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axltxl/m2bk
|
m2bk/mongo.py
|
https://github.com/axltxl/m2bk/blob/980083dfd17e6e783753a946e9aa809714551141/m2bk/mongo.py#L28-L51
|
def _set_mongodb_host_val(key, default, mongodb_host, mongodb_defaults):
"""
Set a value in a 'cascade' fashion for mongodb_host[key]
Within 'mongodb', as a last resort, its hardcoded default value is going to
be picked.
:param key: key name
:param default: default last resort value
:param mongodb_host: mongodb 'host' entry
:param mongodb_defaults: mongodb 'defaults' dict
"""
# If mongodb_host[key] is not already set, its value is going to be picked
# from mongodb_defaults[key]
if key not in mongodb_host:
if key in mongodb_defaults:
mongodb_host[key] = mongodb_defaults[key]
else:
# BUT, if also mongodb_defaults[key] doesn't exist
# the value picked is going to be 'default' as last resort
mongodb_host[key] = default
if key != 'user_name' and key != 'password':
log.msg_debug("Setting default '{key}'='{value}' "
.format(key=key, value=mongodb_host[key]))
|
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Set a value in a 'cascade' fashion for mongodb_host[key]
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:param key: key name
:param default: default last resort value
:param mongodb_host: mongodb 'host' entry
:param mongodb_defaults: mongodb 'defaults' dict
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python
|
train
|
markovmodel/msmtools
|
msmtools/generation/api.py
|
https://github.com/markovmodel/msmtools/blob/54dc76dd2113a0e8f3d15d5316abab41402941be/msmtools/generation/api.py#L133-L151
|
def trajectories(self, M, N, start=None, stop=None):
"""
Generates M trajectories, each of length N, starting from state s
Parameters
----------
M : int
number of trajectories
N : int
trajectory length
start : int, optional, default = None
starting state. If not given, will sample from the stationary distribution of P
stop : int or int-array-like, optional, default = None
stopping set. If given, the trajectory will be stopped before N steps
once a state of the stop set is reached
"""
trajs = [self.trajectory(N, start=start, stop=stop) for _ in range(M)]
return trajs
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Generates M trajectories, each of length N, starting from state s
Parameters
----------
M : int
number of trajectories
N : int
trajectory length
start : int, optional, default = None
starting state. If not given, will sample from the stationary distribution of P
stop : int or int-array-like, optional, default = None
stopping set. If given, the trajectory will be stopped before N steps
once a state of the stop set is reached
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"length",
"N",
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] |
python
|
train
|
log2timeline/plaso
|
plaso/parsers/interface.py
|
https://github.com/log2timeline/plaso/blob/9c564698d2da3ffbe23607a3c54c0582ea18a6cc/plaso/parsers/interface.py#L215-L232
|
def Parse(self, parser_mediator):
"""Parsers the file entry and extracts event objects.
Args:
parser_mediator (ParserMediator): a parser mediator.
Raises:
UnableToParseFile: when the file cannot be parsed.
"""
file_entry = parser_mediator.GetFileEntry()
if not file_entry:
raise errors.UnableToParseFile('Invalid file entry')
parser_mediator.AppendToParserChain(self)
try:
self.ParseFileEntry(parser_mediator, file_entry)
finally:
parser_mediator.PopFromParserChain()
|
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Parsers the file entry and extracts event objects.
Args:
parser_mediator (ParserMediator): a parser mediator.
Raises:
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[
"Parsers",
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"."
] |
python
|
train
|
pygobject/pgi
|
pgi/overrides/__init__.py
|
https://github.com/pygobject/pgi/blob/2090435df6241a15ec2a78379a36b738b728652c/pgi/overrides/__init__.py#L204-L221
|
def deprecated_attr(namespace, attr, replacement):
"""Marks a module level attribute as deprecated. Accessing it will emit
a PyGIDeprecationWarning warning.
e.g. for ``deprecated_attr("GObject", "STATUS_FOO", "GLib.Status.FOO")``
accessing GObject.STATUS_FOO will emit:
"GObject.STATUS_FOO is deprecated; use GLib.Status.FOO instead"
:param str namespace:
The namespace of the override this is called in.
:param str namespace:
The attribute name (which gets added to __all__).
:param str replacement:
The replacement text which will be included in the warning.
"""
_deprecated_attrs.setdefault(namespace, []).append((attr, replacement))
|
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Marks a module level attribute as deprecated. Accessing it will emit
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e.g. for ``deprecated_attr("GObject", "STATUS_FOO", "GLib.Status.FOO")``
accessing GObject.STATUS_FOO will emit:
"GObject.STATUS_FOO is deprecated; use GLib.Status.FOO instead"
:param str namespace:
The namespace of the override this is called in.
:param str namespace:
The attribute name (which gets added to __all__).
:param str replacement:
The replacement text which will be included in the warning.
|
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"emit",
"a",
"PyGIDeprecationWarning",
"warning",
"."
] |
python
|
train
|
zarr-developers/zarr
|
zarr/hierarchy.py
|
https://github.com/zarr-developers/zarr/blob/fb8e6d5ea6bc26e451e5cf0eaaee36977556d5b5/zarr/hierarchy.py#L1002-L1057
|
def group(store=None, overwrite=False, chunk_store=None,
cache_attrs=True, synchronizer=None, path=None):
"""Create a group.
Parameters
----------
store : MutableMapping or string, optional
Store or path to directory in file system.
overwrite : bool, optional
If True, delete any pre-existing data in `store` at `path` before
creating the group.
chunk_store : MutableMapping, optional
Separate storage for chunks. If not provided, `store` will be used
for storage of both chunks and metadata.
cache_attrs : bool, optional
If True (default), user attributes will be cached for attribute read
operations. If False, user attributes are reloaded from the store prior
to all attribute read operations.
synchronizer : object, optional
Array synchronizer.
path : string, optional
Group path within store.
Returns
-------
g : zarr.hierarchy.Group
Examples
--------
Create a group in memory::
>>> import zarr
>>> g = zarr.group()
>>> g
<zarr.hierarchy.Group '/'>
Create a group with a different store::
>>> store = zarr.DirectoryStore('data/example.zarr')
>>> g = zarr.group(store=store, overwrite=True)
>>> g
<zarr.hierarchy.Group '/'>
"""
# handle polymorphic store arg
store = _normalize_store_arg(store)
path = normalize_storage_path(path)
# require group
if overwrite or not contains_group(store):
init_group(store, overwrite=overwrite, chunk_store=chunk_store,
path=path)
return Group(store, read_only=False, chunk_store=chunk_store,
cache_attrs=cache_attrs, synchronizer=synchronizer, path=path)
|
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Create a group.
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If True, delete any pre-existing data in `store` at `path` before
creating the group.
chunk_store : MutableMapping, optional
Separate storage for chunks. If not provided, `store` will be used
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cache_attrs : bool, optional
If True (default), user attributes will be cached for attribute read
operations. If False, user attributes are reloaded from the store prior
to all attribute read operations.
synchronizer : object, optional
Array synchronizer.
path : string, optional
Group path within store.
Returns
-------
g : zarr.hierarchy.Group
Examples
--------
Create a group in memory::
>>> import zarr
>>> g = zarr.group()
>>> g
<zarr.hierarchy.Group '/'>
Create a group with a different store::
>>> store = zarr.DirectoryStore('data/example.zarr')
>>> g = zarr.group(store=store, overwrite=True)
>>> g
<zarr.hierarchy.Group '/'>
|
[
"Create",
"a",
"group",
"."
] |
python
|
train
|
DataDog/integrations-core
|
tokumx/datadog_checks/tokumx/vendor/bson/__init__.py
|
https://github.com/DataDog/integrations-core/blob/ebd41c873cf9f97a8c51bf9459bc6a7536af8acd/tokumx/datadog_checks/tokumx/vendor/bson/__init__.py#L698-L728
|
def _name_value_to_bson(name, value, check_keys, opts):
"""Encode a single name, value pair."""
# First see if the type is already cached. KeyError will only ever
# happen once per subtype.
try:
return _ENCODERS[type(value)](name, value, check_keys, opts)
except KeyError:
pass
# Second, fall back to trying _type_marker. This has to be done
# before the loop below since users could subclass one of our
# custom types that subclasses a python built-in (e.g. Binary)
marker = getattr(value, "_type_marker", None)
if isinstance(marker, int) and marker in _MARKERS:
func = _MARKERS[marker]
# Cache this type for faster subsequent lookup.
_ENCODERS[type(value)] = func
return func(name, value, check_keys, opts)
# If all else fails test each base type. This will only happen once for
# a subtype of a supported base type.
for base in _ENCODERS:
if isinstance(value, base):
func = _ENCODERS[base]
# Cache this type for faster subsequent lookup.
_ENCODERS[type(value)] = func
return func(name, value, check_keys, opts)
raise InvalidDocument("cannot convert value of type %s to bson" %
type(value))
|
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Encode a single name, value pair.
|
[
"Encode",
"a",
"single",
"name",
"value",
"pair",
"."
] |
python
|
train
|
pgjones/quart
|
quart/app.py
|
https://github.com/pgjones/quart/blob/7cb2d3bd98e8746025764f2b933abc12041fa175/quart/app.py#L244-L258
|
def logger(self) -> Logger:
"""A :class:`logging.Logger` logger for the app.
This can be used to log messages in a format as defined in the
app configuration, for example,
.. code-block:: python
app.logger.debug("Request method %s", request.method)
app.logger.error("Error, of some kind")
"""
if self._logger is None:
self._logger = create_logger(self)
return self._logger
|
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".",
"_logger",
"=",
"create_logger",
"(",
"self",
")",
"return",
"self",
".",
"_logger"
] |
A :class:`logging.Logger` logger for the app.
This can be used to log messages in a format as defined in the
app configuration, for example,
.. code-block:: python
app.logger.debug("Request method %s", request.method)
app.logger.error("Error, of some kind")
|
[
"A",
":",
"class",
":",
"logging",
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"Logger",
"logger",
"for",
"the",
"app",
"."
] |
python
|
train
|
twisted/vertex
|
vertex/q2q.py
|
https://github.com/twisted/vertex/blob/feb591aa1b9a3b2b8fdcf53e4962dad2a0bc38ca/vertex/q2q.py#L1910-L1935
|
def requestAvatarId(self, credentials):
"""
Return the ID associated with these credentials.
@param credentials: something which implements one of the interfaces in
self.credentialInterfaces.
@return: a Deferred which will fire a string which identifies an
avatar, an empty tuple to specify an authenticated anonymous user
(provided as checkers.ANONYMOUS) or fire a Failure(UnauthorizedLogin).
@see: L{twisted.cred.credentials}
"""
username, domain = credentials.username.split("@")
key = self.users.key(domain, username)
if key is None:
return defer.fail(UnauthorizedLogin())
def _cbPasswordChecked(passwordIsCorrect):
if passwordIsCorrect:
return username + '@' + domain
else:
raise UnauthorizedLogin()
return defer.maybeDeferred(credentials.checkPassword,
key).addCallback(_cbPasswordChecked)
|
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"key",
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Return the ID associated with these credentials.
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@return: a Deferred which will fire a string which identifies an
avatar, an empty tuple to specify an authenticated anonymous user
(provided as checkers.ANONYMOUS) or fire a Failure(UnauthorizedLogin).
@see: L{twisted.cred.credentials}
|
[
"Return",
"the",
"ID",
"associated",
"with",
"these",
"credentials",
"."
] |
python
|
train
|
numenta/nupic
|
src/nupic/data/generators/distributions.py
|
https://github.com/numenta/nupic/blob/5922fafffdccc8812e72b3324965ad2f7d4bbdad/src/nupic/data/generators/distributions.py#L50-L54
|
def getData(self, n):
"""Returns the next n values for the distribution as a list."""
records = [self.getNext() for x in range(n)]
return records
|
[
"def",
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Returns the next n values for the distribution as a list.
|
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"as",
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"."
] |
python
|
valid
|
PMBio/limix-backup
|
limix/core/old/covar/covariance.py
|
https://github.com/PMBio/limix-backup/blob/1e201fdb5c694d0d5506f207f3de65d8ef66146c/limix/core/old/covar/covariance.py#L50-L56
|
def setParams(self,params):
"""
set hyperParams
"""
self.params = params
self.clear_all()
self._notify()
|
[
"def",
"setParams",
"(",
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"=",
"params",
"self",
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"clear_all",
"(",
")",
"self",
".",
"_notify",
"(",
")"
] |
set hyperParams
|
[
"set",
"hyperParams"
] |
python
|
train
|
lsst-sqre/sqre-apikit
|
apikit/convenience.py
|
https://github.com/lsst-sqre/sqre-apikit/blob/ff505b63d2e29303ff7f05f2bd5eabd0f6d7026e/apikit/convenience.py#L262-L280
|
def raise_from_response(resp):
"""Turn a failed request response into a BackendError. Handy for
reflecting HTTP errors from farther back in the call chain.
Parameters
----------
resp: :class:`requests.Response`
Raises
------
:class:`apikit.BackendError`
If `resp.status_code` is equal to or greater than 400.
"""
if resp.status_code < 400:
# Request was successful. Or at least, not a failure.
return
raise BackendError(status_code=resp.status_code,
reason=resp.reason,
content=resp.text)
|
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")"
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Turn a failed request response into a BackendError. Handy for
reflecting HTTP errors from farther back in the call chain.
Parameters
----------
resp: :class:`requests.Response`
Raises
------
:class:`apikit.BackendError`
If `resp.status_code` is equal to or greater than 400.
|
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"back",
"in",
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"call",
"chain",
"."
] |
python
|
train
|
pydata/xarray
|
xarray/convert.py
|
https://github.com/pydata/xarray/blob/6d93a95d05bdbfc33fff24064f67d29dd891ab58/xarray/convert.py#L139-L178
|
def to_iris(dataarray):
""" Convert a DataArray into a Iris Cube
"""
# Iris not a hard dependency
import iris
from iris.fileformats.netcdf import parse_cell_methods
dim_coords = []
aux_coords = []
for coord_name in dataarray.coords:
coord = encode(dataarray.coords[coord_name])
coord_args = _get_iris_args(coord.attrs)
coord_args['var_name'] = coord_name
axis = None
if coord.dims:
axis = dataarray.get_axis_num(coord.dims)
if coord_name in dataarray.dims:
try:
iris_coord = iris.coords.DimCoord(coord.values, **coord_args)
dim_coords.append((iris_coord, axis))
except ValueError:
iris_coord = iris.coords.AuxCoord(coord.values, **coord_args)
aux_coords.append((iris_coord, axis))
else:
iris_coord = iris.coords.AuxCoord(coord.values, **coord_args)
aux_coords.append((iris_coord, axis))
args = _get_iris_args(dataarray.attrs)
args['var_name'] = dataarray.name
args['dim_coords_and_dims'] = dim_coords
args['aux_coords_and_dims'] = aux_coords
if 'cell_methods' in dataarray.attrs:
args['cell_methods'] = \
parse_cell_methods(dataarray.attrs['cell_methods'])
masked_data = duck_array_ops.masked_invalid(dataarray.data)
cube = iris.cube.Cube(masked_data, **args)
return cube
|
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Convert a DataArray into a Iris Cube
|
[
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] |
python
|
train
|
saltstack/salt
|
salt/modules/kapacitor.py
|
https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/modules/kapacitor.py#L109-L126
|
def _run_cmd(cmd):
'''
Run a Kapacitor task and return a dictionary of info.
'''
ret = {}
env_vars = {
'KAPACITOR_URL': _get_url(),
'KAPACITOR_UNSAFE_SSL': __salt__['config.option']('kapacitor.unsafe_ssl', 'false'),
}
result = __salt__['cmd.run_all'](cmd, env=env_vars)
if result.get('stdout'):
ret['stdout'] = result['stdout']
if result.get('stderr'):
ret['stderr'] = result['stderr']
ret['success'] = result['retcode'] == 0
return ret
|
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Run a Kapacitor task and return a dictionary of info.
|
[
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"a",
"dictionary",
"of",
"info",
"."
] |
python
|
train
|
flatangle/flatlib
|
flatlib/angle.py
|
https://github.com/flatangle/flatlib/blob/44e05b2991a296c678adbc17a1d51b6a21bc867c/flatlib/angle.py#L82-L86
|
def slistFloat(slist):
""" Converts signed list to float. """
values = [v / 60**(i) for (i,v) in enumerate(slist[1:])]
value = sum(values)
return -value if slist[0] == '-' else value
|
[
"def",
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"[",
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Converts signed list to float.
|
[
"Converts",
"signed",
"list",
"to",
"float",
"."
] |
python
|
train
|
oauthlib/oauthlib
|
oauthlib/oauth2/rfc6749/tokens.py
|
https://github.com/oauthlib/oauthlib/blob/30321dd3c0ca784d3508a1970cf90d9f76835c79/oauthlib/oauth2/rfc6749/tokens.py#L245-L262
|
def get_token_from_header(request):
"""
Helper function to extract a token from the request header.
:param request: OAuthlib request.
:type request: oauthlib.common.Request
:return: Return the token or None if the Authorization header is malformed.
"""
token = None
if 'Authorization' in request.headers:
split_header = request.headers.get('Authorization').split()
if len(split_header) == 2 and split_header[0] == 'Bearer':
token = split_header[1]
else:
token = request.access_token
return token
|
[
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] |
Helper function to extract a token from the request header.
:param request: OAuthlib request.
:type request: oauthlib.common.Request
:return: Return the token or None if the Authorization header is malformed.
|
[
"Helper",
"function",
"to",
"extract",
"a",
"token",
"from",
"the",
"request",
"header",
"."
] |
python
|
train
|
saltstack/salt
|
salt/cloud/clouds/opennebula.py
|
https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/cloud/clouds/opennebula.py#L1789-L1894
|
def image_update(call=None, kwargs=None):
'''
Replaces the image template contents.
.. versionadded:: 2016.3.0
image_id
The ID of the image to update. Can be used instead of ``image_name``.
image_name
The name of the image to update. Can be used instead of ``image_id``.
path
The path to a file containing the template of the image. Syntax within the
file can be the usual attribute=value or XML. Can be used instead of ``data``.
data
Contains the template of the image. Syntax can be the usual attribute=value
or XML. Can be used instead of ``path``.
update_type
There are two ways to update an image: ``replace`` the whole template
or ``merge`` the new template with the existing one.
CLI Example:
.. code-block:: bash
salt-cloud -f image_update opennebula image_id=0 file=/path/to/image_update_file.txt update_type=replace
salt-cloud -f image_update opennebula image_name="Ubuntu 14.04" update_type=merge \\
data='NAME="Ubuntu Dev" PATH="/home/one_user/images/ubuntu_desktop.img" \\
DESCRIPTION = "Ubuntu 14.04 for development."'
'''
if call != 'function':
raise SaltCloudSystemExit(
'The image_allocate function must be called with -f or --function.'
)
if kwargs is None:
kwargs = {}
image_id = kwargs.get('image_id', None)
image_name = kwargs.get('image_name', None)
path = kwargs.get('path', None)
data = kwargs.get('data', None)
update_type = kwargs.get('update_type', None)
update_args = ['replace', 'merge']
if update_type is None:
raise SaltCloudSystemExit(
'The image_update function requires an \'update_type\' to be provided.'
)
if update_type == update_args[0]:
update_number = 0
elif update_type == update_args[1]:
update_number = 1
else:
raise SaltCloudSystemExit(
'The update_type argument must be either {0} or {1}.'.format(
update_args[0],
update_args[1]
)
)
if image_id:
if image_name:
log.warning(
'Both the \'image_id\' and \'image_name\' arguments were provided. '
'\'image_id\' will take precedence.'
)
elif image_name:
image_id = get_image_id(kwargs={'name': image_name})
else:
raise SaltCloudSystemExit(
'The image_update function requires either an \'image_id\' or an '
'\'image_name\' to be provided.'
)
if data:
if path:
log.warning(
'Both the \'data\' and \'path\' arguments were provided. '
'\'data\' will take precedence.'
)
elif path:
with salt.utils.files.fopen(path, mode='r') as rfh:
data = rfh.read()
else:
raise SaltCloudSystemExit(
'The image_update function requires either \'data\' or a file \'path\' '
'to be provided.'
)
server, user, password = _get_xml_rpc()
auth = ':'.join([user, password])
response = server.one.image.update(auth, int(image_id), data, int(update_number))
ret = {
'action': 'image.update',
'updated': response[0],
'image_id': response[1],
'error_code': response[2],
}
return ret
|
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Replaces the image template contents.
.. versionadded:: 2016.3.0
image_id
The ID of the image to update. Can be used instead of ``image_name``.
image_name
The name of the image to update. Can be used instead of ``image_id``.
path
The path to a file containing the template of the image. Syntax within the
file can be the usual attribute=value or XML. Can be used instead of ``data``.
data
Contains the template of the image. Syntax can be the usual attribute=value
or XML. Can be used instead of ``path``.
update_type
There are two ways to update an image: ``replace`` the whole template
or ``merge`` the new template with the existing one.
