests/test_money.py::test_sub_negative" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2021-01-10 14:14:52+00:00
bsd-3-clause
1,929
django-money__django-money-604
diff --git a/djmoney/models/fields.py b/djmoney/models/fields.py index 8b812be..e24af66 100644 --- a/djmoney/models/fields.py +++ b/djmoney/models/fields.py @@ -35,7 +35,7 @@ def get_value(obj, expr): else: expr = expr.value if isinstance(expr, OldMoney): - expr.__class__ = Money + expr = Money(expr.amount, expr.currency) return expr @@ -206,7 +206,7 @@ class MoneyField(models.DecimalField): elif isinstance(default, (float, Decimal, int)): default = Money(default, default_currency) elif isinstance(default, OldMoney): - default.__class__ = Money + default = Money(default.amount, default.currency) if default is not None and default is not NOT_PROVIDED and not isinstance(default, Money): raise ValueError("default value must be an instance of Money, is: %s" % default) return default diff --git a/docs/changes.rst b/docs/changes.rst index 1622376..49d3aa1 100644 --- a/docs/changes.rst +++ b/docs/changes.rst @@ -4,6 +4,10 @@ Changelog `Unreleased`_ - TBD ------------------- +**Fixed** + +- Do not mutate the input ``moneyed.Money`` class to ``djmoney.money.Money`` in ``MoneyField.default`` and F-expressions. `#603`_ (`moser`_) + `1.3`_ - 2021-01-10 ------------------- @@ -700,6 +704,7 @@ wrapping with ``money_manager``. .. _0.3: https://github.com/django-money/django-money/compare/0.2...0.3 .. _0.2: https://github.com/django-money/django-money/compare/0.2...a6d90348085332a393abb40b86b5dd9505489b04 +.. _#603: https://github.com/django-money/django-money/issues/603 .. _#595: https://github.com/django-money/django-money/issues/595 .. _#593: https://github.com/django-money/django-money/issues/593 .. _#586: https://github.com/django-money/django-money/issues/586 @@ -852,6 +857,7 @@ wrapping with ``money_manager``. .. _lobziik: https://github.com/lobziik .. _mattions: https://github.com/mattions .. _mithrilstar: https://github.com/mithrilstar +.. _moser: https://github.com/moser .. _MrFus10n: https://github.com/MrFus10n .. _msgre: https://github.com/msgre .. _mstarostik: https://github.com/mstarostik
django-money/django-money
8014bed7968665eb55cc298108fd1922667aec24
diff --git a/tests/test_models.py b/tests/test_models.py index d13ec03..3641356 100644 --- a/tests/test_models.py +++ b/tests/test_models.py @@ -83,6 +83,31 @@ class TestVanillaMoneyField: retrieved = model_class.objects.get(pk=instance.pk) assert retrieved.money == expected + def test_old_money_not_mutated_default(self): + # See GH-603 + money = OldMoney(1, "EUR") + + # When `moneyed.Money` is passed as a default value to a model + class Model(models.Model): + price = MoneyField(default=money, max_digits=10, decimal_places=2) + + class Meta: + abstract = True + + # Its class should remain the same + assert type(money) is OldMoney + + def test_old_money_not_mutated_f_object(self): + # See GH-603 + money = OldMoney(1, "EUR") + + instance = ModelWithVanillaMoneyField.objects.create(money=Money(5, "EUR"), integer=2) + # When `moneyed.Money` is a part of an F-expression + instance.money = F("money") + money + + # Its class should remain the same + assert type(money) is OldMoney + def test_old_money_defaults(self): instance = ModelWithDefaultAsOldMoney.objects.create() assert instance.money == Money(".01", "RUB")
djmoney alters existing objects We have an application that uses `moneyed` and (sub-classes of) its `Money` type in a non-Django environment. We recently started integrating this into a Django app that uses djmoney and started getting weird errors in seemingly unrelated cases because instances of `djmoney.money.Money` started showing up there. We tracked this down to a behavior of the djmoney package in `djmoney.models.fields`: https://github.com/django-money/django-money/blob/bb222ed619f72a0112aef8c0fd9a4823b1e6e388/djmoney/models/fields.py#L38 https://github.com/django-money/django-money/blob/bb222ed619f72a0112aef8c0fd9a4823b1e6e388/djmoney/models/fields.py#L209 The two places alter **the type of an existing object**. Can we change this to copying the objects before altering them?
