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elifesciences/elife-tools
elifetools/parseJATS.py
https://github.com/elifesciences/elife-tools/blob/4b9e38cbe485c61a4ed7cbd8970c6b318334fd86/elifetools/parseJATS.py#L37-L45
def title_prefix(soup): "titlePrefix for article JSON is only articles with certain display_channel values" prefix = None display_channel_match_list = ['feature article', 'insight', 'editorial'] for d_channel in display_channel(soup): if d_channel.lower() in display_channel_match_list: ...
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titlePrefix for article JSON is only articles with certain display_channel values
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python
train
tsroten/pynlpir
pynlpir/pos_map.py
https://github.com/tsroten/pynlpir/blob/8d5e994796a2b5d513f7db8d76d7d24a85d531b1/pynlpir/pos_map.py#L173-L191
def get_pos_name(code, name='parent', english=True, pos_tags=POS_MAP): """Gets the part of speech name for *code*. :param str code: The part of speech code to lookup, e.g. ``'nsf'``. :param str name: Which part of speech name to include in the output. Must be one of ``'parent'``, ``'child'``, or ``...
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Gets the part of speech name for *code*. :param str code: The part of speech code to lookup, e.g. ``'nsf'``. :param str name: Which part of speech name to include in the output. Must be one of ``'parent'``, ``'child'``, or ``'all'``. Defaults to ``'parent'``. ``'parent'`` indicates that only th...
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python
train
Microsoft/azure-devops-python-api
azure-devops/azure/devops/v5_0/symbol/symbol_client.py
https://github.com/Microsoft/azure-devops-python-api/blob/4777ffda2f5052fabbaddb2abe9cb434e0cf1aa8/azure-devops/azure/devops/v5_0/symbol/symbol_client.py#L72-L93
def create_requests_request_id_debug_entries(self, batch, request_id, collection): """CreateRequestsRequestIdDebugEntries. [Preview API] Create debug entries for a symbol request as specified by its identifier. :param :class:`<DebugEntryCreateBatch> <azure.devops.v5_0.symbol.models.DebugEntryCre...
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CreateRequestsRequestIdDebugEntries. [Preview API] Create debug entries for a symbol request as specified by its identifier. :param :class:`<DebugEntryCreateBatch> <azure.devops.v5_0.symbol.models.DebugEntryCreateBatch>` batch: A batch that contains debug entries to create. :param str request_id...
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python
train
nikcub/floyd
floyd/util/dateformat.py
https://github.com/nikcub/floyd/blob/5772d0047efb11c9ce5f7d234a9da4576ce24edc/floyd/util/dateformat.py#L377-L388
def Z(self): """ Time zone offset in seconds (i.e. '-43200' to '43200'). The offset for timezones west of UTC is always negative, and for those east of UTC is always positive. """ if not self.timezone: return 0 offset = self.timezone.utcoffset(self.data) # Only days can be negative...
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Time zone offset in seconds (i.e. '-43200' to '43200'). The offset for timezones west of UTC is always negative, and for those east of UTC is always positive.
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python
train
kislyuk/aegea
aegea/packages/github3/github.py
https://github.com/kislyuk/aegea/blob/94957e9dba036eae3052e2662c208b259c08399a/aegea/packages/github3/github.py#L1052-L1064
def repository(self, owner, repository): """Returns a Repository object for the specified combination of owner and repository :param str owner: (required) :param str repository: (required) :returns: :class:`Repository <github3.repos.Repository>` """ json = None ...
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Returns a Repository object for the specified combination of owner and repository :param str owner: (required) :param str repository: (required) :returns: :class:`Repository <github3.repos.Repository>`
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python
train
hyperledger/sawtooth-core
rest_api/sawtooth_rest_api/route_handlers.py
https://github.com/hyperledger/sawtooth-core/blob/8cf473bc2207e51f02bd182d825158a57d72b098/rest_api/sawtooth_rest_api/route_handlers.py#L124-L185
async def submit_batches(self, request): """Accepts a binary encoded BatchList and submits it to the validator. Request: body: octet-stream BatchList of one or more Batches Response: status: - 202: Batches submitted and pending link: /batches...
