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minhhoit/yacms | yacms/core/templatetags/yacms_tags.py | https://github.com/minhhoit/yacms/blob/2921b706b7107c6e8c5f2bbf790ff11f85a2167f/yacms/core/templatetags/yacms_tags.py#L121-L133 | def sort_by(items, attr):
"""
General sort filter - sorts by either attribute or key.
"""
def key_func(item):
try:
return getattr(item, attr)
except AttributeError:
try:
return item[attr]
except TypeError:
getattr(item, attr) # Reraise AttributeError
return sorted(items, key=key_func) | [
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| python | train | 29.076923 |
apple/turicreate | src/unity/python/turicreate/util/__init__.py | https://github.com/apple/turicreate/blob/74514c3f99e25b46f22c6e02977fe3da69221c2e/src/unity/python/turicreate/util/__init__.py#L394-L405 | def _make_temp_filename(prefix):
'''
Generate a temporary file that would not live beyond the lifetime of
unity_server.
Caller is expected to clean up the temp file as soon as the file is no
longer needed. But temp files created using this method will be cleaned up
when unity_server restarts
'''
temp_location = _get_temp_file_location()
temp_file_name = '/'.join([temp_location, str(prefix)+str(_uuid.uuid4())])
return temp_file_name | [
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| python | train | 38.75 |
django-parler/django-parler | parler/views.py | https://github.com/django-parler/django-parler/blob/11ae4af5e8faddb74c69c848870122df4006a54e/parler/views.py#L243-L253 | def get_language_tabs(self):
"""
Determine the language tabs to show.
"""
current_language = self.get_current_language()
if self.object:
available_languages = list(self.object.get_available_languages())
else:
available_languages = []
return get_language_tabs(self.request, current_language, available_languages) | [
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| python | train | 34.727273 |
zhmcclient/python-zhmcclient | zhmcclient/_user_role.py | https://github.com/zhmcclient/python-zhmcclient/blob/9657563e5d9184c51d3c903442a58b9725fdf335/zhmcclient/_user_role.py#L148-L186 | def create(self, properties):
"""
Create a new (user-defined) User Role in this HMC.
Authorization requirements:
* Task permission to the "Manage User Roles" task.
Parameters:
properties (dict): Initial property values.
Allowable properties are defined in section 'Request body contents'
in section 'Create User Role' in the :term:`HMC API` book.
Returns:
UserRole:
The resource object for the new User Role.
The object will have its 'object-uri' property set as returned by
the HMC, and will also have the input properties set.
Raises:
:exc:`~zhmcclient.HTTPError`
:exc:`~zhmcclient.ParseError`
:exc:`~zhmcclient.AuthError`
:exc:`~zhmcclient.ConnectionError`
"""
result = self.session.post(self.console.uri + '/user-roles',
body=properties)
# There should not be overlaps, but just in case there are, the
# returned props should overwrite the input props:
props = copy.deepcopy(properties)
props.update(result)
name = props.get(self._name_prop, None)
uri = props[self._uri_prop]
user_role = UserRole(self, uri, name, props)
self._name_uri_cache.update(name, uri)
return user_role | [
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Raises:
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| python | train | 34.589744 |
tensorflow/tensor2tensor | tensor2tensor/data_generators/wikitext103.py | https://github.com/tensorflow/tensor2tensor/blob/272500b6efe353aeb638d2745ed56e519462ca31/tensor2tensor/data_generators/wikitext103.py#L62-L104 | def _maybe_download_corpus(tmp_dir, vocab_type):
"""Download and unpack the corpus.
Args:
tmp_dir: directory containing dataset.
vocab_type: which vocabulary are we using.
Returns:
The list of names of files.
"""
if vocab_type == text_problems.VocabType.CHARACTER:
dataset_url = ("https://s3.amazonaws.com/research.metamind.io/wikitext"
"/wikitext-103-raw-v1.zip")
dir_name = "wikitext-103-raw"
else:
dataset_url = ("https://s3.amazonaws.com/research.metamind.io/wikitext"
"/wikitext-103-v1.zip")
dir_name = "wikitext-103"
fname = os.path.basename(dataset_url)
compressed_filepath = generator_utils.maybe_download(tmp_dir, fname,
dataset_url)
zip_ref = zipfile.ZipFile(compressed_filepath, "r")
zip_ref.extractall(tmp_dir)
zip_ref.close()
files = os.path.join(tmp_dir, dir_name, "*")
train_file, valid_file, test_file = None, None, None
for f in tf.gfile.Glob(files):
fname = os.path.basename(f)
if "train" in fname:
train_file = f
elif "valid" in fname:
valid_file = f
elif "test" in fname:
test_file = f
assert train_file, "Training file not found"
assert valid_file, "Validation file not found"
assert test_file, "Testing file not found"
return train_file, valid_file, test_file | [
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| python | train | 31.093023 |
ets-labs/python-dependency-injector | examples/providers/dependency.py | https://github.com/ets-labs/python-dependency-injector/blob/d04fe41eb17f667da38b97525e2d16c8f2d272fe/examples/providers/dependency.py#L34-L38 | def create(self, name):
"""Create user with provided name and return his id."""
with contextlib.closing(self.database.cursor()) as cursor:
cursor.execute('INSERT INTO users(name) VALUES (?)', (name,))
return cursor.lastrowid | [
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| python | train | 52 |
sorgerlab/indra | indra/literature/pubmed_client.py | https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/literature/pubmed_client.py#L106-L127 | def get_id_count(search_term):
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Parameters
----------
search_term : str
A term for which the PubMed search should be performed.
Returns
-------
int or None
The number of citations for the query, or None if the query fails.
"""
params = {'term': search_term,
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'db': 'pubmed'}
tree = send_request(pubmed_search, params)
if tree is None:
return None
else:
count = tree.getchildren()[0].text
return int(count) | [
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| python | train | 26.409091 |
jic-dtool/dtoolcore | dtoolcore/storagebroker.py | https://github.com/jic-dtool/dtoolcore/blob/eeb9a924dc8fcf543340653748a7877be1f98e0f/dtoolcore/storagebroker.py#L245-L250 | def put_manifest(self, manifest):
"""Store the manifest."""
logger.debug("Putting manifest")
text = json.dumps(manifest, indent=2, sort_keys=True)
key = self.get_manifest_key()
self.put_text(key, text) | [
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| python | train | 39.333333 |
0compute/xtraceback | xtraceback/xtraceback.py | https://github.com/0compute/xtraceback/blob/5f4ae11cf21e6eea830d79aed66d3cd91bd013cd/xtraceback/xtraceback.py#L115-L120 | def color(self):
"""
Whether or not color should be output
"""
return self.tty_stream if self.options.color is None \
else self.options.color | [
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| python | train | 30 |
codenerix/django-codenerix | codenerix/views.py | https://github.com/codenerix/django-codenerix/blob/1f5527b352141caaee902b37b2648791a06bd57d/codenerix/views.py#L3532-L3668 | def get_filled_structure(self, subgroup=None):
'''
method in charged of filling an structure containing the object fields
values taking into account the 'group' attribute from the corresponding
form object, which is necesary to fill the details form as it is configured
in the 'group' attribute
'''
# initilize the result structure
result = []
# the object corresponding model content is taken into a dictionary
object_content = model_to_dict(self.object)
# generallically some common or specific fields are not interesting
if 'exclude_fields' not in dir(self):
self.exclude_fields = []
self.exclude_fields.append("id")
for field in (self.exclude_fields):
if field in object_content.keys():
object_content.pop(field)
# following is going to be created an structure with the appropieate caption
# for every existing field in the current model
verbose_names = {}
for field in object_content.keys():
verbose_names[field] = self.model._meta.get_field(field).verbose_name
# the found fields in the groups structure are going to be taked into account
gr_object_content = []
if subgroup:
group_array = subgroup
else:
group_array = self.groups
for group in group_array:
# raise Exception(group)
item = {}
item["name"] = smart_text(group[0])
item["col"] = group[1]
item_elements = group[2:]
sublist = []
idx = 0
for item_element in item_elements:
# the element can contains another groups
if (idx > 1) and (type(item_element) == tuple):
# Recursive
sublist.append(self.get_filled_structure([subgroup]))
else:
filter_field = None
# Check if it is a list
if type(item_element) == list:
# if it is a list, that means that can be found the
# corresponding values for colums and any other
field = item_element[0]
# take into account that field caption can be passed as
# third list element
if len(item_element) >= 3 and item_element[2]:
verbose_names[field] = _(item_element[2])
if len(item_element) >= 9:
filter_field = item_element[8]
else:
field = item_element
if field not in verbose_names:
if field.startswith('get_') and field.endswith('_display'):
label_field = remove_getdisplay(field)
if self.model:
try:
verbose_names[field] = self.model._meta.get_field(label_field).verbose_name
except FieldDoesNotExist:
verbose_names[field] = _(label_field)
else:
verbose_names[field] = _(label_field)
else:
label_field = field
verbose_names[field] = _(label_field)
args = {}
value = None
for field_split in field.split('__'):
if value is None:
try:
verbose_names[field] = self.object._meta.get_field(field_split).verbose_name
except AttributeError:
pass
except FieldDoesNotExist:
pass
value = getattr(self.object, field_split, None)
else:
try:
verbose_names[field] = value._meta.get_field(field_split).verbose_name
except AttributeError:
pass
except FieldDoesNotExist:
pass
value = getattr(value, field_split, None)
if callable(value):
# if 'request' in value.func_code.co_varnames:
related = (getattr(value, 'all', None) is not None)
if related:
value = ", ".join([str(x) for x in value.all()])
else:
if 'request' in value.__code__.co_varnames:
args['request'] = self.request
# Call the method
value = value(**args)
sublist.append({
"name": _(verbose_names[field]),
"value": value,
"filter": filter_field,
})
gr_object_content.append(field)
# Increment index
idx += 1
item["value"] = sublist
result.append(item)
for field in object_content.keys():
item = {}
if field not in gr_object_content:
item["name"] = _(verbose_names[field])
item["value"] = getattr(self.object, field)
result.append(item)
return result | [
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| python | train | 40.80292 |
IntegralDefense/vxstreamlib | bin/vxstreamlib.py | https://github.com/IntegralDefense/vxstreamlib/blob/cd82e3975215085cf929c5976f37083b9a3ac869/bin/vxstreamlib.py#L185-L189 | def wait(self):
"""Waits for all submitted jobs to complete."""
logging.info("waiting for {} jobs to complete".format(len(self.submissions)))
while not self.shutdown:
time.sleep(1) | [
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| python | train | 42.4 |
xu2243051/easyui-menu | easyui/utils.py | https://github.com/xu2243051/easyui-menu/blob/4da0b50cf2d3ddb0f1ec7a4da65fd3c4339f8dfb/easyui/utils.py#L21-L48 | def register_views(app_name, view_filename, urlpatterns=None):
"""
app_name APP名
view_filename views 所在的文件
urlpatterns url中已经存在的urlpatterns
return urlpatterns
只导入View结尾的，是类的视图
"""
app_module = __import__(app_name)
view_module = getattr(app_module, view_filename)
views = dir(view_module)
for view_name in views:
if view_name.endswith('View'):
view = getattr(view_module, view_name)
if isinstance(view, object):
if urlpatterns:
urlpatterns += patterns('',
url(r'^(?i)%s/$' % view_name, view.as_view(), name=view_name),
)
else:
urlpatterns = patterns('',
url(r'^(?i)%s/$' % view_name, view.as_view(), name=view_name),
)
else:
pass
return urlpatterns | [
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| python | valid | 33.25 |
5j9/wikitextparser | wikitextparser/_parser_function.py | https://github.com/5j9/wikitextparser/blob/1347425814361d7955342c53212edbb27f0ff4b5/wikitextparser/_parser_function.py#L66-L71 | def name(self) -> str:
"""Return template's name (includes whitespace)."""
h = self._atomic_partition(self._first_arg_sep)[0]
if len(h) == len(self.string):
return h[2:-2]
return h[2:] | [
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| python | test | 37.166667 |
samirelanduk/quickplots | quickplots/charts.py | https://github.com/samirelanduk/quickplots/blob/59f5e6ff367b2c1c24ba7cf1805d03552034c6d8/quickplots/charts.py#L427-L458 | def x_upper_limit(self, limit=None):
"""Returns or sets (if a value is provided) the value at which the
x-axis should end. By default this is the highest x value in the
associated series.
:param limit: If given, the chart's x_upper_limit will be set to this.
:raises ValueError: if you try to make the upper limit smaller than the\
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if limit is None:
if self._x_upper_limit is None:
if self.smallest_x() == self.largest_x():
if int(self.largest_x()) == float(self.largest_x()):
return self.largest_x() + 1
else:
return math.ceil(self.largest_x())
else:
return self.largest_x()
else:
return self._x_upper_limit
else:
if not is_numeric(limit):
raise TypeError(
"upper x limit must be numeric, not '%s'" % str(limit)
)
if limit <= self.smallest_x():
raise ValueError(
"upper x limit must be greater than lower limit (%s), not %s" % (
str(self.smallest_x()), str(limit)
)
)
self._x_upper_limit = limit | [
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| python | train | 40.5 |
p3trus/slave | slave/quantum_design/ppms.py | https://github.com/p3trus/slave/blob/bdc74e73bd0f47b74a090c43aa2283c469cde3be/slave/quantum_design/ppms.py#L444-L452 | def beep(self, duration, frequency):
"""Generates a beep.
:param duration: The duration in seconds, in the range 0.1 to 5.
:param frequency: The frequency in Hz, in the range 500 to 5000.
"""
cmd = 'BEEP', [Float(min=0.1, max=5.0), Integer(min=500, max=5000)]
self._write(cmd, duration, frequency) | [
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| python | train | 37.666667 |
saltstack/salt | salt/modules/vsphere.py | https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/modules/vsphere.py#L9493-L9529 | def power_on_vm(name, datacenter=None, service_instance=None):
'''
Powers on a virtual machine specified by it's name.
name
Name of the virtual machine
datacenter
Datacenter of the virtual machine
service_instance
Service instance (vim.ServiceInstance) of the vCenter.