0.0
8014bed7968665eb55cc298108fd1922667aec24
[ "tests/test_models.py::TestVanillaMoneyField::test_old_money_not_mutated_default", "tests/test_models.py::TestVanillaMoneyField::test_old_money_not_mutated_f_object" ]
[ "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithVanillaMoneyField-kwargs0-expected0]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithVanillaMoneyField-kwargs1-expected1]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[BaseModel-kwargs2-expected2]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[BaseModel-kwargs3-expected3]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[BaseModel-kwargs4-expected4]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[BaseModel-kwargs5-expected5]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[BaseModel-kwargs6-expected6]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[BaseModel-kwargs7-expected7]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsMoney-kwargs8-expected8]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsFloat-kwargs9-expected9]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsStringWithCurrency-kwargs10-expected10]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsString-kwargs11-expected11]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsInt-kwargs12-expected12]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsDecimal-kwargs13-expected13]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[CryptoModel-kwargs14-expected14]", "tests/test_models.py::TestVanillaMoneyField::test_old_money_defaults", "tests/test_models.py::TestVanillaMoneyField::test_revert_to_default[ModelWithVanillaMoneyField-other_value0]", "tests/test_models.py::TestVanillaMoneyField::test_revert_to_default[BaseModel-other_value1]", "tests/test_models.py::TestVanillaMoneyField::test_revert_to_default[ModelWithDefaultAsMoney-other_value2]", "tests/test_models.py::TestVanillaMoneyField::test_revert_to_default[ModelWithDefaultAsFloat-other_value3]", "tests/test_models.py::TestVanillaMoneyField::test_revert_to_default[ModelWithDefaultAsFloat-other_value4]", "tests/test_models.py::TestVanillaMoneyField::test_invalid_values[value0]", "tests/test_models.py::TestVanillaMoneyField::test_invalid_values[value1]", "tests/test_models.py::TestVanillaMoneyField::test_invalid_values[value2]", "tests/test_models.py::TestVanillaMoneyField::test_save_new_value[money-Money0]", "tests/test_models.py::TestVanillaMoneyField::test_save_new_value[money-Money1]", "tests/test_models.py::TestVanillaMoneyField::test_save_new_value[second_money-Money0]", "tests/test_models.py::TestVanillaMoneyField::test_save_new_value[second_money-Money1]", "tests/test_models.py::TestVanillaMoneyField::test_rounding", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters0-1]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters1-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters2-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters3-0]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters4-3]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters5-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters6-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters7-3]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters8-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters9-1]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters10-2]", 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"tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-exact-3-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-isnull-True-0]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-range-rhs12-4]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-lte-2-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-gt-3-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-icontains-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-in-rhs16-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-startswith-2-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-regex-^[134]-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-iregex-^[134]-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-istartswith-2-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-contains-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-lt-5-4]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-endswith-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-iendswith-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-gte-4-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-iexact-3-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-exact-3-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-isnull-True-0]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-range-rhs12-4]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-lte-2-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-gt-3-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-icontains-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-in-rhs16-1]", "tests/test_models.py::TestVanillaMoneyField::test_exact_match", "tests/test_models.py::TestVanillaMoneyField::test_issue_300_regression", "tests/test_models.py::TestVanillaMoneyField::test_range_search", "tests/test_models.py::TestVanillaMoneyField::test_filter_chaining", "tests/test_models.py::TestVanillaMoneyField::test_currency_querying[ModelWithVanillaMoneyField]", "tests/test_models.py::TestVanillaMoneyField::test_currency_querying[ModelWithChoicesMoneyField]", "tests/test_models.py::TestVanillaMoneyField::test_in_lookup[Money0]", "tests/test_models.py::TestVanillaMoneyField::test_in_lookup[Money1]", "tests/test_models.py::TestVanillaMoneyField::test_in_lookup_f_expression[Money0]", "tests/test_models.py::TestVanillaMoneyField::test_in_lookup_f_expression[Money1]", "tests/test_models.py::TestVanillaMoneyField::test_isnull_lookup", "tests/test_models.py::TestVanillaMoneyField::test_null_default", "tests/test_models.py::TestGetOrCreate::test_get_or_create_respects_currency[ModelWithVanillaMoneyField-money-kwargs0-PLN]", "tests/test_models.py::TestGetOrCreate::test_get_or_create_respects_currency[ModelWithVanillaMoneyField-money-kwargs1-EUR]", "tests/test_models.py::TestGetOrCreate::test_get_or_create_respects_currency[ModelWithVanillaMoneyField-money-kwargs2-EUR]", "tests/test_models.py::TestGetOrCreate::test_get_or_create_respects_currency[ModelWithSharedCurrency-first-kwargs3-CZK]", "tests/test_models.py::TestGetOrCreate::test_get_or_create_respects_defaults", "tests/test_models.py::TestGetOrCreate::test_defaults", "tests/test_models.py::TestGetOrCreate::test_currency_field_lookup", "tests/test_models.py::TestGetOrCreate::test_no_default_model[NullMoneyFieldModel-create_kwargs0-get_kwargs0]", "tests/test_models.py::TestGetOrCreate::test_no_default_model[ModelWithSharedCurrency-create_kwargs1-get_kwargs1]", "tests/test_models.py::TestGetOrCreate::test_shared_currency", "tests/test_models.py::TestNullableCurrency::test_create_nullable", "tests/test_models.py::TestNullableCurrency::test_create_default", "tests/test_models.py::TestNullableCurrency::test_fails_with_null_currency", "tests/test_models.py::TestNullableCurrency::test_fails_with_nullable_but_no_default", "tests/test_models.py::TestNullableCurrency::test_query_not_null", "tests/test_models.py::TestNullableCurrency::test_query_null", "tests/test_models.py::TestFExpressions::test_save[f_obj0-expected0]", "tests/test_models.py::TestFExpressions::test_save[f_obj1-expected1]", "tests/test_models.py::TestFExpressions::test_save[f_obj2-expected2]", "tests/test_models.py::TestFExpressions::test_save[f_obj3-expected3]", "tests/test_models.py::TestFExpressions::test_save[f_obj4-expected4]", "tests/test_models.py::TestFExpressions::test_save[f_obj5-expected5]", "tests/test_models.py::TestFExpressions::test_save[f_obj6-expected6]", "tests/test_models.py::TestFExpressions::test_save[f_obj7-expected7]", "tests/test_models.py::TestFExpressions::test_save[f_obj8-expected8]", "tests/test_models.py::TestFExpressions::test_save[f_obj9-expected9]", "tests/test_models