CLI Example:
.. code-block:: bash
salt-cloud -f image_update opennebula image_id=0 file=/path/to/image_update_file.txt update_type=replace
salt-cloud -f image_update opennebula image_name="Ubuntu 14.04" update_type=merge \\
data='NAME="Ubuntu Dev" PATH="/home/one_user/images/ubuntu_desktop.img" \\
DESCRIPTION = "Ubuntu 14.04 for development."'
|
[
"Replaces",
"the",
"image",
"template",
"contents",
"."
] |
python
|
train
|
librosa/librosa
|
librosa/effects.py
|
https://github.com/librosa/librosa/blob/180e8e6eb8f958fa6b20b8cba389f7945d508247/librosa/effects.py#L145-L186
|
def percussive(y, **kwargs):
'''Extract percussive elements from an audio time-series.
Parameters
----------
y : np.ndarray [shape=(n,)]
audio time series
kwargs : additional keyword arguments.
See `librosa.decompose.hpss` for details.
Returns
-------
y_percussive : np.ndarray [shape=(n,)]
audio time series of just the percussive portion
See Also
--------
hpss : Separate harmonic and percussive components
harmonic : Extract only the harmonic component
librosa.decompose.hpss : HPSS for spectrograms
Examples
--------
>>> # Extract percussive component
>>> y, sr = librosa.load(librosa.util.example_audio_file())
>>> y_percussive = librosa.effects.percussive(y)
>>> # Use a margin > 1.0 for greater percussive separation
>>> y_percussive = librosa.effects.percussive(y, margin=3.0)
'''
# Compute the STFT matrix
stft = core.stft(y)
# Remove harmonics
stft_perc = decompose.hpss(stft, **kwargs)[1]
# Invert the STFT
y_perc = util.fix_length(core.istft(stft_perc, dtype=y.dtype), len(y))
return y_perc
|
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"y_perc"
] |
Extract percussive elements from an audio time-series.
Parameters
----------
y : np.ndarray [shape=(n,)]
audio time series
kwargs : additional keyword arguments.
See `librosa.decompose.hpss` for details.
Returns
-------
y_percussive : np.ndarray [shape=(n,)]
audio time series of just the percussive portion
See Also
--------
hpss : Separate harmonic and percussive components
harmonic : Extract only the harmonic component
librosa.decompose.hpss : HPSS for spectrograms
Examples
--------
>>> # Extract percussive component
>>> y, sr = librosa.load(librosa.util.example_audio_file())
>>> y_percussive = librosa.effects.percussive(y)
>>> # Use a margin > 1.0 for greater percussive separation
>>> y_percussive = librosa.effects.percussive(y, margin=3.0)
|
[
"Extract",
"percussive",
"elements",
"from",
"an",
"audio",
"time",
"-",
"series",
"."
] |
python
|
test
|
raphaelvallat/pingouin
|
pingouin/external/qsturng.py
|
https://github.com/raphaelvallat/pingouin/blob/58b19fa4fffbfe09d58b456e3926a148249e4d9b/pingouin/external/qsturng.py#L787-L818
|
def psturng(q, r, v):
"""Evaluates the probability from 0 to q for a studentized
range having v degrees of freedom and r samples.
Parameters
----------
q : (scalar, array_like)
quantile value of Studentized Range
q >= 0.
r : (scalar, array_like)
The number of samples
r >= 2 and r <= 200
(values over 200 are permitted but not recommended)
v : (scalar, array_like)
The sample degrees of freedom
if p >= .9:
v >=1 and v >= inf
else:
v >=2 and v >= inf
Returns
-------
p : (scalar, array_like)
1. - area from zero to q under the Studentized Range
distribution. When v == 1, p is bound between .001
and .1, when v > 1, p is bound between .001 and .9.
Values between .5 and .9 are 1st order appoximations.
"""
if all(map(_isfloat, [q, r, v])):
return _psturng(q, r, v)
return _vpsturng(q, r, v)
|
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")",
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"(",
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",",
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")"
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Evaluates the probability from 0 to q for a studentized
range having v degrees of freedom and r samples.
Parameters
----------
q : (scalar, array_like)
quantile value of Studentized Range
q >= 0.
r : (scalar, array_like)
The number of samples
r >= 2 and r <= 200
(values over 200 are permitted but not recommended)
v : (scalar, array_like)
The sample degrees of freedom
if p >= .9:
v >=1 and v >= inf
else:
v >=2 and v >= inf
Returns
-------
p : (scalar, array_like)
1. - area from zero to q under the Studentized Range
distribution. When v == 1, p is bound between .001
and .1, when v > 1, p is bound between .001 and .9.
Values between .5 and .9 are 1st order appoximations.
|
[
"Evaluates",
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"for",
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"studentized",
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"having",
"v",
"degrees",
"of",
"freedom",
"and",
"r",
"samples",
"."
] |
python
|
train
|
pyviz/holoviews
|
holoviews/plotting/bokeh/renderer.py
|
https://github.com/pyviz/holoviews/blob/ae0dd2f3de448b0ca5e9065aabd6ef8d84c7e655/holoviews/plotting/bokeh/renderer.py#L253-L303
|
def _figure_data(self, plot, fmt='html', doc=None, as_script=False, **kwargs):
"""
Given a plot instance, an output format and an optional bokeh
document, return the corresponding data. If as_script is True,
the content will be split in an HTML and a JS component.
"""
model = plot.state
if doc is None:
doc = plot.document
else:
plot.document = doc
for m in model.references():
m._document = None
doc.theme = self.theme
doc.add_root(model)
# Bokeh raises warnings about duplicate tools and empty subplots
# but at the holoviews level these are not issues
logger = logging.getLogger(bokeh.core.validation.check.__file__)
logger.disabled = True
if fmt == 'png':
from bokeh.io.export import get_screenshot_as_png
img = get_screenshot_as_png(plot.state, None)
imgByteArr = BytesIO()
img.save(imgByteArr, format='PNG')
data = imgByteArr.getvalue()
if as_script:
b64 = base64.b64encode(data).decode("utf-8")
(mime_type, tag) = MIME_TYPES[fmt], HTML_TAGS[fmt]
src = HTML_TAGS['base64'].format(mime_type=mime_type, b64=b64)
div = tag.format(src=src, mime_type=mime_type, css='')
js = ''
else:
try:
with silence_warnings(EMPTY_LAYOUT, MISSING_RENDERERS):
js, div, _ = notebook_content(model)
html = NOTEBOOK_DIV.format(plot_script=js, plot_div=div)
data = encode_utf8(html)
doc.hold()
except:
logger.disabled = False
raise
logger.disabled = False
plot.document = doc
if as_script:
return div, js
return data
|
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Given a plot instance, an output format and an optional bokeh
document, return the corresponding data. If as_script is True,
the content will be split in an HTML and a JS component.
|
[
"Given",
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"an",
"HTML",
"and",
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"JS",
"component",
"."
] |
python
|
train
|
CGATOxford/UMI-tools
|
umi_tools/umi_methods.py
|
https://github.com/CGATOxford/UMI-tools/blob/c4b5d84aac391d59916d294f8f4f8f5378abcfbe/umi_tools/umi_methods.py#L100-L124
|
def joinedFastqIterate(fastq_iterator1, fastq_iterator2, strict=True):
'''This will return an iterator that returns tuples of fastq records.
At each step it will confirm that the first field of the read name
(before the first whitespace character) is identical between the
two reads. The response if it is not depends on the value of
:param:`strict`. If strict is true an error is returned. If strict
is `False` the second file is advanced until a read that matches
is found.
This allows for protocols where read one contains cell barcodes, and these
reads have been filtered and corrected before processing without regard
to read2
'''
for read1 in fastq_iterator1:
read2 = next(fastq_iterator2)
pair_id = read1.identifier.split()[0]
if not strict:
while read2.identifier.split()[0] != pair_id:
read2 = next(fastq_iterator2)
if not read2.identifier.split()[0] == pair_id:
raise ValueError("\nRead pairs do not match\n%s != %s" %
(pair_id, read2.identifier.split()[0]))
yield (read1, read2)
|
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This will return an iterator that returns tuples of fastq records.
At each step it will confirm that the first field of the read name
(before the first whitespace character) is identical between the
two reads. The response if it is not depends on the value of
:param:`strict`. If strict is true an error is returned. If strict
is `False` the second file is advanced until a read that matches
is found.
This allows for protocols where read one contains cell barcodes, and these
reads have been filtered and corrected before processing without regard
to read2
|
[
"This",
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"until",
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"that",
"matches",
"is",
"found",
"."
] |
python
|
train
|
google/grr
|
api_client/python/grr_api_client/hunt.py
|
https://github.com/google/grr/blob/5cef4e8e2f0d5df43ea4877e9c798e0bf60bfe74/api_client/python/grr_api_client/hunt.py#L172-L193
|
def CreateApproval(self,
reason=None,
notified_users=None,
email_cc_addresses=None):
"""Create a new approval for the current user to access this hunt."""
if not reason:
raise ValueError("reason can't be empty")
if not notified_users:
raise ValueError("notified_users list can't be empty.")
approval = user_pb2.ApiHuntApproval(
reason=reason,
notified_users=notified_users,
email_cc_addresses=email_cc_addresses or [])
args = user_pb2.ApiCreateHuntApprovalArgs(
hunt_id=self.hunt_id, approval=approval)
data = self._context.SendRequest("CreateHuntApproval", args)
return HuntApproval(
data=data, username=self._context.username, context=self._context)
|
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Create a new approval for the current user to access this hunt.
|
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python
|
train
|
bwohlberg/sporco
|
sporco/admm/pdcsc.py
|
https://github.com/bwohlberg/sporco/blob/8946a04331106f4e39904fbdf2dc7351900baa04/sporco/admm/pdcsc.py#L479-L506
|
def setdict(self, D=None, B=None):
"""Set dictionary array."""
if D is not None:
self.D = np.asarray(D, dtype=self.dtype)
if B is not None:
self.B = np.asarray(B, dtype=self.dtype)
if B is not None or not hasattr(self, 'Gamma'):
self.Gamma, self.Q = np.linalg.eigh(self.B.T.dot(self.B))
self.Gamma = np.abs(self.Gamma)
if D is not None or not hasattr(self, 'Df'):
self.Df = sl.rfftn(self.D, self.cri.Nv, self.cri.axisN)
# Fold square root of Gamma into the dictionary array to enable
# use of the solvedbi_sm solver
shpg = [1] * len(self.cri.shpD)
shpg[self.cri.axisC] = self.Gamma.shape[0]
Gamma2 = np.sqrt(self.Gamma).reshape(shpg)
self.gDf = Gamma2 * self.Df
if self.opt['HighMemSolve']:
self.c = sl.solvedbd_sm_c(
self.gDf, np.conj(self.gDf),
(self.mu / self.rho) * self.GHGf + 1.0, self.cri.axisM)
else:
self.c = None
|
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] |
Set dictionary array.
|
[
"Set",
"dictionary",
"array",
"."
] |
python
|
train
|
NaPs/Kolekto
|
kolekto/commands/link.py
|
https://github.com/NaPs/Kolekto/blob/29c5469da8782780a06bf9a76c59414bb6fd8fe3/kolekto/commands/link.py#L26-L36
|
def format_all(format_string, env):
""" Format the input string using each possible combination of lists
in the provided environment. Returns a list of formated strings.
"""
prepared_env = parse_pattern(format_string, env, lambda x, y: [FormatWrapper(x, z) for z in y])
# Generate each possible combination, format the string with it and yield
# the resulting string:
for field_values in product(*prepared_env.itervalues()):
format_env = dict(izip(prepared_env.iterkeys(), field_values))
yield format_string.format(**format_env)
|
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Format the input string using each possible combination of lists
in the provided environment. Returns a list of formated strings.
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] |
python
|
train
|
BradRuderman/pyhs2
|
pyhs2/cursor.py
|
https://github.com/BradRuderman/pyhs2/blob/1094d4b3a1e9032ee17eeb41f3381bbbd95862c1/pyhs2/cursor.py#L104-L141
|
def fetchone(self):
""" fetch a single row. a lock object is used to assure that a single
record will be fetched and all housekeeping done properly in a
multithreaded environment.
as getting a block is currently synchronous, this also protects
against multiple block requests (but does not protect against
explicit calls to to _fetchBlock())
"""
self._cursorLock.acquire()
# if there are available records in current block,
# return one and advance counter
if self._currentBlock is not None and self._currentRecordNum < len(self._currentBlock):
x = self._currentRecordNum
self._currentRecordNum += 1
self._cursorLock.release()
return self._currentBlock[x]
# if no standby block is waiting, fetch a block
if self._standbyBlock is None:
# TODO - make sure exceptions due to problems in getting the block
# of records from the server are handled properly
self._fetchBlock()
# if we still do not have a standby block (or it is empty),
# return None - no more data is available
if self._standbyBlock is None or len(self._standbyBlock)==0:
self._cursorLock.release()
return None
# move the standby to current
self._currentBlock = self._standbyBlock
self._standbyBlock = None
self._currentRecordNum = 1
# return the first record
self._cursorLock.release()
return self._currentBlock[0]
|
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fetch a single row. a lock object is used to assure that a single
record will be fetched and all housekeeping done properly in a
multithreaded environment.
as getting a block is currently synchronous, this also protects
against multiple block requests (but does not protect against
explicit calls to to _fetchBlock())
|
[
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] |
python
|
train
|
limpyd/redis-limpyd-jobs
|
limpyd_jobs/workers.py
|
https://github.com/limpyd/redis-limpyd-jobs/blob/264c71029bad4377d6132bf8bb9c55c44f3b03a2/limpyd_jobs/workers.py#L888-L914
|
def prepare_worker(self):
"""
Prepare the worker, ready to be launched: prepare options, create a
log handler if none, and manage dry_run options
"""
worker_options = self.prepare_worker_options()
self.worker = self.options.worker_class(**worker_options)
if self.update_title:
self.worker._add_update_status_callback(self.update_proc_title)
self.update_proc_title()
if not self.worker.logger.handlers:
handler = logging.StreamHandler()
handler.setFormatter(logging.Formatter(
' '.join(['[%(process)d]',
# '%(asctime)s,%(msecs).03d',
'%(asctime)s',
'(%(name)s)',
'%(levelname)-8s',
'%(message)s',
])
# , '%y.%m.%d:%H.%M.%S'
))
self.worker.logger.addHandler(handler)
if self.options.dry_run:
self.worker.end_forced = True
|
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Prepare the worker, ready to be launched: prepare options, create a
log handler if none, and manage dry_run options
|
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"create",
"a",
"log",
"handler",
"if",
"none",
"and",
"manage",
"dry_run",
"options"
] |
python
|
train
|
delfick/nose-of-yeti
|
noseOfYeti/tokeniser/config.py
|
https://github.com/delfick/nose-of-yeti/blob/0b545ff350cebd59b40b601333c13033ce40d6dc/noseOfYeti/tokeniser/config.py#L82-L102
|
def find_config_file(self):
"""
Find where our config file is if there is any
If the value for the config file is a default and it doesn't exist
then it is silently ignored.
If however, the value isn't a default and it doesn't exist, an error is raised
"""
filename = self.values.get('config_file', Default('noy.json'))
ignore_missing = False
if isinstance(filename, Default):
filename = filename.val
ignore_missing = True
filename = os.path.abspath(filename)
if os.path.exists(filename):
return filename
elif not ignore_missing:
raise MissingConfigFile("Config file doesn't exist at {}".format(filename))
|
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Find where our config file is if there is any
If the value for the config file is a default and it doesn't exist
then it is silently ignored.
If however, the value isn't a default and it doesn't exist, an error is raised
|
[
"Find",
"where",
"our",
"config",
"file",
"is",
"if",
"there",
"is",
"any"
] |
python
|
train
|
inasafe/inasafe
|
safe/report/expressions/map_report.py
|
https://github.com/inasafe/inasafe/blob/831d60abba919f6d481dc94a8d988cc205130724/safe/report/expressions/map_report.py#L509-L513
|
def aggregation_not_used_text_element(feature, parent):
"""Retrieve reference title header string from definitions."""
_ = feature, parent # NOQA
header = aggregation_not_used_text['string_format']
return header.capitalize()
|
[
"def",
"aggregation_not_used_text_element",
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"feature",
",",
"parent",
")",
":",
"_",
"=",
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"# NOQA",
"header",
"=",
"aggregation_not_used_text",
"[",
"'string_format'",
"]",
"return",
"header",
".",
"capitalize",
"(",
")"
] |
Retrieve reference title header string from definitions.
|
[
"Retrieve",
"reference",
"title",
"header",
"string",
"from",
"definitions",
"."
] |
python
|
train
|
dailymuse/oz
|
oz/__init__.py
|
https://github.com/dailymuse/oz/blob/4329f6a207dc9d2a8fbeb4d16d415dbe4570b5bd/oz/__init__.py#L106-L125
|
def trigger(self, name, *args, **kwargs):
"""
Triggers an event to run through middleware. This method will execute
a chain of relevant trigger callbacks, until one of the callbacks
returns the `break_trigger`.
"""
# Relevant middleware is cached so we don't have to rediscover it
# every time. Fetch the cached value if possible.
listeners = self._triggers.get(name, [])
# Execute each piece of middleware
for listener in listeners:
result = listener(*args, **kwargs)
if result == break_trigger:
return False
return True
|
[
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Triggers an event to run through middleware. This method will execute
a chain of relevant trigger callbacks, until one of the callbacks
returns the `break_trigger`.
|
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"Triggers",
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"break_trigger",
"."
] |
python
|
train
|
dlintott/gns3-converter
|
gns3converter/converter.py
|
https://github.com/dlintott/gns3-converter/blob/acbc55da51de86388dc5b5f6da55809b3c86b7ca/gns3converter/converter.py#L163-L263
|
def generate_nodes(self, topology):
"""
Generate a list of nodes for the new topology
:param dict topology: processed topology from
:py:meth:`process_topology`
:return: a list of dicts on nodes
:rtype: list
"""
nodes = []
devices = topology['devices']
hypervisors = topology['conf']
for device in sorted(devices):
hv_id = devices[device]['hv_id']
try:
tmp_node = Node(hypervisors[hv_id], self.port_id)
except IndexError:
tmp_node = Node({}, self.port_id)
# Start building the structure
tmp_node.node['properties']['name'] = device
tmp_node.node['id'] = devices[device]['node_id']
tmp_node.node['x'] = devices[device]['x']
tmp_node.node['y'] = devices[device]['y']
tmp_node.device_info['from'] = devices[device]['from']
tmp_node.device_info['type'] = devices[device]['type']
tmp_node.device_info['desc'] = devices[device]['desc']
if 'ext_conf' in devices[device]:
tmp_node.device_info['ext_conf'] = devices[device]['ext_conf']
# Node Label
tmp_node.node['label']['text'] = device
if 'hx' in devices[device] and 'hy' in devices[device]:
tmp_node.node['label']['x'] = devices[device]['hx']
tmp_node.node['label']['y'] = devices[device]['hy']
if 'model' in devices[device]:
tmp_node.device_info['model'] = devices[device]['model']
else:
tmp_node.device_info['model'] = ''
tmp_node.set_description()
tmp_node.set_type()
# Now lets process the rest
for item in sorted(devices[device]):
tmp_node.add_device_items(item, devices[device])
if tmp_node.device_info['type'] == 'Router':
tmp_node.add_info_from_hv()
tmp_node.node['router_id'] = devices[device]['node_id']
tmp_node.calc_mb_ports()
for item in sorted(tmp_node.node['properties']):
if item.startswith('slot'):
tmp_node.add_slot_ports(item)
elif item.startswith('wic'):
tmp_node.add_wic_ports(item)
# Add default ports to 7200 and 3660
if tmp_node.device_info['model'] == 'c7200':
# tmp_node.add_slot_ports('slot0')
# C7200 doesnt have any ports by default
pass
elif tmp_node.device_info['model'] == 'c3600' \
and tmp_node.device_info['chassis'] == '3660':
tmp_node.node['properties']['slot0'] = 'Leopard-2FE'
# Calculate the router links
tmp_node.calc_device_links()
elif tmp_node.device_info['type'] == 'Cloud':
try:
tmp_node.calc_cloud_connection()
except RuntimeError as err:
print(err)
elif tmp_node.device_info['type'] == 'FrameRelaySwitch':
tmp_node.process_mappings()
elif tmp_node.device_info['type'] == 'VirtualBoxVM':
tmp_node.add_to_virtualbox()
tmp_node.add_vm_ethernet_ports()
tmp_node.calc_device_links()
elif tmp_node.device_info['type'] == 'QemuVM':
tmp_node.add_to_qemu()
tmp_node.set_qemu_symbol()
tmp_node.add_vm_ethernet_ports()
tmp_node.calc_device_links()
# Get the data we need back from the node instance
self.links.extend(tmp_node.links)
self.configs.extend(tmp_node.config)
self.port_id += tmp_node.get_nb_added_ports(self.port_id)
nodes.append(tmp_node.node)
return nodes
|
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] |
Generate a list of nodes for the new topology
:param dict topology: processed topology from
:py:meth:`process_topology`
:return: a list of dicts on nodes
:rtype: list
|
[
"Generate",
"a",
"list",
"of",
"nodes",
"for",
"the",
"new",
"topology"
] |
python
|
train
|
mosdef-hub/mbuild
|
mbuild/packing.py
|
https://github.com/mosdef-hub/mbuild/blob/dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3/mbuild/packing.py#L56-L217
|
def fill_box(compound, n_compounds=None, box=None, density=None, overlap=0.2,
seed=12345, edge=0.2, compound_ratio=None,
aspect_ratio=None, fix_orientation=False, temp_file=None):
"""Fill a box with a compound using packmol.