Default is None.
.. code-block:: bash
salt '*' vsphere.power_on_vm name=my_vm
'''
log.trace('Powering on virtual machine %s', name)
vm_properties = [
'name',
'summary.runtime.powerState'
]
virtual_machine = salt.utils.vmware.get_vm_by_property(
service_instance,
name,
datacenter=datacenter,
vm_properties=vm_properties)
if virtual_machine['summary.runtime.powerState'] == 'poweredOn':
result = {'comment': 'Virtual machine is already powered on',
'changes': {'power_on': True}}
return result
salt.utils.vmware.power_cycle_vm(virtual_machine['object'], action='on')
result = {'comment': 'Virtual machine power on action succeeded',
'changes': {'power_on': True}}
return result | [
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Datacenter of the virtual machine
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Service instance (vim.ServiceInstance) of the vCenter.
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.. code-block:: bash
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| python | train | 30.027027 |
i3visio/deepify | deepify/tor.py | https://github.com/i3visio/deepify/blob/2af04e0bea3eaabe96b0565e10f7eeb29b042a2b/deepify/tor.py#L53-L93 | def _grabContentFromUrl(self, url):
"""
Function that abstracts capturing a URL. This method rewrites the one from Wrapper.
:param url: The URL to be processed.
:return: The response in a Json format.
"""
# Defining an empty object for the response
response = {}
# This part has to be modified...
try:
# Configuring the socket
socks.setdefaultproxy(socks.PROXY_TYPE_SOCKS5, self.info["host"], int(self.info["port"]), True)
s = socks.socksocket()
# Extracting the domain from the URL
domain = self.getDomainFromUrl(url)
s.connect((domain, 80))
message = 'GET ' + url + ' HTTP/1.0\r\n\r\n'
s.sendall(message)
data = ""
while True:
reply = s.recv(4096)
if not reply:
break
else:
data += reply
# Processing data as expected
response = self._createDataStructure(data)
# Try to make the errors clear for other users
except socks.ProxyConnectionError, sPCE:
errMsg = "ERROR socks.ProxyConnectionError. Something seems to be wrong with the Tor Bundler."
raise Exception( errMsg + " " + str(sPCE))
return response | [
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| python | train | 36.121951 |
msoulier/tftpy | tftpy/TftpStates.py | https://github.com/msoulier/tftpy/blob/af2f2fe89a3bf45748b78703820efb0986a8207a/tftpy/TftpStates.py#L55-L80 | def returnSupportedOptions(self, options):
"""This method takes a requested options list from a client, and
returns the ones that are supported."""
# We support the options blksize and tsize right now.
# FIXME - put this somewhere else?
accepted_options = {}
for option in options:
if option == 'blksize':
# Make sure it's valid.
if int(options[option]) > MAX_BLKSIZE:
log.info("Client requested blksize greater than %d "
"setting to maximum" % MAX_BLKSIZE)
accepted_options[option] = MAX_BLKSIZE
elif int(options[option]) < MIN_BLKSIZE:
log.info("Client requested blksize less than %d "
"setting to minimum" % MIN_BLKSIZE)
accepted_options[option] = MIN_BLKSIZE
else:
accepted_options[option] = options[option]
elif option == 'tsize':
log.debug("tsize option is set")
accepted_options['tsize'] = 0
else:
log.info("Dropping unsupported option '%s'" % option)
log.debug("Returning these accepted options: %s", accepted_options)
return accepted_options | [
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| python | train | 49.807692 |
csparpa/pyowm | pyowm/commons/tile.py | https://github.com/csparpa/pyowm/blob/cdd59eb72f32f7238624ceef9b2e2329a5ebd472/pyowm/commons/tile.py#L71-L87 | def geoocoords_to_tile_coords(cls, lon, lat, zoom):
"""
Calculates the tile numbers corresponding to the specified geocoordinates at the specified zoom level
Coordinates shall be provided in degrees and using the Mercator Projection (http://en.wikipedia.org/wiki/Mercator_projection)
:param lon: longitude
:type lon: int or float
:param lat: latitude
:type lat: int or float
:param zoom: zoom level
:type zoom: int
:return: a tuple (x, y) containing the tile-coordinates
"""
n = 2.0 ** zoom
x = int((lon + 180.0) / 360.0 * n)
y = int((1.0 - math.log(math.tan(math.radians(lat)) + (1 / math.cos(math.radians(lat)))) / math.pi) / 2.0 * n)
return x, y | [
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| python | train | 44.294118 |
RedHatInsights/insights-core | insights/parsers/oracle.py | https://github.com/RedHatInsights/insights-core/blob/b57cbf8ed7c089672426ede0441e0a4f789ef4a1/insights/parsers/oracle.py#L18-L41 | def _parse_oracle(lines):
"""
Performs the actual file parsing, returning a dict of the config values
in a given Oracle DB config file.
Despite their differences, the two filetypes are similar enough to
allow idential parsing.
"""
config = {}
for line in get_active_lines(lines):
# Check for NULL in line to begin control char removal
if '\00' in line:
line = cleanup.sub('', line)
if '=' in line:
(key, value) = line.split('=', 1)
key = key.strip(whitespace + '"\'').lower()
if ',' in line:
value = [s.strip(whitespace + '"\'').lower() for s in value.split(',')]
else:
value = value.strip(whitespace + '"\'').lower()
config[key] = value
return config | [
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| python | train | 33.125 |
openstack/networking-cisco | networking_cisco/apps/saf/agent/vdp/ovs_vdp.py | https://github.com/openstack/networking-cisco/blob/aa58a30aec25b86f9aa5952b0863045975debfa9/networking_cisco/apps/saf/agent/vdp/ovs_vdp.py#L205-L236 | def _flow_check_handler_internal(self):
"""Periodic handler to check if installed flows are present.
This handler runs periodically to check if installed flows are present.
This function cannot detect and delete the stale flows, if present.
It requires more complexity to delete stale flows. Generally, stale
flows are not present. So, that logic is not put here.
"""
integ_flow = self.integ_br_obj.dump_flows_for(
in_port=self.int_peer_port_num)
ext_flow = self.ext_br_obj.dump_flows_for(
in_port=self.phy_peer_port_num)
for net_uuid, lvm in six.iteritems(self.local_vlan_map):
vdp_vlan = lvm.any_consistent_vlan()
flow_required = False
if not (vdp_vlan and ovs_lib.is_valid_vlan_tag(vdp_vlan)):
return
if not self._check_bridge_flow(integ_flow, vdp_vlan, lvm.lvid):
LOG.error("Flow for VDP Vlan %(vdp_vlan)s, Local vlan "
"%(lvid)s not present on Integ bridge",
{'vdp_vlan': vdp_vlan, 'lvid': lvm.lvid})
flow_required = True
if not self._check_bridge_flow(ext_flow, lvm.lvid, vdp_vlan):
LOG.error("Flow for VDP Vlan %(vdp_vlan)s, Local vlan "
"%(lvid)s not present on External bridge",
{'vdp_vlan': vdp_vlan, 'lvid': lvm.lvid})
flow_required = True
if flow_required:
LOG.info("Programming flows for lvid %(lvid)s vdp vlan"
" %(vdp)s",
{'lvid': lvm.lvid, 'vdp': vdp_vlan})
self.program_vm_ovs_flows(lvm.lvid, 0, vdp_vlan) | [
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This function cannot detect and delete the stale flows, if present.
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| python | train | 53.9375 |
googlefonts/fontbakery | Lib/fontbakery/profiles/googlefonts.py | https://github.com/googlefonts/fontbakery/blob/b355aea2e619a4477769e060d24c32448aa65399/Lib/fontbakery/profiles/googlefonts.py#L2029-L2061 | def com_google_fonts_check_metadata_italic_style(ttFont, font_metadata):
"""METADATA.pb font.style "italic" matches font internals?"""
from fontbakery.utils import get_name_entry_strings
from fontbakery.constants import MacStyle
if font_metadata.style != "italic":
yield SKIP, "This check only applies to italic fonts."
else:
font_fullname = get_name_entry_strings(ttFont, NameID.FULL_FONT_NAME)
if len(font_fullname) == 0:
yield SKIP, "Font lacks fullname entries in name table."
# this fail scenario was already checked above
# (passing those previous checks is a prerequisite for this one)
# FIXME: Could we pack this into a condition ?
else:
# FIXME: here we only check the first name entry.
# Should we iterate over them all ? Or should we check
# if they're all the same?
font_fullname = font_fullname[0]
if not bool(ttFont["head"].macStyle & MacStyle.ITALIC):
yield FAIL, Message("bad-macstyle",
"METADATA.pb style has been set to italic"
" but font macStyle is improperly set.")
elif not font_fullname.split("-")[-1].endswith("Italic"):
yield FAIL, Message("bad-fullfont-name",
("Font macStyle Italic bit is set"
" but nameID {} (\"{}\") is not ended with"
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font_fullname))
else:
yield PASS, ("OK: METADATA.pb font.style \"italic\""
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| python | train | 49.272727 |
alerta/python-alerta-client | alertaclient/commands/cmd_top.py | https://github.com/alerta/python-alerta-client/blob/7eb367b5fe87d5fc20b54dea8cddd7f09e251afa/alertaclient/commands/cmd_top.py#L9-L15 | def cli(obj):
"""Display alerts like unix "top" command."""
client = obj['client']
timezone = obj['timezone']
screen = Screen(client, timezone)
screen.run() | [
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| Display alerts like unix "top" command. | [
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| python | train | 24.428571 |
watchforstock/evohome-client | evohomeclient2/__init__.py | https://github.com/watchforstock/evohome-client/blob/f1cb9273e97946d79c0651f00a218abbf7ada53a/evohomeclient2/__init__.py#L236-L243 | def gateway(self):
"""Return the detail of the gateway."""
url = 'https://tccna.honeywell.com/WebAPI/emea/api/v1/gateway'
response = requests.get(url, headers=self._headers())
response.raise_for_status()
return response.json() | [
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| python | train | 32.625 |
Becksteinlab/GromacsWrapper | gromacs/setup.py | https://github.com/Becksteinlab/GromacsWrapper/blob/d4f9a8cb6f48292732cf7c7e4ef4a6d2ccbc51b9/gromacs/setup.py#L761-L822 | def em_schedule(**kwargs):
"""Run multiple energy minimizations one after each other.
:Keywords:
*integrators*
list of integrators (from 'l-bfgs', 'cg', 'steep')
[['bfgs', 'steep']]
*nsteps*
list of maximum number of steps; one for each integrator in
in the *integrators* list [[100,1000]]
*kwargs*
mostly passed to :func:`gromacs.setup.energy_minimize`
:Returns: dictionary with paths to final structure ('struct') and
other files
:Example:
Conduct three minimizations:
1. low memory Broyden-Goldfarb-Fletcher-Shannon (BFGS) for 30 steps
2. steepest descent for 200 steps
3. finish with BFGS for another 30 steps
We also do a multi-processor minimization when possible (i.e. for steep
(and conjugate gradient) by using a :class:`gromacs.run.MDrunner` class
for a :program:`mdrun` executable compiled for OpenMP in 64 bit (see
:mod:`gromacs.run` for details)::
import gromacs.run
gromacs.setup.em_schedule(struct='solvate/ionized.gro',
mdrunner=gromacs.run.MDrunnerOpenMP64,
integrators=['l-bfgs', 'steep', 'l-bfgs'],
nsteps=[50,200, 50])
.. Note:: You might have to prepare the mdp file carefully because at the
moment one can only modify the *nsteps* parameter on a
per-minimizer basis.
"""
mdrunner = kwargs.pop('mdrunner', None)
integrators = kwargs.pop('integrators', ['l-bfgs', 'steep'])
kwargs.pop('integrator', None) # clean input; we set intgerator from integrators
nsteps = kwargs.pop('nsteps', [100, 1000])
outputs = ['em{0:03d}_{1!s}.pdb'.format(i, integrator) for i,integrator in enumerate(integrators)]
outputs[-1] = kwargs.pop('output', 'em.pdb')
files = {'struct': kwargs.pop('struct', None)} # fake output from energy_minimize()
for i, integrator in enumerate(integrators):
struct = files['struct']
logger.info("[em %d] energy minimize with %s for maximum %d steps", i, integrator, nsteps[i])
kwargs.update({'struct':struct, 'output':outputs[i],
'integrator':integrator, 'nsteps': nsteps[i]})
if not integrator == 'l-bfgs':
kwargs['mdrunner'] = mdrunner
else:
kwargs['mdrunner'] = None
logger.warning("[em %d] Not using mdrunner for L-BFGS because it cannot "
"do parallel runs.", i)
files = energy_minimize(**kwargs)
return files | [
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*nsteps*
list of maximum number of steps; one for each integrator in
in the *integrators* list [[100,1000]]
*kwargs*
mostly passed to :func:`gromacs.setup.energy_minimize`
:Returns: dictionary with paths to final structure ('struct') and
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:Example:
Conduct three minimizations:
1. low memory Broyden-Goldfarb-Fletcher-Shannon (BFGS) for 30 steps
2. steepest descent for 200 steps
3. finish with BFGS for another 30 steps
We also do a multi-processor minimization when possible (i.e. for steep
(and conjugate gradient) by using a :class:`gromacs.run.MDrunner` class
for a :program:`mdrun` executable compiled for OpenMP in 64 bit (see
:mod:`gromacs.run` for details)::
import gromacs.run
gromacs.setup.em_schedule(struct='solvate/ionized.gro',
mdrunner=gromacs.run.MDrunnerOpenMP64,
integrators=['l-bfgs', 'steep', 'l-bfgs'],
nsteps=[50,200, 50])
.. Note:: You might have to prepare the mdp file carefully because at the
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| python | valid | 41.145161 |
h2oai/h2o-3 | h2o-py/h2o/frame.py | https://github.com/h2oai/h2o-3/blob/dd62aaa1e7f680a8b16ee14bc66b0fb5195c2ad8/h2o-py/h2o/frame.py#L2924-L2930 | def toupper(self):
"""
Translate characters from lower to upper case for a particular column.