.py::TestFExpressions::test_save[f_obj10-expected10]", "tests/test_models.py::TestFExpressions::test_save[f_obj11-expected11]", "tests/test_models.py::TestFExpressions::test_save[f_obj12-expected12]", "tests/test_models.py::TestFExpressions::test_save[f_obj13-expected13]", "tests/test_models.py::TestFExpressions::test_save[f_obj14-expected14]", "tests/test_models.py::TestFExpressions::test_save[f_obj15-expected15]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj0-expected0]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj1-expected1]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj2-expected2]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj3-expected3]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj4-expected4]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj5-expected5]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj6-expected6]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj7-expected7]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj8-expected8]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj9-expected9]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj10-expected10]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj11-expected11]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj12-expected12]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj13-expected13]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj14-expected14]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj15-expected15]", "tests/test_models.py::TestFExpressions::test_default_update", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs0-filter_value0-True]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs1-filter_value1-True]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs2-filter_value2-False]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs3-filter_value3-True]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs4-filter_value4-True]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs5-filter_value5-False]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs6-filter_value6-False]", "tests/test_models.py::TestFExpressions::test_update_fields_save", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj0]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj1]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj2]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj3]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj4]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj5]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj6]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj7]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj8]", "tests/test_models.py::TestExpressions::test_bulk_update", "tests/test_models.py::TestExpressions::test_conditional_update", "tests/test_models.py::TestExpressions::test_create_func", "tests/test_models.py::TestExpressions::test_value_create[None-None]", "tests/test_models.py::TestExpressions::test_value_create[10-expected1]", "tests/test_models.py::TestExpressions::test_value_create[value2-expected2]", "tests/test_models.py::TestExpressions::test_value_create_invalid", "tests/test_models.py::TestExpressions::test_expressions_for_non_money_fields", "tests/test_models.py::test_find_models_related_to_money_models", "tests/test_models.py::test_allow_expression_nodes_without_money", "tests/test_models.py::test_base_model", "tests/test_models.py::TestInheritance::test_model[InheritedModel]", "tests/test_models.py::TestInheritance::test_model[InheritorModel]", "tests/test_models.py::TestInheritance::test_fields[InheritedModel]", "tests/test_models.py::TestInheritance::test_fields[InheritorModel]", "tests/test_models.py::TestManager::test_manager", "tests/test_models.py::TestManager::test_objects_creation", "tests/test_models.py::TestProxyModel::test_instances", "tests/test_models.py::TestProxyModel::test_patching", "tests/test_models.py::TestDifferentCurrencies::test_add_default", "tests/test_models.py::TestDifferentCurrencies::test_sub_default", "tests/test_models.py::TestDifferentCurrencies::test_eq", "tests/test_models.py::TestDifferentCurrencies::test_ne", "tests/test_models.py::TestDifferentCurrencies::test_ne_currency", "tests/test_models.py::test_manager_instance_access[ModelWithNonMoneyField]", "tests/test_models.py::test_manager_instance_access[InheritorModel]", "tests/test_models.py::test_manager_instance_access[InheritedModel]", "tests/test_models.py::test_manager_instance_access[ProxyModel]", "tests/test_models.py::test_different_hashes", "tests/test_models.py::test_migration_serialization", "tests/test_models.py::test_clear_meta_cache[ModelWithVanillaMoneyField-objects]", "tests/test_models.py::test_clear_meta_cache[ModelWithCustomDefaultManager-custom]", "tests/test_models.py::TestFieldAttributes::test_missing_attributes", "tests/test_models.py::TestFieldAttributes::test_default_currency", "tests/test_models.py::TestCustomManager::test_method", "tests/test_models.py::test_package_is_importable", "tests/test_models.py::test_hash_uniqueness", "tests/test_models.py::test_override_decorator", "tests/test_models.py::TestSharedCurrency::test_attributes", "tests/test_models.py::TestSharedCurrency::test_filter_by_money_match[args0-kwargs0]", "tests/test_models.py::TestSharedCurrency::test_filter_by_money_match[args1-kwargs1]", "tests/test_models.py::TestSharedCurrency::test_filter_by_money_no_match[args0-kwargs0]", "tests/test_models.py::TestSharedCurrency::test_filter_by_money_no_match[args1-kwargs1]", "tests/test_models.py::TestSharedCurrency::test_f_query[args0-kwargs0]", "tests/test_models.py::TestSharedCurrency::test_f_query[args1-kwargs1]", "tests/test_models.py::TestSharedCurrency::test_in_lookup[args0-kwargs0]", "tests/test_models.py::TestSharedCurrency::test_in_lookup[args1-kwargs1]", "tests/test_models.py::TestSharedCurrency::test_create_with_money", "tests/test_models.py::test_order_by", "tests/test_models.py::test_distinct_through_wrapper", "tests/test_models.py::test_mixer_blend" ]
{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2021-02-02 14:03:40+00:00
bsd-3-clause
1,930
django-money__django-money-647
diff --git a/djmoney/models/fields.py b/djmoney/models/fields.py index 9b7195e..9d42575 100644 --- a/djmoney/models/fields.py +++ b/djmoney/models/fields.py @@ -298,8 +298,11 @@ class MoneyField(models.DecimalField): if self._has_default: kwargs["default"] = self.default.amount - if self.default_currency is not None and self.default_currency != DEFAULT_CURRENCY: - kwargs["default_currency"] = str(self.default_currency) + if self.default_currency != DEFAULT_CURRENCY: + if self.default_currency is not None: + kwargs["default_currency"] = str(self.default_currency) + else: + kwargs["default_currency"] = None if self.currency_choices != CURRENCY_CHOICES: kwargs["currency_choices"] = self.currency_choices if self.currency_field_name:
django-money/django-money
2040eff83fef2d4a1d882c016ab2b5e0853d2f84
diff --git a/tests/test_models.py b/tests/test_models.py index f573ed3..506fac4 100644 --- a/tests/test_models.py +++ b/tests/test_models.py @@ -787,3 +787,11 @@ def test_mixer_blend(): instance = mixer.blend(ModelWithTwoMoneyFields) assert isinstance(instance.amount1, Money) assert isinstance(instance.amount2, Money) + + +def test_deconstruct_includes_default_currency_as_none(): + instance = ModelWithNullableCurrency()._meta.get_field("money") + __, ___, args, kwargs = instance.deconstruct() + new = MoneyField(*args, **kwargs) + assert new.default_currency == instance.default_currency + assert new.default_currency is None
default_currency=None keeps detecting migration changes Based on the comment in the discussion found here: https://github.com/django-money/django-money/issues/530#issuecomment-650166087 If `MoneyField(..., default_currency=None)` is added to an already existing model, so that the field is triggering migration operations `AddField` or `AlterField`. Django keeps detecting changes on the field/model when running `python manage.py makemigrations`.