Two arguments of `n_compounds, box, and density` must be specified.
If `n_compounds` and `box` are not None, the specified number of
n_compounds will be inserted into a box of the specified size.
If `n_compounds` and `density` are not None, the corresponding box
size will be calculated internally. In this case, `n_compounds`
must be an int and not a list of int.
If `box` and `density` are not None, the corresponding number of
compounds will be calculated internally.
For the cases in which `box` is not specified but generated internally,
the default behavior is to calculate a cubic box. Optionally,
`aspect_ratio` can be passed to generate a non-cubic box.
Parameters
----------
compound : mb.Compound or list of mb.Compound
Compound or list of compounds to be put in box.
n_compounds : int or list of int
Number of compounds to be put in box.
box : mb.Box
Box to be filled by compounds.
density : float, units kg/m^3, default=None
Target density for the system in macroscale units. If not None, one of
`n_compounds` or `box`, but not both, must be specified.
overlap : float, units nm, default=0.2
Minimum separation between atoms of different molecules.
seed : int, default=12345
Random seed to be passed to PACKMOL.
edge : float, units nm, default=0.2
Buffer at the edge of the box to not place molecules. This is necessary
in some systems because PACKMOL does not account for periodic boundary
conditions in its optimization.
compound_ratio : list, default=None
Ratio of number of each compound to be put in box. Only used in the
case of `density` and `box` having been specified, `n_compounds` not
specified, and more than one `compound`.
aspect_ratio : list of float
If a non-cubic box is desired, the ratio of box lengths in the x, y,
and z directions.
fix_orientation : bool or list of bools
Specify that compounds should not be rotated when filling the box,
default=False.
temp_file : str, default=None
File name to write PACKMOL's raw output to.
Returns
-------
filled : mb.Compound
"""
_check_packmol(PACKMOL)
arg_count = 3 - [n_compounds, box, density].count(None)
if arg_count != 2:
msg = ("Exactly 2 of `n_compounds`, `box`, and `density` "
"must be specified. {} were given.".format(arg_count))
raise ValueError(msg)
if box is not None:
box = _validate_box(box)
if not isinstance(compound, (list, set)):
compound = [compound]
if n_compounds is not None and not isinstance(n_compounds, (list, set)):
n_compounds = [n_compounds]
if not isinstance(fix_orientation, (list, set)):
fix_orientation = [fix_orientation]*len(compound)
if compound is not None and n_compounds is not None:
if len(compound) != len(n_compounds):
msg = ("`compound` and `n_compounds` must be of equal length.")
raise ValueError(msg)
if compound is not None:
if len(compound) != len(fix_orientation):
msg = ("`compound`, `n_compounds`, and `fix_orientation` must be of equal length.")
raise ValueError(msg)
if density is not None:
if box is None and n_compounds is not None:
total_mass = np.sum([n*np.sum([a.mass for a in c.to_parmed().atoms])
for c, n in zip(compound, n_compounds)])
# Conversion from (amu/(kg/m^3))**(1/3) to nm
L = (total_mass/density)**(1/3)*1.1841763
if aspect_ratio is None:
box = _validate_box(Box(3*[L]))
else:
L *= np.prod(aspect_ratio) ** (-1/3)
box = _validate_box(Box([val*L for val in aspect_ratio]))
if n_compounds is None and box is not None:
if len(compound) == 1:
compound_mass = np.sum([a.mass for a in compound[0].to_parmed().atoms])
# Conversion from kg/m^3 / amu * nm^3 to dimensionless units
n_compounds = [int(density/compound_mass*np.prod(box.lengths)*.60224)]
else:
if compound_ratio is None:
msg = ("Determing `n_compounds` from `density` and `box` "
"for systems with more than one compound type requires"
"`compound_ratio`")
raise ValueError(msg)
if len(compound) != len(compound_ratio):
msg = ("Length of `compound_ratio` must equal length of "
"`compound`")
raise ValueError(msg)
prototype_mass = 0
for c, r in zip(compound, compound_ratio):
prototype_mass += r * np.sum([a.mass for a in c.to_parmed().atoms])
# Conversion from kg/m^3 / amu * nm^3 to dimensionless units
n_prototypes = int(density/prototype_mass*np.prod(box.lengths)*.60224)
n_compounds = list()
for c in compound_ratio:
n_compounds.append(int(n_prototypes * c))
# In angstroms for packmol.
box_mins = box.mins * 10
box_maxs = box.maxs * 10
overlap *= 10
# Apply edge buffer
box_maxs -= edge * 10
# Build the input file for each compound and call packmol.
filled_xyz = _new_xyz_file()
# create a list to contain the file handles for the compound temp files
compound_xyz_list = list()
try:
input_text = PACKMOL_HEADER.format(overlap, filled_xyz.name, seed)
for comp, m_compounds, rotate in zip(compound, n_compounds, fix_orientation):
m_compounds = int(m_compounds)
compound_xyz = _new_xyz_file()
compound_xyz_list.append(compound_xyz)
comp.save(compound_xyz.name, overwrite=True)
input_text += PACKMOL_BOX.format(compound_xyz.name, m_compounds,
box_mins[0], box_mins[1],
box_mins[2], box_maxs[0],
box_maxs[1], box_maxs[2],
PACKMOL_CONSTRAIN if rotate else "")
_run_packmol(input_text, filled_xyz, temp_file)
# Create the topology and update the coordinates.
filled = Compound()
filled = _create_topology(filled, compound, n_compounds)
filled.update_coordinates(filled_xyz.name)
filled.periodicity = np.asarray(box.lengths, dtype=np.float32)
finally:
for file_handle in compound_xyz_list:
file_handle.close()
os.unlink(file_handle.name)
filled_xyz.close()
os.unlink(filled_xyz.name)
return filled
|
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Fill a box with a compound using packmol.
Two arguments of `n_compounds, box, and density` must be specified.
If `n_compounds` and `box` are not None, the specified number of
n_compounds will be inserted into a box of the specified size.
If `n_compounds` and `density` are not None, the corresponding box
size will be calculated internally. In this case, `n_compounds`
must be an int and not a list of int.
If `box` and `density` are not None, the corresponding number of
compounds will be calculated internally.
For the cases in which `box` is not specified but generated internally,
the default behavior is to calculate a cubic box. Optionally,
`aspect_ratio` can be passed to generate a non-cubic box.
Parameters
----------
compound : mb.Compound or list of mb.Compound
Compound or list of compounds to be put in box.
n_compounds : int or list of int
Number of compounds to be put in box.
box : mb.Box
Box to be filled by compounds.
density : float, units kg/m^3, default=None
Target density for the system in macroscale units. If not None, one of
`n_compounds` or `box`, but not both, must be specified.
overlap : float, units nm, default=0.2
Minimum separation between atoms of different molecules.
seed : int, default=12345
Random seed to be passed to PACKMOL.
edge : float, units nm, default=0.2
Buffer at the edge of the box to not place molecules. This is necessary
in some systems because PACKMOL does not account for periodic boundary
conditions in its optimization.
compound_ratio : list, default=None
Ratio of number of each compound to be put in box. Only used in the
case of `density` and `box` having been specified, `n_compounds` not
specified, and more than one `compound`.
aspect_ratio : list of float
If a non-cubic box is desired, the ratio of box lengths in the x, y,
and z directions.
fix_orientation : bool or list of bools
Specify that compounds should not be rotated when filling the box,
default=False.
temp_file : str, default=None
File name to write PACKMOL's raw output to.
Returns
-------
filled : mb.Compound
|
[
"Fill",
"a",
"box",
"with",
"a",
"compound",
"using",
"packmol",
"."
] |
python
|
train
|
asphalt-framework/asphalt
|
asphalt/core/context.py
|
https://github.com/asphalt-framework/asphalt/blob/4114b3ac9743cbd9facb374a3f53e19d3afef22d/asphalt/core/context.py#L176-L184
|
def context_chain(self) -> List['Context']:
"""Return a list of contexts starting from this one, its parent and so on."""
contexts = []
ctx = self # type: Optional[Context]
while ctx is not None:
contexts.append(ctx)
ctx = ctx.parent
return contexts
|
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Return a list of contexts starting from this one, its parent and so on.
|
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] |
python
|
train
|
django-dbbackup/django-dbbackup
|
dbbackup/db/base.py
|
https://github.com/django-dbbackup/django-dbbackup/blob/77de209e2d5317e51510d0f888e085ee0c400d66/dbbackup/db/base.py#L118-L155
|
def run_command(self, command, stdin=None, env=None):
"""
Launch a shell command line.
:param command: Command line to launch
:type command: str
:param stdin: Standard input of command
:type stdin: file
:param env: Environment variable used in command
:type env: dict
:return: Standard output of command
:rtype: file
"""
cmd = shlex.split(command)
stdout = SpooledTemporaryFile(max_size=settings.TMP_FILE_MAX_SIZE,
dir=settings.TMP_DIR)
stderr = SpooledTemporaryFile(max_size=settings.TMP_FILE_MAX_SIZE,
dir=settings.TMP_DIR)
full_env = os.environ.copy() if self.use_parent_env else {}
full_env.update(self.env)
full_env.update(env or {})
try:
if isinstance(stdin, (ContentFile, SFTPStorageFile)):
process = Popen(cmd, stdin=PIPE, stdout=stdout, stderr=stderr, env=full_env)
process.communicate(input=stdin.read())
else:
process = Popen(cmd, stdin=stdin, stdout=stdout, stderr=stderr, env=full_env)
process.wait()
if process.poll():
stderr.seek(0)
raise exceptions.CommandConnectorError(
"Error running: {}\n{}".format(command, stderr.read().decode('utf-8')))
stdout.seek(0)
stderr.seek(0)
return stdout, stderr
except OSError as err:
raise exceptions.CommandConnectorError(
"Error running: {}\n{}".format(command, str(err)))
|
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".",
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"(",
"command",
",",
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"(",
"err",
")",
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")"
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Launch a shell command line.
:param command: Command line to launch
:type command: str
:param stdin: Standard input of command
:type stdin: file
:param env: Environment variable used in command
:type env: dict
:return: Standard output of command
:rtype: file
|
[
"Launch",
"a",
"shell",
"command",
"line",
"."
] |
python
|
train
|
tradenity/python-sdk
|
tradenity/resources/store_credit_transaction.py
|
https://github.com/tradenity/python-sdk/blob/d13fbe23f4d6ff22554c6d8d2deaf209371adaf1/tradenity/resources/store_credit_transaction.py#L553-L575
|
def list_all_store_credit_transactions(cls, **kwargs):
"""List StoreCreditTransactions
Return a list of StoreCreditTransactions
This method makes a synchronous HTTP request by default. To make an
asynchronous HTTP request, please pass async=True
>>> thread = api.list_all_store_credit_transactions(async=True)
>>> result = thread.get()
:param async bool
:param int page: page number
:param int size: page size
:param str sort: page order
:return: page[StoreCreditTransaction]
If the method is called asynchronously,
returns the request thread.
"""
kwargs['_return_http_data_only'] = True
if kwargs.get('async'):
return cls._list_all_store_credit_transactions_with_http_info(**kwargs)
else:
(data) = cls._list_all_store_credit_transactions_with_http_info(**kwargs)
return data
|
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List StoreCreditTransactions
Return a list of StoreCreditTransactions
This method makes a synchronous HTTP request by default. To make an
asynchronous HTTP request, please pass async=True
>>> thread = api.list_all_store_credit_transactions(async=True)
>>> result = thread.get()
:param async bool
:param int page: page number
:param int size: page size
:param str sort: page order
:return: page[StoreCreditTransaction]
If the method is called asynchronously,
returns the request thread.
|
[
"List",
"StoreCreditTransactions"
] |
python
|
train
|
jlaine/python-netfilter
|
netfilter/rule.py
|
https://github.com/jlaine/python-netfilter/blob/e4942c0f6a654a985049b629ead3dc6dcdb30145/netfilter/rule.py#L91-L95
|
def log(self, level, prefix = ''):
"""Writes the contents of the Extension to the logging system.
"""
logging.log(level, "%sname: %s", prefix, self.__name)
logging.log(level, "%soptions: %s", prefix, self.__options)
|
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Writes the contents of the Extension to the logging system.
|
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"Extension",
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"logging",
"system",
"."
] |
python
|
train
|
MisterWil/abodepy
|
abodepy/devices/cover.py
|
https://github.com/MisterWil/abodepy/blob/6f84bb428fd1da98855f55083cd427bebbcc57ae/abodepy/devices/cover.py#L19-L26
|
def switch_off(self):
"""Turn the switch off."""
success = self.set_status(CONST.STATUS_CLOSED_INT)
if success:
self._json_state['status'] = CONST.STATUS_CLOSED
return success
|
[
"def",
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"[",
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"STATUS_CLOSED",
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] |
Turn the switch off.
|
[
"Turn",
"the",
"switch",
"off",
"."
] |
python
|
train
|
gbowerman/azurerm
|
azurerm/restfns.py
|
https://github.com/gbowerman/azurerm/blob/79d40431d3b13f8a36aadbff5029888383d72674/azurerm/restfns.py#L110-L123
|
def do_put(endpoint, body, access_token):
'''Do an HTTP PUT request and return JSON.
Args:
endpoint (str): Azure Resource Manager management endpoint.
body (str): JSON body of information to put.
access_token (str): A valid Azure authentication token.
Returns:
HTTP response. JSON body.
'''
headers = {"content-type": "application/json", "Authorization": 'Bearer ' + access_token}
headers['User-Agent'] = get_user_agent()
return requests.put(endpoint, data=body, headers=headers)
|
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"(",
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"data",
"=",
"body",
",",
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"=",
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")"
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Do an HTTP PUT request and return JSON.
Args:
endpoint (str): Azure Resource Manager management endpoint.
body (str): JSON body of information to put.
access_token (str): A valid Azure authentication token.
Returns:
HTTP response. JSON body.
|
[
"Do",
"an",
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"PUT",
"request",
"and",
"return",
"JSON",
"."
] |
python
|
train
|
lsst-sqre/zenodio
|
zenodio/harvest.py
|
https://github.com/lsst-sqre/zenodio/blob/24283e84bee5714450e4f206ec024c4d32f2e761/zenodio/harvest.py#L156-L164
|
def authors(self):
"""List of :class:`~zenodio.harvest.Author`\ s
(:class:`zenodio.harvest.Author`).
Authors correspond to `creators` in the Datacite schema.
"""
creators = _pluralize(self._r['creators'], 'creator')
authors = [Author.from_xmldict(c) for c in creators]
return authors
|
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"from_xmldict",
"(",
"c",
")",
"for",
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"in",
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"]",
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"authors"
] |
List of :class:`~zenodio.harvest.Author`\ s
(:class:`zenodio.harvest.Author`).
Authors correspond to `creators` in the Datacite schema.
|
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"Author",
")",
"."
] |
python
|
train
|
dims/etcd3-gateway
|
etcd3gw/utils.py
|
https://github.com/dims/etcd3-gateway/blob/ad566c29cbde135aee20cfd32e0a4815ca3b5ee6/etcd3gw/utils.py#L33-L41
|
def _decode(data):
"""Decode the base-64 encoded string
:param data:
:return: decoded data
"""
if not isinstance(data, bytes_types):
data = six.b(str(data))
return base64.b64decode(data.decode("utf-8"))
|
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"def",
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"data",
")",
":",
"if",
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"isinstance",
"(",
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",",
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"(",
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"(",
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")",
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] |
Decode the base-64 encoded string
:param data:
:return: decoded data
|
[
"Decode",
"the",
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"64",
"encoded",
"string"
] |
python
|
train
|
dshean/demcoreg
|
demcoreg/dem_mask.py
|
https://github.com/dshean/demcoreg/blob/abd6be75d326b35f52826ee30dff01f9e86b4b52/demcoreg/dem_mask.py#L108-L141
|
def get_nlcd_mask(nlcd_ds, filter='not_forest', out_fn=None):
"""Generate raster mask for specified NLCD LULC filter
"""
print("Loading NLCD LULC")
b = nlcd_ds.GetRasterBand(1)
l = b.ReadAsArray()
print("Filtering NLCD LULC with: %s" % filter)
#Original nlcd products have nan as ndv
#12 - ice
#31 - rock
#11 - open water, includes rivers
#52 - shrub, <5 m tall, >20%
#42 - evergreeen forest
#Should use data dictionary here for general masking
#Using 'rock+ice+water' preserves the most pixels, although could be problematic over areas with lakes
if filter == 'rock':
mask = (l==31)
elif filter == 'rock+ice':
mask = np.logical_or((l==31),(l==12))
elif filter == 'rock+ice+water':
mask = np.logical_or(np.logical_or((l==31),(l==12)),(l==11))
elif filter == 'not_forest':
mask = ~(np.logical_or(np.logical_or((l==41),(l==42)),(l==43)))
elif filter == 'not_forest+not_water':
mask = ~(np.logical_or(np.logical_or(np.logical_or((l==41),(l==42)),(l==43)),(l==11)))
else:
print("Invalid mask type")
mask = None
#Write out original data
if out_fn is not None:
print("Writing out %s" % out_fn)
iolib.writeGTiff(l, out_fn, nlcd_ds)
l = None
return mask
|
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Generate raster mask for specified NLCD LULC filter
|
[
"Generate",
"raster",
"mask",
"for",
"specified",
"NLCD",
"LULC",
"filter"
] |
python
|
train
|
Tinche/cattrs
|
src/cattr/converters.py
|
https://github.com/Tinche/cattrs/blob/481bc9bdb69b2190d699b54f331c8c5c075506d5/src/cattr/converters.py#L227-L236
|
def _unstructure_mapping(self, mapping):
"""Convert a mapping of attr classes to primitive equivalents."""
# We can reuse the mapping class, so dicts stay dicts and OrderedDicts
# stay OrderedDicts.
dispatch = self._unstructure_func.dispatch
return mapping.__class__(
(dispatch(k.__class__)(k), dispatch(v.__class__)(v))
for k, v in mapping.items()
)
|
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Convert a mapping of attr classes to primitive equivalents.
|
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"equivalents",
"."
] |
python
|
train
|
openstack/networking-cisco
|
networking_cisco/ml2_drivers/nexus/nexus_db_v2.py
|
https://github.com/openstack/networking-cisco/blob/aa58a30aec25b86f9aa5952b0863045975debfa9/networking_cisco/ml2_drivers/nexus/nexus_db_v2.py#L399-L407
|
def get_nve_vni_switch_bindings(vni, switch_ip):
"""Return the nexus nve binding(s) per switch."""
LOG.debug("get_nve_vni_switch_bindings() called")
session = bc.get_reader_session()
try:
return (session.query(nexus_models_v2.NexusNVEBinding).
filter_by(vni=vni, switch_ip=switch_ip).all())
except sa_exc.NoResultFound:
return None
|
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Return the nexus nve binding(s) per switch.
|
[
"Return",
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"nve",
"binding",
"(",
"s",
")",
"per",
"switch",
"."
] |
python
|
train
|
Azure/azure-sdk-for-python
|
azure-servicebus/azure/servicebus/control_client/servicebusservice.py
|
https://github.com/Azure/azure-sdk-for-python/blob/d7306fde32f60a293a7567678692bdad31e4b667/azure-servicebus/azure/servicebus/control_client/servicebusservice.py#L1129-L1151
|
def update_event_hub(self, hub_name, hub=None):
'''
Updates an Event Hub.
hub_name:
Name of event hub.
hub:
Optional. Event hub properties. Instance of EventHub class.
hub.message_retention_in_days:
Number of days to retain the events for this Event Hub.
'''
_validate_not_none('hub_name', hub_name)
request = HTTPRequest()
request.method = 'PUT'
request.host = self._get_host()
request.path = '/' + _str(hub_name) + '?api-version=2014-01'
request.body = _get_request_body(_convert_event_hub_to_xml(hub))
request.path, request.query = self._httpclient._update_request_uri_query(request) # pylint: disable=protected-access
request.headers.append(('If-Match', '*'))
request.headers = self._update_service_bus_header(request)
response = self._perform_request(request)
return _convert_response_to_event_hub(response)
|
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")",
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"_convert_response_to_event_hub",
"(",
"response",
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Updates an Event Hub.
hub_name:
Name of event hub.
hub:
Optional. Event hub properties. Instance of EventHub class.
hub.message_retention_in_days:
Number of days to retain the events for this Event Hub.
|
[
"Updates",
"an",
"Event",
"Hub",
"."