:returns: new H2OFrame with all strings in the current frame converted to the uppercase.
"""
return H2OFrame._expr(expr=ExprNode("toupper", self), cache=self._ex._cache) | [
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| python | test | 42.571429 |
caffeinehit/django-oauth2-provider | provider/views.py | https://github.com/caffeinehit/django-oauth2-provider/blob/6b5bc0d3ad706d2aaa47fa476f38406cddd01236/provider/views.py#L60-L68 | def cache_data(self, request, data, key='params'):
"""
Cache data in the session store.
:param request: :attr:`django.http.HttpRequest`
:param data: Arbitrary data to store.
:param key: `str` The key under which to store the data.
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| python | train | 38.444444 |
bykof/billomapy | billomapy/billomapy.py | https://github.com/bykof/billomapy/blob/a28ba69fd37654fa145d0411d52c200e7f8984ab/billomapy/billomapy.py#L2187-L2198 | def mark_offer_as_lose(self, offer_id):
"""
Mark offer as lose
:param offer_id: the offer id
:return Response
"""
return self._create_put_request(
resource=OFFERS,
billomat_id=offer_id,
command=LOSE,
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| python | train | 23.583333 |
tensorflow/tensor2tensor | tensor2tensor/trax/trax.py | https://github.com/tensorflow/tensor2tensor/blob/272500b6efe353aeb638d2745ed56e519462ca31/tensor2tensor/trax/trax.py#L336-L348 | def _reshape_by_device_single(x, num_devices):
"""Reshape x into a shape [num_devices, ...]."""
x_shape = list(x.shape)
batch_size = x_shape[0]
batch_size_per_device = batch_size // num_devices
# We require that num_devices divides batch_size evenly.
if batch_size_per_device * num_devices != batch_size:
logging.fatal(
"We require that num_devices[%d] divides batch_size[%d] evenly.",
num_devices, batch_size)
# New shape.
new_shape_prefix = [num_devices, batch_size_per_device]
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| python | train | 42.923077 |
jonathf/chaospy | chaospy/descriptives/expected.py | https://github.com/jonathf/chaospy/blob/25ecfa7bf5608dc10c0b31d142ded0e3755f5d74/chaospy/descriptives/expected.py#L7-L69 | def E(poly, dist=None, **kws):
"""
Expected value operator.
1st order statistics of a probability distribution or polynomial on a given
probability space.
Args:
poly (Poly, Dist):
Input to take expected value on.
dist (Dist):
Defines the space the expected value is taken on. It is ignored if
``poly`` is a distribution.
Returns:
(numpy.ndarray):
The expected value of the polynomial or distribution, where
``expected.shape == poly.shape``.
Examples:
>>> dist = chaospy.J(chaospy.Gamma(1, 1), chaospy.Normal(0, 2))
>>> print(chaospy.E(dist))
[1. 0.]
>>> x, y = chaospy.variable(2)
>>> poly = chaospy.Poly([1, x, y, 10*x*y])
>>> print(chaospy.E(poly, dist))
[1. 1. 0. 0.]
"""
if not isinstance(poly, (distributions.Dist, polynomials.Poly)):
print(type(poly))
print("Approximating expected value...")
out = quadrature.quad(poly, dist, veceval=True, **kws)
print("done")
return out
if isinstance(poly, distributions.Dist):
dist, poly = poly, polynomials.variable(len(poly))
if not poly.keys:
return numpy.zeros(poly.shape, dtype=int)
if isinstance(poly, (list, tuple, numpy.ndarray)):
return [E(_, dist, **kws) for _ in poly]
if poly.dim < len(dist):
poly = polynomials.setdim(poly, len(dist))
shape = poly.shape
poly = polynomials.flatten(poly)
keys = poly.keys
mom = dist.mom(numpy.array(keys).T, **kws)
A = poly.A
if len(dist) == 1:
mom = mom[0]
out = numpy.zeros(poly.shape)
for i in range(len(keys)):
out += A[keys[i]]*mom[i]
out = numpy.reshape(out, shape)
return out | [
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Returns:
(numpy.ndarray):
The expected value of the polynomial or distribution, where
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>>> dist = chaospy.J(chaospy.Gamma(1, 1), chaospy.Normal(0, 2))
>>> print(chaospy.E(dist))
[1. 0.]
>>> x, y = chaospy.variable(2)
>>> poly = chaospy.Poly([1, x, y, 10*x*y])
>>> print(chaospy.E(poly, dist))
[1. 1. 0. 0.] | [
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| python | train | 27.634921 |
bwhite/hadoopy | hadoopy/thirdparty/pyinstaller/PyInstaller/lib/pefile.py | https://github.com/bwhite/hadoopy/blob/ff39b4e6d4e6efaf1f571cf0f2c0e0d7ab28c2d6/hadoopy/thirdparty/pyinstaller/PyInstaller/lib/pefile.py#L663-L676 | def ask_pascal_16(self, next_rva_ptr):
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length = self.__get_pascal_16_length()
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self.length = length
return True
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| python | train | 34.357143 |
senaite/senaite.core | bika/lims/exportimport/instruments/sysmex/xt/i1800.py | https://github.com/senaite/senaite.core/blob/7602ce2ea2f9e81eb34e20ce17b98a3e70713f85/bika/lims/exportimport/instruments/sysmex/xt/i1800.py#L142-L155 | def _handle_result_line(self, sline):
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Parses the data line and adds to the dictionary.
:param sline: a split data line to parse
:returns: the number of rows to jump and parse the next data line or
return the code error -1
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as_kw = sline[3]
a_result = str(sline[5].split('^')[0])
self._cur_values[as_kw] = {
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return 0 | [
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:param sline: a split data line to parse
:returns: the number of rows to jump and parse the next data line or
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| python | train | 33.5 |
micha030201/aionationstates | aionationstates/nation_.py | https://github.com/micha030201/aionationstates/blob/dc86b86d994cbab830b69ab8023601c73e778b3a/aionationstates/nation_.py#L502-L519 | async def freedomscores(self, root):
"""Nation's `Freedoms`: three basic indicators of the nation's
Civil Rights, Economy, and Political Freedom, as percentages.
Returns
-------
an :class:`ApiQuery` of :class:`collections.OrderedDict` with \
keys of str and values of int
Keys being, in order: ``Civil Rights``, ``Economy``, and
``Political Freedom``.
"""
elem = root.find('FREEDOMSCORES')
result = OrderedDict()
result['Civil Rights'] = int(elem.find('CIVILRIGHTS').text)
result['Economy'] = int(elem.find('ECONOMY').text)
result['Political Freedom'] = int(elem.find('POLITICALFREEDOM').text)
return result | [
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| python | train | 40 |
EnergieID/smappy | smappy/smappy.py | https://github.com/EnergieID/smappy/blob/1ada3abc9a51c76205c072369258f6f4f4e8fd0f/smappy/smappy.py#L276-L311 | def get_events(self, service_location_id, appliance_id, start, end,
max_number=None):
"""
Request events for a given appliance
Parameters
----------
service_location_id : int
appliance_id : int
start : int | dt.datetime | pd.Timestamp
end : int | dt.datetime | pd.Timestamp
start and end support epoch (in milliseconds),
datetime and Pandas Timestamp
timezone-naive datetimes are assumed to be in UTC
max_number : int, optional
The maximum number of events that should be returned by this query
Default returns all events in the selected period
Returns
-------
dict
"""
start = self._to_milliseconds(start)
end = self._to_milliseconds(end)
url = urljoin(URLS['servicelocation'], service_location_id, "events")
headers = {"Authorization": "Bearer {}".format(self.access_token)}
params = {
"from": start,
"to": end,
"applianceId": appliance_id,
"maxNumber": max_number
}
r = requests.get(url, headers=headers, params=params)
r.raise_for_status()
return r.json() | [
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end : int | dt.datetime | pd.Timestamp
start and end support epoch (in milliseconds),
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| python | train | 34.166667 |
tanghaibao/jcvi | jcvi/assembly/bambus.py | https://github.com/tanghaibao/jcvi/blob/d2e31a77b6ade7f41f3b321febc2b4744d1cdeca/jcvi/assembly/bambus.py#L22-L99 | def scaffold(args):
"""
%prog scaffold ctgfasta reads1.fasta mapping1.bed
reads2.fasta mapping2.bed ...
Run BAMBUS on set of contigs, reads and read mappings.
"""
from jcvi.formats.base import FileMerger
from jcvi.formats.bed import mates
from jcvi.formats.contig import frombed
from jcvi.formats.fasta import join
from jcvi.utils.iter import grouper
p = OptionParser(scaffold.__doc__)
p.set_rclip(rclip=1)
p.add_option("--conf", help="BAMBUS configuration file [default: %default]")
p.add_option("--prefix", default=False, action="store_true",
help="Only keep links between IDs with same prefix [default: %default]")
opts, args = p.parse_args(args)
nargs = len(args)
if nargs < 3 or nargs % 2 != 1:
sys.exit(not p.print_help())
rclip = opts.rclip
ctgfasta = args[0]
duos = list(grouper(args[1:], 2))
trios = []
for fastafile, bedfile in duos:
prefix = bedfile.rsplit(".", 1)[0]
matefile = prefix + ".mates"
matebedfile = matefile + ".bed"
if need_update(bedfile, [matefile, matebedfile]):
matesopt = [bedfile, "--lib", "--nointra",
"--rclip={0}".format(rclip),
"--cutoff={0}".format(opts.cutoff)]
if opts.prefix:
matesopt += ["--prefix"]
matefile, matebedfile = mates(matesopt)
trios.append((fastafile, matebedfile, matefile))
# Merge the readfasta, bedfile and matefile
bbfasta, bbbed, bbmate = "bambus.reads.fasta", "bambus.bed", "bambus.mates"
for files, outfile in zip(zip(*trios), (bbfasta, bbbed, bbmate)):
FileMerger(files, outfile=outfile).merge(checkexists=True)
ctgfile = "bambus.contig"
idsfile = "bambus.ids"
frombedInputs = [bbbed, ctgfasta, bbfasta]
if need_update(frombedInputs, ctgfile):
frombed(frombedInputs)
inputfasta = "bambus.contigs.fasta"
singletonfasta = "bambus.singletons.fasta"
cmd = "faSomeRecords {0} {1} ".format(ctgfasta, idsfile)
sh(cmd + inputfasta)
sh(cmd + singletonfasta + " -exclude")
# Run bambus
prefix = "bambus"
cmd = "goBambus -c {0} -m {1} -o {2}".format(ctgfile, bbmate, prefix)
if opts.conf:
cmd += " -C {0}".format(opts.conf)
sh(cmd)
cmd = "untangle -e {0}.evidence.xml -s {0}.out.xml -o {0}.untangle.xml".\
format(prefix)
sh(cmd)
final = "final"
cmd = "printScaff -e {0}.evidence.xml -s {0}.untangle.xml -l {0}.lib " \
"-merge -detail -oo -sum -o {1}".format(prefix, final)
sh(cmd)
oofile = final + ".oo"
join([inputfasta, "--oo={0}".format(oofile)]) | [
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| %prog scaffold ctgfasta reads1.fasta mapping1.bed
reads2.fasta mapping2.bed ...
Run BAMBUS on set of contigs, reads and read mappings. | [
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| python | train | 33.961538 |
majerteam/sqla_inspect | sqla_inspect/py3o.py | https://github.com/majerteam/sqla_inspect/blob/67edb5541e6a56b0a657d3774d1e19c1110cd402/sqla_inspect/py3o.py#L205-L226 | def gen_xml_doc(self):
"""
Generate the text tags that should be inserted in the content.xml of a
full model
"""
res = self.make_doc()
var_tag = """
<text:user-field-decl office:value-type="string"
office:string-value="%s" text:name="py3o.%s"/>"""
text_tag = """<text:p text:style-name="P1">
<text:user-field-get text:name="py3o.%s">%s</text:user-field-get>
</text:p>
"""
keys = res.keys()
keys.sort()
texts = ""
vars = ""
for key in keys:
value = res[key]
vars += var_tag % (value, key)
texts += text_tag % (key, value)
return CONTENT_TMPL % (vars, texts) | [
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| python | train | 32.681818 |
isambard-uob/ampal | src/ampal/dssp.py | https://github.com/isambard-uob/ampal/blob/906e2afacb435ffb129b381f262ff8e7bfb324c5/src/ampal/dssp.py#L111-L163 | def find_ss_regions(dssp_residues, loop_assignments=(' ', 'B', 'S', 'T')):
"""Separates parsed DSSP data into groups of secondary structure.
Notes
-----
Example: all residues in a single helix/loop/strand will be gathered
into a list, then the next secondary structure element will be
gathered into a separate list, and so on.
Parameters
----------
dssp_residues : [tuple]
Each internal list contains:
[0] int Residue number
[1] str Secondary structure type
[2] str Chain identifier
[3] str Residue type
[4] float Phi torsion angle
[5] float Psi torsion angle
[6] int dssp solvent accessibility
Returns
-------
fragments : [[list]]
Lists grouped in continuous regions of secondary structure.
Innermost list has the same format as above.
"""
loops = loop_assignments
previous_ele = None
fragment = []
fragments = []
for ele in dssp_residues:
if previous_ele is None:
fragment.append(ele)
elif ele[2] != previous_ele[2]:
fragments.append(fragment)
fragment = [ele]
elif previous_ele[1] in loops:
if ele[1] in loops:
fragment.append(ele)
else:
fragments.append(fragment)
fragment = [ele]
else:
if ele[1] == previous_ele[1]:
fragment.append(ele)
else:
fragments.append(fragment)
fragment = [ele]
previous_ele = ele
fragments.append(fragment)
return fragments | [
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| Separates parsed DSSP data into groups of secondary structure.