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Accepts a binary encoded BatchList and submits it to the validator. Request: body: octet-stream BatchList of one or more Batches Response: status: - 202: Batches submitted and pending link: /batches or /batch_statuses link for submitted batches
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python
train
hectane/python-hectane
pyhectane/django.py
https://github.com/hectane/python-hectane/blob/e0fe1df576f776566e813f71782f8adf60146383/pyhectane/django.py#L55-L78
def send_messages(self, emails): """ Attempt to send the specified emails. """ num_sent = 0 for e in emails: html = None if isinstance(e, EmailMultiAlternatives): for a in e.alternatives: if a[1] == 'text/html': ...
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Attempt to send the specified emails.
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python
train
gusutabopb/aioinflux
aioinflux/serialization/usertype.py
https://github.com/gusutabopb/aioinflux/blob/2e4b7b3e13604e7618c686d89a0673f0bc70b24e/aioinflux/serialization/usertype.py#L67-L122
def _make_serializer(meas, schema, rm_none, extra_tags, placeholder): # noqa: C901 """Factory of line protocol parsers""" _validate_schema(schema, placeholder) tags = [] fields = [] ts = None meas = meas for k, t in schema.items(): if t is MEASUREMENT: meas = f"{{i.{k}}}...
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Factory of line protocol parsers
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python
train
jfear/sramongo
sramongo/services/entrez.py
https://github.com/jfear/sramongo/blob/82a9a157e44bda4100be385c644b3ac21be66038/sramongo/services/entrez.py#L86-L115
def epost(database, ids: List[str], webenv=False, api_key=False, email=False, **kwargs) -> Optional[EpostResult]: """Post IDs using the Entrez ESearch API. Parameters ---------- database : str Entez database to search. ids : list List of IDs to submit to the server. webenv : str...
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Post IDs using the Entrez ESearch API. Parameters ---------- database : str Entez database to search. ids : list List of IDs to submit to the server. webenv : str An Entrez WebEnv to post ids to. api_key : str A users API key which allows more requests per second...
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python
train
libtcod/python-tcod
tcod/random.py
https://github.com/libtcod/python-tcod/blob/8ba10c5cfb813eaf3e834de971ba2d6acb7838e4/tcod/random.py#L58-L62
def _new_from_cdata(cls, cdata: Any) -> "Random": """Return a new instance encapsulating this cdata.""" self = object.__new__(cls) # type: "Random" self.random_c = cdata return self
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Return a new instance encapsulating this cdata.
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python
train
biolink/ontobio
ontobio/sparql/rdflib_bridge.py
https://github.com/biolink/ontobio/blob/4e512a7831cfe6bc1b32f2c3be2ba41bc5cf7345/ontobio/sparql/rdflib_bridge.py#L15-L44
def rdfgraph_to_ontol(rg): """ Return an Ontology object from an rdflib graph object Status: Incomplete """ digraph = networkx.MultiDiGraph() from rdflib.namespace import RDF label_map = {} for c in rg.subjects(RDF.type, OWL.Class): cid = contract_uri_wrap(c) logging.inf...
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Return an Ontology object from an rdflib graph object Status: Incomplete
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python
train
aiortc/aiortc
aiortc/rtcpeerconnection.py
https://github.com/aiortc/aiortc/blob/60ed036abf4575bd63985724b4493d569e6da29b/aiortc/rtcpeerconnection.py#L319-L343
def addTrack(self, track): """ Add a :class:`MediaStreamTrack` to the set of media tracks which will be transmitted to the remote peer. """ # check state is valid self.__assertNotClosed() if track.kind not in ['audio', 'video']: raise InternalError('In...
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Add a :class:`MediaStreamTrack` to the set of media tracks which will be transmitted to the remote peer.
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python
train
molmod/molmod
molmod/io/cube.py
https://github.com/molmod/molmod/blob/a7b5b4364ed514ad4c465856c05b5eda1cb561e0/molmod/io/cube.py#L260-L267
def copy(self, newdata=None): '''Return a copy of the cube with optionally new data.''' if newdata is None: newdata = self.data.copy() return self.__class__( self.molecule, self.origin.copy(), self.axes.copy(), self.nrep.copy(), newdata, self.subtitle, self.nu...
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Return a copy of the cube with optionally new data.