] |
python
|
test
|
mobinrg/rpi_spark_drives
|
JMRPiSpark/Drives/Attitude/MPU6050.py
|
https://github.com/mobinrg/rpi_spark_drives/blob/e1602d8268a5ef48e9e0a8b37de89e0233f946ea/JMRPiSpark/Drives/Attitude/MPU6050.py#L533-L555
|
def getAllData(self, temp = True, accel = True, gyro = True):
"""!
Get all the available data.
@param temp: True - Allow to return Temperature data
@param accel: True - Allow to return Accelerometer data
@param gyro: True - Allow to return Gyroscope data
@return a dictionary data
@retval {} Did not read any data
@retval {"temp":32.3,"accel":{"x":0.45634,"y":0.2124,"z":1.334},"gyro":{"x":0.45634,"y":0.2124,"z":1.334}} Returned all data
"""
allData = {}
if temp:
allData["temp"] = self.getTemp()
if accel:
allData["accel"] = self.getAccelData( raw = False )
if gyro:
allData["gyro"] = self.getGyroData()
return allData
|
[
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"[",
"\"gyro\"",
"]",
"=",
"self",
".",
"getGyroData",
"(",
")",
"return",
"allData"
] |
!
Get all the available data.
@param temp: True - Allow to return Temperature data
@param accel: True - Allow to return Accelerometer data
@param gyro: True - Allow to return Gyroscope data
@return a dictionary data
@retval {} Did not read any data
@retval {"temp":32.3,"accel":{"x":0.45634,"y":0.2124,"z":1.334},"gyro":{"x":0.45634,"y":0.2124,"z":1.334}} Returned all data
|
[
"!",
"Get",
"all",
"the",
"available",
"data",
"."
] |
python
|
train
|
peterldowns/lggr
|
lggr/__init__.py
|
https://github.com/peterldowns/lggr/blob/622968f17133e02d9a46a4900dd20fb3b19fe961/lggr/__init__.py#L345-L360
|
def SocketWriter(host, port, af=None, st=None):
""" Writes messages to a socket/host. """
import socket
if af is None:
af = socket.AF_INET
if st is None:
st = socket.SOCK_STREAM
message = '({0}): {1}'
s = socket.socket(af, st)
s.connect(host, port)
try:
while True:
logstr = (yield)
s.send(logstr)
except GeneratorExit:
s.close()
|
[
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",",
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"(",
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"GeneratorExit",
":",
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"close",
"(",
")"
] |
Writes messages to a socket/host.
|
[
"Writes",
"messages",
"to",
"a",
"socket",
"/",
"host",
"."
] |
python
|
train
|
ansible/ansible-container
|
container/docker/engine.py
|
https://github.com/ansible/ansible-container/blob/d031c1a6133d5482a5d054fcbdbecafb923f8b4b/container/docker/engine.py#L766-L892
|
def generate_orchestration_playbook(self, url=None, namespace=None, vault_files=None, **kwargs):
"""
Generate an Ansible playbook to orchestrate services.
:param url: registry URL where images will be pulled from
:param namespace: registry namespace
:return: playbook dict
"""
states = ['start', 'restart', 'stop', 'destroy']
service_def = {}
for service_name, service in iteritems(self.services):
service_definition = {}
if service.get('roles'):
if url and namespace:
# Reference previously pushed image
service_definition[u'image'] = '{}/{}/{}'.format(re.sub(r'/$', '', url), namespace,
self.image_name_for_service(service_name))
else:
# Check that the image was built
image = self.get_latest_image_for_service(service_name)
if image is None:
raise exceptions.AnsibleContainerConductorException(
u"No image found for service {}, make sure you've run `ansible-container "
u"build`".format(service_name)
)
service_definition[u'image'] = image.tags[0]
else:
try:
# Check if the image is already local
image = self.client.images.get(service['from'])
image_from = image.tags[0]
except docker.errors.ImageNotFound:
image_from = service['from']
logger.warning(u"Image {} for service {} not found. "
u"An attempt will be made to pull it.".format(service['from'], service_name))
service_definition[u'image'] = image_from
for extra in self.COMPOSE_WHITELIST:
if extra in service:
service_definition[extra] = service[extra]
if 'secrets' in service:
service_secrets = []
for secret, secret_engines in iteritems(service[u'secrets']):
if 'docker' in secret_engines:
service_secrets += secret_engines[u'docker']
if service_secrets:
service_definition[u'secrets'] = service_secrets
if self.CAP_SIM_SECRETS:
# Simulate external secrets using a Docker volume
if not 'volumes' in service_definition:
service_definition['volumes'] = []
service_definition['volumes'].append("{}:/run/secrets:ro".format(self.secrets_volume_name))
logger.debug(u'Adding new service to definition',
service=service_name, definition=service_definition)
service_def[service_name] = service_definition
tasks = []
top_level_secrets = self._get_top_level_secrets()
if self.CAP_SIM_SECRETS and top_level_secrets:
# Let compose know that we're using a named volume to simulate external secrets
if not isinstance(self.volumes, dict):
self.volumes = dict()
self.volumes[self.secrets_volume_name] = dict(external=True)
for desired_state in states:
task_params = {
u'project_name': self.project_name,
u'definition': {
u'version': u'3.1' if top_level_secrets else u'2',
u'services': service_def,
}
}
if self.secrets:
task_params[u'definition'][u'secrets'] = top_level_secrets
if self.volumes:
task_params[u'definition'][u'volumes'] = dict(self.volumes)
if desired_state in {'restart', 'start', 'stop'}:
task_params[u'state'] = u'present'
if desired_state == 'restart':
task_params[u'restarted'] = True
if desired_state == 'stop':
task_params[u'stopped'] = True
elif desired_state == 'destroy':
task_params[u'state'] = u'absent'
task_params[u'remove_volumes'] = u'yes'
tasks.append({u'docker_service': task_params, u'tags': [desired_state]})
playbook = []
if self.secrets and self.CAP_SIM_SECRETS:
playbook.append(self.generate_secrets_play(vault_files=vault_files))
playbook.append(CommentedMap([
(u'name', 'Deploy {}'.format(self.project_name)),
(u'hosts', u'localhost'),
(u'gather_facts', False)
]))
if vault_files:
playbook[len(playbook) - 1][u'vars_files'] = [os.path.normpath(os.path.abspath(v)) for v in vault_files]
playbook[len(playbook) - 1][u'tasks'] = tasks
for service in list(self.services.keys()) + ['conductor']:
image_name = self.image_name_for_service(service)
for image in self.client.images.list(name=image_name):
logger.debug('Found image for service', tags=image.tags, id=image.short_id)
for tag in image.tags:
if tag.startswith(self.project_name):
logger.debug('Adding task to destroy image', tag=tag)
playbook[len(playbook) - 1][u'tasks'].append({
u'docker_image': {
u'name': tag,
u'state': u'absent',
u'force': u'yes'
},
u'tags': u'destroy'
})
if self.secrets and self.CAP_SIM_SECRETS:
playbook.append(self.generate_remove_volume_play())
logger.debug(u'Created playbook to run project', playbook=playbook)
return playbook
|
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")",
")",
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"in",
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"]",
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"[",
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")",
"-",
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"]",
"[",
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"]",
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"tasks",
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"(",
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"(",
")",
")",
"+",
"[",
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"]",
":",
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"(",
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",",
"tag",
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"tag",
")",
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"[",
"len",
"(",
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"-",
"1",
"]",
"[",
"u'tasks'",
"]",
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"(",
"{",
"u'docker_image'",
":",
"{",
"u'name'",
":",
"tag",
",",
"u'state'",
":",
"u'absent'",
",",
"u'force'",
":",
"u'yes'",
"}",
",",
"u'tags'",
":",
"u'destroy'",
"}",
")",
"if",
"self",
".",
"secrets",
"and",
"self",
".",
"CAP_SIM_SECRETS",
":",
"playbook",
".",
"append",
"(",
"self",
".",
"generate_remove_volume_play",
"(",
")",
")",
"logger",
".",
"debug",
"(",
"u'Created playbook to run project'",
",",
"playbook",
"=",
"playbook",
")",
"return",
"playbook"
] |
Generate an Ansible playbook to orchestrate services.
:param url: registry URL where images will be pulled from
:param namespace: registry namespace
:return: playbook dict
|
[
"Generate",
"an",
"Ansible",
"playbook",
"to",
"orchestrate",
"services",
".",
":",
"param",
"url",
":",
"registry",
"URL",
"where",
"images",
"will",
"be",
"pulled",
"from",
":",
"param",
"namespace",
":",
"registry",
"namespace",
":",
"return",
":",
"playbook",
"dict"
] |
python
|
train
|
python-rope/rope
|
rope/base/project.py
|
https://github.com/python-rope/rope/blob/1c9f9cd5964b099a99a9111e998f0dc728860688/rope/base/project.py#L85-L93
|
def validate(self, folder):
"""Validate files and folders contained in this folder
It validates all of the files and folders contained in this
folder if some observers are interested in them.
"""
for observer in list(self.observers):
observer.validate(folder)
|
[
"def",
"validate",
"(",
"self",
",",
"folder",
")",
":",
"for",
"observer",
"in",
"list",
"(",
"self",
".",
"observers",
")",
":",
"observer",
".",
"validate",
"(",
"folder",
")"
] |
Validate files and folders contained in this folder
It validates all of the files and folders contained in this
folder if some observers are interested in them.
|
[
"Validate",
"files",
"and",
"folders",
"contained",
"in",
"this",
"folder"
] |
python
|
train
|
PyThaiNLP/pythainlp
|
pythainlp/util/keyboard.py
|
https://github.com/PyThaiNLP/pythainlp/blob/e9a300b8a99dfd1a67a955e7c06f62e4afe0fbca/pythainlp/util/keyboard.py#L116-L125
|
def thai_to_eng(text: str) -> str:
"""
Correct text in one language that is incorrectly-typed with a keyboard layout in another language. (type Thai with English keyboard)
:param str text: Incorrect input (type English with Thai keyboard)
:return: English text
"""
return "".join(
[TH_EN_KEYB_PAIRS[ch] if (ch in TH_EN_KEYB_PAIRS) else ch for ch in text]
)
|
[
"def",
"thai_to_eng",
"(",
"text",
":",
"str",
")",
"->",
"str",
":",
"return",
"\"\"",
".",
"join",
"(",
"[",
"TH_EN_KEYB_PAIRS",
"[",
"ch",
"]",
"if",
"(",
"ch",
"in",
"TH_EN_KEYB_PAIRS",
")",
"else",
"ch",
"for",
"ch",
"in",
"text",
"]",
")"
] |
Correct text in one language that is incorrectly-typed with a keyboard layout in another language. (type Thai with English keyboard)
:param str text: Incorrect input (type English with Thai keyboard)
:return: English text
|
[
"Correct",
"text",
"in",
"one",
"language",
"that",
"is",
"incorrectly",
"-",
"typed",
"with",
"a",
"keyboard",
"layout",
"in",
"another",
"language",
".",
"(",
"type",
"Thai",
"with",
"English",
"keyboard",
")"
] |
python
|
train
|
saltstack/salt
|
salt/states/pcs.py
|
https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/states/pcs.py#L939-L981
|
def stonith_present(name, stonith_id, stonith_device_type, stonith_device_options=None, cibname=None):
'''
Ensure that a fencing resource is created
Should be run on one cluster node only
(there may be races)
Can only be run on a node with a functional pacemaker/corosync
name
Irrelevant, not used (recommended: pcs_stonith__created_{{stonith_id}})
stonith_id
name for the stonith resource
stonith_device_type
name of the stonith agent fence_eps, fence_xvm f.e.
stonith_device_options
additional options for creating the stonith resource
cibname
use a cached CIB-file named like cibname instead of the live CIB
Example:
.. code-block:: yaml
pcs_stonith__created_eps_fence:
pcs.stonith_present:
- stonith_id: eps_fence
- stonith_device_type: fence_eps
- stonith_device_options:
- 'pcmk_host_map=node1.example.org:01;node2.example.org:02'
- 'ipaddr=myepsdevice.example.org'
- 'power_wait=5'
- 'verbose=1'
- 'debug=/var/log/pcsd/eps_fence.log'
- 'login=hidden'
- 'passwd=hoonetorg'
- cibname: cib_for_stonith
'''
return _item_present(name=name,
item='stonith',
item_id=stonith_id,
item_type=stonith_device_type,
extra_args=stonith_device_options,
cibname=cibname)
|
[
"def",
"stonith_present",
"(",
"name",
",",
"stonith_id",
",",
"stonith_device_type",
",",
"stonith_device_options",
"=",
"None",
",",
"cibname",
"=",
"None",
")",
":",
"return",
"_item_present",
"(",
"name",
"=",
"name",
",",
"item",
"=",
"'stonith'",
",",
"item_id",
"=",
"stonith_id",
",",
"item_type",
"=",
"stonith_device_type",
",",
"extra_args",
"=",
"stonith_device_options",
",",
"cibname",
"=",
"cibname",
")"
] |
Ensure that a fencing resource is created
Should be run on one cluster node only
(there may be races)
Can only be run on a node with a functional pacemaker/corosync
name
Irrelevant, not used (recommended: pcs_stonith__created_{{stonith_id}})
stonith_id
name for the stonith resource
stonith_device_type
name of the stonith agent fence_eps, fence_xvm f.e.
stonith_device_options
additional options for creating the stonith resource
cibname
use a cached CIB-file named like cibname instead of the live CIB
Example:
.. code-block:: yaml
pcs_stonith__created_eps_fence:
pcs.stonith_present:
- stonith_id: eps_fence
- stonith_device_type: fence_eps
- stonith_device_options:
- 'pcmk_host_map=node1.example.org:01;node2.example.org:02'
- 'ipaddr=myepsdevice.example.org'
- 'power_wait=5'
- 'verbose=1'
- 'debug=/var/log/pcsd/eps_fence.log'
- 'login=hidden'
- 'passwd=hoonetorg'
- cibname: cib_for_stonith
|
[
"Ensure",
"that",
"a",
"fencing",
"resource",
"is",
"created"
] |
python
|
train
|
line/line-bot-sdk-python
|
linebot/api.py
|
https://github.com/line/line-bot-sdk-python/blob/1b38bfc2497ff3e3c75be4b50e0f1b7425a07ce0/linebot/api.py#L468-L487
|
def get_rich_menu_image(self, rich_menu_id, timeout=None):
"""Call download rich menu image API.
https://developers.line.me/en/docs/messaging-api/reference/#download-rich-menu-image
:param str rich_menu_id: ID of the rich menu with the image to be downloaded
:param timeout: (optional) How long to wait for the server
to send data before giving up, as a float,
or a (connect timeout, read timeout) float tuple.
Default is self.http_client.timeout
:type timeout: float | tuple(float, float)
:rtype: :py:class:`linebot.models.responses.Content`
:return: Content instance
"""
response = self._get(
'/v2/bot/richmenu/{rich_menu_id}/content'.format(rich_menu_id=rich_menu_id),
timeout=timeout
)
return Content(response)
|
[
"def",
"get_rich_menu_image",
"(",
"self",
",",
"rich_menu_id",
",",
"timeout",
"=",
"None",
")",
":",
"response",
"=",
"self",
".",
"_get",
"(",
"'/v2/bot/richmenu/{rich_menu_id}/content'",
".",
"format",
"(",
"rich_menu_id",
"=",
"rich_menu_id",
")",
",",
"timeout",
"=",
"timeout",
")",
"return",
"Content",
"(",
"response",
")"
] |
Call download rich menu image API.
https://developers.line.me/en/docs/messaging-api/reference/#download-rich-menu-image
:param str rich_menu_id: ID of the rich menu with the image to be downloaded
:param timeout: (optional) How long to wait for the server
to send data before giving up, as a float,
or a (connect timeout, read timeout) float tuple.
Default is self.http_client.timeout
:type timeout: float | tuple(float, float)
:rtype: :py:class:`linebot.models.responses.Content`
:return: Content instance
|
[
"Call",
"download",
"rich",
"menu",
"image",
"API",
"."
] |
python
|
train
|
richardkiss/pycoin
|
pycoin/satoshi/intops.py
|
https://github.com/richardkiss/pycoin/blob/1e8d0d9fe20ce0347b97847bb529cd1bd84c7442/pycoin/satoshi/intops.py#L72-L88
|
def do_OP_RIGHT(vm):
"""
>>> s = [b'abcdef', b'\\3']
>>> do_OP_RIGHT(s, require_minimal=True)
>>> print(s==[b'def'])
True
>>> s = [b'abcdef', b'\\0']
>>> do_OP_RIGHT(s, require_minimal=False)
>>> print(s==[b''])
True
"""
pos = vm.pop_nonnegative()
if pos > 0:
vm.append(vm.pop()[-pos:])
else:
vm.pop()
vm.append(b'')
|
[
"def",
"do_OP_RIGHT",
"(",
"vm",
")",
":",
"pos",
"=",
"vm",
".",
"pop_nonnegative",
"(",
")",
"if",
"pos",
">",
"0",
":",
"vm",
".",
"append",
"(",
"vm",
".",
"pop",
"(",
")",
"[",
"-",
"pos",
":",
"]",
")",
"else",
":",
"vm",
".",
"pop",
"(",
")",
"vm",
".",
"append",
"(",
"b''",
")"
] |
>>> s = [b'abcdef', b'\\3']
>>> do_OP_RIGHT(s, require_minimal=True)
>>> print(s==[b'def'])
True
>>> s = [b'abcdef', b'\\0']
>>> do_OP_RIGHT(s, require_minimal=False)
>>> print(s==[b''])
True
|
[
">>>",
"s",
"=",
"[",
"b",
"abcdef",
"b",
"\\\\",
"3",
"]",
">>>",
"do_OP_RIGHT",
"(",
"s",
"require_minimal",
"=",
"True",
")",
">>>",
"print",
"(",
"s",
"==",
"[",
"b",
"def",
"]",
")",
"True",
">>>",
"s",
"=",
"[",
"b",
"abcdef",
"b",
"\\\\",
"0",
"]",
">>>",
"do_OP_RIGHT",
"(",
"s",
"require_minimal",
"=",
"False",
")",
">>>",
"print",
"(",
"s",
"==",
"[",
"b",
"]",
")",
"True"
] |
python
|
train
|
openthread/openthread
|
tools/harness-thci/OpenThread.py
|
https://github.com/openthread/openthread/blob/0208d10563aa21c518092985c78ecf9cd223ab74/tools/harness-thci/OpenThread.py#L2409-L2474
|
def MGMT_PENDING_SET(self, sAddr='', xCommissionerSessionId=None, listPendingTimestamp=None, listActiveTimestamp=None, xDelayTimer=None,
xChannel=None, xPanId=None, xMasterKey=None, sMeshLocalPrefix=None, sNetworkName=None):
"""send MGMT_PENDING_SET command
Returns:
True: successful to send MGMT_PENDING_SET
False: fail to send MGMT_PENDING_SET
"""
print '%s call MGMT_PENDING_SET' % self.port
try:
cmd = 'dataset mgmtsetcommand pending'
if listPendingTimestamp != None:
cmd += ' pendingtimestamp '
cmd += str(listPendingTimestamp[0])
if listActiveTimestamp != None:
cmd += ' activetimestamp '
cmd += str(listActiveTimestamp[0])
if xDelayTimer != None:
cmd += ' delaytimer '
cmd += str(xDelayTimer)
#cmd += ' delaytimer 3000000'
if xChannel != None:
cmd += ' channel '
cmd += str(xChannel)
if xPanId != None:
cmd += ' panid '
cmd += str(xPanId)
if xMasterKey != None:
cmd += ' masterkey '
key = self.__convertLongToString(xMasterKey)
if len(key) < 32:
key = key.zfill(32)
cmd += key
if sMeshLocalPrefix != None:
cmd += ' localprefix '
cmd += str(sMeshLocalPrefix)
if sNetworkName != None:
cmd += ' networkname '
cmd += str(sNetworkName)
if xCommissionerSessionId != None:
cmd += ' binary '
cmd += '0b02'
sessionid = str(hex(xCommissionerSessionId))[2:]
if len(sessionid) < 4:
sessionid = sessionid.zfill(4)
cmd += sessionid
print cmd
return self.__sendCommand(cmd)[0] == 'Done'
except Exception, e:
ModuleHelper.WriteIntoDebugLogger("MGMT_PENDING_SET() Error: " + str(e))
|
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",",
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"=",
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"' delaytimer '",
"cmd",
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"str",
"(",
"xDelayTimer",
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"' channel '",
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"' panid '",
"cmd",
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"(",
"xPanId",
")",
"if",
"xMasterKey",
"!=",
"None",
":",
"cmd",
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"' masterkey '",
"key",
"=",
"self",
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"__convertLongToString",
"(",
"xMasterKey",
")",
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"(",
"sMeshLocalPrefix",
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"sNetworkName",
"!=",
"None",
":",
"cmd",
"+=",
"' networkname '",
"cmd",
"+=",
"str",
"(",
"sNetworkName",
")",
"if",
"xCommissionerSessionId",
"!=",
"None",
":",
"cmd",
"+=",
"' binary '",
"cmd",
"+=",
"'0b02'",
"sessionid",
"=",
"str",
"(",
"hex",
"(",
"xCommissionerSessionId",
")",
")",
"[",
"2",
":",
"]",
"if",
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"(",
"sessionid",
")",
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"4",
":",
"sessionid",
"=",
"sessionid",
".",
"zfill",
"(",
"4",
")",
"cmd",
"+=",
"sessionid",
"print",
"cmd",
"return",
"self",
".",
"__sendCommand",
"(",
"cmd",
")",
"[",
"0",
"]",
"==",
"'Done'",
"except",
"Exception",
",",
"e",
":",
"ModuleHelper",
".",
"WriteIntoDebugLogger",
"(",
"\"MGMT_PENDING_SET() Error: \"",
"+",
"str",
"(",
"e",
")",
")"
] |
send MGMT_PENDING_SET command
Returns:
True: successful to send MGMT_PENDING_SET
False: fail to send MGMT_PENDING_SET
|
[
"send",
"MGMT_PENDING_SET",
"command"
] |
python
|
train
|
ianepperson/telnetsrvlib
|
telnetsrv/telnetsrvlib.py
|
https://github.com/ianepperson/telnetsrvlib/blob/fac52a4a333c2d373d53d295a76a0bbd71e5d682/telnetsrv/telnetsrvlib.py#L992-L995
|
def handleException(self, exc_type, exc_param, exc_tb):
"Exception handler (False to abort)"
self.writeline(''.join( traceback.format_exception(exc_type, exc_param, exc_tb) ))
return True
|
[
"def",
"handleException",
"(",
"self",
",",
"exc_type",
",",
"exc_param",
",",
"exc_tb",
")",
":",
"self",
".",
"writeline",
"(",
"''",
".",
"join",
"(",
"traceback",
".",
"format_exception",
"(",
"exc_type",
",",
"exc_param",
",",
"exc_tb",
")",
")",
")",
"return",
"True"
] |
Exception handler (False to abort)
|
[
"Exception",
"handler",
"(",
"False",
"to",
"abort",
")"
] |
python
|
train
|
openstax/cnx-publishing
|
cnxpublishing/views/moderation.py
|
https://github.com/openstax/cnx-publishing/blob/f55b4a2c45d8618737288f1b74b4139d5ac74154/cnxpublishing/views/moderation.py#L17-L31
|
def get_moderation(request):
"""Return the list of publications that need moderation."""