Notes
-----
Example: all residues in a single helix/loop/strand will be gathered
into a list, then the next secondary structure element will be
gathered into a separate list, and so on.
Parameters
----------
dssp_residues : [tuple]
Each internal list contains:
[0] int Residue number
[1] str Secondary structure type
[2] str Chain identifier
[3] str Residue type
[4] float Phi torsion angle
[5] float Psi torsion angle
[6] int dssp solvent accessibility
Returns
-------
fragments : [[list]]
Lists grouped in continuous regions of secondary structure.
Innermost list has the same format as above. | [
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]
| python | train | 30.45283 |
alphatwirl/alphatwirl | alphatwirl/selection/factories/expand.py | https://github.com/alphatwirl/alphatwirl/blob/5138eeba6cd8a334ba52d6c2c022b33c61e3ba38/alphatwirl/selection/factories/expand.py#L4-L20 | def expand_path_cfg(path_cfg, alias_dict={ }, overriding_kargs={ }):
"""expand a path config
Args:
path_cfg (str, tuple, dict): a config for path
alias_dict (dict): a dict for aliases
overriding_kargs (dict): to be used for recursive call
"""
if isinstance(path_cfg, str):
return _expand_str(path_cfg, alias_dict, overriding_kargs)
if isinstance(path_cfg, dict):
return _expand_dict(path_cfg, alias_dict)
# assume tuple or list
return _expand_tuple(path_cfg, alias_dict, overriding_kargs) | [
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Args:
path_cfg (str, tuple, dict): a config for path
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| python | valid | 32 |
jxtech/wechatpy | wechatpy/client/api/customservice.py | https://github.com/jxtech/wechatpy/blob/4df0da795618c0895a10f1c2cde9e9d5c0a93aaa/wechatpy/client/api/customservice.py#L92-L110 | def upload_headimg(self, account, media_file):
"""
上传客服账号头像
详情请参考
http://mp.weixin.qq.com/wiki/1/70a29afed17f56d537c833f89be979c9.html
:param account: 完整客服账号
:param media_file: 要上传的头像文件，一个 File-Object
:return: 返回的 JSON 数据包
"""
return self._post(
'https://api.weixin.qq.com/customservice/kfaccount/uploadheadimg',
params={
'kf_account': account
},
files={
'media': media_file
}
) | [
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:param account: 完整客服账号
:param media_file: 要上传的头像文件，一个 File-Object
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| python | train | 28.052632 |
numenta/nupic | src/nupic/algorithms/utils.py | https://github.com/numenta/nupic/blob/5922fafffdccc8812e72b3324965ad2f7d4bbdad/src/nupic/algorithms/utils.py#L86-L103 | def transferCoincidences(network, fromElementName, toElementName):
"""
Gets the coincidence matrix from one element and sets it on
another element
(using locked handles, a la nupic.bindings.research.lockHandle).
TODO: Generalize to more node types, parameter name pairs, etc.
Does not work across processes.
"""
coincidenceHandle = getLockedHandle(
runtimeElement=network.getElement(fromElementName),
# TODO: Re-purpose for use with nodes other than PMXClassifierNode.
expression="self._cd._W"
)
network.getElement(toElementName).setParameter("coincidencesAbove",
coincidenceHandle) | [
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| python | valid | 34.111111 |
chromy/essence | src/essence/world.py | https://github.com/chromy/essence/blob/6cd18821ec91edf022619d9f0c0878f38c22a763/src/essence/world.py#L56-L72 | def add_component(self, entity, component):
"""Add component to entity.
Long-hand for :func:`essence.Entity.add`.
:param entity: entity to associate
:type entity: :class:`essence.Entity`
:param component: component to add to the entity
:type component: :class:`essence.Component`"""
component_type = type(component)
relation = self._get_relation(component_type)
if entity in relation:
# PYTHON2.6: Numbers required in format string.
msg = "Component {0} can't be added to entity {1} since it already has a component of type {2}.".format(component, entity, component_type)
raise DuplicateComponentError(msg)
relation[entity] = component
self._entities_with(component_type).add(entity) | [
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Long-hand for :func:`essence.Entity.add`.
:param entity: entity to associate
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:param component: component to add to the entity
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| python | train | 46.647059 |
hazelcast/hazelcast-python-client | hazelcast/protocol/codec/multi_map_add_entry_listener_codec.py | https://github.com/hazelcast/hazelcast-python-client/blob/3f6639443c23d6d036aa343f8e094f052250d2c1/hazelcast/protocol/codec/multi_map_add_entry_listener_codec.py#L11-L17 | def calculate_size(name, include_value, local_only):
""" Calculates the request payload size"""
data_size = 0
data_size += calculate_size_str(name)
data_size += BOOLEAN_SIZE_IN_BYTES
data_size += BOOLEAN_SIZE_IN_BYTES
return data_size | [
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| Calculates the request payload size | [
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| python | train | 36 |
ejeschke/ginga | ginga/rv/plugins/PlotTable.py | https://github.com/ejeschke/ginga/blob/a78c893ec6f37a837de851947e9bb4625c597915/ginga/rv/plugins/PlotTable.py#L292-L329 | def _get_plot_data(self):
"""Extract only good data point for plotting."""
_marker_type = self.settings.get('markerstyle', 'o')
if self.x_col == self._idxname:
x_data = self._idx
else:
x_data = self.tab[self.x_col].data
if self.y_col == self._idxname:
y_data = self._idx
else:
y_data = self.tab[self.y_col].data
if self.tab.masked:
if self.x_col == self._idxname:
x_mask = np.ones_like(self._idx, dtype=np.bool)
else:
x_mask = ~self.tab[self.x_col].mask
if self.y_col == self._idxname:
y_mask = np.ones_like(self._idx, dtype=np.bool)
else:
y_mask = ~self.tab[self.y_col].mask
mask = x_mask & y_mask
x_data = x_data[mask]
y_data = y_data[mask]
if len(x_data) > 1:
i = np.argsort(x_data) # Sort X-axis to avoid messy line plot
x_data = x_data[i]
y_data = y_data[i]
if not self.w.show_marker.get_state():
_marker_type = None
return x_data, y_data, _marker_type | [
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| python | train | 30.552632 |
spyder-ide/spyder | spyder/plugins/editor/widgets/editor.py | https://github.com/spyder-ide/spyder/blob/f76836ce1b924bcc4efd3f74f2960d26a4e528e0/spyder/plugins/editor/widgets/editor.py#L1734-L1750 | def file_saved_in_other_editorstack(self, original_filename, filename):
"""
File was just saved in another editorstack, let's synchronize!
This avoids file being automatically reloaded.
The original filename is passed instead of an index in case the tabs
on the editor stacks were moved and are now in a different order - see
issue 5703.
Filename is passed in case file was just saved as another name.
"""
index = self.has_filename(original_filename)
if index is None:
return
finfo = self.data[index]
finfo.newly_created = False
finfo.filename = to_text_string(filename)
finfo.lastmodified = QFileInfo(finfo.filename).lastModified() | [
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| python | train | 44.529412 |
OSSOS/MOP | src/ossos/core/ossos/wcs.py | https://github.com/OSSOS/MOP/blob/94f91d32ad5ec081d5a1ebd67604a838003465af/src/ossos/core/ossos/wcs.py#L389-L425 | def parse_pv(header):
"""
Parses the PV array from an astropy FITS header.
Args:
header: astropy.io.fits.header.Header
The header containing the PV values.
Returns:
cd: 2d array (list(list(float))
[[PV1_0, PV1_1, ... PV1_N], [PV2_0, PV2_1, ... PV2_N]]
Note that N depends on the order of the fit. For example, an
order 3 fit goes up to PV?_10.
"""
order_fit = parse_order_fit(header)
def parse_with_base(i):
key_base = "PV%d_" % i
pvi_x = [header[key_base + "0"]]
def parse_range(lower, upper):
for j in range(lower, upper + 1):
pvi_x.append(header[key_base + str(j)])
if order_fit >= 1:
parse_range(1, 3)
if order_fit >= 2:
parse_range(4, 6)
if order_fit >= 3:
parse_range(7, 10)
return pvi_x
return [parse_with_base(1), parse_with_base(2)] | [
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cd: 2d array (list(list(float))
[[PV1_0, PV1_1, ... PV1_N], [PV2_0, PV2_1, ... PV2_N]]
Note that N depends on the order of the fit. For example, an
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| python | train | 24.648649 |
wummel/dosage | scripts/comicgenesis.py | https://github.com/wummel/dosage/blob/a0109c3a46219f280e6e5e77183674e40da0f304/scripts/comicgenesis.py#L371-L407 | def handle_url(url, session, res):
"""Parse one search result page."""
print("Parsing", url, file=sys.stderr)
try:
data = getPageContent(url, session)
except IOError as msg:
print("ERROR:", msg, file=sys.stderr)
return
for match in url_matcher.finditer(data):
url = match.group(1) + '/'
name = unescape(match.group(2))
name = asciify(name.replace('&', 'And').replace('@', 'At'))
name = capfirst(name)
if name in exclude_comics:
continue
if contains_case_insensitive(res, name):
# we cannot handle two comics that only differ in case
print("INFO: skipping possible duplicate", repr(name), file=sys.stderr)
continue
# find out how many images this comic has
end = match.end()
mo = num_matcher.search(data[end:])
if not mo:
print("ERROR:", repr(data[end:end+300]), file=sys.stderr)
continue
num = int(mo.group(1))
url = url_overrides.get(name, url)
try:
if "/d/" not in url:
check_robotstxt(url+"d/", session)
else:
check_robotstxt(url, session)
except IOError:
print("INFO: robots.txt denied for comicgenesis", repr(name))
continue
else:
res[name] = (url, num) | [
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| python | train | 36.486486 |
angr/angr | angr/state_plugins/posix.py | https://github.com/angr/angr/blob/4e2f97d56af5419ee73bdb30482c8dd8ff5f3e40/angr/state_plugins/posix.py#L553-L569 | def dumps(self, fd, **kwargs):
"""
Returns the concrete content for a file descriptor.
BACKWARD COMPATIBILITY: if you ask for file descriptors 0 1 or 2, it will return the data from stdin, stdout,
or stderr as a flat string.
:param fd: A file descriptor.
:return: The concrete content.
:rtype: str
"""
if 0 <= fd <= 2:
data = [self.stdin, self.stdout, self.stderr][fd].concretize(**kwargs)
if type(data) is list:
data = b''.join(data)
return data
return self.get_fd(fd).concretize(**kwargs) | [
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| python | train | 36.235294 |
hydpy-dev/hydpy | hydpy/models/hland/hland_model.py | https://github.com/hydpy-dev/hydpy/blob/1bc6a82cf30786521d86b36e27900c6717d3348d/hydpy/models/hland/hland_model.py#L2184-L2231 | def calc_qt_v1(self):
"""Calculate the total discharge after possible abstractions.
Required control parameter:
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Required flux sequence:
|OutUH|
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Basic equation:
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Examples:
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>>> from hydpy.models.hland import *
>>> parameterstep('1d')
>>> simulationstep('12h')
>>> abstr(2.0)
>>> fluxes.outuh = 2.0
>>> model.calc_qt_v1()
>>> fluxes.qt
qt(1.0)
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>>> fluxes.outuh = 1.0
>>> model.calc_qt_v1()
>>> fluxes.qt
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"""
con = self.parameters.control.fastaccess
flu = self.sequences.fluxes.fastaccess
flu.qt = max(flu.outuh-con.abstr, 0.) | [
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| python | train | 23.3125 |
BernardFW/bernard | src/bernard/layers/stack.py | https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/layers/stack.py#L77-L89 | def _make_index(self):
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out = {}
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cls = layer.__class__
out[cls] = out.get(cls, []) + [layer]
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| python | train | 23.538462 |
Carreau/telemetry | telemetry/__init__.py | https://github.com/Carreau/telemetry/blob/6d456e982e3d7fd4eb6a8f43cd94925bb69ab855/telemetry/__init__.py#L47-L55 | def collect_basic_info():
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| python | train | 25.222222 |
wglass/zoonado | zoonado/connection.py | https://github.com/wglass/zoonado/blob/8f143b3dd26be88131356f731e7ca51809bc69cb/zoonado/connection.py#L196-L215 | def abort(self, exception=exc.ConnectError):
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"""
log.warn("Aborting connection to %s:%s", self.host, self.port)
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exc_info = sys.exc_info()
if any(exc_info):
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f.set_exception(exception(self.host, self.port))
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| python | train | 37.75 |
hammerlab/cohorts | cohorts/cohort.py | https://github.com/hammerlab/cohorts/blob/278b05e609e6c4d4a77c57d49446460be53ea33e/cohorts/cohort.py#L538-L570 | def _hash_filter_fn(self, filter_fn, **kwargs):
""" Construct string representing state of filter_fn
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"""
filter_fn_name = self._get_function_name(filter_fn, default="filter-none")
logger.debug("Computing hash for filter_fn: {} with kwargs {}".format(filter_fn_name, str(dict(**kwargs))))
# hash function source code
fn_source = str(dill.source.getsource(filter_fn))
pickled_fn_source = pickle.dumps(fn_source) ## encode as byte string
hashed_fn_source = int(hashlib.sha1(pickled_fn_source).hexdigest(), 16) % (10 ** 11)
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kw_dict = dict(**kwargs)
kw_hash = list()
if not kw_dict:
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closure = []
nonlocals = inspect.getclosurevars(filter_fn).nonlocals
for (key, val) in nonlocals.items():
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if inspect.isfunction(val):
closure.append(self._hash_filter_fn(val))
closure.sort() # Sorted for file name consistency
closure_str = "null" if len(closure) == 0 else "-".join(closure)
# construct final string comprising hashed components
hashed_fn = ".".join(["-".join([filter_fn_name,
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| python | train | 52.69697 |
mweb/appconfig | appconfig/appconfig.py | https://github.com/mweb/appconfig/blob/780c1fe3b2f537463a46e335186b7741add88a1e/appconfig/appconfig.py#L370-L407 | def _format_message(value, line_length, indent="", first_indent=None):
''' Return a string with newlines so that the given string fits into this
line length. At the start of the line the indent is added. This can
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if indent.find('\t'):
indent = indent.replace('\t', ' ')
result = []
if first_indent is None:
first_indent = indent
cindent = first_indent
tmp = "*" * line_length
for ele in value.split(' '):
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ele = ele.replace('\t', ' ')
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tmp = '{0}{1}'.format(cindent, ele)
cindent = indent
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| python | train | 36.605263 |
HolmesNL/confidence | confidence/models.py | https://github.com/HolmesNL/confidence/blob/e14d2d8769a01fa55676716f7a2f22714c2616d3/confidence/models.py#L113-L161 | def get(self, path, default=_NoDefault, as_type=None, resolve_references=True):
"""
Gets a value for the specified path.