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python
train
SavinaRoja/OpenAccess_EPUB
src/openaccess_epub/publisher/plos.py
https://github.com/SavinaRoja/OpenAccess_EPUB/blob/6b77ba30b7394fd003920e7a7957bca963a90656/src/openaccess_epub/publisher/plos.py#L1192-L1216
def convert_ref_list_elements(self): """ List of references (citations) for an article, which is often called “References”, “Bibliography”, or “Additional Reading”. No distinction is made between lists of cited references and lists of suggested references. This method s...
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List of references (citations) for an article, which is often called “References”, “Bibliography”, or “Additional Reading”. No distinction is made between lists of cited references and lists of suggested references. This method should not be confused with the method(s) employed for the...
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python
train
night-crawler/django-docker-helpers
django_docker_helpers/utils.py
https://github.com/night-crawler/django-docker-helpers/blob/b64f8009101a8eb61d3841124ba19e3ab881aa2f/django_docker_helpers/utils.py#L143-L156
def dotkey(obj: dict, path: str, default=None, separator='.'): """ Provides an interface to traverse nested dict values by dot-separated paths. Wrapper for ``dpath.util.get``. :param obj: dict like ``{'some': {'value': 3}}`` :param path: ``'some.value'`` :param separator: ``'.'`` or ``'/'`` or what...
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Provides an interface to traverse nested dict values by dot-separated paths. Wrapper for ``dpath.util.get``. :param obj: dict like ``{'some': {'value': 3}}`` :param path: ``'some.value'`` :param separator: ``'.'`` or ``'/'`` or whatever :param default: default for KeyError :return: dict value or de...
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python
train
saltstack/salt
salt/loader.py
https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/loader.py#L913-L926
def call(fun, **kwargs): ''' Directly call a function inside a loader directory ''' args = kwargs.get('args', []) dirs = kwargs.get('dirs', []) funcs = LazyLoader( [os.path.join(SALT_BASE_PATH, 'modules')] + dirs, None, tag='modules', virtual_enable=False, ) ...
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Directly call a function inside a loader directory
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python
train
materialsproject/pymatgen
pymatgen/electronic_structure/bandstructure.py
https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/electronic_structure/bandstructure.py#L922-L959
def from_old_dict(cls, d): """ Args: d (dict): A dict with all data for a band structure symm line object. Returns: A BandStructureSymmLine object """ # Strip the label to recover initial string (see trick used in as_dict to handle $ chars)...
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Args: d (dict): A dict with all data for a band structure symm line object. Returns: A BandStructureSymmLine object
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python
train
pudo/jsongraph
jsongraph/context.py
https://github.com/pudo/jsongraph/blob/35e4f397dbe69cd5553cf9cb9ab98859c3620f03/jsongraph/context.py#L51-L59
def delete(self): """ Delete all statements matching the current context identifier from the main store. """ if self.parent.buffered: query = 'CLEAR SILENT GRAPH %s ;' % self.identifier.n3() self.parent.graph.update(query) self.flush() else: ...
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Delete all statements matching the current context identifier from the main store.
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python
train
CitrineInformatics/pif-dft
dfttopif/parsers/base.py
https://github.com/CitrineInformatics/pif-dft/blob/d5411dc1f6c6e8d454b132977ca7ab3bb8131a80/dfttopif/parsers/base.py#L196-L205
def is_converged(self): '''Whether the calculation has converged Returns: Property where "scalar" is a boolean indicating ''' # Check for cached result if self._converged is None: self._converged = self._is_converged() return Property(scalars=[Scalar...
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Whether the calculation has converged Returns: Property where "scalar" is a boolean indicating
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python
train
tango-controls/pytango
tango/utils.py
https://github.com/tango-controls/pytango/blob/9cf78c517c9cdc1081ff6d080a9646a740cc1d36/tango/utils.py#L1170-L1180
def findentry(self, item): """A caseless way of checking if an item is in the list or not. It returns None or the entry.""" if not isinstance(item, str): raise TypeError( 'Members of this object must be strings. ' 'You supplied \"%s\"' % type(item)) ...
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A caseless way of checking if an item is in the list or not. It returns None or the entry.