0.0
2040eff83fef2d4a1d882c016ab2b5e0853d2f84
[ "tests/test_models.py::test_deconstruct_includes_default_currency_as_none" ]
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"tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsFloat-kwargs9-expected9]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsStringWithCurrency-kwargs10-expected10]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsString-kwargs11-expected11]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsInt-kwargs12-expected12]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[ModelWithDefaultAsDecimal-kwargs13-expected13]", "tests/test_models.py::TestVanillaMoneyField::test_create_defaults[CryptoModel-kwargs14-expected14]", "tests/test_models.py::TestVanillaMoneyField::test_old_money_not_mutated_default", "tests/test_models.py::TestVanillaMoneyField::test_old_money_not_mutated_f_object", "tests/test_models.py::TestVanillaMoneyField::test_old_money_defaults", "tests/test_models.py::TestVanillaMoneyField::test_revert_to_default[ModelWithVanillaMoneyField-other_value0]", "tests/test_models.py::TestVanillaMoneyField::test_revert_to_default[BaseModel-other_value1]", "tests/test_models.py::TestVanillaMoneyField::test_revert_to_default[ModelWithDefaultAsMoney-other_value2]", "tests/test_models.py::TestVanillaMoneyField::test_revert_to_default[ModelWithDefaultAsFloat-other_value3]", "tests/test_models.py::TestVanillaMoneyField::test_revert_to_default[ModelWithDefaultAsFloat-other_value4]", "tests/test_models.py::TestVanillaMoneyField::test_invalid_values[value0]", "tests/test_models.py::TestVanillaMoneyField::test_invalid_values[value1]", "tests/test_models.py::TestVanillaMoneyField::test_invalid_values[value2]", "tests/test_models.py::TestVanillaMoneyField::test_save_new_value[money-Money0]", "tests/test_models.py::TestVanillaMoneyField::test_save_new_value[money-Money1]", "tests/test_models.py::TestVanillaMoneyField::test_save_new_value[second_money-Money0]", "tests/test_models.py::TestVanillaMoneyField::test_save_new_value[second_money-Money1]", "tests/test_models.py::TestVanillaMoneyField::test_rounding", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters0-1]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters1-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters2-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters3-0]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters4-3]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters5-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters6-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters7-3]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters8-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters9-1]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money0-filters10-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters0-1]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters1-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters2-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters3-0]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters4-3]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters5-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters6-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters7-3]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters8-2]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters9-1]", "tests/test_models.py::TestVanillaMoneyField::test_comparison_lookup[Money1-filters10-2]", "tests/test_models.py::TestVanillaMoneyField::test_date_lookup", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-startswith-2-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-regex-^[134]-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-iregex-^[134]-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-istartswith-2-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-contains-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-lt-5-4]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-endswith-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-iendswith-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-gte-4-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-iexact-3-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-exact-3-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-isnull-True-0]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-range-rhs12-4]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-lte-2-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-gt-3-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-icontains-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money0-in-rhs16-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-startswith-2-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-regex-^[134]-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-iregex-^[134]-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-istartswith-2-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-contains-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-lt-5-4]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-endswith-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-iendswith-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-gte-4-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-iexact-3-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-exact-3-1]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-isnull-True-0]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-range-rhs12-4]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-lte-2-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-gt-3-3]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-icontains-5-2]", "tests/test_models.py::TestVanillaMoneyField::test_all_lookups[Money1-in-rhs16-1]", "tests/test_models.py::TestVanillaMoneyField::test_exact_match", "tests/test_models.py::TestVanillaMoneyField::test_issue_300_regression", "tests/test_models.py::TestVanillaMoneyField::test_range_search", "tests/test_models.py::TestVanillaMoneyField::test_filter_chaining", "tests/test_models.py::TestVanillaMoneyField::test_currency_querying[ModelWithVanillaMoneyField]", "tests/test_models.py::TestVanillaMoneyField::test_currency_querying[ModelWithChoicesMoneyField]", "tests/test_models.py::TestVanillaMoneyField::test_in_lookup[Money0]", "tests/test_models.py::TestVanillaMoneyField::test_in_lookup[Money1]", "tests/test_models.py::TestVanillaMoneyField::