:param path: the configuration key to fetch a value for, steps
separated by the separator supplied to the constructor (default
``.``)
:param default: a value to return if no value is found for the
supplied path (``None`` is allowed)
:param as_type: an optional callable to apply to the value found for
the supplied path (possibly raising exceptions of its own if the
value can not be coerced to the expected type)
:param resolve_references: whether to resolve references in values
:return: the value associated with the supplied configuration key, if
available, or a supplied default value if the key was not found
:raises ConfigurationError: when no value was found for *path* and
*default* was not provided or a reference could not be resolved
"""
value = self._source
steps_taken = []
try:
# walk through the values dictionary
for step in path.split(self._separator):
steps_taken.append(step)
value = value[step]
if as_type:
return as_type(value)
elif isinstance(value, Mapping):
# create an instance of our current type, copying 'configured' properties / policies
namespace = type(self)(separator=self._separator, missing=self._missing)
namespace._source = value
# carry the root object from namespace to namespace, references are always resolved from root
namespace._root = self._root
return namespace
elif resolve_references and isinstance(value, str):
# only resolve references in str-type values (the only way they can be expressed)
return self._resolve(value)
else:
return value
except ConfiguredReferenceError:
# also a KeyError, but this one should bubble to caller
raise
except KeyError as e:
if default is not _NoDefault:
return default
else:
missing_key = self._separator.join(steps_taken)
raise NotConfiguredError('no configuration for key {}'.format(missing_key), key=missing_key) from e | [
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:return: the value associated with the supplied configuration key, if
available, or a supplied default value if the key was not found
:raises ConfigurationError: when no value was found for *path* and
*default* was not provided or a reference could not be resolved | [
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| python | train | 49.673469 |
jldantas/libmft | libmft/attribute.py | https://github.com/jldantas/libmft/blob/65a988605fe7663b788bd81dcb52c0a4eaad1549/libmft/attribute.py#L1909-L1920 | def _from_binary_ace_header(cls, binary_stream):
"""See base class."""
''' ACE Type - 1
ACE Control flags - 1
Size - 2 (includes header size)
'''
type, control_flags, size = cls._REPR.unpack(binary_stream)
nw_obj = cls((ACEType(type), ACEControlFlags(control_flags), size))
_MOD_LOGGER.debug("Attempted to unpack ACE Header from \"%s\"\nResult: %s", binary_stream.tobytes(), nw_obj)
return nw_obj | [
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| python | train | 35.916667 |
mozillazg/python-pinyin | pypinyin/core.py | https://github.com/mozillazg/python-pinyin/blob/b44756c852e0d2f50f251e3098cbbfef51774979/pypinyin/core.py#L155-L179 | def phrase_pinyin(phrase, style, heteronym, errors='default', strict=True):
"""词语拼音转换.
:param phrase: 词语
:param errors: 指定如何处理没有拼音的字符
:param strict: 是否严格遵照《汉语拼音方案》来处理声母和韵母
:return: 拼音列表
:rtype: list
"""
py = []
if phrase in PHRASES_DICT:
py = deepcopy(PHRASES_DICT[phrase])
for idx, item in enumerate(py):
if heteronym:
py[idx] = _remove_dup_items([
_to_fixed(x, style=style, strict=strict) for x in item])
else:
py[idx] = [_to_fixed(item[0], style=style, strict=strict)]
else:
for i in phrase:
single = single_pinyin(i, style=style, heteronym=heteronym,
errors=errors, strict=strict)
if single:
py.extend(single)
return py | [
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:return: 拼音列表
:rtype: list | [
"词语拼音转换",
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| python | train | 32.76 |
pandas-dev/pandas | pandas/core/dtypes/cast.py | https://github.com/pandas-dev/pandas/blob/9feb3ad92cc0397a04b665803a49299ee7aa1037/pandas/core/dtypes/cast.py#L486-L516 | def maybe_infer_dtype_type(element):
"""Try to infer an object's dtype, for use in arithmetic ops
Uses `element.dtype` if that's available.
Objects implementing the iterator protocol are cast to a NumPy array,
and from there the array's type is used.
Parameters
----------
element : object
Possibly has a `.dtype` attribute, and possibly the iterator
protocol.
Returns
-------
tipo : type
Examples
--------
>>> from collections import namedtuple
>>> Foo = namedtuple("Foo", "dtype")
>>> maybe_infer_dtype_type(Foo(np.dtype("i8")))
numpy.int64
"""
tipo = None
if hasattr(element, 'dtype'):
tipo = element.dtype
elif is_list_like(element):
element = np.asarray(element)
tipo = element.dtype
return tipo | [
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Uses `element.dtype` if that's available.
Objects implementing the iterator protocol are cast to a NumPy array,
and from there the array's type is used.
Parameters
----------
element : object
Possibly has a `.dtype` attribute, and possibly the iterator
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Returns
-------
tipo : type
Examples
--------
>>> from collections import namedtuple
>>> Foo = namedtuple("Foo", "dtype")
>>> maybe_infer_dtype_type(Foo(np.dtype("i8")))
numpy.int64 | [
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| python | train | 25.741935 |
razor-x/scipy-data_fitting | scipy_data_fitting/figure/plot.py | https://github.com/razor-x/scipy-data_fitting/blob/c756a645da8629699b3f22244bfb7d5d4d88b179/scipy_data_fitting/figure/plot.py#L103-L110 | def add_ylabel(self, text=None):
"""
Add a label to the y-axis.
"""
y = self.fit.meta['dependent']
if not text:
text = '$' + y['tex_symbol'] + r'$ $(\si{' + y['siunitx'] + r'})$'
self.plt.set_ylabel(text) | [
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| python | train | 32.25 |
wtolson/gnsq | gnsq/nsqd.py | https://github.com/wtolson/gnsq/blob/0fd02578b2c9c5fa30626d78579db2a46c10edac/gnsq/nsqd.py#L682-L687 | def publish_tcp(self, topic, data, **kwargs):
"""Use :meth:`NsqdTCPClient.publish` instead.
.. deprecated:: 1.0.0
"""
return self.__tcp_client.publish(topic, data, **kwargs) | [
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.. deprecated:: 1.0.0 | [
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| python | train | 33.5 |
zagaran/mongolia | mongolia/mongo_connection.py | https://github.com/zagaran/mongolia/blob/82c499345f0a8610c7289545e19f5f633e8a81c0/mongolia/mongo_connection.py#L64-L71 | def connect(self, host=None, port=None, connect=False, **kwargs):
""" Explicitly creates the MongoClient; this method must be used
in order to specify a non-default host or port to the MongoClient.
Takes arguments identical to MongoClient.__init__"""
try:
self.__connection = MongoClient(host=host, port=port, connect=connect, **kwargs)
except (AutoReconnect, ConnectionFailure, ServerSelectionTimeoutError):
raise DatabaseIsDownError("No mongod process is running.") | [
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| python | train | 66.5 |
hydraplatform/hydra-base | hydra_base/lib/template.py | https://github.com/hydraplatform/hydra-base/blob/9251ff7946505f7a272c87837390acd1c435bc6e/hydra_base/lib/template.py#L71-L102 | def get_types_by_attr(resource, template_id=None):
"""
Using the attributes of the resource, get all the
types that this resource matches.
@returns a dictionary, keyed on the template name, with the
value being the list of type names which match the resources
attributes.
"""
resource_type_templates = []
#Create a list of all of this resources attributes.
attr_ids = []
for res_attr in resource.attributes:
attr_ids.append(res_attr.attr_id)
all_resource_attr_ids = set(attr_ids)
all_types = db.DBSession.query(TemplateType).options(joinedload_all('typeattrs')).filter(TemplateType.resource_type==resource.ref_key)
if template_id is not None:
all_types = all_types.filter(TemplateType.template_id==template_id)
all_types = all_types.all()
#tmpl type attrs must be a subset of the resource's attrs
for ttype in all_types:
type_attr_ids = []
for typeattr in ttype.typeattrs:
type_attr_ids.append(typeattr.attr_id)
if set(type_attr_ids).issubset(all_resource_attr_ids):
resource_type_templates.append(ttype)
return resource_type_templates | [
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| python | train | 36.4375 |
joke2k/faker | faker/providers/address/__init__.py | https://github.com/joke2k/faker/blob/965824b61132e52d92d1a6ce470396dbbe01c96c/faker/providers/address/__init__.py#L52-L57 | def street_name(self):
"""
:example 'Crist Parks'
"""
pattern = self.random_element(self.street_name_formats)
return self.generator.parse(pattern) | [
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| python | train | 30.166667 |
hsolbrig/PyShEx | pyshex/shape_expressions_language/p5_2_validation_definition.py | https://github.com/hsolbrig/PyShEx/blob/9d659cc36e808afd66d4a6d60e8ea21cb12eb744/pyshex/shape_expressions_language/p5_2_validation_definition.py#L14-L53 | def isValid(cntxt: Context, m: FixedShapeMap) -> Tuple[bool, List[str]]:
"""`5.2 Validation Definition <http://shex.io/shex-semantics/#validation>`_
The expression isValid(G, m) indicates that for every nodeSelector/shapeLabel pair (n, s) in m, s has a
corresponding shape expression se and satisfies(n, se, G, m). satisfies is defined below for each form
of shape expression
:param cntxt: evaluation context - includes graph and schema
:param m: list of NodeShape pairs to test
:return: Success/failure indicator and, if fail, a list of failure reasons
"""
if not cntxt.is_valid:
return False, cntxt.error_list
parse_nodes = []
for nodeshapepair in m:
n = nodeshapepair.nodeSelector
if not isinstance_(n, Node):
return False, [f"{n}: Triple patterns are not implemented"]
# The third test below is because the spec asserts that completely empty graphs pass in certain circumstances
elif not (next(cntxt.graph.predicate_objects(nodeshapepair.nodeSelector), None) or
next(cntxt.graph.subject_predicates(nodeshapepair.nodeSelector), None) or
not next(cntxt.graph.triples((None, None, None)), None)):
return False, [f"Focus: {nodeshapepair.nodeSelector} not in graph"]
else:
s = cntxt.shapeExprFor(START if nodeshapepair.shapeLabel is None or nodeshapepair.shapeLabel is START
else nodeshapepair.shapeLabel)
cntxt.current_node = ParseNode(satisfies, s, n, cntxt)
if not s:
if nodeshapepair.shapeLabel is START or nodeshapepair.shapeLabel is None:
cntxt.fail_reason = "START node is not specified or is invalid"
else:
cntxt.fail_reason = f"Shape: {nodeshapepair.shapeLabel} not found in Schema"
return False, cntxt.process_reasons()
parse_nodes.append(cntxt.current_node)
if not satisfies(cntxt, n, s):
cntxt.current_node.result = False
return False, cntxt.process_reasons()
else:
cntxt.current_node.result = True
return True, [] | [
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| `5.2 Validation Definition <http://shex.io/shex-semantics/#validation>`_
The expression isValid(G, m) indicates that for every nodeSelector/shapeLabel pair (n, s) in m, s has a
corresponding shape expression se and satisfies(n, se, G, m). satisfies is defined below for each form
of shape expression
:param cntxt: evaluation context - includes graph and schema
:param m: list of NodeShape pairs to test
:return: Success/failure indicator and, if fail, a list of failure reasons | [
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| python | train | 54.875 |
galactics/beyond | beyond/utils/ccsds.py | https://github.com/galactics/beyond/blob/7a7590ff0fd4c0bac3e8e383ecca03caa98e5742/beyond/utils/ccsds.py#L105-L167 | def _read_oem(string):
"""
Args:
string (str): String containing the OEM
Return:
Ephem:
"""
ephems = []
required = ('REF_FRAME', 'CENTER_NAME', 'TIME_SYSTEM', 'OBJECT_ID', 'OBJECT_NAME')
mode = None
for line in string.splitlines():
if not line or line.startswith("COMMENT"): # pragma: no cover
continue
elif line.startswith("META_START"):
mode = "meta"
ephem = {'orbits': []}
ephems.append(ephem)
elif line.startswith("META_STOP"):
mode = "data"
# Check for required fields
for k in required:
if k not in ephem:
raise ValueError("Missing field '{}'".format(k))
# Conversion to be compliant with beyond.env.jpl dynamic reference
# frames naming convention.
if ephem['CENTER_NAME'].lower() != "earth":
ephem['REF_FRAME'] = ephem['CENTER_NAME'].title().replace(" ", "")
elif mode == "meta":
key, _, value = line.partition("=")
ephem[key.strip()] = value.strip()
elif mode == "data":
date, *state_vector = line.split()
date = Date.strptime(date, "%Y-%m-%dT%H:%M:%S.%f", scale=ephem['TIME_SYSTEM'])
# Conversion from km to m, from km/s to m/s
# and discard acceleration if present
state_vector = np.array([float(x) for x in state_vector[:6]]) * 1000
ephem['orbits'].append(Orbit(date, state_vector, 'cartesian', ephem['REF_FRAME'], None))
for i, ephem_dict in enumerate(ephems):
if not ephem_dict['orbits']:
raise ValueError("Empty ephemeris")
# In case there is no recommendation for interpolation
# default to a Lagrange 8th order
method = ephem_dict.get('INTERPOLATION', 'Lagrange').lower()
order = int(ephem_dict.get('INTERPOLATION_DEGREE', 7)) + 1
ephem = Ephem(ephem_dict['orbits'], method=method, order=order)
ephem.name = ephem_dict['OBJECT_NAME']
ephem.cospar_id = ephem_dict['OBJECT_ID']
ephems[i] = ephem
if len(ephems) == 1:
return ephems[0]
return ephems | [
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| Args:
string (str): String containing the OEM
Return:
Ephem: | [
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| python | train | 34.492063 |
NASA-AMMOS/AIT-Core | ait/core/bsc.py | https://github.com/NASA-AMMOS/AIT-Core/blob/9d85bd9c738e7a6a6fbdff672bea708238b02a3a/ait/core/bsc.py#L229-L238 | def socket_monitor_loop(self):
''' Monitor the socket and log captured data. '''
try:
while True:
gevent.socket.wait_read(self.socket.fileno())
self._handle_log_rotations()
self.capture_packet()
finally:
self.clean_up() | [
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| python | train | 30.7 |
apple/turicreate | deps/src/libxml2-2.9.1/python/libxml2.py | https://github.com/apple/turicreate/blob/74514c3f99e25b46f22c6e02977fe3da69221c2e/deps/src/libxml2-2.9.1/python/libxml2.py#L705-L710 | def setValidityErrorHandler(self, err_func, warn_func, arg=None):
"""
Register error and warning handlers for RelaxNG validation.