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python
train
Ceasar/easywatch
easywatch/easywatch.py
https://github.com/Ceasar/easywatch/blob/1dd464d2acca5932473759b187dec4eb63dab2d9/easywatch/easywatch.py#L13-L36
def watch(path, handler): """Watch a directory for events. - path should be the directory to watch - handler should a function which takes an event_type and src_path and does something interesting. event_type will be one of 'created', 'deleted', 'modified', or 'moved'. src_path will be t...
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Watch a directory for events. - path should be the directory to watch - handler should a function which takes an event_type and src_path and does something interesting. event_type will be one of 'created', 'deleted', 'modified', or 'moved'. src_path will be the absolute path to the f...
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python
train
PyGithub/PyGithub
github/AuthenticatedUser.py
https://github.com/PyGithub/PyGithub/blob/f716df86bbe7dc276c6596699fa9712b61ef974c/github/AuthenticatedUser.py#L657-L667
def get_authorizations(self): """ :calls: `GET /authorizations <http://developer.github.com/v3/oauth>`_ :rtype: :class:`github.PaginatedList.PaginatedList` of :class:`github.Authorization.Authorization` """ return github.PaginatedList.PaginatedList( github.Authorizati...
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:calls: `GET /authorizations <http://developer.github.com/v3/oauth>`_ :rtype: :class:`github.PaginatedList.PaginatedList` of :class:`github.Authorization.Authorization`
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python
train
soravux/scoop
scoop/backports/dictconfig.py
https://github.com/soravux/scoop/blob/d391dfa62f47e49d48328ee9cf08aa114256fd33/scoop/backports/dictconfig.py#L153-L174
def resolve(self, s): """ Resolve strings to objects using standard import and attribute syntax. """ name = s.split('.') used = name.pop(0) try: found = self.importer(used) for frag in name: used += '.' + frag ...
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Resolve strings to objects using standard import and attribute syntax.
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python
train
googledatalab/pydatalab
google/datalab/_context.py
https://github.com/googledatalab/pydatalab/blob/d9031901d5bca22fe0d5925d204e6698df9852e1/google/datalab/_context.py#L102-L124
def default(): """Retrieves a default Context object, creating it if necessary. The default Context is a global shared instance used every time the default context is retrieved. Attempting to use a Context with no project_id will raise an exception, so on first use set_project_id must be c...
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Retrieves a default Context object, creating it if necessary. The default Context is a global shared instance used every time the default context is retrieved. Attempting to use a Context with no project_id will raise an exception, so on first use set_project_id must be called. Returns: ...
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python
train
josuebrunel/myql
myql/contrib/finance/stockscraper/stockretriever.py
https://github.com/josuebrunel/myql/blob/891bad29cc83a81b3f5ebc4d0401d6f2c22f119e/myql/contrib/finance/stockscraper/stockretriever.py#L49-L54
def get_historical_info(self, symbol,items=None, startDate=None, endDate=None, limit=None): """get_historical_info() uses the csv datatable to retrieve all available historical data on a typical historical prices page """ startDate, endDate = self.__get_time_range(startDate, endDate) res...
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get_historical_info() uses the csv datatable to retrieve all available historical data on a typical historical prices page
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python
train
hovren/crisp
crisp/imu.py
https://github.com/hovren/crisp/blob/65cae19e7cfae5a397859096c9ef666e0f4e7f1b/crisp/imu.py#L66-L77
def rate(self): """Get the sample rate in Hz. Returns --------- rate : float The sample rate, in Hz, calculated from the timestamps """ N = len(self.timestamps) t = self.timestamps[-1] - self.timestamps[0] rate = 1.0 * N / ...
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Get the sample rate in Hz. Returns --------- rate : float The sample rate, in Hz, calculated from the timestamps
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python
train
rochacbruno/python-pagseguro
pagseguro/__init__.py
https://github.com/rochacbruno/python-pagseguro/blob/18a9ca3301783cb323e838574b59f9ddffa9a593/pagseguro/__init__.py#L209-L211
def get(self, url): """ do a get transaction """ return requests.get(url, params=self.data, headers=self.config.HEADERS)
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do a get transaction
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python
train
shmir/PyIxNetwork
ixnetwork/ixn_interface.py
https://github.com/shmir/PyIxNetwork/blob/e7d7a89c08a5d3a1382b4dcfd915bbfc7eedd33f/ixnetwork/ixn_interface.py#L55-L68
def _create(self, **attributes): """ Create new interface on IxNetwork. Set enabled and description (==name). :return: interface object reference. """ attributes['enabled'] = True if 'name' in self._data: attributes['description'] = self._data['name'] ...