test_in_lookup_f_expression[Money0]", "tests/test_models.py::TestVanillaMoneyField::test_in_lookup_f_expression[Money1]", "tests/test_models.py::TestVanillaMoneyField::test_isnull_lookup", "tests/test_models.py::TestVanillaMoneyField::test_null_default", "tests/test_models.py::TestGetOrCreate::test_get_or_create_respects_currency[ModelWithVanillaMoneyField-money-kwargs0-PLN]", "tests/test_models.py::TestGetOrCreate::test_get_or_create_respects_currency[ModelWithVanillaMoneyField-money-kwargs1-EUR]", "tests/test_models.py::TestGetOrCreate::test_get_or_create_respects_currency[ModelWithVanillaMoneyField-money-kwargs2-EUR]", "tests/test_models.py::TestGetOrCreate::test_get_or_create_respects_currency[ModelWithSharedCurrency-first-kwargs3-CZK]", "tests/test_models.py::TestGetOrCreate::test_get_or_create_respects_defaults", "tests/test_models.py::TestGetOrCreate::test_defaults", "tests/test_models.py::TestGetOrCreate::test_currency_field_lookup", "tests/test_models.py::TestGetOrCreate::test_no_default_model[NullMoneyFieldModel-create_kwargs0-get_kwargs0]", "tests/test_models.py::TestGetOrCreate::test_no_default_model[ModelWithSharedCurrency-create_kwargs1-get_kwargs1]", "tests/test_models.py::TestGetOrCreate::test_shared_currency", "tests/test_models.py::TestNullableCurrency::test_create_nullable", "tests/test_models.py::TestNullableCurrency::test_create_default", "tests/test_models.py::TestNullableCurrency::test_fails_with_null_currency", "tests/test_models.py::TestNullableCurrency::test_fails_with_nullable_but_no_default", "tests/test_models.py::TestNullableCurrency::test_query_not_null", "tests/test_models.py::TestNullableCurrency::test_query_null", "tests/test_models.py::TestFExpressions::test_save[f_obj0-expected0]", "tests/test_models.py::TestFExpressions::test_save[f_obj1-expected1]", "tests/test_models.py::TestFExpressions::test_save[f_obj2-expected2]", "tests/test_models.py::TestFExpressions::test_save[f_obj3-expected3]", "tests/test_models.py::TestFExpressions::test_save[f_obj4-expected4]", "tests/test_models.py::TestFExpressions::test_save[f_obj5-expected5]", "tests/test_models.py::TestFExpressions::test_save[f_obj6-expected6]", "tests/test_models.py::TestFExpressions::test_save[f_obj7-expected7]", "tests/test_models.py::TestFExpressions::test_save[f_obj8-expected8]", "tests/test_models.py::TestFExpressions::test_save[f_obj9-expected9]", "tests/test_models.py::TestFExpressions::test_save[f_obj10-expected10]", "tests/test_models.py::TestFExpressions::test_save[f_obj11-expected11]", "tests/test_models.py::TestFExpressions::test_save[f_obj12-expected12]", "tests/test_models.py::TestFExpressions::test_save[f_obj13-expected13]", "tests/test_models.py::TestFExpressions::test_save[f_obj14-expected14]", "tests/test_models.py::TestFExpressions::test_save[f_obj15-expected15]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj0-expected0]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj1-expected1]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj2-expected2]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj3-expected3]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj4-expected4]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj5-expected5]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj6-expected6]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj7-expected7]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj8-expected8]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj9-expected9]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj10-expected10]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj11-expected11]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj12-expected12]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj13-expected13]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj14-expected14]", "tests/test_models.py::TestFExpressions::test_f_update[f_obj15-expected15]", "tests/test_models.py::TestFExpressions::test_default_update", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs0-filter_value0-True]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs1-filter_value1-True]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs2-filter_value2-False]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs3-filter_value3-True]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs4-filter_value4-True]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs5-filter_value5-False]", "tests/test_models.py::TestFExpressions::test_filtration[create_kwargs6-filter_value6-False]", "tests/test_models.py::TestFExpressions::test_update_fields_save", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj0]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj1]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj2]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj3]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj4]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj5]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj6]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj7]", "tests/test_models.py::TestFExpressions::test_invalid_expressions_access[f_obj8]", "tests/test_models.py::TestExpressions::test_bulk_update", "tests/test_models.py::TestExpressions::test_conditional_update", "tests/test_models.py::TestExpressions::test_create_func", "tests/test_models.py::TestExpressions::test_value_create[None-None]", "tests/test_models.py::TestExpressions::test_value_create[10-expected1]", "tests/test_models.py::TestExpressions::test_value_create[value2-expected2]", "tests/test_models.py::TestExpressions::test_value_create_invalid", "tests/test_models.py::TestExpressions::test_expressions_for_non_money_fields", "tests/test_models.py::test_find_models_related_to_money_models", "tests/test_models.py::test_allow_expression_nodes_without_money", "tests/test_models.py::test_base_model", "tests/test_models.py::TestInheritance::test_model[InheritedModel]", "tests/test_models.py::TestInheritance::test_model[InheritorModel]", "tests/test_models.py::TestInheritance::test_fields[InheritedModel]", "tests/test_models.py::TestInheritance::test_fields[InheritorModel]", "tests/test_models.py::TestManager::test_manager", "tests/test_models.py::TestManager::test_objects_creation", "tests/test_models.py::TestProxyModel::test_instances", "tests/test_models.py::TestProxyModel::test_patching", "tests/test_models.py::TestDifferentCurrencies::test_add_default", "tests/test