These will be called back as f(msg,arg)
"""
libxml2mod.xmlRelaxNGSetValidErrors(self._o, err_func, warn_func, arg) | [
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| python | train | 46.5 |
echinopsii/net.echinopsii.ariane.community.cli.python3 | ariane_clip3/natsd/driver.py | https://github.com/echinopsii/net.echinopsii.ariane.community.cli.python3/blob/0a7feddebf66fee4bef38d64f456d93a7e9fcd68/ariane_clip3/natsd/driver.py#L243-L308 | def on_response(self, msg):
"""
setup response if correlation id is the good one
"""
LOGGER.debug("natsd.Requester.on_response: " + str(sys.getsizeof(msg)) + " bytes received")
working_response = json.loads(msg.data.decode())
working_properties = DriverTools.json2properties(working_response['properties'])
working_body = b''+bytes(working_response['body'], 'utf8') if 'body' in working_response else None
if DriverTools.MSG_CORRELATION_ID in working_properties:
if self.corr_id == working_properties[DriverTools.MSG_CORRELATION_ID]:
if DriverTools.MSG_SPLIT_COUNT in working_properties and \
int(working_properties[DriverTools.MSG_SPLIT_COUNT]) > 1:
working_body_decoded = base64.b64decode(working_body) if working_body is not None else None
if self.split_responses is None:
self.split_responses = []
self.split_responses_mid = working_properties[DriverTools.MSG_SPLIT_MID]
if working_properties[DriverTools.MSG_SPLIT_MID] == self.split_responses_mid:
response = {
'properties': working_properties,
'body': working_body_decoded
}
self.split_responses.insert(int(working_properties[DriverTools.MSG_SPLIT_OID]), response)
if self.split_responses.__len__() == int(working_properties[DriverTools.MSG_SPLIT_COUNT]):
properties = {}
body = b''
for num in range(0, self.split_responses.__len__()):
properties.update(self.split_responses[num]['properties'])
body += self.split_responses[num]['body']
self.response = {
'properties': properties,
'body': body
}
self.split_responses = None
self.split_responses_mid = None
else:
LOGGER.warn("natsd.Requester.on_response - discarded response : (" +
str(working_properties[DriverTools.MSG_CORRELATION_ID]) + "," +
str(working_properties[DriverTools.MSG_SPLIT_MID]) + ")")
LOGGER.debug("natsd.Requester.on_response - discarded response : " + str({
'properties': working_properties,
'body': working_body_decoded
}))
else:
working_body_decoded = base64.b64decode(working_body) if working_body is not None else \
bytes(json.dumps({}), 'utf8')
self.response = {
'properties': working_properties,
'body': working_body_decoded
}
else:
working_body_decoded = base64.b64decode(working_body) if working_body is not None else None
LOGGER.warn("natsd.Requester.on_response - discarded response : " +
str(working_properties[DriverTools.MSG_CORRELATION_ID]))
LOGGER.debug("natsd.Requester.on_response - discarded response : " + str({
'properties': working_properties,
'body': working_body_decoded
}))
else:
working_body_decoded = base64.b64decode(working_body) if working_body is not None else None
LOGGER.warn("natsd.Requester.on_response - discarded response (no correlation ID)")
LOGGER.debug("natsd.Requester.on_response - discarded response : " + str({
'properties': working_properties,
'body': working_body_decoded
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| setup response if correlation id is the good one | [
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| python | train | 60.363636 |
codeforamerica/three | three/core.py | https://github.com/codeforamerica/three/blob/67b4a4b233a57aa7995d01f6b0f69c2e85aea6c0/three/core.py#L142-L146 | def _format_dates(self, start, end):
"""Format start and end dates."""
start = self._split_date(start)
end = self._split_date(end)
return start, end | [
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| python | train | 35.2 |
KeplerGO/K2fov | K2fov/greatcircle.py | https://github.com/KeplerGO/K2fov/blob/fb122b35687340e0357cba9e0dd47b3be0760693/K2fov/greatcircle.py#L10-L42 | def sphericalAngSep(ra0, dec0, ra1, dec1, radians=False):
"""
Compute the spherical angular separation between two
points on the sky.
//Taken from http://www.movable-type.co.uk/scripts/gis-faq-5.1.html
NB: For small distances you can probably use
sqrt( dDec**2 + cos^2(dec)*dRa)
where dDec = dec1 - dec0 and
dRa = ra1 - ra0
and dec1 \approx dec \approx dec0
"""
if radians==False:
ra0 = np.radians(ra0)
dec0 = np.radians(dec0)
ra1 = np.radians(ra1)
dec1 = np.radians(dec1)
deltaRa= ra1-ra0
deltaDec= dec1-dec0
val = haversine(deltaDec)
val += np.cos(dec0) * np.cos(dec1) * haversine(deltaRa)
val = min(1, np.sqrt(val)) ; #Guard against round off error?
val = 2*np.arcsin(val)
#Convert back to degrees if necessary
if radians==False:
val = np.degrees(val)
return val | [
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sqrt( dDec**2 + cos^2(dec)*dRa)
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| python | train | 27.515152 |
mitsei/dlkit | dlkit/json_/assessment_authoring/sessions.py | https://github.com/mitsei/dlkit/blob/445f968a175d61c8d92c0f617a3c17dc1dc7c584/dlkit/json_/assessment_authoring/sessions.py#L1079-L1114 | def delete_assessment_part(self, assessment_part_id):
"""Removes an asessment part and all mapped items.
arg: assessment_part_id (osid.id.Id): the ``Id`` of the
``AssessmentPart``
raise: NotFound - ``assessment_part_id`` not found
raise: NullArgument - ``assessment_part_id`` is ``null``
raise: OperationFailed - unable to complete request
raise: PermissionDenied - authorization failure occurred
*compliance: mandatory -- This method must be implemented.*
"""
# Should be implemented from template for
# osid.learning.ObjectiveAdminSession.delete_objective_template
# but need to handle magic part delete ...
if not isinstance(assessment_part_id, ABCId):
raise errors.InvalidArgument('the argument is not a valid OSID Id')
collection = JSONClientValidated('assessment_authoring',
collection='AssessmentPart',
runtime=self._runtime)
if collection.find({'assessmentPartId': str(assessment_part_id)}).count() != 0:
raise errors.IllegalState('there are still AssessmentParts associated with this AssessmentPart')
collection = JSONClientValidated('assessment_authoring',
collection='AssessmentPart',
runtime=self._runtime)
try:
apls = get_assessment_part_lookup_session(runtime=self._runtime,
proxy=self._proxy)
apls.use_unsequestered_assessment_part_view()
apls.use_federated_bank_view()
part = apls.get_assessment_part(assessment_part_id)
part.delete()
except AttributeError:
collection.delete_one({'_id': ObjectId(assessment_part_id.get_identifier())}) | [
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raise: NotFound - ``assessment_part_id`` not found
raise: NullArgument - ``assessment_part_id`` is ``null``
raise: OperationFailed - unable to complete request
raise: PermissionDenied - authorization failure occurred
*compliance: mandatory -- This method must be implemented.* | [
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| python | train | 52.583333 |
ska-sa/katcp-python | katcp/resource.py | https://github.com/ska-sa/katcp-python/blob/9127c826a1d030c53b84d0e95743e20e5c5ea153/katcp/resource.py#L824-L828 | def set_value(self, value, status=Sensor.NOMINAL, timestamp=None):
"""Set sensor value with optinal specification of status and timestamp"""
if timestamp is None:
timestamp = self._manager.time()
self.set(timestamp, status, value) | [
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| python | train | 52.4 |
ianmiell/shutit | shutit_setup.py | https://github.com/ianmiell/shutit/blob/19cd64cdfb23515b106b40213dccff4101617076/shutit_setup.py#L170-L184 | def build(self, shutit):
"""Initializes target ready for build and updating package management if in container.
"""
if shutit.build['delivery'] in ('docker','dockerfile'):
if shutit.get_current_shutit_pexpect_session_environment().install_type == 'apt':
shutit.add_to_bashrc('export DEBIAN_FRONTEND=noninteractive')
if not shutit.command_available('lsb_release'):
shutit.install('lsb-release')
shutit.lsb_release()
elif shutit.get_current_shutit_pexpect_session_environment().install_type == 'yum':
# yum updates are so often "bad" that we let exit codes of 1 through.
# TODO: make this more sophisticated
shutit.send('yum update -y', timeout=9999, exit_values=['0', '1'])
shutit.pause_point('Anything you want to do to the target host ' + 'before the build starts?', level=2)
return True | [
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| python | train | 54.666667 |
DLR-RM/RAFCON | source/rafcon/gui/controllers/state_editor/outcomes.py | https://github.com/DLR-RM/RAFCON/blob/24942ef1a904531f49ab8830a1dbb604441be498/source/rafcon/gui/controllers/state_editor/outcomes.py#L225-L232 | def remove_core_element(self, model):
"""Remove respective core element of handed outcome model
:param OutcomeModel model: Outcome model which core element should be removed
:return:
"""
assert model.outcome.parent is self.model.state
gui_helper_state_machine.delete_core_element_of_model(model) | [
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:param OutcomeModel model: Outcome model which core element should be removed
:return: | [
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| python | train | 42.125 |
bitlabstudio/django-dashboard-app | dashboard_app/widget_pool.py | https://github.com/bitlabstudio/django-dashboard-app/blob/ed98f2bca91a4ced36d0dd1aa1baee78e989cf64/dashboard_app/widget_pool.py#L69-L91 | def register_widget(self, widget_cls, **widget_kwargs):
"""
Registers the given widget.
Widgets must inherit ``DashboardWidgetBase`` and you cannot register
the same widget twice.
:widget_cls: A class that inherits ``DashboardWidgetBase``.
"""
if not issubclass(widget_cls, DashboardWidgetBase):
raise ImproperlyConfigured(
'DashboardWidgets must be subclasses of DashboardWidgetBase,'
' {0} is not.'.format(widget_cls))
widget = widget_cls(**widget_kwargs)
widget_name = widget.get_name()
if widget_name in self.widgets:
raise WidgetAlreadyRegistered(
'Cannot register {0}, a plugin with this name {1} is already '
'registered.'.format(widget_cls, widget_name))
self.widgets[widget_name] = widget | [
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| python | test | 37.217391 |
draperjames/qtpandas | qtpandas/utils.py | https://github.com/draperjames/qtpandas/blob/64294fb69f1839e53dee5ea453337266bfaf24f4/qtpandas/utils.py#L208-L218 | def dedupe_cols(frame):
"""
Need to dedupe columns that have the same name.
"""
cols = list(frame.columns)
for i, item in enumerate(frame.columns):
if item in frame.columns[:i]:
cols[i] = "toDROP"
frame.columns = cols
return frame.drop("toDROP", 1, errors='ignore') | [
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| python | train | 27.636364 |
manahl/arctic | arctic/chunkstore/chunkstore.py | https://github.com/manahl/arctic/blob/57e110b6e182dbab00e7e214dc26f7d9ec47c120/arctic/chunkstore/chunkstore.py#L119-L168 | def delete(self, symbol, chunk_range=None, audit=None):
"""
Delete all chunks for a symbol, or optionally, chunks within a range
Parameters
----------
symbol : str
symbol name for the item
chunk_range: range object
a date range to delete
audit: dict
dict to store in the audit log
"""
if chunk_range is not None:
sym = self._get_symbol_info(symbol)
# read out chunks that fall within the range and filter out
# data within the range
df = self.read(symbol, chunk_range=chunk_range, filter_data=False)
row_adjust = len(df)
if not df.empty:
df = CHUNKER_MAP[sym[CHUNKER]].exclude(df, chunk_range)
# remove chunks, and update any remaining data
query = {SYMBOL: symbol}
query.update(CHUNKER_MAP[sym[CHUNKER]].to_mongo(chunk_range))
self._collection.delete_many(query)
self._mdata.delete_many(query)
self.update(symbol, df)
# update symbol metadata (rows and chunk count)
sym = self._get_symbol_info(symbol)
sym[LEN] -= row_adjust
sym[CHUNK_COUNT] = mongo_count(self._collection, filter={SYMBOL: symbol})
self._symbols.replace_one({SYMBOL: symbol}, sym)
else:
query = {SYMBOL: symbol}
self._collection.delete_many(query)
self._symbols.delete_many(query)
self._mdata.delete_many(query)
if audit is not None:
audit['symbol'] = symbol
if chunk_range is not None:
audit['rows_deleted'] = row_adjust
audit['action'] = 'range delete'
else:
audit['action'] = 'symbol delete'
self._audit.insert_one(audit) | [
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| python | train | 37.62 |
CxAalto/gtfspy | gtfspy/routing/profile_block_analyzer.py | https://github.com/CxAalto/gtfspy/blob/bddba4b74faae6c1b91202f19184811e326547e5/gtfspy/routing/profile_block_analyzer.py#L185-L213 | def _temporal_distance_pdf(self):
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Temporal distance probability density function.