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
cursor.execute("""\
SELECT row_to_json(combined_rows) FROM (
SELECT id, created, publisher, publication_message,
(select array_agg(row_to_json(pd))
from pending_documents as pd
where pd.publication_id = p.id) AS models
FROM publications AS p
WHERE state = 'Waiting for moderation') AS combined_rows""")
moderations = [x[0] for x in cursor.fetchall()]
return moderations
|
[
"def",
"get_moderation",
"(",
"request",
")",
":",
"with",
"db_connect",
"(",
")",
"as",
"db_conn",
":",
"with",
"db_conn",
".",
"cursor",
"(",
")",
"as",
"cursor",
":",
"cursor",
".",
"execute",
"(",
"\"\"\"\\\nSELECT row_to_json(combined_rows) FROM (\n SELECT id, created, publisher, publication_message,\n (select array_agg(row_to_json(pd))\n from pending_documents as pd\n where pd.publication_id = p.id) AS models\n FROM publications AS p\n WHERE state = 'Waiting for moderation') AS combined_rows\"\"\"",
")",
"moderations",
"=",
"[",
"x",
"[",
"0",
"]",
"for",
"x",
"in",
"cursor",
".",
"fetchall",
"(",
")",
"]",
"return",
"moderations"
] |
Return the list of publications that need moderation.
|
[
"Return",
"the",
"list",
"of",
"publications",
"that",
"need",
"moderation",
"."
] |
python
|
valid
|
gopalkoduri/intonation
|
intonation/pitch.py
|
https://github.com/gopalkoduri/intonation/blob/7f50d2b572755840be960ea990416a7b27f20312/intonation/pitch.py#L16-L54
|
def discretize(self, intervals, slope_thresh=1500, cents_thresh=50):
"""
This function takes the pitch data and returns it quantized to given
set of intervals. All transactions must happen in cent scale.
slope_thresh is the bound beyond which the pitch contour is said to transit
from one svara to another. It is specified in cents/sec.
cents_thresh is a limit within which two pitch values are considered the same.
This is what pushes the quantization limit.
The function returns quantized pitch data.
"""
#eps = np.finfo(float).eps
#pitch = median_filter(pitch, 7)+eps
self.pitch = median_filter(self.pitch, 7)
pitch_quantized = np.zeros(len(self.pitch))
pitch_quantized[0] = utils.find_nearest_index(intervals, self.pitch[0])
pitch_quantized[-1] = utils.find_nearest_index(intervals, self.pitch[-1])
for i in xrange(1, len(self.pitch)-1):
if self.pitch[i] == -10000:
pitch_quantized[i] = -10000
continue
slope_back = abs((self.pitch[i] - self.pitch[i-1])/(self.timestamps[i] - self.timestamps[i-1]))
slope_front = abs((self.pitch[i+1] - self.pitch[i])/(self.timestamps[i+1] - self.timestamps[i]))
if slope_front < slope_thresh or slope_back < slope_thresh:
ind = utils.find_nearest_index(intervals, self.pitch[i])
cents_diff = abs(self.pitch[i] - intervals[ind])
if cents_diff <= cents_thresh:
pitch_quantized[i] = intervals[ind]
else:
pitch_quantized[i] = -10000
else:
pitch_quantized[i] = -10000
self.pitch = pitch_quantized
|
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This function takes the pitch data and returns it quantized to given
set of intervals. All transactions must happen in cent scale.
slope_thresh is the bound beyond which the pitch contour is said to transit
from one svara to another. It is specified in cents/sec.
cents_thresh is a limit within which two pitch values are considered the same.
This is what pushes the quantization limit.
The function returns quantized pitch data.
|
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"All",
"transactions",
"must",
"happen",
"in",
"cent",
"scale",
"."
] |
python
|
train
|
apache/incubator-superset
|
superset/views/core.py
|
https://github.com/apache/incubator-superset/blob/ca2996c78f679260eb79c6008e276733df5fb653/superset/views/core.py#L2171-L2246
|
def dashboard(self, dashboard_id):
"""Server side rendering for a dashboard"""
session = db.session()
qry = session.query(models.Dashboard)
if dashboard_id.isdigit():
qry = qry.filter_by(id=int(dashboard_id))
else:
qry = qry.filter_by(slug=dashboard_id)
dash = qry.one_or_none()
if not dash:
abort(404)
datasources = set()
for slc in dash.slices:
datasource = slc.datasource
if datasource:
datasources.add(datasource)
if config.get('ENABLE_ACCESS_REQUEST'):
for datasource in datasources:
if datasource and not security_manager.datasource_access(datasource):
flash(
__(security_manager.get_datasource_access_error_msg(datasource)),
'danger')
return redirect(
'superset/request_access/?'
f'dashboard_id={dash.id}&')
dash_edit_perm = check_ownership(dash, raise_if_false=False) and \
security_manager.can_access('can_save_dash', 'Superset')
dash_save_perm = security_manager.can_access('can_save_dash', 'Superset')
superset_can_explore = security_manager.can_access('can_explore', 'Superset')
superset_can_csv = security_manager.can_access('can_csv', 'Superset')
slice_can_edit = security_manager.can_access('can_edit', 'SliceModelView')
standalone_mode = request.args.get('standalone') == 'true'
edit_mode = request.args.get('edit') == 'true'
# Hack to log the dashboard_id properly, even when getting a slug
@log_this
def dashboard(**kwargs): # noqa
pass
dashboard(
dashboard_id=dash.id,
dashboard_version='v2',
dash_edit_perm=dash_edit_perm,
edit_mode=edit_mode)
dashboard_data = dash.data
dashboard_data.update({
'standalone_mode': standalone_mode,
'dash_save_perm': dash_save_perm,
'dash_edit_perm': dash_edit_perm,
'superset_can_explore': superset_can_explore,
'superset_can_csv': superset_can_csv,
'slice_can_edit': slice_can_edit,
})
bootstrap_data = {
'user_id': g.user.get_id(),
'dashboard_data': dashboard_data,
'datasources': {ds.uid: ds.data for ds in datasources},
'common': self.common_bootsrap_payload(),
'editMode': edit_mode,
}
if request.args.get('json') == 'true':
return json_success(json.dumps(bootstrap_data))
return self.render_template(
'superset/dashboard.html',
entry='dashboard',
standalone_mode=standalone_mode,
title=dash.dashboard_title,
bootstrap_data=json.dumps(bootstrap_data),
)
|
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Server side rendering for a dashboard
|
[
"Server",
"side",
"rendering",
"for",
"a",
"dashboard"
] |
python
|
train
|
openearth/mmi-python
|
mmi/mmi_client.py
|
https://github.com/openearth/mmi-python/blob/a2f4ac96b1e7f2fa903f668b3e05c4e86ad42e8d/mmi/mmi_client.py#L56-L69
|
def initialize(self, configfile=None):
"""
Initialize the module
"""
method = "initialize"
A = None
metadata = {method: configfile}
send_array(self.socket, A, metadata)
A, metadata = recv_array(
self.socket, poll=self.poll, poll_timeout=self.poll_timeout,
flags=self.zmq_flags)
|
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"def",
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] |
Initialize the module
|
[
"Initialize",
"the",
"module"
] |
python
|
train
|
Workiva/furious
|
example/callback.py
|
https://github.com/Workiva/furious/blob/c29823ec8b98549e7439d7273aa064d1e5830632/example/callback.py#L125-L140
|
def handle_an_error():
"""Will be run if the async task raises an unhandled exception."""
import os
from furious.context import get_current_async
async = get_current_async()
async_exception = async.result.payload
exc_info = async_exception.traceback
logging.info('async job blew up, exception info: %r', exc_info)
retries = int(os.environ['HTTP_X_APPENGINE_TASKRETRYCOUNT'])
if retries < 2:
raise Exception(async_exception.error)
else:
logging.info('Caught too many errors, giving up now.')
|
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"info",
"(",
"'Caught too many errors, giving up now.'",
")"
] |
Will be run if the async task raises an unhandled exception.
|
[
"Will",
"be",
"run",
"if",
"the",
"async",
"task",
"raises",
"an",
"unhandled",
"exception",
"."
] |
python
|
train
|
spoqa/dodotable
|
dodotable/schema.py
|
https://github.com/spoqa/dodotable/blob/083ebdeb8ceb109a8f67264b44a652af49b64250/dodotable/schema.py#L244-L247
|
def append(self, cell):
"""행에 cell을 붙입니다. """
assert isinstance(cell, Cell)
super(Row, self).append(cell)
|
[
"def",
"append",
"(",
"self",
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")",
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"(",
"Row",
",",
"self",
")",
".",
"append",
"(",
"cell",
")"
] |
행에 cell을 붙입니다.
|
[
"행에",
"cell을",
"붙입니다",
"."
] |
python
|
train
|
cuihantao/andes
|
andes/models/line.py
|
https://github.com/cuihantao/andes/blob/7067898d4f26ce7534e968b8486c4aa8fe3a511a/andes/models/line.py#L392-L396
|
def v2(self):
"""Return voltage phasors at the "to buses" (bus2)"""
Vm = self.system.dae.y[self.v]
Va = self.system.dae.y[self.a]
return polar(Vm[self.a2], Va[self.a2])
|
[
"def",
"v2",
"(",
"self",
")",
":",
"Vm",
"=",
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"[",
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"a2",
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",",
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"[",
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Return voltage phasors at the "to buses" (bus2)
|
[
"Return",
"voltage",
"phasors",
"at",
"the",
"to",
"buses",
"(",
"bus2",
")"
] |
python
|
train
|
googleapis/google-cloud-python
|
dns/google/cloud/dns/zone.py
|
https://github.com/googleapis/google-cloud-python/blob/85e80125a59cb10f8cb105f25ecc099e4b940b50/dns/google/cloud/dns/zone.py#L138-L148
|
def description(self, value):
"""Update description of the zone.
:type value: str
:param value: (Optional) new description
:raises: ValueError for invalid value types.
"""
if not isinstance(value, six.string_types) and value is not None:
raise ValueError("Pass a string, or None")
self._properties["description"] = value
|
[
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"if",
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"\"Pass a string, or None\"",
")",
"self",
".",
"_properties",
"[",
"\"description\"",
"]",
"=",
"value"
] |
Update description of the zone.
:type value: str
:param value: (Optional) new description
:raises: ValueError for invalid value types.
|
[
"Update",
"description",
"of",
"the",
"zone",
"."
] |
python
|
train
|
albahnsen/CostSensitiveClassification
|
costcla/models/regression.py
|
https://github.com/albahnsen/CostSensitiveClassification/blob/75778ae32c70671c0cdde6c4651277b6a8b58871/costcla/models/regression.py#L259-L276
|
def predict_proba(self, X):
"""Probability estimates.
The returned estimates.
Parameters
----------
X : array-like, shape = [n_samples, n_features]
Returns
-------
T : array-like, shape = [n_samples, 2]
Returns the probability of the sample for each class in the model.
"""
y_prob = np.zeros((X.shape[0], 2))
y_prob[:, 1] = _sigmoid(np.dot(X, self.coef_) + self.intercept_)
y_prob[:, 0] = 1 - y_prob[:, 1]
return y_prob
|
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Probability estimates.
The returned estimates.
Parameters
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Returns
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Returns the probability of the sample for each class in the model.
|
[
"Probability",
"estimates",
"."
] |
python
|
train
|
saltstack/salt
|
salt/states/boto_cloudtrail.py
|
https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/states/boto_cloudtrail.py#L75-L315
|
def present(name, Name,
S3BucketName, S3KeyPrefix=None,
SnsTopicName=None,
IncludeGlobalServiceEvents=True,
IsMultiRegionTrail=None,
EnableLogFileValidation=False,
CloudWatchLogsLogGroupArn=None,
CloudWatchLogsRoleArn=None,
KmsKeyId=None,
LoggingEnabled=True,
Tags=None,
region=None, key=None, keyid=None, profile=None):
'''
Ensure trail exists.
name
The name of the state definition
Name
Name of the trail.
S3BucketName
Specifies the name of the Amazon S3 bucket designated for publishing log
files.
S3KeyPrefix
Specifies the Amazon S3 key prefix that comes after the name of the
bucket you have designated for log file delivery.
SnsTopicName
Specifies the name of the Amazon SNS topic defined for notification of
log file delivery. The maximum length is 256 characters.
IncludeGlobalServiceEvents
Specifies whether the trail is publishing events from global services
such as IAM to the log files.
EnableLogFileValidation
Specifies whether log file integrity validation is enabled. The default
is false.
CloudWatchLogsLogGroupArn
Specifies a log group name using an Amazon Resource Name (ARN), a unique
identifier that represents the log group to which CloudTrail logs will
be delivered. Not required unless you specify CloudWatchLogsRoleArn.
CloudWatchLogsRoleArn
Specifies the role for the CloudWatch Logs endpoint to assume to write
to a user's log group.
KmsKeyId
Specifies the KMS key ID to use to encrypt the logs delivered by
CloudTrail. The value can be a an alias name prefixed by "alias/", a
fully specified ARN to an alias, a fully specified ARN to a key, or a
globally unique identifier.
LoggingEnabled
Whether logging should be enabled for the trail
Tags
A dictionary of tags that should be set on the trail
region
Region to connect to.
key
Secret key to be used.
keyid
Access key to be used.
profile
A dict with region, key and keyid, or a pillar key (string) that
contains a dict with region, key and keyid.
'''
ret = {'name': Name,
'result': True,
'comment': '',
'changes': {}
}
r = __salt__['boto_cloudtrail.exists'](Name=Name,
region=region, key=key, keyid=keyid, profile=profile)
if 'error' in r:
ret['result'] = False
ret['comment'] = 'Failed to create trail: {0}.'.format(r['error']['message'])
return ret
if not r.get('exists'):
if __opts__['test']:
ret['comment'] = 'CloudTrail {0} is set to be created.'.format(Name)
ret['result'] = None
return ret
r = __salt__['boto_cloudtrail.create'](Name=Name,
S3BucketName=S3BucketName,
S3KeyPrefix=S3KeyPrefix,
SnsTopicName=SnsTopicName,
IncludeGlobalServiceEvents=IncludeGlobalServiceEvents,
IsMultiRegionTrail=IsMultiRegionTrail,
EnableLogFileValidation=EnableLogFileValidation,
CloudWatchLogsLogGroupArn=CloudWatchLogsLogGroupArn,
CloudWatchLogsRoleArn=CloudWatchLogsRoleArn,
KmsKeyId=KmsKeyId,
region=region, key=key, keyid=keyid, profile=profile)
if not r.get('created'):
ret['result'] = False
ret['comment'] = 'Failed to create trail: {0}.'.format(r['error']['message'])
return ret
_describe = __salt__['boto_cloudtrail.describe'](Name,
region=region, key=key, keyid=keyid, profile=profile)
ret['changes']['old'] = {'trail': None}
ret['changes']['new'] = _describe
ret['comment'] = 'CloudTrail {0} created.'.format(Name)
if LoggingEnabled:
r = __salt__['boto_cloudtrail.start_logging'](Name=Name,
region=region, key=key, keyid=keyid, profile=profile)
if 'error' in r:
ret['result'] = False
ret['comment'] = 'Failed to create trail: {0}.'.format(r['error']['message'])
ret['changes'] = {}
return ret
ret['changes']['new']['trail']['LoggingEnabled'] = True
else:
ret['changes']['new']['trail']['LoggingEnabled'] = False
if bool(Tags):
r = __salt__['boto_cloudtrail.add_tags'](Name=Name,
region=region, key=key, keyid=keyid, profile=profile, **Tags)
if not r.get('tagged'):
ret['result'] = False
ret['comment'] = 'Failed to create trail: {0}.'.format(r['error']['message'])
ret['changes'] = {}
return ret
ret['changes']['new']['trail']['Tags'] = Tags
return ret
ret['comment'] = os.linesep.join([ret['comment'], 'CloudTrail {0} is present.'.format(Name)])
ret['changes'] = {}
# trail exists, ensure config matches
_describe = __salt__['boto_cloudtrail.describe'](Name=Name,
region=region, key=key, keyid=keyid, profile=profile)
if 'error' in _describe:
ret['result'] = False
ret['comment'] = 'Failed to update trail: {0}.'.format(_describe['error']['message'])
ret['changes'] = {}
return ret
_describe = _describe.get('trail')
r = __salt__['boto_cloudtrail.status'](Name=Name,
region=region, key=key, keyid=keyid, profile=profile)
_describe['LoggingEnabled'] = r.get('trail', {}).get('IsLogging', False)
need_update = False
bucket_vars = {'S3BucketName': 'S3BucketName',
'S3KeyPrefix': 'S3KeyPrefix',
'SnsTopicName': 'SnsTopicName',
'IncludeGlobalServiceEvents': 'IncludeGlobalServiceEvents',
'IsMultiRegionTrail': 'IsMultiRegionTrail',
'EnableLogFileValidation': 'LogFileValidationEnabled',
'CloudWatchLogsLogGroupArn': 'CloudWatchLogsLogGroupArn',
'CloudWatchLogsRoleArn': 'CloudWatchLogsRoleArn',
'KmsKeyId': 'KmsKeyId',
'LoggingEnabled': 'LoggingEnabled'}
for invar, outvar in six.iteritems(bucket_vars):
if _describe[outvar] != locals()[invar]:
need_update = True
ret['changes'].setdefault('new', {})[invar] = locals()[invar]
ret['changes'].setdefault('old', {})[invar] = _describe[outvar]
r = __salt__['boto_cloudtrail.list_tags'](Name=Name,
region=region, key=key, keyid=keyid, profile=profile)
_describe['Tags'] = r.get('tags', {})
tagchange = salt.utils.data.compare_dicts(_describe['Tags'], Tags)
if bool(tagchange):
need_update = True
ret['changes'].setdefault('new', {})['Tags'] = Tags
ret['changes'].setdefault('old', {})['Tags'] = _describe['Tags']
if need_update:
if __opts__['test']:
msg = 'CloudTrail {0} set to be modified.'.format(Name)
ret['comment'] = msg
ret['result'] = None
return ret
ret['comment'] = os.linesep.join([ret['comment'], 'CloudTrail to be modified'])
r = __salt__['boto_cloudtrail.update'](Name=Name,
S3BucketName=S3BucketName,
S3KeyPrefix=S3KeyPrefix,
SnsTopicName=SnsTopicName,
IncludeGlobalServiceEvents=IncludeGlobalServiceEvents,
IsMultiRegionTrail=IsMultiRegionTrail,
EnableLogFileValidation=EnableLogFileValidation,
CloudWatchLogsLogGroupArn=CloudWatchLogsLogGroupArn,
CloudWatchLogsRoleArn=CloudWatchLogsRoleArn,
KmsKeyId=KmsKeyId,
region=region, key=key, keyid=keyid, profile=profile)
if not r.get('updated'):
ret['result'] = False
ret['comment'] = 'Failed to update trail: {0}.'.format(r['error']['message'])
ret['changes'] = {}
return ret
if LoggingEnabled:
r = __salt__['boto_cloudtrail.start_logging'](Name=Name,
region=region, key=key, keyid=keyid, profile=profile)
if not r.get('started'):
ret['result'] = False
ret['comment'] = 'Failed to update trail: {0}.'.format(r['error']['message'])
ret['changes'] = {}
return ret
else:
r = __salt__['boto_cloudtrail.stop_logging'](Name=Name,
region=region, key=key, keyid=keyid, profile=profile)
if not r.get('stopped'):
ret['result'] = False
ret['comment'] = 'Failed to update trail: {0}.'.format(r['error']['message'])
ret['changes'] = {}
return ret
if bool(tagchange):
adds = {}
removes = {}
for k, diff in six.iteritems(tagchange):
if diff.get('new', '') != '':
# there's an update for this key
adds[k] = Tags[k]
elif diff.get('old', '') != '':
removes[k] = _describe['Tags'][k]
if bool(adds):
r = __salt__['boto_cloudtrail.add_tags'](Name=Name,
region=region, key=key, keyid=keyid, profile=profile, **adds)
if bool(removes):
r = __salt__['boto_cloudtrail.remove_tags'](Name=Name,
region=region, key=key, keyid=keyid, profile=profile,
**removes)
return ret
|
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",",
"profile",
"=",
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",",
"*",
"*",
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")",
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"ret"
] |
Ensure trail exists.
name
The name of the state definition
Name
Name of the trail.