_models.py::TestDifferentCurrencies::test_sub_default", "tests/test_models.py::TestDifferentCurrencies::test_eq", "tests/test_models.py::TestDifferentCurrencies::test_ne", "tests/test_models.py::TestDifferentCurrencies::test_ne_currency", "tests/test_models.py::test_manager_instance_access[ModelWithNonMoneyField]", "tests/test_models.py::test_manager_instance_access[InheritorModel]", "tests/test_models.py::test_manager_instance_access[InheritedModel]", "tests/test_models.py::test_manager_instance_access[ProxyModel]", "tests/test_models.py::test_different_hashes", "tests/test_models.py::test_migration_serialization", "tests/test_models.py::test_clear_meta_cache[ModelWithVanillaMoneyField-objects]", "tests/test_models.py::test_clear_meta_cache[ModelWithCustomDefaultManager-custom]", "tests/test_models.py::TestFieldAttributes::test_missing_attributes", "tests/test_models.py::TestFieldAttributes::test_default_currency", "tests/test_models.py::TestCustomManager::test_method", "tests/test_models.py::test_package_is_importable", "tests/test_models.py::test_hash_uniqueness", "tests/test_models.py::test_override_decorator", "tests/test_models.py::TestSharedCurrency::test_attributes", "tests/test_models.py::TestSharedCurrency::test_filter_by_money_match[args0-kwargs0]", "tests/test_models.py::TestSharedCurrency::test_filter_by_money_match[args1-kwargs1]", "tests/test_models.py::TestSharedCurrency::test_filter_by_money_no_match[args0-kwargs0]", "tests/test_models.py::TestSharedCurrency::test_filter_by_money_no_match[args1-kwargs1]", "tests/test_models.py::TestSharedCurrency::test_f_query[args0-kwargs0]", "tests/test_models.py::TestSharedCurrency::test_f_query[args1-kwargs1]", "tests/test_models.py::TestSharedCurrency::test_in_lookup[args0-kwargs0]", "tests/test_models.py::TestSharedCurrency::test_in_lookup[args1-kwargs1]", "tests/test_models.py::TestSharedCurrency::test_create_with_money", "tests/test_models.py::test_order_by", "tests/test_models.py::test_distinct_through_wrapper", "tests/test_models.py::test_mixer_blend" ]
{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }
2021-12-27 14:25:56+00:00
bsd-3-clause
1,931
django-money__django-money-689
diff --git a/djmoney/contrib/exchange/models.py b/djmoney/contrib/exchange/models.py index 4d97846..7963967 100644 --- a/djmoney/contrib/exchange/models.py +++ b/djmoney/contrib/exchange/models.py @@ -40,6 +40,8 @@ def get_rate(source, target, backend=None): Converts exchange rate on the DB side if there is no backends with given base currency. Uses data from the default backend if the backend is not specified. """ + if str(source) == str(target): + return 1 if backend is None: backend = get_default_backend_name() key = f"djmoney:get_rate:{source}:{target}:{backend}" @@ -53,8 +55,6 @@ def get_rate(source, target, backend=None): def _get_rate(source, target, backend): source, target = str(source), str(target) - if str(source) == target: - return 1 rates = Rate.objects.filter(currency__in=(source, target), backend=backend).select_related("backend") if not rates: raise MissingRate(f"Rate {source} -> {target} does not exist")
django-money/django-money
94f279562b252a0ce631d3929534a68f83e93711
diff --git a/tests/contrib/exchange/test_model.py b/tests/contrib/exchange/test_model.py index 4bd6b75..4d37c78 100644 --- a/tests/contrib/exchange/test_model.py +++ b/tests/contrib/exchange/test_model.py @@ -64,8 +64,10 @@ def test_string_representation(backend): def test_cache(): with patch("djmoney.contrib.exchange.models._get_rate", wraps=_get_rate) as original: assert get_rate("USD", "USD") == 1 + assert original.call_count == 0 + assert get_rate("USD", "EUR") == 2 assert original.call_count == 1 - assert get_rate("USD", "USD") == 1 + assert get_rate("USD", "EUR") == 2 assert original.call_count == 1 diff --git a/tests/contrib/test_django_rest_framework.py b/tests/contrib/test_django_rest_framework.py index 4a7e4a2..5372a91 100644 --- a/tests/contrib/test_django_rest_framework.py +++ b/tests/contrib/test_django_rest_framework.py @@ -106,7 +106,7 @@ class TestMoneyField: def test_serializer_with_fields(self): serializer = self.get_serializer(ModelWithVanillaMoneyField, data={"money": "10.00"}, fields_=("money",)) - serializer.is_valid(True) + serializer.is_valid(raise_exception=True) assert serializer.data == {"money": "10.00"} @pytest.mark.parametrize(
calling get_rate with identical source and target currency should be a noop - it is always exactly 1 - that doesn't even have to hit the cache ;)
0.0
94f279562b252a0ce631d3929534a68f83e93711
[ "tests/contrib/exchange/test_model.py::test_cache" ]
[ "tests/contrib/exchange/test_model.py::test_unknown_currency_with_partially_exiting_currencies[NOK-ZAR]", "tests/contrib/exchange/test_model.py::test_unknown_currency_with_partially_exiting_currencies[USD-ZAR]", "tests/contrib/exchange/test_model.py::test_get_rate[EUR-USD-expected2-1]", "tests/contrib/exchange/test_model.py::test_bad_configuration", "tests/contrib/exchange/test_model.py::test_rates_via_base[SEK-NOK-expected1]", "tests/contrib/exchange/test_model.py::test_unknown_currency[SEK-ZWL]", "tests/contrib/exchange/test_model.py::test_rates_via_base[NOK-SEK-expected0]", "tests/contrib/exchange/test_model.py::test_without_installed_exchange", "tests/contrib/exchange/test_model.py::test_get_rate[source3-USD-1-0]", "tests/contrib/exchange/test_model.py::test_get_rate[USD-USD-1-0]", "tests/contrib/exchange/test_model.py::test_unknown_currency_with_partially_exiting_currencies[ZAR-USD]", "tests/contrib/exchange/test_model.py::test_get_rate[USD-target4-1-0]", "tests/contrib/exchange/test_model.py::test_get_rate[USD-EUR-2-1]", "tests/contrib/exchange/test_model.py::test_string_representation", "tests/contrib/exchange/test_model.py::test_unknown_currency_with_partially_exiting_currencies[ZAR-NOK]", "tests/contrib/exchange/test_model.py::test_unknown_currency[USD-EUR]" ]
{ "failed_lite_validators": [ "has_short_problem_statement" ], "has_test_patch": true, "is_lite": false }
2022-09-27 10:03:46+00:00
bsd-3-clause
1,932
django-treebeard__django-treebeard-186