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Create new interface on IxNetwork. Set enabled and description (==name). :return: interface object reference.
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python
train
hazelcast/hazelcast-python-client
hazelcast/proxy/transactional_map.py
https://github.com/hazelcast/hazelcast-python-client/blob/3f6639443c23d6d036aa343f8e094f052250d2c1/hazelcast/proxy/transactional_map.py#L25-L33
def get(self, key): """ Transactional implementation of :func:`Map.get(key) <hazelcast.proxy.map.Map.get>` :param key: (object), the specified key. :return: (object), the value for the specified key. """ check_not_none(key, "key can't be none") return self._encod...
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Transactional implementation of :func:`Map.get(key) <hazelcast.proxy.map.Map.get>` :param key: (object), the specified key. :return: (object), the value for the specified key.
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python
train
summa-tx/riemann
riemann/tx/tx_builder.py
https://github.com/summa-tx/riemann/blob/04ae336dfd4007ceaed748daadc91cc32fa278ec/riemann/tx/tx_builder.py#L263-L319
def make_tx(version, tx_ins, tx_outs, lock_time, expiry=None, value_balance=0, tx_shielded_spends=None, tx_shielded_outputs=None, tx_witnesses=None, tx_joinsplits=None, joinsplit_pubkey=None, joinsplit_sig=None, binding_sig=None): ''' int, list(TxIn), list(TxOut), int, list(I...
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int, list(TxIn), list(TxOut), int, list(InputWitness) -> Tx
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python
train
Opentrons/opentrons
api/src/opentrons/protocol_api/labware.py
https://github.com/Opentrons/opentrons/blob/a7c15cc2636ecb64ab56c7edc1d8a57163aaeadf/api/src/opentrons/protocol_api/labware.py#L124-L157
def _from_center_cartesian( self, x: float, y: float, z: float) -> Point: """ Specifies an arbitrary point relative to the center of the well based on percentages of the radius in each axis. For example, to specify the back-right corner of a well at 1/4 of the well depth from...
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Specifies an arbitrary point relative to the center of the well based on percentages of the radius in each axis. For example, to specify the back-right corner of a well at 1/4 of the well depth from the bottom, the call would be `_from_center_cartesian(1, 1, -0.5)`. No checks are perfor...
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python
train
pennlabs/penn-sdk-python
penn/dining.py
https://github.com/pennlabs/penn-sdk-python/blob/31ff12c20d69438d63bc7a796f83ce4f4c828396/penn/dining.py#L157-L173
def venues(self): """Get a list of all venue objects. >>> venues = din.venues() """ response = self._request(V2_ENDPOINTS['VENUES']) # Normalize `dateHours` to array for venue in response["result_data"]["document"]["venue"]: if venue.get("id") in VENUE_NAME...
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Get a list of all venue objects. >>> venues = din.venues()
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python
train
houtianze/bypy
bypy/bypy.py
https://github.com/houtianze/bypy/blob/c59b6183e2fca45f11138bbcdec6247449b2eaad/bypy/bypy.py#L2912-L2920
def dumpcache(self): ''' Usage: dumpcache - display file hash cache''' if cached.cacheloaded: #pprint.pprint(cached.cache) MyPrettyPrinter().pprint(cached.cache) return const.ENoError else: perr("Cache not loaded.") return const.ECacheNotLoaded
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Usage: dumpcache - display file hash cache
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python
train
kristianfoerster/melodist
melodist/humidity.py
https://github.com/kristianfoerster/melodist/blob/ddc155c77b65f791be0021dbbaf68c6bac42ecbd/melodist/humidity.py#L33-L109
def disaggregate_humidity(data_daily, method='equal', temp=None, a0=None, a1=None, kr=None, month_hour_precip_mean=None, preserve_daily_mean=False): """general function for humidity disaggregation Args: daily_data: daily values method: keyword...
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general function for humidity disaggregation Args: daily_data: daily values method: keyword specifying the disaggregation method to be used temp: hourly temperature time series (necessary for some methods) kr: parameter for linear_dewpoint_variation method (6 or 12) month_ho...