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non_delta_peak_densities: numpy.array
len(density) == len(temporal_distance_split_points_ordered) -1
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"""
temporal_distance_split_points_ordered, norm_cdf = self._temporal_distance_cdf()
delta_peak_loc_to_probability_mass = {}
non_delta_peak_split_points = [temporal_distance_split_points_ordered[0]]
non_delta_peak_densities = []
for i in range(0, len(temporal_distance_split_points_ordered) - 1):
left = temporal_distance_split_points_ordered[i]
right = temporal_distance_split_points_ordered[i + 1]
width = right - left
prob_mass = norm_cdf[i + 1] - norm_cdf[i]
if width == 0.0:
delta_peak_loc_to_probability_mass[left] = prob_mass
else:
non_delta_peak_split_points.append(right)
non_delta_peak_densities.append(prob_mass / float(width))
assert (len(non_delta_peak_densities) == len(non_delta_peak_split_points) - 1)
return numpy.array(non_delta_peak_split_points), \
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| python | valid | 47.206897 |
andela-sjames/paystack-python | paystackapi/base.py | https://github.com/andela-sjames/paystack-python/blob/c9e4bddcb76e1490fefc362e71a21486400dccd4/paystackapi/base.py#L45-L60 | def _request(self, method, resource_uri, **kwargs):
"""Perform a method on a resource.
Args:
method: requests.`method`
resource_uri: resource endpoint
Raises:
HTTPError
Returns:
JSON Response
"""
data = kwargs.get('data')
response = method(self.API_BASE_URL + resource_uri,
json=data, headers=self.headers)
response.raise_for_status()
return response.json() | [
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| python | train | 30.5625 |
MisterY/gnucash-portfolio | reports/report_vanguard_prices/report_vanguard_prices.py | https://github.com/MisterY/gnucash-portfolio/blob/bfaad8345a5479d1cd111acee1939e25c2a638c2/reports/report_vanguard_prices/report_vanguard_prices.py#L18-L27 | def generate_report(
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documentation_string="Comma-separated list of fund ids.",
default_value="8123,8146,8148,8147")
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"""Generates the report output"""
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| python | train | 32.5 |
pymupdf/PyMuPDF | fitz/fitz.py | https://github.com/pymupdf/PyMuPDF/blob/917f2d83482510e26ba0ff01fd2392c26f3a8e90/fitz/fitz.py#L2894-L2906 | def MediaBoxSize(self):
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| python | train | 21.153846 |
nugget/python-insteonplm | insteonplm/states/onOff.py | https://github.com/nugget/python-insteonplm/blob/65548041f1b0729ae1ae904443dd81b0c6cbf1bf/insteonplm/states/onOff.py#L365-L369 | def close(self):
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| python | train | 49 |
apple/turicreate | deps/src/boost_1_68_0/libs/metaparse/tools/benchmark/generate.py | https://github.com/apple/turicreate/blob/74514c3f99e25b46f22c6e02977fe3da69221c2e/deps/src/boost_1_68_0/libs/metaparse/tools/benchmark/generate.py#L233-L235 | def out_filename(template, n_val, mode):
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| python | train | 51 |
pycontribs/jira | jira/resources.py | https://github.com/pycontribs/jira/blob/397db5d78441ed6a680a9b7db4c62030ade1fd8a/jira/resources.py#L251-L347 | def update(self, fields=None, async_=None, jira=None, notify=True, **kwargs):
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"""
if async_ is None:
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data = {}
if fields is not None:
data.update(fields)
data.update(kwargs)
data = json.dumps(data)
if not notify:
querystring = "?notifyUsers=false"
else:
querystring = ""
r = self._session.put(
self.self + querystring, data=data)
if 'autofix' in self._options and \
r.status_code == 400:
user = None
error_list = get_error_list(r)
logging.error(error_list)
if "The reporter specified is not a user." in error_list:
if 'reporter' not in data['fields']:
logging.warning(
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data['fields']['reporter'] = {
'name': self._options['autofix']}
if "Issues must be assigned." in error_list:
if 'assignee' not in data['fields']:
logging.warning("autofix: setting assignee to '%s' for %s and retrying the update." % (
self._options['autofix'], self.key))
data['fields']['assignee'] = {
'name': self._options['autofix']}
# for some reason the above approach fails on Jira 5.2.11
# so we need to change the assignee before
if "Issue type is a sub-task but parent issue key or id not specified." in error_list:
logging.warning(
"autofix: trying to fix sub-task without parent by converting to it to bug")
data['fields']['issuetype'] = {"name": "Bug"}
if "The summary is invalid because it contains newline characters." in error_list:
logging.warning("autofix: trying to fix newline in summary")
data['fields'][
'summary'] = self.fields.summary.replace("/n", "")
for error in error_list:
if re.search(r"^User '(.*)' was not found in the system\.", error, re.U):
m = re.search(
r"^User '(.*)' was not found in the system\.", error, re.U)
if m:
user = m.groups()[0]
else:
raise NotImplementedError()
if re.search(r"^User '(.*)' does not exist\.", error):
m = re.search(r"^User '(.*)' does not exist\.", error)
if m:
user = m.groups()[0]
else:
raise NotImplementedError()
if user:
logging.warning(
"Trying to add missing orphan user '%s' in order to complete the previous failed operation." % user)
jira.add_user(user, '[email protected]', 10100, active=False)
# if 'assignee' not in data['fields']:
# logging.warning("autofix: setting assignee to '%s' and retrying the update." % self._options['autofix'])
# data['fields']['assignee'] = {'name': self._options['autofix']}
# EXPERIMENTAL --->
if async_:
if not hasattr(self._session, '_async_jobs'):
self._session._async_jobs = set()
self._session._async_jobs.add(threaded_requests.put(
self.self, data=json.dumps(data)))
else:
r = self._session.put(
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self._load(self.self) | [
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Keyword arguments are marshalled into a dict before being sent. If this
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will only raise errors in case of user error.
:param fields: Fields which should be updated for the object.
:type fields: Optional[Dict[str, Any]]
:param async_: If true the request will be added to the queue so it can be executed later using async_run()
:type async_: bool
:param jira: Instance of JIRA Client
:type jira: jira.JIRA
:param notify: Whether or not to notify users about the update. (Default: True)
:type notify: bool
:type kwargs: **Any | [
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| python | train | 46.876289 |
etesync/radicale_storage_etesync | radicale_storage_etesync/__init__.py | https://github.com/etesync/radicale_storage_etesync/blob/73d549bad7a37f060ece65c653c18a859a9962f2/radicale_storage_etesync/__init__.py#L321-L332 | def sync(self, old_token=None):
"""Get the current sync token and changed items for synchronization.
``old_token`` an old sync token which is used as the base of the
delta update. If sync token is missing, all items are returned.
ValueError is raised for invalid or old tokens.
"""
# FIXME: Actually implement
token = "http://radicale.org/ns/sync/%s" % self.etag.strip("\"")
if old_token:
raise ValueError("Sync token are not supported (you can ignore this warning)")
return token, self.list() | [
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| python | train | 47.25 |
erijo/tellcore-py | tellcore/telldus.py | https://github.com/erijo/tellcore-py/blob/7a1eb53e12ef039a2350933e502633df7560f6a8/tellcore/telldus.py#L48-L62 | def process_callback(self, block=True):
"""Dispatch a single callback in the current thread.
:param boolean block: If True, blocks waiting for a callback to come.
:return: True if a callback was processed; otherwise False.
"""
try:
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try:
callback(*args)
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self._queue.task_done()
except queue.Empty:
return False
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| python | train | 33.4 |
aetros/aetros-cli | aetros/git.py | https://github.com/aetros/aetros-cli/blob/a2a1f38d6af1660e1e2680c7d413ec2aef45faab/aetros/git.py#L582-L651 | def stream_file(self, path, fast_lane=True):
"""
Create a temp file, stream it to the server if online and append its content using the write() method.
This makes sure that we have all newest data of this file on the server directly.
At the end of the job, the content the server received is stored as git blob on the server. It is then committed
locally and pushed. Git detects that the server already has the version (through the continuous streaming)
and won't push it again. Very handy for rather large files that will append over time (like channel data, logs)
Example:
self.log_stream = git.stream_file('log.txt')
self.log_stream.write("new line\n");
self.log_stream.write("another line\n");
"""
# create temp file
# open temp file
# register stream file and write locally
# on end() git_commit that file locally
# create socket connection to server
# stream file to server
# on end() send server end signal, so he can store its content in git as blob as well.
# A git push would detect that both sides have the same content already,
# except when server connection broke between start() and end().
# Result -> already transmitted logs/channel data (probably many MBs) won't transfered twice
# when doing a git-push.
# return handler to write to this file
full_path = os.path.normpath(self.temp_path + '/stream-blob/' + self.job_id + '/' + path)
if not os.path.exists(os.path.dirname(full_path)):
os.makedirs(os.path.dirname(full_path))
handle = open(full_path, 'wb')
self.streamed_files[path] = handle
class Stream():
def __init__(self, git):
self.git = git
def write(self, data):
if path not in self.git.streamed_files:
# already committed to server
return
if hasattr(data, 'encode'):
data = data.encode("utf-8", 'replace')
try:
self.git.stream_files_lock.acquire()
if not handle.closed:
handle.write(data)
handle.flush()
except IOError as e:
handle.close()
if 'No space left' in e.__str__():
sys.stderr.write(traceback.format_exc() + '\n')
self.git.logger.error(e.__str__())
finally:
self.git.stream_files_lock.release()
if self.git.client.online is not False:
self.git.client.send({'type': 'stream-blob', 'path': path, 'data': data}, channel='' if fast_lane else 'files')
return Stream(self) | [
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self.log_stream = git.stream_file('log.txt')
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| python | train | 40.557143 |
UDST/urbansim | urbansim/models/regression.py | https://github.com/UDST/urbansim/blob/79f815a6503e109f50be270cee92d0f4a34f49ef/urbansim/models/regression.py#L546-L559 | def add_model(self, model):
"""
Add a `RegressionModel` instance.
Parameters
----------
model : `RegressionModel`
Should have a ``.name`` attribute matching one of
the groupby segments.
"""
logger.debug(
'adding model {} to group {}'.format(model.name, self.name))
self.models[model.name] = model | [
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| python | train | 27.5 |
intuition-io/intuition | intuition/api/portfolio.py | https://github.com/intuition-io/intuition/blob/cd517e6b3b315a743eb4d0d0dc294e264ab913ce/intuition/api/portfolio.py#L77-L84 | def update(self, portfolio, date, perfs=None):
'''
Actualizes the portfolio universe with the alog state
'''
# Make the manager aware of current simulation
self.portfolio = portfolio
self.perfs = perfs
self.date = date | [
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| python | train | 33.375 |
robotools/fontMath | Lib/fontMath/mathGlyph.py | https://github.com/robotools/fontMath/blob/6abcb9d5a1ca19788fbde4418d7b5630c60990d8/Lib/fontMath/mathGlyph.py#L276-L286 | def drawPoints(self, pointPen, filterRedundantPoints=False):
"""draw self using pointPen"""
if filterRedundantPoints:
pointPen = FilterRedundantPointPen(pointPen)
for contour in self.contours:
pointPen.beginPath(identifier=contour["identifier"])
for segmentType, pt, smooth, name, identifier in contour["points"]:
pointPen.addPoint(pt=pt, segmentType=segmentType, smooth=smooth, name=name, identifier=identifier)
pointPen.endPath()
for component in self.components:
pointPen.addComponent(component["baseGlyph"], component["transformation"], identifier=component["identifier"]) | [
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| python | train | 61.272727 |
ethereum/py-evm | eth/chains/base.py | https://github.com/ethereum/py-evm/blob/58346848f076116381d3274bbcea96b9e2cfcbdf/eth/chains/base.py#L545-L551 | def get_block_by_hash(self, block_hash: Hash32) -> BaseBlock:
"""
Returns the requested block as specified by block hash.