diff --git a/CHANGES b/CHANGES index 4b8acb7..ef16948 100644 --- a/CHANGES +++ b/CHANGES @@ -1,3 +1,13 @@ +Release 4.4 (Oct 26, 2020) +---------------------------- + +* Implement a non-destructive path-fixing algorithm for ``MP_Node.fix_tree``. +* Ensure ``post_save`` is triggered *after* the parent node is updated in ``MP_AddChildHandler``. +* Fix static URL generation to use ``static`` template tag instead of constructing the URL manually. +* Declare support for Django 2.2, 3.0 and 3.1. +* Drop support for Django 2.1 and lower. +* Drop support for Python 2.7 and Python 3.5. + Release 4.3.1 (Dec 25, 2019) ---------------------------- @@ -221,7 +231,7 @@ New features added - script to build documentation - updated numconv.py - + Bugs fixed ~~~~~~~~~~ @@ -230,7 +240,7 @@ Bugs fixed Solves bug in postgres when the table isn't created by syncdb. * Removing unused method NS_Node._find_next_node - + * Fixed MP_Node.get_tree to include the given parent when given a leaf node diff --git a/README.rst b/README.rst index 8e31be6..688ea51 100644 --- a/README.rst +++ b/README.rst @@ -16,6 +16,9 @@ Status .. image:: https://travis-ci.org/django-treebeard/django-treebeard.svg?branch=master :target: https://travis-ci.org/django-treebeard/django-treebeard +.. image:: https://ci.appveyor.com/api/projects/status/mwbf062v68lhw05c?svg=true + :target: https://ci.appveyor.com/project/mvantellingen/django-treebeard + .. image:: https://img.shields.io/pypi/v/django-treebeard.svg :target: https://pypi.org/project/django-treebeard/ diff --git a/appveyor.yml b/appveyor.yml index 5ee9a8f..807ce95 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -1,7 +1,25 @@ -# Do a dummy build so that AppVeyor doesn't fail -# while we're waiting for it to be disconnected altogether +services: + - mssql2016 -branches: - only: [] +environment: + matrix: + - TOXENV: py36-dj22-mssql + - TOXENV: py37-dj22-mssql + - TOXENV: py38-dj22-mssql + - TOXENV: py36-dj30-mssql + - TOXENV: py37-dj30-mssql + - TOXENV: py38-dj30-mssql + - TOXENV: py36-dj31-mssql + - TOXENV: py37-dj31-mssql + - TOXENV: py38-dj31-mssql -build: false # i.e. do nut run msbuild +matrix: + fast_finish: true + +install: + - C:\Python36\python -m pip install tox + +build: false # Not a C# project + +test_script: + - C:\Python36\scripts\tox diff --git a/tox.ini b/tox.ini index d909363..2105bd3 100644 --- a/tox.ini +++ b/tox.ini @@ -6,7 +6,7 @@ [tox] envlist = - py{36,37,38}-dj{22,30,31}-{sqlite,postgres,mysql} + py{36,37,38}-dj{22,30,31}-{sqlite,postgres,mysql,mssql} [testenv:docs] basepython = python @@ -25,9 +25,11 @@ deps = dj31: Django>=3.1,<3.2 postgres: psycopg2>=2.6 mysql: mysqlclient>=1.3.9 + mssql: django-mssql-backend>=2.8.1 setenv = sqlite: DATABASE_ENGINE=sqlite postgres: DATABASE_ENGINE=psql mysql: DATABASE_ENGINE=mysql + mssql: DATABASE_ENGINE=mssql commands = pytest diff --git a/treebeard/__init__.py b/treebeard/__init__.py index 00d37f5..80f4727 100644 --- a/treebeard/__init__.py +++ b/treebeard/__init__.py @@ -10,10 +10,13 @@ Release logic: 5. git push 6. assure that all tests pass on https://travis-ci.org/django-treebeard/django-treebeard/builds/ 7. git push --tags - 8. python setup.py sdist upload - 9. bump the version, append ".dev0" to __version__ -10. git add treebeard/__init__.py -11. git commit -m 'Start with <version>' -12. git push + 8. pip install --upgrade pip wheel twine + 9. python setup.py clean --all + 9. python setup.py sdist bdist_wheel +10. twine upload dist/* +11. bump the version, append ".dev0" to __version__ +12. git add treebeard/__init__.py +13. git commit -m 'Start with <version>' +14. git push """ -__version__ = '4.3.1' +__version__ = '4.4.0' diff --git a/treebeard/forms.py b/treebeard/forms.py index 4f9ef11..547c6d9 100644 --- a/treebeard/forms.py +++ b/treebeard/forms.py @@ -178,11 +178,8 @@ class MoveNodeForm(forms.ModelForm): def add_subtree(cls, for_node, node, options): """ Recursively build options tree. """ if cls.is_loop_safe(for_node, node): - options.append( - (node.pk, - mark_safe(cls.mk_indent(node.get_depth()) + escape(node)))) - for subnode in node.get_children(): - cls.add_subtree(for_node, subnode, options) + for item, _ in node.get_annotated_list(node): + options.append((item.pk, mark_safe(cls.mk_indent(item.get_depth()) + escape(item)))) @classmethod def mk_dropdown_tree(cls, model, for_node=None):
django-treebeard/django-treebeard
c3abc0c812da30a9ab5b2a8bcf976c860a44ee95
diff --git a/treebeard/tests/settings.py b/treebeard/tests/settings.py index c8a2745..47cc1c8 100644 --- a/treebeard/tests/settings.py +++ b/treebeard/tests/settings.py @@ -36,6 +36,19 @@ def get_db_conf(): 'HOST': '127.0.0.1', 'PORT': '', } + elif database_engine == "mssql": + return { + 'ENGINE': 'sql_server.pyodbc', + 'NAME': 'master', + 'USER': 'sa', + 'PASSWORD': 'Password12!', + 'HOST': '(local)\\SQL2016', + 'PORT': '', + 'OPTIONS': { + 'driver': 'SQL Server Native Client 11.0', + 'MARS_Connection': 'True', + }, + } DATABASES = {'default': get_db_conf()} SECRET_KEY = '7r33b34rd' diff --git a/treebeard/tests/test_treebeard.py b/treebeard/tests/test_treebeard.py index 03e7619..c68963d 100644 --- a/treebeard/tests/test_treebeard.py +++ b/treebeard/tests/test_treebeard.py @@ -2164,8 +2164,8 @@ class TestMoveNodeForm(TestNonEmptyTree): def test_form_leaf_node(self, model): nodes = list(model.get_tree()) - node = nodes.pop() safe_parent_nodes = self._get_node_ids_and_depths(nodes) + node = nodes.pop() self._move_node_helper(node, safe_parent_nodes) def test_form_admin(self, model): @@ -2725,3 +2725,16 @@ class TestTreeAdmin(TestNonEmptyTree): ('4', 1, 1), ('41', 2, 0)] assert self.got(model) == expected + + +class TestMPFormPerformance(TestCase): + @classmethod + def setup_class(cls): + cls.model = models.MP_TestNode + cls.model.load_bulk(BASE_DATA) + + def test_form_add_subtree_no_of_queries(self): + form_class = movenodeform_factory(self.model) + form = form_class() + with self.assertNumQueries(len(self.model.get_root_nodes()) + 1): + form.mk_dropdown_tree(self.model)
Publish releases as wheels? I see on PyPI that the package’s releases only contain source distribution, for example for the latest [4.3.1](https://pypi.org/project/django-treebeard/4.3.1/#files). Would it be possible to additionally publish wheels? The project is already set up for universal wheels since #130, and will switch to Python3-only wheels once #153 is merged – so I think this should just be a matter of adding `bdist_wheel` to the release process as described here: https://github.com/django-treebeard/django-treebeard/blob/3a8062cf4584336cc63551f332e9926e1af207ed/treebeard/__init__.py#L14 More general info on wheels: https://pythonwheels.com/. For me I’m particularly interested in speeding up installations.