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python
train
googleapis/google-cloud-python
bigquery/google/cloud/bigquery/external_config.py
https://github.com/googleapis/google-cloud-python/blob/85e80125a59cb10f8cb105f25ecc099e4b940b50/bigquery/google/cloud/bigquery/external_config.py#L697-L718
def from_api_repr(cls, resource): """Factory: construct an :class:`~.external_config.ExternalConfig` instance given its API representation. Args: resource (Dict[str, Any]): Definition of an :class:`~.external_config.ExternalConfig` instance in the sam...
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Factory: construct an :class:`~.external_config.ExternalConfig` instance given its API representation. Args: resource (Dict[str, Any]): Definition of an :class:`~.external_config.ExternalConfig` instance in the same representation as is returned from the ...
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python
train
GetmeUK/MongoFrames
mongoframes/frames.py
https://github.com/GetmeUK/MongoFrames/blob/7d2bd792235dfa77a9deecab5366f5f73480823d/mongoframes/frames.py#L771-L775
def get_db(cls): """Return the database for the collection""" if cls._db: return getattr(cls._client, cls._db) return cls._client.get_default_database()
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Return the database for the collection
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python
train
mdeous/fatbotslim
fatbotslim/handlers.py
https://github.com/mdeous/fatbotslim/blob/341595d24454a79caee23750eac271f9d0626c88/fatbotslim/handlers.py#L284-L306
def handle_rights(self, msg): """ Catch-all command that is called whenever a restricted command is triggered. :param msg: message that triggered the command. :type msg: :class:`fatbotslim.irc.Message` """ command = msg.args[0][1:] if command in self.commands_rig...
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Catch-all command that is called whenever a restricted command is triggered. :param msg: message that triggered the command. :type msg: :class:`fatbotslim.irc.Message`
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python
train
edx/edx-enterprise
enterprise/messages.py
https://github.com/edx/edx-enterprise/blob/aea91379ab0a87cd3bc798961fce28b60ee49a80/enterprise/messages.py#L77-L97
def add_unenrollable_item_message(request, item): """ Add a message to the Django message store indicating that the item (i.e. course run, program) is unenrollable. :param request: The current request. :param item: The item that is unenrollable (i.e. a course run). """ messages.info( re...
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Add a message to the Django message store indicating that the item (i.e. course run, program) is unenrollable. :param request: The current request. :param item: The item that is unenrollable (i.e. a course run).
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python
valid
OpenGov/python_data_wrap
datawrap/listwrap.py
https://github.com/OpenGov/python_data_wrap/blob/7de38bb30d7a500adc336a4a7999528d753e5600/datawrap/listwrap.py#L393-L431
def _get_single_index_request(self, index, set_to_value=False, value=None): ''' Helper function which implements single index requests for __getitem__. ''' adjusted_index = index # Multiply by step length if self.range.step: step = self.range.step ...
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Helper function which implements single index requests for __getitem__.
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python
train
googleapis/google-cloud-python
irm/google/cloud/irm_v1alpha2/gapic/incident_service_client.py
https://github.com/googleapis/google-cloud-python/blob/85e80125a59cb10f8cb105f25ecc099e4b940b50/irm/google/cloud/irm_v1alpha2/gapic/incident_service_client.py#L82-L88
def incident_path(cls, project, incident): """Return a fully-qualified incident string.""" return google.api_core.path_template.expand( "projects/{project}/incidents/{incident}", project=project, incident=incident, )
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Return a fully-qualified incident string.
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python
train
ARMmbed/icetea
icetea_lib/tools/GenericProcess.py
https://github.com/ARMmbed/icetea/blob/b2b97ac607429830cf7d62dae2e3903692c7c778/icetea_lib/tools/GenericProcess.py#L247-L260
def readline(self): """ Readline implementation. :return: popped line from descriptor queue. None if nothing found :raises: RuntimeError if errors happened while reading PIPE """ try: return self._descriptor.read_queue.pop() except IndexError: ...