"""
validate_word(block_hash, title="Block Hash")
block_header = self.get_block_header_by_hash(block_hash)
return self.get_block_by_header(block_header) | [
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| python | train | 45.142857 |
SoCo/SoCo | dev_tools/analyse_ws.py | https://github.com/SoCo/SoCo/blob/671937e07d7973b78c0cbee153d4f3ad68ec48c6/dev_tools/analyse_ws.py#L268-L310 | def __update_window(self, width, height, message_no, page_no):
""" Update the window with the menu and the new text """
file_exists_label = '-F-ILE'
if not os.path.exists(self.__create_file_name(message_no)):
file_exists_label = '(f)ile'
# Clear the screen
if PLATFORM == 'win32':
# Ugly hack until someone figures out a better way for Windows
# probably something with a cls command, but I cannot test it
for _ in range(50):
print
else:
sys.stdout.write('\x1b[2J\x1b[H') # Clear screen
# Content
content = self.messages[message_no].output.rstrip('\n')
out = content
if self.args.color:
out = pygments.highlight(content, XmlLexer(), TerminalFormatter())
# Paging functionality
if message_no not in self.pages:
self._form_pages(message_no, content, out, height, width)
# Coerce in range
page_no = max(min(len(self.pages[message_no]) - 1, page_no), 0)
page_content = self.pages[message_no][page_no]
# Menu
max_message = str(len(self.messages) - 1)
position_string = u'{{0: >{0}}}/{{1: <{0}}}'.format(len(max_message))
position_string = position_string.format(message_no, max_message)
# Assume less than 100 pages
current_max_page = len(self.pages[message_no]) - 1
pages_string = u'{0: >2}/{1: <2}'.format(page_no, current_max_page)
menu = (u'(b)rowser | {0} | Message {1} \u2193 (s)\u2191 (w) | '
u'Page {2} \u2190 (a)\u2192 (d) | (q)uit\n{3}').\
format(file_exists_label, position_string, pages_string,
'-' * width)
print menu
print page_content
return page_no | [
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| python | train | 41.348837 |
tensorflow/datasets | tensorflow_datasets/translate/wmt.py | https://github.com/tensorflow/datasets/blob/46ceb0cf7b4690f38ecbbc689e4d659a903d08dc/tensorflow_datasets/translate/wmt.py#L838-L858 | def _parse_tmx(path):
"""Generates examples from TMX file."""
def _get_tuv_lang(tuv):
for k, v in tuv.items():
if k.endswith("}lang"):
return v
raise AssertionError("Language not found in `tuv` attributes.")
def _get_tuv_seg(tuv):
segs = tuv.findall("seg")
assert len(segs) == 1, "Invalid number of segments: %d" % len(segs)
return segs[0].text
with tf.io.gfile.GFile(path) as f:
for _, elem in ElementTree.iterparse(f):
if elem.tag == "tu":
yield {
_get_tuv_lang(tuv):
_get_tuv_seg(tuv) for tuv in elem.iterfind("tuv")
}
elem.clear() | [
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| python | train | 29.52381 |
gregreen/dustmaps | dustmaps/iphas.py | https://github.com/gregreen/dustmaps/blob/c8f571a71da0d951bf8ea865621bee14492bdfd9/dustmaps/iphas.py#L76-L212 | def query(self, coords, mode='random_sample'):
"""
Returns A0 at the given coordinates. There are several different query
modes, which handle the probabilistic nature of the map differently.
Args:
coords (:obj:`astropy.coordinates.SkyCoord`): The coordinates to query.
mode (Optional[:obj:`str`]): Five different query modes are available:
``'random_sample'``, ``'random_sample_per_pix'``, ``'samples'``,
``'median'`` and ``'mean'``. The ``mode`` determines how the output
will reflect the probabilistic nature of the IPHAS dust map.
Returns:
Monochromatic extinction, A0, at the specified coordinates, in mags.
The shape of the output depends on the ``mode``, and on whether
``coords`` contains distances.
If ``coords`` does not specify distance(s), then the shape of the
output begins with `coords.shape`. If `coords` does specify
distance(s), then the shape of the output begins with
``coords.shape + ([number of distance bins],)``.
If ``mode`` is ``'random_sample'``, then at each coordinate/distance, a
random sample of reddening is given.
If ``mode`` is ``'random_sample_per_pix'``, then the sample chosen for
each angular pixel of the map will be consistent. For example, if
two query coordinates lie in the same map pixel, then the same
random sample will be chosen from the map for both query
coordinates.
If ``mode`` is ``'median'``, then at each coordinate/distance, the
median reddening is returned.
If ``mode`` is ``'mean'``, then at each coordinate/distance, the mean
reddening is returned.
Finally, if ``mode`` is ``'samples'``, then all at each
coordinate/distance, all samples are returned.
"""
# Check that the query mode is supported
valid_modes = [
'random_sample',
'random_sample_per_pix',
'samples',
'median',
'mean']
if mode not in valid_modes:
raise ValueError(
'"{}" is not a valid `mode`. Valid modes are:\n'
' {}'.format(mode, valid_modes))
n_coords_ret = coords.shape[0]
# Determine if distance has been requested
has_dist = hasattr(coords.distance, 'kpc')
d = coords.distance.kpc if has_dist else None
# Convert coordinates to pixel indices
pix_idx = self._coords2idx(coords)
# Determine which coordinates are out of bounds
mask_idx = (pix_idx == self._n_pix)
if np.any(mask_idx):
pix_idx[mask_idx] = 0
# Which samples to extract
if mode == 'random_sample':
samp_idx = np.random.randint(0, self._n_samples, pix_idx.size)
n_samp_ret = 1
elif mode == 'random_sample_per_pix':
samp_idx = np.random.randint(0, self._n_samples, self._n_pix)[pix_idx]
n_sample_ret = 1
else:
samp_idx = slice(None)
n_samp_ret = self._n_samples
# Which distances to extract
if has_dist:
d = coords.distance.pc
dist_idx_ceil = np.searchsorted(self._dists, d)
if isinstance(samp_idx, slice):
ret = np.empty((n_coords_ret, n_samp_ret), dtype='f4')
else:
ret = np.empty((n_coords_ret,), dtype='f4')
# d < d(nearest distance slice)
idx_near = (dist_idx_ceil == 0)
if np.any(idx_near):
a = d[idx_near] / self._dists[0]
if isinstance(samp_idx, slice):
ret[idx_near] = a[:,None] * self._data['A0'][pix_idx[idx_near], 0, samp_idx]
else:
ret[idx_near] = a[:] * self._data['A0'][pix_idx[idx_near], 0, samp_idx[idx_near]]
# d > d(farthest distance slice)
idx_far = (dist_idx_ceil == self._n_dists)
if np.any(idx_far):
if isinstance(samp_idx, slice):
ret[idx_far] = self._data['A0'][pix_idx[idx_far], -1, samp_idx]
else:
ret[idx_far] = self._data['A0'][pix_idx[idx_far], -1, samp_idx[idx_far]]
# d(nearest distance slice) < d < d(farthest distance slice)
idx_btw = ~idx_near & ~idx_far
if np.any(idx_btw):
d_ceil = self._dists[dist_idx_ceil[idx_btw]]
d_floor = self._dists[dist_idx_ceil[idx_btw]-1]
a = (d_ceil - d[idx_btw]) / (d_ceil - d_floor)
if isinstance(samp_idx, slice):
ret[idx_btw] = (
(1.-a[:,None]) * self._data['A0'][pix_idx[idx_btw], dist_idx_ceil[idx_btw], samp_idx]
+ a[:,None] * self._data['A0'][pix_idx[idx_btw], dist_idx_ceil[idx_btw]-1, samp_idx])
else:
ret[idx_btw] = (
(1.-a[:]) * self._data['A0'][pix_idx[idx_btw], dist_idx_ceil[idx_btw], samp_idx[idx_btw]]
+ a[:] * self._data['A0'][pix_idx[idx_btw], dist_idx_ceil[idx_btw]-1, samp_idx[idx_btw]])
else:
# TODO: Harmonize order of distances & samples with Bayestar.
ret = self._data['A0'][pix_idx, :, samp_idx]
# Reduce the samples in the requested manner
samp_axis = 1 if has_dist else 2
if mode == 'median':
ret = np.median(ret, axis=samp_axis)
elif mode == 'mean':
ret = np.mean(ret, axis=samp_axis)
if np.any(mask_idx):
ret[mask_idx] = np.nan
return ret | [
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mode (Optional[:obj:`str`]): Five different query modes are available:
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Returns:
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The shape of the output depends on the ``mode``, and on whether
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If ``coords`` does not specify distance(s), then the shape of the
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If ``mode`` is ``'median'``, then at each coordinate/distance, the
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If ``mode`` is ``'mean'``, then at each coordinate/distance, the mean
reddening is returned.
Finally, if ``mode`` is ``'samples'``, then all at each
coordinate/distance, all samples are returned. | [
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| python | train | 41.518248 |
inveniosoftware-contrib/invenio-workflows | invenio_workflows/engine.py | https://github.com/inveniosoftware-contrib/invenio-workflows/blob/9c09fd29509a3db975ac2aba337e6760d8cfd3c2/invenio_workflows/engine.py#L161-L164 | def running_objects(self):
"""Return the objects associated with this workflow."""
return [obj for obj in self.database_objects
if obj.status in [obj.known_statuses.RUNNING]] | [
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| python | train | 50.75 |
JdeRobot/base | src/drivers/MAVLinkServer/MAVProxy/modules/mavproxy_sensors.py | https://github.com/JdeRobot/base/blob/303b18992785b2fe802212f2d758a60873007f1f/src/drivers/MAVLinkServer/MAVProxy/modules/mavproxy_sensors.py#L82-L93 | def report(self, name, ok, msg=None, deltat=20):
'''report a sensor error'''
r = self.reports[name]
if time.time() < r.last_report + deltat:
r.ok = ok
return
r.last_report = time.time()
if ok and not r.ok:
self.say("%s OK" % name)
r.ok = ok
if not r.ok:
self.say(msg) | [
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| python | train | 30 |
juju/charm-helpers | charmhelpers/core/hookenv.py | https://github.com/juju/charm-helpers/blob/aa785c40c3b7a8c69dbfbc7921d6b9f30142e171/charmhelpers/core/hookenv.py#L394-L425 | def config(scope=None):
"""
Get the juju charm configuration (scope==None) or individual key,
(scope=str). The returned value is a Python data structure loaded as
JSON from the Juju config command.
:param scope: If set, return the value for the specified key.
:type scope: Optional[str]
:returns: Either the whole config as a Config, or a key from it.
:rtype: Any
"""
global _cache_config
config_cmd_line = ['config-get', '--all', '--format=json']
try:
# JSON Decode Exception for Python3.5+
exc_json = json.decoder.JSONDecodeError
except AttributeError:
# JSON Decode Exception for Python2.7 through Python3.4
exc_json = ValueError
try:
if _cache_config is None:
config_data = json.loads(
subprocess.check_output(config_cmd_line).decode('UTF-8'))
_cache_config = Config(config_data)
if scope is not None:
return _cache_config.get(scope)
return _cache_config
except (exc_json, UnicodeDecodeError) as e:
log('Unable to parse output from config-get: config_cmd_line="{}" '
'message="{}"'
.format(config_cmd_line, str(e)), level=ERROR)
return None | [
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| python | train | 38.21875 |
pypa/pipenv | pipenv/patched/notpip/_internal/req/req_uninstall.py | https://github.com/pypa/pipenv/blob/cae8d76c210b9777e90aab76e9c4b0e53bb19cde/pipenv/patched/notpip/_internal/req/req_uninstall.py#L337-L366 | def remove(self, auto_confirm=False, verbose=False):
"""Remove paths in ``self.paths`` with confirmation (unless
``auto_confirm`` is True)."""
if not self.paths:
logger.info(
"Can't uninstall '%s'. No files were found to uninstall.",
self.dist.project_name,
)
return
dist_name_version = (
self.dist.project_name + "-" + self.dist.version
)
logger.info('Uninstalling %s:', dist_name_version)
with indent_log():
if auto_confirm or self._allowed_to_proceed(verbose):
moved = self._moved_paths
for_rename = compress_for_rename(self.paths)
for path in sorted(compact(for_rename)):
moved.stash(path)
logger.debug('Removing file or directory %s', path)
for pth in self.pth.values():
pth.remove()
logger.info('Successfully uninstalled %s', dist_name_version) | [
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| python | train | 33.866667 |
nteract/papermill | papermill/preprocess.py | https://github.com/nteract/papermill/blob/7423a303f3fa22ec6d03edf5fd9700d659b5a6fa/papermill/preprocess.py#L14-L26 | def preprocess(self, nb_man, resources, km=None):
"""
Wraps the parent class process call slightly
"""
with self.setup_preprocessor(nb_man.nb, resources, km=km):
if self.log_output:
self.log.info("Executing notebook with kernel: {}".format(self.kernel_name))
nb, resources = self.papermill_process(nb_man, resources)
info_msg = self._wait_for_reply(self.kc.kernel_info())
nb.metadata['language_info'] = info_msg['content']['language_info']
self.set_widgets_metadata()
return nb, resources | [
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| python | train | 45.615385 |
wilson-eft/wilson | wilson/match/smeft.py | https://github.com/wilson-eft/wilson/blob/4164f55ff663d4f668c6e2b4575fd41562662cc9/wilson/match/smeft.py#L206-L221 | def match_all(d_SMEFT, parameters=None):
"""Match the SMEFT Warsaw basis onto the WET JMS basis."""
p = default_parameters.copy()
if parameters is not None:
# if parameters are passed in, overwrite the default values
p.update(parameters)
C = wilson.util.smeftutil.wcxf2arrays_symmetrized(d_SMEFT)
C['vT'] = 246.22
C_WET = match_all_array(C, p)
C_WET = wilson.translate.wet.rotate_down(C_WET, p)
C_WET = wetutil.unscale_dict_wet(C_WET)
d_WET = wilson.util.smeftutil.arrays2wcxf(C_WET)
basis = wcxf.Basis['WET', 'JMS']
keys = set(d_WET.keys()) & set(basis.all_wcs)
d_WET = {k: d_WET[k] for k in keys}
return d_WET | [
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| python | train | 41.5 |
riga/tfdeploy | tfdeploy.py | https://github.com/riga/tfdeploy/blob/8481f657d6e3a51d76185a195b993e45f448828a/tfdeploy.py#L863-L877 | def print_tensor(td_tensor, indent="| ", max_depth=-1, depth=0):
""" print_tensor(td_tensor, indent=" ", max_depth=-1)
Prints the dependency graph of a :py:class:`Tensor` *td_tensor*, where each new level is
indented by *indent*. When *max_depth* is positive, the graph is truncated at that depth, where
each tensor and each op count as a level.
"""
offset = depth * indent
line = "td tensor: %s" % td_tensor.name
if td_tensor.value is not None:
line += " (%s)" % (",".join(str(i) for i in td_tensor.value.shape),)
print(offset + line)
if td_tensor.op and (max_depth < 0 or max_depth > depth):
print_op(td_tensor.op, indent=indent, max_depth=max_depth, depth=depth+1) | [
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| python | train | 47.733333 |
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