S3BucketName
Specifies the name of the Amazon S3 bucket designated for publishing log
files.
S3KeyPrefix
Specifies the Amazon S3 key prefix that comes after the name of the
bucket you have designated for log file delivery.
SnsTopicName
Specifies the name of the Amazon SNS topic defined for notification of
log file delivery. The maximum length is 256 characters.
IncludeGlobalServiceEvents
Specifies whether the trail is publishing events from global services
such as IAM to the log files.
EnableLogFileValidation
Specifies whether log file integrity validation is enabled. The default
is false.
CloudWatchLogsLogGroupArn
Specifies a log group name using an Amazon Resource Name (ARN), a unique
identifier that represents the log group to which CloudTrail logs will
be delivered. Not required unless you specify CloudWatchLogsRoleArn.
CloudWatchLogsRoleArn
Specifies the role for the CloudWatch Logs endpoint to assume to write
to a user's log group.
KmsKeyId
Specifies the KMS key ID to use to encrypt the logs delivered by
CloudTrail. The value can be a an alias name prefixed by "alias/", a
fully specified ARN to an alias, a fully specified ARN to a key, or a
globally unique identifier.
LoggingEnabled
Whether logging should be enabled for the trail
Tags
A dictionary of tags that should be set on the trail
region
Region to connect to.
key
Secret key to be used.
keyid
Access key to be used.
profile
A dict with region, key and keyid, or a pillar key (string) that
contains a dict with region, key and keyid.
|
[
"Ensure",
"trail",
"exists",
"."
] |
python
|
train
|
etcher-be/emiz
|
emiz/weather/custom_metar/custom_metar.py
|
https://github.com/etcher-be/emiz/blob/1c3e32711921d7e600e85558ffe5d337956372de/emiz/weather/custom_metar/custom_metar.py#L27-L60
|
def get_metar(
metar: typing.Union[str, 'CustomMetar']
) -> typing.Tuple[typing.Union[str, None], typing.Union['CustomMetar', None]]:
"""
Builds a CustomMetar object from a CustomMetar object (returns it), an ICAO code or a METAR string
Args:
metar: CustomMetar object, ICAO string or METAR string
Returns: CustomMetar object
"""
error: typing.Optional[str] = None
if isinstance(metar, CustomMetar):
return None, metar
if isinstance(metar, str):
LOGGER.debug('building CustomMetar from: %s', metar)
if len(metar) == 4:
LOGGER.debug('retrieving METAR from ICAO')
# NOAA has discontinued their hosting of raw METAR text files ...
# error, metar = noaa.retrieve_metar(metar)
# metar = avwx.AVWX.query_icao(metar).rawreport
metar = AWC.query_icao(metar).raw_metar
else:
error = f'expected a string or or a CustomMetar object, got: {type(metar)}'
if error:
return error, None
try:
return None, CustomMetar(metar_code=metar)
except ParserError:
return f'Unable to parse METAR: {metar}', None
|
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":",
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",",
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Builds a CustomMetar object from a CustomMetar object (returns it), an ICAO code or a METAR string
Args:
metar: CustomMetar object, ICAO string or METAR string
Returns: CustomMetar object
|
[
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"(",
"returns",
"it",
")",
"an",
"ICAO",
"code",
"or",
"a",
"METAR",
"string"
] |
python
|
train
|
Tanganelli/CoAPthon3
|
coapthon/resources/resource.py
|
https://github.com/Tanganelli/CoAPthon3/blob/985763bfe2eb9e00f49ec100c5b8877c2ed7d531/coapthon/resources/resource.py#L417-L427
|
def init_resource(self, request, res):
"""
Helper function to initialize a new resource.
:param request: the request that generate the new resource
:param res: the resource
:return: the edited resource
"""
res.location_query = request.uri_query
res.payload = (request.content_type, request.payload)
return res
|
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"(",
"request",
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"content_type",
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] |
Helper function to initialize a new resource.
:param request: the request that generate the new resource
:param res: the resource
:return: the edited resource
|
[
"Helper",
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"initialize",
"a",
"new",
"resource",
"."
] |
python
|
train
|
Unidata/MetPy
|
metpy/io/_nexrad_msgs/parse_spec.py
|
https://github.com/Unidata/MetPy/blob/16f68a94919b9a82dcf9cada2169cf039129e67b/metpy/io/_nexrad_msgs/parse_spec.py#L58-L92
|
def process_msg18(fname):
"""Handle information for message type 18."""
with open(fname, 'r') as infile:
info = []
for lineno, line in enumerate(infile):
parts = line.split(' ')
try:
if len(parts) == 8:
parts = parts[:6] + [parts[6] + parts[7]]
var_name, desc, typ, units, rng, prec, byte_range = parts
start, end = map(int, byte_range.split('-'))
size = end - start + 1
assert size >= 4
fmt = fix_type(typ, size,
additional=[('See Note (5)', ('{size}s', 1172))])
if ' ' in var_name:
warnings.warn('Space in {}'.format(var_name))
if not desc:
warnings.warn('null description for {}'.format(var_name))
var_name = fix_var_name(var_name)
full_desc = fix_desc(desc, units)
info.append({'name': var_name, 'desc': full_desc, 'fmt': fmt})
if (ignored_item(info[-1]) and var_name != 'SPARE'
and 'SPARE' not in full_desc):
warnings.warn('{} has type {}. Setting as SPARE'.format(var_name, typ))
except (ValueError, AssertionError):
warnings.warn('{} > {}'.format(lineno + 1, ':'.join(parts)))
raise
return info
|
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Handle information for message type 18.
|
[
"Handle",
"information",
"for",
"message",
"type",
"18",
"."
] |
python
|
train
|
Kortemme-Lab/klab
|
klab/general/strutil.py
|
https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/general/strutil.py#L57-L63
|
def split_pdb_residue(s):
'''Splits a PDB residue into the numeric and insertion code components.'''
if s.isdigit():
return (int(s), ' ')
else:
assert(s[:-1].isdigit())
return ((s[:-1], s[-1]))
|
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"def",
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"-",
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Splits a PDB residue into the numeric and insertion code components.
|
[
"Splits",
"a",
"PDB",
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"into",
"the",
"numeric",
"and",
"insertion",
"code",
"components",
"."
] |
python
|
train
|
gersolar/goescalibration
|
goescalibration/instrument.py
|
https://github.com/gersolar/goescalibration/blob/aab7f3e3cede9694e90048ceeaea74566578bc75/goescalibration/instrument.py#L37-L53
|
def calibrate(filename):
"""
Append the calibration parameters as variables of the netcdf file.
Keyword arguments:
filename -- the name of a netcdf file.
"""
params = calibration_to(filename)
with nc.loader(filename) as root:
for key, value in params.items():
nc.getdim(root, 'xc_1', 1)
nc.getdim(root, 'yc_1', 1)
if isinstance(value, list):
for i in range(len(value)):
nc.getvar(root, '%s_%i' % (key, i), 'f4', ('time', 'yc_1', 'xc_1' ))[:] = value[i]
else:
nc.getvar(root, key, 'f4', ('time', 'yc_1', 'xc_1'))[:] = value
|
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Append the calibration parameters as variables of the netcdf file.
Keyword arguments:
filename -- the name of a netcdf file.
|
[
"Append",
"the",
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"parameters",
"as",
"variables",
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"the",
"netcdf",
"file",
"."
] |
python
|
train
|
trailofbits/manticore
|
manticore/platforms/evm.py
|
https://github.com/trailofbits/manticore/blob/54c5a15b1119c523ae54c09972413e8b97f11629/manticore/platforms/evm.py#L2376-L2432
|
def create_account(self, address=None, balance=0, code=None, storage=None, nonce=None):
"""
Low level account creation. No transaction is done.
:param address: the address of the account, if known. If omitted, a new address will be generated as closely to the Yellow Paper as possible.
:param balance: the initial balance of the account in Wei
:param code: the runtime code of the account, if a contract
:param storage: storage array
:param nonce: the nonce for the account; contracts should have a nonce greater than or equal to 1
"""
if code is None:
code = bytes()
else:
if not isinstance(code, (bytes, Array)):
raise EthereumError('Wrong code type')
# nonce default to initial nonce
if nonce is None:
# As per EIP 161, contract accounts are initialized with a nonce of 1
nonce = 1 if code else 0
if address is None:
address = self.new_address()
if not isinstance(address, int):
raise EthereumError('You must provide an address')
if address in self.accounts:
# FIXME account may have been created via selfdestruct destination
# or CALL and may contain some ether already, though if it was a
# selfdestructed address, it can not be reused
raise EthereumError('The account already exists')
if storage is None:
# Uninitialized values in a storage are 0 by spec
storage = self.constraints.new_array(index_bits=256, value_bits=256, name=f'STORAGE_{address:x}', avoid_collisions=True, default=0)
else:
if isinstance(storage, ArrayProxy):
if storage.index_bits != 256 or storage.value_bits != 256:
raise TypeError("An ArrayProxy 256bits -> 256bits is needed")
else:
if any((k < 0 or k >= 1 << 256 for k, v in storage.items())):
raise TypeError("Need a dict like object that maps 256 bits keys to 256 bits values")
# Hopefully here we have a mapping from 256b to 256b
self._world_state[address] = {}
self._world_state[address]['nonce'] = nonce
self._world_state[address]['balance'] = balance
self._world_state[address]['storage'] = storage
self._world_state[address]['code'] = code
# adds hash of new address
data = binascii.unhexlify('{:064x}{:064x}'.format(address, 0))
value = sha3.keccak_256(data).hexdigest()
value = int(value, 16)
self._publish('on_concrete_sha3', data, value)
return address
|
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"[",
"'balance'",
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"(",
"'on_concrete_sha3'",
",",
"data",
",",
"value",
")",
"return",
"address"
] |
Low level account creation. No transaction is done.
:param address: the address of the account, if known. If omitted, a new address will be generated as closely to the Yellow Paper as possible.
:param balance: the initial balance of the account in Wei
:param code: the runtime code of the account, if a contract
:param storage: storage array
:param nonce: the nonce for the account; contracts should have a nonce greater than or equal to 1
|
[
"Low",
"level",
"account",
"creation",
".",
"No",
"transaction",
"is",
"done",
".",
":",
"param",
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"the",
"address",
"of",
"the",
"account",
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"known",
".",
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"address",
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"be",
"generated",
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"Paper",
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"param",
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"the",
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"account",
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"param",
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";",
"contracts",
"should",
"have",
"a",
"nonce",
"greater",
"than",
"or",
"equal",
"to",
"1"
] |
python
|
valid
|
Nic30/hwt
|
hwt/hdl/transPart.py
|
https://github.com/Nic30/hwt/blob/8cbb399e326da3b22c233b98188a9d08dec057e6/hwt/hdl/transPart.py#L38-L43
|
def getBusWordBitRange(self) -> Tuple[int, int]:
"""
:return: bit range which contains data of this part on bus data signal
"""
offset = self.startOfPart % self.parent.wordWidth
return (offset + self.bit_length(), offset)
|
[
"def",
"getBusWordBitRange",
"(",
"self",
")",
"->",
"Tuple",
"[",
"int",
",",
"int",
"]",
":",
"offset",
"=",
"self",
".",
"startOfPart",
"%",
"self",
".",
"parent",
".",
"wordWidth",
"return",
"(",
"offset",
"+",
"self",
".",
"bit_length",
"(",
")",
",",
"offset",
")"
] |
:return: bit range which contains data of this part on bus data signal
|
[
":",
"return",
":",
"bit",
"range",
"which",
"contains",
"data",
"of",
"this",
"part",
"on",
"bus",
"data",
"signal"
] |
python
|
test
|
chrisspen/burlap
|
burlap/host.py
|
https://github.com/chrisspen/burlap/blob/a92b0a8e5206850bb777c74af8421ea8b33779bd/burlap/host.py#L200-L288
|
def initrole(self, check=True):
"""
Called to set default password login for systems that do not yet have passwordless
login setup.
"""
if self.env.original_user is None:
self.env.original_user = self.genv.user
if self.env.original_key_filename is None:
self.env.original_key_filename = self.genv.key_filename
host_string = None
user = None
password = None
if self.env.login_check:
host_string, user, password = self.find_working_password(
usernames=[self.genv.user, self.env.default_user],
host_strings=[self.genv.host_string, self.env.default_hostname],
)
if self.verbose:
print('host.initrole.host_string:', host_string)
print('host.initrole.user:', user)
print('host.initrole.password:', password)
# needs = True
# if check:
# needs = self.needs_initrole(stop_on_error=True)
needs = False
if host_string is not None:
self.genv.host_string = host_string
if user is not None:
self.genv.user = user
if password is not None:
self.genv.password = password
if not needs:
return
assert self.env.default_hostname, 'No default hostname set.'
assert self.env.default_user, 'No default user set.'
self.genv.host_string = self.env.default_hostname
if self.env.default_hosts:
self.genv.hosts = self.env.default_hosts
else:
self.genv.hosts = [self.env.default_hostname]
self.genv.user = self.env.default_user
self.genv.password = self.env.default_password
self.genv.key_filename = self.env.default_key_filename
# If the host has been reformatted, the SSH keys will mismatch, throwing an error, so clear them.
self.purge_keys()
# Do a test login with the default password to determine which password we should use.
# r.env.password = self.env.default_password
# with settings(warn_only=True):
# ret = r._local("sshpass -p '{password}' ssh -o StrictHostKeyChecking=no {user}@{host_string} echo hello", capture=True)
# print('ret.return_code:', ret.return_code)
# # print('ret000:[%s]' % ret)
# #code 1 = good password, but prompts needed
# #code 5 = bad password
# #code 6 = good password, but host public key is unknown
# if ret.return_code in (1, 6) or 'hello' in ret:
# # Login succeeded, so we haven't yet changed the password, so use the default password.
# self.genv.password = self.env.default_password
# elif self.genv.user in self.genv.user_passwords:
# # Otherwise, use the password or key set in the config.
# self.genv.password = self.genv.user_passwords[self.genv.user]
# else:
# # Default password fails and there's no current password, so clear.
# self.genv.password = None
# self.genv.password = self.find_working_password()
# print('host.initrole,using password:', self.genv.password)
# Execute post-init callbacks.
for task_name in self.env.post_initrole_tasks:
if self.verbose:
print('Calling post initrole task %s' % task_name)
satchel_name, method_name = task_name.split('.')
satchel = self.get_satchel(name=satchel_name)
getattr(satchel, method_name)()
print('^'*80)
print('host.initrole.host_string:', self.genv.host_string)
print('host.initrole.user:', self.genv.user)
print('host.initrole.password:', self.genv.password)
|
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"# Do a test login with the default password to determine which password we should use.",
"# r.env.password = self.env.default_password",
"# with settings(warn_only=True):",
"# ret = r._local(\"sshpass -p '{password}' ssh -o StrictHostKeyChecking=no {user}@{host_string} echo hello\", capture=True)",
"# print('ret.return_code:', ret.return_code)",
"# # print('ret000:[%s]' % ret)",
"# #code 1 = good password, but prompts needed",
"# #code 5 = bad password",
"# #code 6 = good password, but host public key is unknown",
"# if ret.return_code in (1, 6) or 'hello' in ret:",
"# # Login succeeded, so we haven't yet changed the password, so use the default password.",
"# self.genv.password = self.env.default_password",
"# elif self.genv.user in self.genv.user_passwords:",
"# # Otherwise, use the password or key set in the config.",
"# self.genv.password = self.genv.user_passwords[self.genv.user]",
"# else:",
"# # Default password fails and there's no current password, so clear.",
"# self.genv.password = None",
"# self.genv.password = self.find_working_password()",
"# print('host.initrole,using password:', self.genv.password)",
"# Execute post-init callbacks.",
"for",
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",",
"method_name",
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"'host.initrole.password:'",
",",
"self",
".",
"genv",
".",
"password",
")"
] |
Called to set default password login for systems that do not yet have passwordless
login setup.
|
[
"Called",
"to",
"set",
"default",
"password",
"login",
"for",
"systems",
"that",
"do",
"not",
"yet",
"have",
"passwordless",
"login",
"setup",
"."
] |
python
|
valid
|
materialsproject/pymatgen
|
pymatgen/core/structure.py
|
https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2012-L2022
|
def center_of_mass(self):
"""
Center of mass of molecule.
"""
center = np.zeros(3)
total_weight = 0
for site in self:
wt = site.species.weight
center += site.coords * wt
total_weight += wt
return center / total_weight
|
[
"def",
"center_of_mass",
"(",
"self",
")",
":",
"center",
"=",
"np",
".",
"zeros",
"(",
"3",
")",
"total_weight",
"=",
"0",
"for",
"site",
"in",
"self",
":",
"wt",
"=",
"site",
".",
"species",
".",
"weight",
"center",
"+=",
"site",
".",
"coords",
"*",
"wt",
"total_weight",
"+=",
"wt",
"return",
"center",
"/",
"total_weight"
] |
Center of mass of molecule.
|
[
"Center",
"of",
"mass",
"of",
"molecule",
"."
] |
python
|
train
|
gamechanger/schemer
|
schemer/validators.py
|
https://github.com/gamechanger/schemer/blob/1d1dd7da433d3b84ce5a80ded5a84ab4a65825ee/schemer/validators.py#L68-L80
|
def between(min_value, max_value):
"""
Validates that a field value is between the two values
given to this validator.
"""
def validate(value):
if value < min_value:
return e("{} is not greater than or equal to {}",
value, min_value)
if value > max_value:
return e("{} is not less than or equal to {}",
value, max_value)
return validate
|
[
"def",
"between",
"(",
"min_value",
",",
"max_value",
")",
":",
"def",
"validate",
"(",
"value",
")",
":",
"if",
"value",
"<",
"min_value",
":",
"return",
"e",
"(",
"\"{} is not greater than or equal to {}\"",
",",
"value",
",",
"min_value",
")",
"if",
"value",
">",
"max_value",
":",
"return",
"e",
"(",
"\"{} is not less than or equal to {}\"",
",",
"value",
",",
"max_value",
")",
"return",
"validate"
] |
Validates that a field value is between the two values
given to this validator.
|
[
"Validates",
"that",
"a",
"field",
"value",
"is",
"between",
"the",
"two",
"values",
"given",
"to",
"this",
"validator",
"."
] |
python
|
train
|
vladsaveliev/TargQC
|
targqc/utilz/file_utils.py
|
https://github.com/vladsaveliev/TargQC/blob/e887c36b2194dbd73c6ea32989b6cb84c6c0e58d/targqc/utilz/file_utils.py#L903-L928
|
def tx_tmpdir(base_dir, rollback_dirpath):
"""Context manager to create and remove a transactional temporary directory.