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Readline implementation. :return: popped line from descriptor queue. None if nothing found :raises: RuntimeError if errors happened while reading PIPE
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python
train
carlosp420/dataset-creator
dataset_creator/utils.py
https://github.com/carlosp420/dataset-creator/blob/ea27340b145cb566a36c1836ff42263f1b2003a0/dataset_creator/utils.py#L89-L126
def make_dataset_header(data, file_format, aminoacids): """Creates the dataset header for NEXUS files from ``#NEXUS`` to ``MATRIX``. Parameters: data (namedtuple): with necessary info for dataset creation. file_format (str): TNT, PHYLIP, NEXUS, FASTA aminoacids (boolean): If ``ami...
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Creates the dataset header for NEXUS files from ``#NEXUS`` to ``MATRIX``. Parameters: data (namedtuple): with necessary info for dataset creation. file_format (str): TNT, PHYLIP, NEXUS, FASTA aminoacids (boolean): If ``aminoacids is True`` the header will show ...
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python
train
bitshares/python-bitshares
bitshares/bitshares.py
https://github.com/bitshares/python-bitshares/blob/8a3b5954a6abcaaff7c6a5c41d910e58eea3142f/bitshares/bitshares.py#L895-L922
def set_proxy(self, proxy_account, account=None, **kwargs): """ Set a specific proxy for account :param bitshares.account.Account proxy_account: Account to be proxied :param str account: (optional) the account to allow access to (defaults to ``default...
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python
train
openstax/rhaptos.cnxmlutils
rhaptos/cnxmlutils/utils.py
https://github.com/openstax/rhaptos.cnxmlutils/blob/c32b1a7428dc652e8cd745f3fdf4019a20543649/rhaptos/cnxmlutils/utils.py#L233-L238
def aloha_to_etree(html_source): """ Converts HTML5 from Aloha editor output to a lxml etree. """ xml = _tidy2xhtml5(html_source) for i, transform in enumerate(ALOHA2HTML_TRANSFORM_PIPELINE): xml = transform(xml) return xml
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Converts HTML5 from Aloha editor output to a lxml etree.
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python
train
nschloe/colorio
experiments/new-cs.py
https://github.com/nschloe/colorio/blob/357d6001b3cf30f752e23726bf429dc1d1c60b3a/experiments/new-cs.py#L309-L346
def build_grad_matrices(V, points): """Build the sparse m-by-n matrices that map a coefficient set for a function in V to the values of dx and dy at a number m of points. """ # See <https://www.allanswered.com/post/lkbkm/#zxqgk> mesh = V.mesh() bbt = BoundingBoxTree() bbt.build(mesh) do...
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Build the sparse m-by-n matrices that map a coefficient set for a function in V to the values of dx and dy at a number m of points.
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python
train
konstantint/PassportEye
passporteye/mrz/image.py
https://github.com/konstantint/PassportEye/blob/b32afba0f5dc4eb600c4edc4f49e5d49959c5415/passporteye/mrz/image.py#L254-L267
def _try_larger_image(self, roi, cur_text, cur_mrz, filter_order=3): """Attempts to improve the OCR result by scaling the image. If the new mrz is better, returns it, otherwise returns the old mrz.""" if roi.shape[1] <= 700: scale_by = int(1050.0 / roi.shape[1] + 0.5) roi...
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python
train
hamperbot/hamper
hamper/commander.py
https://github.com/hamperbot/hamper/blob/6f841ec4dcc319fdd7bb3ca1f990e3b7a458771b/hamper/commander.py#L348-L368
def runPlugins(self, category, func, protocol, *args): """ Run the specified set of plugins against a given protocol. """ # Plugins are already sorted by priority for plugin in self.plugins: # If a plugin throws an exception, we should catch it gracefully. ...
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Run the specified set of plugins against a given protocol.
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python
train
twilio/twilio-python
twilio/rest/sync/v1/service/sync_map/__init__.py
https://github.com/twilio/twilio-python/blob/c867895f55dcc29f522e6e8b8868d0d18483132f/twilio/rest/sync/v1/service/sync_map/__init__.py#L372-L386
def _proxy(self): """ Generate an instance context for the instance, the context is capable of performing various actions. All instance actions are proxied to the context :returns: SyncMapContext for this SyncMapInstance :rtype: twilio.rest.sync.v1.service.sync_map.SyncMapConte...