0.0
c3abc0c812da30a9ab5b2a8bcf976c860a44ee95
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"treebeard/tests/test_treebeard.py::TestForm::test_clean_cleaned_data[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestForm::test_clean_cleaned_data[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestForm::test_clean_cleaned_data[NS_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestForm::test_save_edit[AL_TestNode]", "treebeard/tests/test_treebeard.py::TestForm::test_save_edit[MP_TestNode]", "treebeard/tests/test_treebeard.py::TestForm::test_save_edit[NS_TestNode]", "treebeard/tests/test_treebeard.py::TestForm::test_save_edit[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestForm::test_save_edit[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestForm::test_save_edit[NS_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestForm::test_save_new[AL_TestNode]", "treebeard/tests/test_treebeard.py::TestForm::test_save_new[MP_TestNode]", "treebeard/tests/test_treebeard.py::TestForm::test_save_new[NS_TestNode]", "treebeard/tests/test_treebeard.py::TestForm::test_save_new[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestForm::test_save_new[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestForm::test_save_new[NS_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestAdminTreeTemplateTags::test_treebeard_css", "treebeard/tests/test_treebeard.py::TestAdminTreeTemplateTags::test_treebeard_js", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_changelist_view", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_get_node[AL_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_get_node[MP_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_get_node[NS_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_get_node[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_get_node[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_get_node[NS_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_keyerror[AL_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_keyerror[MP_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_keyerror[NS_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_keyerror[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_keyerror[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_keyerror[NS_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_valueerror[AL_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_valueerror[MP_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_valueerror[NS_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_valueerror[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_valueerror[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_node_validate_valueerror[NS_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_missing_nodeorderby[AL_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_missing_nodeorderby[MP_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_missing_nodeorderby[NS_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_missing_nodeorderby[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_missing_nodeorderby[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_missing_nodeorderby[NS_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_invalid_pos[AL_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_invalid_pos[MP_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_invalid_pos[NS_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_invalid_pos[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_invalid_pos[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_invalid_pos[NS_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_to_descendant[AL_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_to_descendant[MP_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_to_descendant[NS_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_to_descendant[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_to_descendant[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_validate_to_descendant[NS_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_left[AL_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_left[MP_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_left[NS_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_left[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_left[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_left[NS_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_last_child[AL_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_last_child[MP_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_last_child[NS_TestNode]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_last_child[AL_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_last_child[MP_TestNode_Proxy]", "treebeard/tests/test_treebeard.py::TestTreeAdmin::test_move_last_child[NS_TestNode_Proxy]" ]
{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }
2020-10-26 06:31:31+00:00
apache-2.0
1,933
django__asgiref-183
diff --git a/asgiref/wsgi.py b/asgiref/wsgi.py index 7155ab2..8811118 100644 --- a/asgiref/wsgi.py +++ b/asgiref/wsgi.py @@ -55,8 +55,8 @@ class WsgiToAsgiInstance: """ environ = { "REQUEST_METHOD": scope["method"], - "SCRIPT_NAME": scope.get("root_path", ""), - "PATH_INFO": scope["path"], + "SCRIPT_NAME": scope.get("root_path", "").encode("utf8").decode("latin1"), + "PATH_INFO": scope["path"].encode("utf8").decode("latin1"), "QUERY_STRING": scope["query_string"].decode("ascii"), "SERVER_PROTOCOL": "HTTP/%s" % scope["http_version"], "wsgi.version": (1, 0),
django/asgiref
3020b4a309033ad0b7041dda7712b0ed729e338f
diff --git a/tests/test_wsgi.py b/tests/test_wsgi.py index 647f465..3490573 100644 --- a/tests/test_wsgi.py +++ b/tests/test_wsgi.py @@ -50,6 +50,48 @@ async def test_basic_wsgi(): assert (await instance.receive_output(1)) == {"type": "http.response.body"} [email protected] +async def test_wsgi_path_encoding(): + """ + Makes sure the WSGI wrapper has basic functionality. + """ + # Define WSGI app + def wsgi_application(environ, start_response): + assert environ["SCRIPT_NAME"] == "/中国".encode("utf8").decode("latin-1") + assert environ["PATH_INFO"] == "/中文".encode("utf8").decode("latin-1") + start_response("200 OK", []) + yield b"" + + # Wrap it + application = WsgiToAsgi(wsgi_application) + # Launch it as a test application + instance = ApplicationCommunicator( + application, + { + "type": "http", + "http_version": "1.0", + "method": "GET", + "path": "/中文", + "root_path": "/中国", + "query_string": b"bar=baz", + "headers": [], + }, + ) + await instance.send_input({"type": "http.request"}) + # Check they send stuff + assert (await instance.receive_output(1)) == { + "type": "http.response.start", + "status": 200, + "headers": [], + } + assert (await instance.receive_output(1)) == { + "type": "http.response.body", + "body": b"", + "more_body": True, + } + assert (await instance.receive_output(1)) == {"type": "http.response.body"} + + @pytest.mark.asyncio async def test_wsgi_empty_body(): """
WSGI Error in non-ascii path https://github.com/encode/starlette/issues/997 I noticed that the ASGI document clearly states that utf8 encoding is required, but WSGI seems to require latin-1 encoding. https://www.python.org/dev/peps/pep-3333/#a-note-on-string-types https://asgi.readthedocs.io/en/latest/specs/www.html#connection-scope
0.0
3020b4a309033ad0b7041dda7712b0ed729e338f
[ "tests/test_wsgi.py::test_wsgi_path_encoding" ]
[ "tests/test_wsgi.py::test_basic_wsgi", "tests/test_wsgi.py::test_wsgi_empty_body", "tests/test_wsgi.py::test_wsgi_multi_body" ]
{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }
2020-07-14 02:53:15+00:00
bsd-3-clause
1,934