"""
# tmp_dir_base = join(base_dir, 'tx', str(uuid.uuid4()))
# unique_attempts = 0
# while os.path.exists(tmp_dir_base):
# if unique_attempts > 5:
# break
# tmp_dir_base = join(base_dir, 'tx', str(uuid.uuid4()))
# time.sleep(1)
# unique_attempts += 1
# if base_dir is not None:
# tmp_dir_base = os.path.join(base_dir, "tx")
# else:
# tmp_dir_base = os.path.join(os.getcwd(), "tx")
if exists(rollback_dirpath):
critical(rollback_dirpath + ' already exists')
tmp_dir = tempfile.mkdtemp(dir=base_dir)
safe_mkdir(tmp_dir)
try:
yield tmp_dir
finally:
if tmp_dir and exists(tmp_dir):
os.rename(tmp_dir, rollback_dirpath)
|
[
"def",
"tx_tmpdir",
"(",
"base_dir",
",",
"rollback_dirpath",
")",
":",
"# tmp_dir_base = join(base_dir, 'tx', str(uuid.uuid4()))",
"# unique_attempts = 0",
"# while os.path.exists(tmp_dir_base):",
"# if unique_attempts > 5:",
"# break",
"# tmp_dir_base = join(base_dir, 'tx', str(uuid.uuid4()))",
"# time.sleep(1)",
"# unique_attempts += 1",
"# if base_dir is not None:",
"# tmp_dir_base = os.path.join(base_dir, \"tx\")",
"# else:",
"# tmp_dir_base = os.path.join(os.getcwd(), \"tx\")",
"if",
"exists",
"(",
"rollback_dirpath",
")",
":",
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"(",
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"+",
"' already exists'",
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"(",
"dir",
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")",
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"(",
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":",
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"(",
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")",
":",
"os",
".",
"rename",
"(",
"tmp_dir",
",",
"rollback_dirpath",
")"
] |
Context manager to create and remove a transactional temporary directory.
|
[
"Context",
"manager",
"to",
"create",
"and",
"remove",
"a",
"transactional",
"temporary",
"directory",
"."
] |
python
|
train
|
mikekatz04/BOWIE
|
bowie/plotutils/forminput.py
|
https://github.com/mikekatz04/BOWIE/blob/a941342a3536cb57c817a1643896d99a3f354a86/bowie/plotutils/forminput.py#L665-L685
|
def savefig(self, output_path, **kwargs):
"""Save figure during generation.
This method is used to save a completed figure during the main function run.
It represents a call to ``matplotlib.pyplot.fig.savefig``.
# TODO: Switch to kwargs for matplotlib.pyplot.savefig
Args:
output_path (str): Relative path to the WORKING_DIRECTORY to save the figure.
Keyword Arguments:
dpi (int, optional): Dots per inch of figure. Default is 200.
Note: Other kwargs are available. See:
https://matplotlib.org/api/_as_gen/matplotlib.pyplot.savefig.html
"""
self.figure.save_figure = True
self.figure.output_path = output_path
self.figure.savefig_kwargs = kwargs
return
|
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"def",
"savefig",
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",",
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",",
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"output_path",
"=",
"output_path",
"self",
".",
"figure",
".",
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"=",
"kwargs",
"return"
] |
Save figure during generation.
This method is used to save a completed figure during the main function run.
It represents a call to ``matplotlib.pyplot.fig.savefig``.
# TODO: Switch to kwargs for matplotlib.pyplot.savefig
Args:
output_path (str): Relative path to the WORKING_DIRECTORY to save the figure.
Keyword Arguments:
dpi (int, optional): Dots per inch of figure. Default is 200.
Note: Other kwargs are available. See:
https://matplotlib.org/api/_as_gen/matplotlib.pyplot.savefig.html
|
[
"Save",
"figure",
"during",
"generation",
"."
] |
python
|
train
|
spyder-ide/spyder
|
spyder/plugins/explorer/widgets.py
|
https://github.com/spyder-ide/spyder/blob/f76836ce1b924bcc4efd3f74f2960d26a4e528e0/spyder/plugins/explorer/widgets.py#L1348-L1385
|
def chdir(self, directory=None, browsing_history=False):
"""Set directory as working directory"""
if directory is not None:
directory = osp.abspath(to_text_string(directory))
if browsing_history:
directory = self.history[self.histindex]
elif directory in self.history:
self.histindex = self.history.index(directory)
else:
if self.histindex is None:
self.history = []
else:
self.history = self.history[:self.histindex+1]
if len(self.history) == 0 or \
(self.history and self.history[-1] != directory):
self.history.append(directory)
self.histindex = len(self.history)-1
directory = to_text_string(directory)
try:
PermissionError
FileNotFoundError
except NameError:
PermissionError = OSError
if os.name == 'nt':
FileNotFoundError = WindowsError
else:
FileNotFoundError = IOError
try:
os.chdir(directory)
self.sig_open_dir.emit(directory)
self.refresh(new_path=directory, force_current=True)
except PermissionError:
QMessageBox.critical(self.parent_widget, "Error",
_("You don't have the right permissions to "
"open this directory"))
except FileNotFoundError:
# Handle renaming directories on the fly. See issue #5183
self.history.pop(self.histindex)
|
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"self",
".",
"history",
".",
"pop",
"(",
"self",
".",
"histindex",
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] |
Set directory as working directory
|
[
"Set",
"directory",
"as",
"working",
"directory"
] |
python
|
train
|
cloudendpoints/endpoints-management-python
|
endpoints_management/control/wsgi.py
|
https://github.com/cloudendpoints/endpoints-management-python/blob/ec3c4a330ae9d65738861ce6df4dd6c3cb9f7731/endpoints_management/control/wsgi.py#L658-L688
|
def _create_authenticator(a_service):
"""Create an instance of :class:`google.auth.tokens.Authenticator`.
Args:
a_service (:class:`endpoints_management.gen.servicemanagement_v1_messages.Service`): a
service instance
"""
if not isinstance(a_service, sm_messages.Service):
raise ValueError(u"service is None or not an instance of Service")
authentication = a_service.authentication
if not authentication:
_logger.info(u"authentication is not configured in service, "
u"authentication checks will be disabled")
return
issuers_to_provider_ids = {}
issuer_uri_configs = {}
for provider in authentication.providers:
issuer = provider.issuer
jwks_uri = provider.jwksUri
# Enable openID discovery if jwks_uri is unset
open_id = jwks_uri is None
issuer_uri_configs[issuer] = suppliers.IssuerUriConfig(open_id, jwks_uri)
issuers_to_provider_ids[issuer] = provider.id
key_uri_supplier = suppliers.KeyUriSupplier(issuer_uri_configs)
jwks_supplier = suppliers.JwksSupplier(key_uri_supplier)
authenticator = tokens.Authenticator(issuers_to_provider_ids, jwks_supplier)
return authenticator
|
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".",
"Authenticator",
"(",
"issuers_to_provider_ids",
",",
"jwks_supplier",
")",
"return",
"authenticator"
] |
Create an instance of :class:`google.auth.tokens.Authenticator`.
Args:
a_service (:class:`endpoints_management.gen.servicemanagement_v1_messages.Service`): a
service instance
|
[
"Create",
"an",
"instance",
"of",
":",
"class",
":",
"google",
".",
"auth",
".",
"tokens",
".",
"Authenticator",
"."
] |
python
|
train
|
oscarbranson/latools
|
latools/helpers/stat_fns.py
|
https://github.com/oscarbranson/latools/blob/cd25a650cfee318152f234d992708511f7047fbe/latools/helpers/stat_fns.py#L51-L96
|
def gauss_weighted_stats(x, yarray, x_new, fwhm):
"""
Calculate gaussian weigted moving mean, SD and SE.
Parameters
----------
x : array-like
The independent variable
yarray : (n,m) array
Where n = x.size, and m is the number of
dependent variables to smooth.
x_new : array-like
The new x-scale to interpolate the data
fwhm : int
FWHM of the gaussian kernel.
Returns
-------
(mean, std, se) : tuple
"""
sigma = fwhm / (2 * np.sqrt(2 * np.log(2)))
# create empty mask array
mask = np.zeros((x.size, yarray.shape[1], x_new.size))
# fill mask
for i, xni in enumerate(x_new):
mask[:, :, i] = gauss(x[:, np.newaxis], 1, xni, sigma)
# normalise mask
nmask = mask / mask.sum(0) # sum of each gaussian = 1
# calculate moving average
av = (nmask * yarray[:, :, np.newaxis]).sum(0) # apply mask to data
# sum along xn axis to get means
# calculate moving sd
diff = np.power(av - yarray[:, :, np.newaxis], 2)
std = np.sqrt((diff * nmask).sum(0))
# sqrt of weighted average of data-mean
# calculate moving se
se = std / np.sqrt(mask.sum(0))
# max amplitude of weights is 1, so sum of weights scales
# a fn of how many points are nearby. Use this as 'n' in
# SE calculation.
return av, std, se
|
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"# SE calculation.",
"return",
"av",
",",
"std",
",",
"se"
] |
Calculate gaussian weigted moving mean, SD and SE.
Parameters
----------
x : array-like
The independent variable
yarray : (n,m) array
Where n = x.size, and m is the number of
dependent variables to smooth.
x_new : array-like
The new x-scale to interpolate the data
fwhm : int
FWHM of the gaussian kernel.
Returns
-------
(mean, std, se) : tuple
|
[
"Calculate",
"gaussian",
"weigted",
"moving",
"mean",
"SD",
"and",
"SE",
"."
] |
python
|
test
|
SpriteLink/NIPAP
|
pynipap/pynipap.py
|
https://github.com/SpriteLink/NIPAP/blob/f96069f11ab952d80b13cab06e0528f2d24b3de9/pynipap/pynipap.py#L585-L639
|
def save(self):
""" Save changes made to object to NIPAP.
If the object represents a new VRF unknown to NIPAP (attribute `id`
is `None`) this function maps to the function
:py:func:`nipap.backend.Nipap.add_vrf` in the backend, used to
create a new VRF. Otherwise it maps to the function
:py:func:`nipap.backend.Nipap.edit_vrf` in the backend, used to
modify the VRF. Please see the documentation for the backend
functions for information regarding input arguments and return
values.
"""
xmlrpc = XMLRPCConnection()
data = {
'rt': self.rt,
'name': self.name,
'description': self.description,
'tags': [],
'avps': self.avps
}
for tag_name in self.tags:
data['tags'].append(tag_name)
if self.id is None:
# New object, create
try:
vrf = xmlrpc.connection.add_vrf(
{
'attr': data,
'auth': self._auth_opts.options
})
except xmlrpclib.Fault as xml_fault:
raise _fault_to_exception(xml_fault)
else:
# Old object, edit
try:
vrfs = xmlrpc.connection.edit_vrf(
{
'vrf': { 'id': self.id },
'attr': data,
'auth': self._auth_opts.options
})
except xmlrpclib.Fault as xml_fault:
raise _fault_to_exception(xml_fault)
if len(vrfs) != 1:
raise NipapError('VRF edit returned %d entries, should be 1.' % len(vrfs))
vrf = vrfs[0]
# Refresh object data with attributes from add/edit operation
VRF.from_dict(vrf, self)
_cache['VRF'][self.id] = self
|
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"self",
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"_cache",
"[",
"'VRF'",
"]",
"[",
"self",
".",
"id",
"]",
"=",
"self"
] |
Save changes made to object to NIPAP.
If the object represents a new VRF unknown to NIPAP (attribute `id`
is `None`) this function maps to the function
:py:func:`nipap.backend.Nipap.add_vrf` in the backend, used to
create a new VRF. Otherwise it maps to the function
:py:func:`nipap.backend.Nipap.edit_vrf` in the backend, used to
modify the VRF. Please see the documentation for the backend
functions for information regarding input arguments and return
values.
|
[
"Save",
"changes",
"made",
"to",
"object",
"to",
"NIPAP",
"."
] |
python
|
train
|
annoviko/pyclustering
|
pyclustering/cluster/examples/xmeans_examples.py
|
https://github.com/annoviko/pyclustering/blob/98aa0dd89fd36f701668fb1eb29c8fb5662bf7d0/pyclustering/cluster/examples/xmeans_examples.py#L121-L125
|
def cluster_target():
"Not so applicable for this sample"
start_centers = [[0.2, 0.2], [0.0, -2.0], [3.0, -3.0], [3.0, 3.0], [-3.0, 3.0], [-3.0, -3.0]]
template_clustering(start_centers, FCPS_SAMPLES.SAMPLE_TARGET, criterion = splitting_type.BAYESIAN_INFORMATION_CRITERION)
template_clustering(start_centers, FCPS_SAMPLES.SAMPLE_TARGET, criterion = splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH)
|
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",",
"[",
"0.0",
",",
"-",
"2.0",
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",",
"[",
"3.0",
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"-",
"3.0",
"]",
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"[",
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",",
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"[",
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"3.0",
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"3.0",
"]",
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"[",
"-",
"3.0",
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"]",
"]",
"template_clustering",
"(",
"start_centers",
",",
"FCPS_SAMPLES",
".",
"SAMPLE_TARGET",
",",
"criterion",
"=",
"splitting_type",
".",
"BAYESIAN_INFORMATION_CRITERION",
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"template_clustering",
"(",
"start_centers",
",",
"FCPS_SAMPLES",
".",
"SAMPLE_TARGET",
",",
"criterion",
"=",
"splitting_type",
".",
"MINIMUM_NOISELESS_DESCRIPTION_LENGTH",
")"
] |
Not so applicable for this sample
|
[
"Not",
"so",
"applicable",
"for",
"this",
"sample"
] |
python
|
valid
|
majerteam/sqla_inspect
|
sqla_inspect/export.py
|
https://github.com/majerteam/sqla_inspect/blob/67edb5541e6a56b0a657d3774d1e19c1110cd402/sqla_inspect/export.py#L308-L326
|
def _merge_many_to_one_field_from_fkey(self, main_infos, prop, result):
"""
Find the relationship associated with this fkey and set the title
:param dict main_infos: The already collected datas about this column
:param obj prop: The property mapper of the relationship
:param list result: The actual collected headers
:returns: a main_infos dict or None
"""
if prop.columns[0].foreign_keys and prop.key.endswith('_id'):
# We have a foreign key, we'll try to merge it with the
# associated foreign key
rel_name = prop.key[0:-3]
for val in result:
if val["name"] == rel_name:
val["label"] = main_infos['label']
main_infos = None # We can forget this field in export
break
return main_infos
|
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"[",
"'label'",
"]",
"main_infos",
"=",
"None",
"# We can forget this field in export",
"break",
"return",
"main_infos"
] |
Find the relationship associated with this fkey and set the title
:param dict main_infos: The already collected datas about this column
:param obj prop: The property mapper of the relationship
:param list result: The actual collected headers
:returns: a main_infos dict or None
|
[
"Find",
"the",
"relationship",
"associated",
"with",
"this",
"fkey",
"and",
"set",
"the",
"title"
] |
python
|
train
|
ellethee/argparseinator
|
argparseinator/__init__.py
|
https://github.com/ellethee/argparseinator/blob/05e9c00dfaa938b9c4ee2aadc6206f5e0918e24e/argparseinator/__init__.py#L552-L555
|
def _self_event(self, event_name, cmd, *pargs, **kwargs):
"""Call self event"""
if hasattr(self, event_name):
getattr(self, event_name)(cmd, *pargs, **kwargs)
|
[
"def",
"_self_event",
"(",
"self",
",",
"event_name",
",",
"cmd",
",",
"*",
"pargs",
",",
"*",
"*",
"kwargs",
")",
":",
"if",
"hasattr",
"(",
"self",
",",
"event_name",
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":",
"getattr",
"(",
"self",
",",
"event_name",
")",
"(",
"cmd",
",",
"*",
"pargs",
",",
"*",
"*",
"kwargs",
")"
] |
Call self event
|
[
"Call",
"self",
"event"
] |
python
|
train
|
10gen/mongo-orchestration
|
mongo_orchestration/sharded_clusters.py
|
https://github.com/10gen/mongo-orchestration/blob/81fd2224205922ea2178b08190b53a33aec47261/mongo_orchestration/sharded_clusters.py#L214-L226
|
def __init_configrs(self, rs_cfg):
"""Create and start a config replica set."""
# Use 'rs_id' to set the id for consistency, but need to rename
# to 'id' to use with ReplicaSets.create()
rs_cfg['id'] = rs_cfg.pop('rs_id', None)
for member in rs_cfg.setdefault('members', [{}]):
member['procParams'] = self._strip_auth(
member.get('procParams', {}))
member['procParams']['configsvr'] = True
if self.enable_ipv6:
common.enable_ipv6_single(member['procParams'])
rs_cfg['sslParams'] = self.sslParams
self._configsvrs.append(ReplicaSets().create(rs_cfg))
|
[
"def",
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":",
"# Use 'rs_id' to set the id for consistency, but need to rename",
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"rs_cfg",
"[",
"'id'",
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"=",
"rs_cfg",
".",
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",",
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"setdefault",
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"_strip_auth",
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"get",
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"}",
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")",
"member",
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"=",
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".",
"enable_ipv6",
":",
"common",
".",
"enable_ipv6_single",
"(",
"member",
"[",
"'procParams'",
"]",
")",
"rs_cfg",
"[",
"'sslParams'",
"]",
"=",
"self",
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"sslParams",
"self",
".",
"_configsvrs",
".",
"append",
"(",
"ReplicaSets",
"(",
")",
".",
"create",
"(",
"rs_cfg",
")",
")"
] |
Create and start a config replica set.
|
[
"Create",
"and",
"start",
"a",
"config",
"replica",
"set",
"."
] |
python
|
train
|
Azure/azure-sdk-for-python
|
azure-servicemanagement-legacy/azure/servicemanagement/servicebusmanagementservice.py
|
https://github.com/Azure/azure-sdk-for-python/blob/d7306fde32f60a293a7567678692bdad31e4b667/azure-servicemanagement-legacy/azure/servicemanagement/servicebusmanagementservice.py#L134-L145
|
def delete_namespace(self, name):
'''
Delete a service bus namespace.
name:
Name of the service bus namespace to delete.
'''
_validate_not_none('name', name)
return self._perform_delete(
self._get_path('services/serviceBus/Namespaces', name),
None)
|
[
"def",
"delete_namespace",
"(",
"self",
",",
"name",
")",
":",
"_validate_not_none",
"(",
"'name'",
",",
"name",
")",
"return",
"self",
".",
"_perform_delete",
"(",
"self",
".",
"_get_path",
"(",
"'services/serviceBus/Namespaces'",
",",
"name",
")",
",",
"None",
")"
] |
Delete a service bus namespace.
name:
Name of the service bus namespace to delete.
|
[
"Delete",
"a",
"service",
"bus",
"namespace",
"."
] |
python
|
test
|
TUNE-Archive/freight_forwarder
|
freight_forwarder/cli/quality_control.py
|
https://github.com/TUNE-Archive/freight_forwarder/blob/6ea4a49f474ec04abb8bb81b175c774a16b5312f/freight_forwarder/cli/quality_control.py#L96-L130
|
def _quality_control(self, args, **extra_args):
"""
Export is the entry point for exporting docker images.
"""
if not isinstance(args, argparse.Namespace):
raise Exception("args should of an instance of argparse.Namespace")
# create new freight forwarder object
# config_override=manifest_override
freight_forwarder = FreightForwarder()
# create commercial invoice this is the contact given to freight forwarder dispatch containers and images
commercial_invoice = freight_forwarder.commercial_invoice(
'quality_control',
args.data_center,
args.environment,
args.service
)
# call quality control with commercial invoice and additional arguments
bill_of_lading = freight_forwarder.quality_control(
commercial_invoice,
attach=args.attach,
clean=args.clean,
test=args.test,
configs=args.configs,
use_cache=args.use_cache,
env=args.env
)
# pretty lame... Need to work on return values through to app to make them consistent.
exit_code = 0 if bill_of_lading else 1
if exit_code != 0:
exit(exit_code)
|
[
"def",
"_quality_control",
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"*",
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"# create new freight forwarder object",
"# config_override=manifest_override",
"freight_forwarder",
"=",
"FreightForwarder",
"(",
")",
"# create commercial invoice this is the contact given to freight forwarder dispatch containers and images",
"commercial_invoice",
"=",
"freight_forwarder",
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"'quality_control'",
",",
"args",
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"data_center",
",",
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"environment",
",",
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"service",
")",
"# call quality control with commercial invoice and additional arguments",
"bill_of_lading",
"=",
"freight_forwarder",
".",
"quality_control",
"(",
"commercial_invoice",
",",
"attach",
"=",
"args",
".",
"attach",
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"clean",
"=",
"args",
".",
"clean",
",",
"test",
"=",
"args",
".",
"test",
",",
"configs",
"=",
"args",
".",
"configs",
",",
"use_cache",
"=",
"args",
".",
"use_cache",
",",
"env",
"=",
"args",
".",
"env",
")",
"# pretty lame... Need to work on return values through to app to make them consistent.",
"exit_code",
"=",
"0",
"if",
"bill_of_lading",
"else",
"1",
"if",
"exit_code",
"!=",
"0",
":",
"exit",
"(",
"exit_code",
")"
] |
Export is the entry point for exporting docker images.
|
[
"Export",
"is",
"the",
"entry",
"point",
"for",
"exporting",
"docker",
"images",
"."
] |
python
|
train
|
apache/incubator-heron
|
heron/tools/cli/src/python/help.py
|
https://github.com/apache/incubator-heron/blob/ad10325a0febe89ad337e561ebcbe37ec5d9a5ac/heron/tools/cli/src/python/help.py#L51-L74
|
def run(command, parser, args, unknown_args):
'''
:param command:
:param parser:
:param args:
:param unknown_args:
:return:
'''
# get the command for detailed help
command_help = args['help-command']
# if no command is provided, just print main help
if command_help == 'help':
parser.print_help()
return SimpleResult(Status.Ok)
# get the subparser for the specific command
subparser = config.get_subparser(parser, command_help)
if subparser:
print(subparser.format_help())
return SimpleResult(Status.Ok)
else:
Log.error("Unknown subcommand \'%s\'", command_help)
return SimpleResult(Status.InvocationError)
|
[
"def",
"run",
"(",
"command",
",",
"parser",
",",
"args",
",",
"unknown_args",
")",
":",
"# get the command for detailed help",
"command_help",
"=",
"args",
"[",
"'help-command'",
"]",
"# if no command is provided, just print main help",
"if",
"command_help",
"==",
"'help'",
":",
"parser",
".",
"print_help",
"(",
")",
"return",
"SimpleResult",
"(",
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"Ok",
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"subparser",
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"config",
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"get_subparser",
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",",
"command_help",
")",
"return",
"SimpleResult",
"(",
"Status",
".",
"InvocationError",
")"
] |
:param command:
:param parser:
:param args:
:param unknown_args:
:return:
|
[
":",
"param",
"command",
":",
":",
"param",
"parser",
":",
":",
"param",
"args",
":",
":",
"param",
"unknown_args",
":",
":",
"return",
":"
] |
python
|
valid
|
PMBio/limix-backup
|
limix/deprecated/archive/varianceDecompositionOld.py
|
https://github.com/PMBio/limix-backup/blob/1e201fdb5c694d0d5506f207f3de65d8ef66146c/limix/deprecated/archive/varianceDecompositionOld.py#L112-L155
|
def addSingleTraitTerm(self,K=None,is_noise=False,normalize=True,Ks=None):
"""
add random effects term for single trait models (no trait-trait covariance matrix)
Args:
K: NxN sample covariance matrix
is_noise: bool labeling the noise term (noise term has K=eye)
normalize: if True, K and Ks are scales such that K.diagonal().mean()==1
Ks: NxN test cross covariance for predictions
"""
assert self.P == 1, 'Incompatible number of traits'
assert K!=None or is_noise, 'Specify covariance structure'
if is_noise:
assert self.noisPos==None, 'noise term already exists'
K = SP.eye(self.Nt)
self.noisPos = self.n_terms
else:
assert K.shape[0]==self.Nt, 'Incompatible shape'
assert K.shape[1]==self.Nt, 'Incompatible shape'
if Ks!=None:
assert Ks.shape[0]==self.N, 'Incompatible shape'
if normalize:
Norm = 1/K.diagonal().mean()
K *= Norm
if Ks!=None: Ks *= Norm
self.vd.addTerm(limix.CSingleTraitTerm(K))
if Ks!=None: self.setKstar(self.n_terms,Ks)
self.n_terms+=1
self.gp = None
self.init = False
self.fast = False
self.optimum = None
self.cache['Sigma'] = None
self.cache['Hessian'] = None
self.cache['Lparams'] = None
self.cache['paramsST']= None
|
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"]",
"=",
"None",
"self",
".",
"cache",
"[",
"'paramsST'",
"]",
"=",
"None"
] |
add random effects term for single trait models (no trait-trait covariance matrix)
Args:
K: NxN sample covariance matrix
is_noise: bool labeling the noise term (noise term has K=eye)
normalize: if True, K and Ks are scales such that K.diagonal().mean()==1
Ks: NxN test cross covariance for predictions
|
[
"add",
"random",
"effects",
"term",
"for",
"single",
"trait",
"models",
"(",
"no",
"trait",
"-",
"trait",
"covariance",
"matrix",
")",
"Args",
":",
"K",
":",
"NxN",
"sample",
"covariance",
"matrix",
"is_noise",
":",
"bool",
"labeling",
"the",
"noise",
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"(",
"noise",
"term",
"has",
"K",
"=",
"eye",
")",
"normalize",
":",
"if",
"True",
"K",
"and",
"Ks",
"are",
"scales",
"such",
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"K",
".",
"diagonal",
"()",
".",
"mean",
"()",
"==",
"1",
"Ks",
":",
"NxN",
"test",
"cross",
"covariance",
"for",
"predictions"
] |
python
|
train
|
UB-UNIBAS/simple-elastic
|
simple_elastic/index.py
|
https://github.com/UB-UNIBAS/simple-elastic/blob/54f2fdd3405a7eafbf8873f337da263b8d47532a/simple_elastic/index.py#L75-L84
|
def create(self):
"""Create the corresponding index. Will overwrite existing indexes of the same name."""
body = dict()
if self.mapping is not None:
body['mappings'] = self.mapping
if self.settings is not None:
body['settings'] = self.settings
else:
body['settings'] = self._default_settings()
self.instance.indices.create(self.index, body)
|
[
"def",
"create",
"(",
"self",
")",
":",
"body",
"=",
"dict",
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")",
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".",
"indices",
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"create",
"(",
"self",
".",
"index",
",",
"body",
")"
] |
Create the corresponding index. Will overwrite existing indexes of the same name.
|
[
"Create",
"the",
"corresponding",
"index",
".",
"Will",
"overwrite",
"existing",
"indexes",
"of",
"the",
"same",
"name",
"."
] |
python
|
train
|
DLR-RM/RAFCON
|
source/rafcon/core/states/state.py
|
https://github.com/DLR-RM/RAFCON/blob/24942ef1a904531f49ab8830a1dbb604441be498/source/rafcon/core/states/state.py#L1410-L1417
|
def is_root_state_of_library(self):
""" If self is the attribute LibraryState.state_copy of a LibraryState its the library root state and its parent
is a LibraryState
:return True or False
:rtype bool
"""
from rafcon.core.states.library_state import LibraryState
return isinstance(self.parent, LibraryState)
|
[
"def",
"is_root_state_of_library",
"(",
"self",
")",
":",
"from",
"rafcon",
".",
"core",
".",
"states",
".",
"library_state",
"import",
"LibraryState",
"return",
"isinstance",
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".",
"parent",
",",
"LibraryState",
")"
] |
If self is the attribute LibraryState.state_copy of a LibraryState its the library root state and its parent
is a LibraryState
:return True or False
:rtype bool
|
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python
|
train
|
OpenGov/carpenter
|
carpenter/blocks/block.py
|
https://github.com/OpenGov/carpenter/blob/0ab3c54c05133b9b0468c63e834a7ce3a6fb575b/carpenter/blocks/block.py#L441-L463
|
def _check_interpret_cell(self, cell, prior_cell, row_index, column_index):
'''
Helper function which checks cell type and performs cell translation to strings where
necessary.
Returns:
A tuple of the form '(cell, changed)' where 'changed' indicates if 'cell' differs from
input.
'''
changed = False
if (not is_empty_cell(cell) and
not is_text_cell(cell)):
self.flag_change(self.flags, 'interpreted', (row_index, column_index),
self.worksheet, self.FLAGS['converted-to-string'])
cell = str(cell)
changed = True
# If we find a blank cell, propagate the prior title
elif is_empty_cell(cell):
self.flag_change(self.flags, 'interpreted', (row_index, column_index),
self.worksheet, self.FLAGS['copied-title'])
cell = prior_cell
changed = True
return cell, changed
|
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Helper function which checks cell type and performs cell translation to strings where
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python
|
train
|
quantmind/pulsar
|
pulsar/utils/config.py
|
https://github.com/quantmind/pulsar/blob/fee44e871954aa6ca36d00bb5a3739abfdb89b26/pulsar/utils/config.py#L594-L611
|
def set(self, val, default=False, imported=False):
"""Set ``val`` as the :attr:`value` for this :class:`Setting`.
If ``default`` is ``True`` set also the :attr:`default` value.
"""
if hasattr(self.validator, '__call__'):
try:
val = self.validator(val)
except Exception as exc:
raise type(exc)(
'Could not validate value for "%s" setting: %s' %
(self.name, exc)
) from None
self.value = val
self.imported = imported
if default:
self.default = val
self.modified = True
|
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Set ``val`` as the :attr:`value` for this :class:`Setting`.
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|
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python
|
train
|
alex-kostirin/pyatomac
|
atomac/AXClasses.py
|
https://github.com/alex-kostirin/pyatomac/blob/3f46f6feb4504315eec07abb18bb41be4d257aeb/atomac/AXClasses.py#L1301-L1308
|
def _convenienceMatch(self, role, attr, match):
"""Method used by role based convenience functions to find a match"""
kwargs = {}
# If the user supplied some text to search for,
# supply that in the kwargs
if match:
kwargs[attr] = match
return self.findAll(AXRole=role, **kwargs)
|
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python
|
valid
|
MisterY/gnucash-portfolio
|
gnucash_portfolio/lib/datetimeutils.py
|
https://github.com/MisterY/gnucash-portfolio/blob/bfaad8345a5479d1cd111acee1939e25c2a638c2/gnucash_portfolio/lib/datetimeutils.py#L15-L19
|
def get_from_gnucash26_date(date_str: str) -> date:
""" Creates a datetime from GnuCash 2.6 date string """
date_format = "%Y%m%d"
result = datetime.strptime(date_str, date_format).date()
return result
|
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Creates a datetime from GnuCash 2.6 date string
|
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"Creates",
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"from",
"GnuCash",
"2",
".",
"6",
"date",
"string"
] |
python
|
train
|
onelogin/python3-saml
|
src/onelogin/saml2/response.py
|
https://github.com/onelogin/python3-saml/blob/064b7275fba1e5f39a9116ba1cdcc5d01fc34daa/src/onelogin/saml2/response.py#L330-L348
|
def check_status(self):
"""
Check if the status of the response is success or not
:raises: Exception. If the status is not success
"""
status = OneLogin_Saml2_Utils.get_status(self.document)
code = status.get('code', None)
if code and code != OneLogin_Saml2_Constants.STATUS_SUCCESS:
splited_code = code.split(':')
printable_code = splited_code.pop()
status_exception_msg = 'The status code of the Response was not Success, was %s' % printable_code
status_msg = status.get('msg', None)
if status_msg:
status_exception_msg += ' -> ' + status_msg
raise OneLogin_Saml2_ValidationError(
status_exception_msg,
OneLogin_Saml2_ValidationError.STATUS_CODE_IS_NOT_SUCCESS
)
|
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Check if the status of the response is success or not
:raises: Exception. If the status is not success
|
[
"Check",
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"or",
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] |
python
|
train
|
ev3dev/ev3dev-lang-python
|
ev3dev2/motor.py
|
https://github.com/ev3dev/ev3dev-lang-python/blob/afc98d35004b533dc161a01f7c966e78607d7c1e/ev3dev2/motor.py#L1962-L1967
|
def on_for_seconds(self, steering, speed, seconds, brake=True, block=True):
"""
Rotate the motors according to the provided ``steering`` for ``seconds``.
"""
(left_speed, right_speed) = self.get_speed_steering(steering, speed)
MoveTank.on_for_seconds(self, SpeedNativeUnits(left_speed), SpeedNativeUnits(right_speed), seconds, brake, block)
|
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Rotate the motors according to the provided ``steering`` for ``seconds``.
|
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"steering",
"for",
"seconds",
"."
] |
python
|
train
|
Galarzaa90/tibia.py
|
tibiapy/character.py
|
https://github.com/Galarzaa90/tibia.py/blob/02ba1a8f1e18177ef5c7dcd44affc8d761d59e12/tibiapy/character.py#L401-L442
|
def _parse_deaths(self, rows):
"""
Parses the character's recent deaths
Parameters
----------
rows: :class:`list` of :class:`bs4.Tag`
A list of all rows contained in the table.
"""
for row in rows:
cols = row.find_all('td')
death_time_str = cols[0].text.replace("\xa0", " ").strip()
death_time = parse_tibia_datetime(death_time_str)
death = str(cols[1]).replace("\xa0", " ")
death_info = death_regexp.search(death)
if death_info:
level = int(death_info.group("level"))
killers_desc = death_info.group("killers")
else:
continue
death = Death(self.name, level, time=death_time)
assists_name_list = []
# Check if the killers list contains assists
assist_match = death_assisted.search(killers_desc)
if assist_match:
# Filter out assists
killers_desc = assist_match.group("killers")
# Split assists into a list.
assists_name_list = self._split_list(assist_match.group("assists"))
killers_name_list = self._split_list(killers_desc)
for killer in killers_name_list:
killer_dict = self._parse_killer(killer)
death.killers.append(Killer(**killer_dict))
for assist in assists_name_list:
# Extract names from character links in assists list.
assist_dict = {"name": link_content.search(assist).group(1), "player": True}
death.assists.append(Killer(**assist_dict))
try:
self.deaths.append(death)
except ValueError:
# Some pvp deaths have no level, so they are raising a ValueError, they will be ignored for now.
continue
|
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Parses the character's recent deaths
Parameters
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rows: :class:`list` of :class:`bs4.Tag`
A list of all rows contained in the table.
|
[
"Parses",
"the",
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"s",
"recent",
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] |
python
|
train
|
tensorpack/tensorpack
|
tensorpack/dataflow/imgaug/geometry.py
|
https://github.com/tensorpack/tensorpack/blob/d7a13cb74c9066bc791d7aafc3b744b60ee79a9f/tensorpack/dataflow/imgaug/geometry.py#L128-L152
|
def largest_rotated_rect(w, h, angle):
"""
Get largest rectangle after rotation.
http://stackoverflow.com/questions/16702966/rotate-image-and-crop-out-black-borders
"""
angle = angle / 180.0 * math.pi
if w <= 0 or h <= 0:
return 0, 0
width_is_longer = w >= h
side_long, side_short = (w, h) if width_is_longer else (h, w)
# since the solutions for angle, -angle and 180-angle are all the same,
# if suffices to look at the first quadrant and the absolute values of sin,cos:
sin_a, cos_a = abs(math.sin(angle)), abs(math.cos(angle))
if side_short <= 2. * sin_a * cos_a * side_long:
# half constrained case: two crop corners touch the longer side,
# the other two corners are on the mid-line parallel to the longer line
x = 0.5 * side_short
wr, hr = (x / sin_a, x / cos_a) if width_is_longer else (x / cos_a, x / sin_a)
else:
# fully constrained case: crop touches all 4 sides
cos_2a = cos_a * cos_a - sin_a * sin_a
wr, hr = (w * cos_a - h * sin_a) / cos_2a, (h * cos_a - w * sin_a) / cos_2a
return int(np.round(wr)), int(np.round(hr))
|
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Get largest rectangle after rotation.
http://stackoverflow.com/questions/16702966/rotate-image-and-crop-out-black-borders
|
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"-",
"and",
"-",
"crop",
"-",
"out",
"-",
"black",
"-",
"borders"
] |
python
|
train
|
softlayer/softlayer-python
|
SoftLayer/managers/account.py
|
https://github.com/softlayer/softlayer-python/blob/9f181be08cc3668353b05a6de0cb324f52cff6fa/SoftLayer/managers/account.py#L94-L118
|
def get_invoices(self, limit=50, closed=False, get_all=False):
"""Gets an accounts invoices.
:param int limit: Number of invoices to get back in a single call.
:param bool closed: If True, will also get CLOSED invoices
:param bool get_all: If True, will paginate through invoices until all have been retrieved.
:return: Billing_Invoice
"""
mask = "mask[invoiceTotalAmount, itemCount]"
_filter = {
'invoices': {
'createDate': {
'operation': 'orderBy',
'options': [{
'name': 'sort',
'value': ['DESC']
}]
},
'statusCode': {'operation': 'OPEN'},
}
}
if closed:
del _filter['invoices']['statusCode']
return self.client.call('Account', 'getInvoices', mask=mask, filter=_filter, iter=get_all, limit=limit)
|
[
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",",
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"_filter",
",",
"iter",
"=",
"get_all",
",",
"limit",
"=",
"limit",
")"
] |
Gets an accounts invoices.
:param int limit: Number of invoices to get back in a single call.
:param bool closed: If True, will also get CLOSED invoices
:param bool get_all: If True, will paginate through invoices until all have been retrieved.
:return: Billing_Invoice
|
[
"Gets",
"an",
"accounts",
"invoices",
"."
] |
python
|
train
|
pmacosta/pexdoc
|
pexdoc/pinspect.py
|
https://github.com/pmacosta/pexdoc/blob/201ac243e5781347feb75896a4231429fe6da4b1/pexdoc/pinspect.py#L989-L1029
|
def visit_Assign(self, node):
"""
Implement assignment walker.
Parse class properties defined via the property() function
"""
# [[[cog
# cog.out("print(pcolor('Enter assign visitor', 'magenta'))")
# ]]]
# [[[end]]]
# ###
# Class-level assignment may also be a class attribute that is not
# a managed attribute, record it anyway, no harm in doing so as it
# is not attached to a callable
if self._in_class(node):
element_full_name = self._pop_indent_stack(node, "prop")
code_id = (self._fname, node.lineno)
self._processed_line = node.lineno
self._callables_db[element_full_name] = {
"name": element_full_name,
"type": "prop",
"code_id": code_id,
"last_lineno": None,
}
self._reverse_callables_db[code_id] = element_full_name
# [[[cog
# code = """
# print(
# pcolor(
# 'Visiting property {0} @ {1}'.format(
# element_full_name, code_id[1]
# ),
# 'green'
# )
# )
# """
# cog.out(code)
# ]]]
# [[[end]]]
# Get property actions
self.generic_visit(node)
|
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"def",
"visit_Assign",
"(",
"self",
",",
"node",
")",
":",
"# [[[cog",
"# cog.out(\"print(pcolor('Enter assign visitor', 'magenta'))\")",
"# ]]]",
"# [[[end]]]",
"# ###",
"# Class-level assignment may also be a class attribute that is not",
"# a managed attribute, record it anyway, no harm in doing so as it",
"# is not attached to a callable",
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".",
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",",
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"{",
"\"name\"",
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",",
"\"code_id\"",
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",",
"\"last_lineno\"",
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"None",
",",
"}",
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".",
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"[",
"code_id",
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"=",
"element_full_name",
"# [[[cog",
"# code = \"\"\"",
"# print(",
"# pcolor(",
"# 'Visiting property {0} @ {1}'.format(",
"# element_full_name, code_id[1]",
"# ),",
"# 'green'",
"# )",
"# )",
"# \"\"\"",
"# cog.out(code)",
"# ]]]",
"# [[[end]]]",
"# Get property actions",
"self",
".",
"generic_visit",
"(",
"node",
")"
] |
Implement assignment walker.
Parse class properties defined via the property() function
|
[
"Implement",
"assignment",
"walker",
"."
] |
python
|
train
|
pydata/pandas-gbq
|
pandas_gbq/gbq.py
|
https://github.com/pydata/pandas-gbq/blob/e590317b3325939ede7563f49aa6b163bb803b77/pandas_gbq/gbq.py#L1328-L1349
|
def exists(self, dataset_id):
""" Check if a dataset exists in Google BigQuery
Parameters
----------
dataset_id : str
Name of dataset to be verified
Returns
-------
boolean
true if dataset exists, otherwise false
"""
from google.api_core.exceptions import NotFound
try:
self.client.get_dataset(self.client.dataset(dataset_id))
return True
except NotFound:
return False
except self.http_error as ex:
self.process_http_error(ex)
|
[
"def",
"exists",
"(",
"self",
",",
"dataset_id",
")",
":",
"from",
"google",
".",
"api_core",
".",
"exceptions",
"import",
"NotFound",
"try",
":",
"self",
".",
"client",
".",
"get_dataset",
"(",
"self",
".",
"client",
".",
"dataset",
"(",
"dataset_id",
")",
")",
"return",
"True",
"except",
"NotFound",
":",
"return",
"False",
"except",
"self",
".",
"http_error",
"as",
"ex",
":",
"self",
".",
"process_http_error",
"(",
"ex",
")"
] |
Check if a dataset exists in Google BigQuery
Parameters
----------
dataset_id : str
Name of dataset to be verified
Returns
-------
boolean
true if dataset exists, otherwise false
|
[
"Check",
"if",
"a",
"dataset",
"exists",
"in",
"Google",
"BigQuery"
] |
python
|
train
|
openstates/billy
|
billy/web/public/views/region.py
|
https://github.com/openstates/billy/blob/5fc795347f12a949e410a8cfad0c911ea6bced67/billy/web/public/views/region.py#L17-L23
|
def region_selection(request):
'''Handle submission of the region selection form in the base template. '''
form = get_region_select_form(request.GET)
abbr = form.data.get('abbr')
if not abbr or len(abbr) != 2:
return redirect('homepage')
return redirect('region', abbr=abbr)
|
[
"def",
"region_selection",
"(",
"request",
")",
":",
"form",
"=",
"get_region_select_form",
"(",
"request",
".",
"GET",
")",
"abbr",
"=",
"form",
".",
"data",
".",
"get",
"(",
"'abbr'",
")",
"if",
"not",
"abbr",
"or",
"len",
"(",
"abbr",
")",
"!=",
"2",
":",
"return",
"redirect",
"(",
"'homepage'",
")",
"return",
"redirect",
"(",
"'region'",
",",
"abbr",
"=",
"abbr",
")"
] |
Handle submission of the region selection form in the base template.
|
[
"Handle",
"submission",
"of",
"the",
"region",
"selection",
"form",
"in",
"the",
"base",
"template",
"."
] |
python
|
train
|
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