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Generate an instance context for the instance, the context is capable of performing various actions. All instance actions are proxied to the context :returns: SyncMapContext for this SyncMapInstance :rtype: twilio.rest.sync.v1.service.sync_map.SyncMapContext
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python
train
ranaroussi/ezibpy
ezibpy/ezibpy.py
https://github.com/ranaroussi/ezibpy/blob/1a9d4bf52018abd2a01af7c991d7cf00cda53e0c/ezibpy/ezibpy.py#L1892-L1929
def requestHistoricalData(self, contracts=None, resolution="1 min", lookback="1 D", data="TRADES", end_datetime=None, rth=False, csv_path=None, format_date=2, utc=False): """ Download to historical data https://www.interactivebrokers.com/en/software/api/apiguide/java/req...
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Download to historical data https://www.interactivebrokers.com/en/software/api/apiguide/java/reqhistoricaldata.htm
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python
train
nccgroup/Scout2
AWSScout2/services/cloudwatch.py
https://github.com/nccgroup/Scout2/blob/5d86d46d7ed91a92000496189e9cfa6b98243937/AWSScout2/services/cloudwatch.py#L21-L35
def parse_alarm(self, global_params, region, alarm): """ Parse a single CloudWatch trail :param global_params: Parameters shared for all regions :param region: Name of the AWS region :param alarm: Alarm """ alarm['arn'...
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Parse a single CloudWatch trail :param global_params: Parameters shared for all regions :param region: Name of the AWS region :param alarm: Alarm
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python
train
cloud-custodian/cloud-custodian
tools/c7n_azure/c7n_azure/utils.py
https://github.com/cloud-custodian/cloud-custodian/blob/52ef732eb3d7bc939d1579faf519314814695c08/tools/c7n_azure/c7n_azure/utils.py#L259-L270
def _get_port_range(range_str): """ Given a string with a port or port range: '80', '80-120' Returns tuple with range start and end ports: (80, 80), (80, 120) """ if range_str == '*': return PortsRangeHelper.PortsRange(start=0, end=65535) s = range_str.split('-')...
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Given a string with a port or port range: '80', '80-120' Returns tuple with range start and end ports: (80, 80), (80, 120)
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python
train
GaryLee/cmdlet
cmdlet/cmds.py
https://github.com/GaryLee/cmdlet/blob/5852a63fc2c7dd723a3d7abe18455f8dacb49433/cmdlet/cmds.py#L691-L695
def substitute(prev, *args, **kw): '''alias of string.Template.substitute''' template_obj = string.Template(*args, **kw) for data in prev: yield template_obj.substitute(data)
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alias of string.Template.substitute
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python
valid
nccgroup/Scout2
AWSScout2/services/redshift.py
https://github.com/nccgroup/Scout2/blob/5d86d46d7ed91a92000496189e9cfa6b98243937/AWSScout2/services/redshift.py#L60-L70
def parse_security_group(self, global_params, region, security_group): """ Parse a single Redsfhit security group :param global_params: Parameters shared for all regions :param region: Name of the AWS region :param security)_group: Security gro...
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Parse a single Redsfhit security group :param global_params: Parameters shared for all regions :param region: Name of the AWS region :param security)_group: Security group
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python
train
Projectplace/basepage
basepage/base_page.py
https://github.com/Projectplace/basepage/blob/735476877eb100db0981590a6d12140e68652167/basepage/base_page.py#L722-L738
def wait_for_non_empty_text(self, locator, params=None, timeout=5): """ Wait and get elements when they're populated with any text. :param locator: locator tuple :param params: (optional) locator params :param timeout: (optional) maximum waiting time (in seconds) (default: 5) ...
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Wait and get elements when they're populated with any text. :param locator: locator tuple :param params: (optional) locator params :param timeout: (optional) maximum waiting time (in seconds) (default: 5) :return: list of WebElements
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python
train
fitnr/twitter_bot_utils
twitter_bot_utils/helpers.py
https://github.com/fitnr/twitter_bot_utils/blob/21f35afa5048cd3efa54db8cb87d405f69a78a62/twitter_bot_utils/helpers.py#L98-L113
def remove_entities(status, entitylist): '''Remove entities for a list of items.''' try: entities = status.entities text = status.text except AttributeError: entities = status.get('entities', dict()) text = status['text'] indices = [ent['indices'] for etype, entval in li...
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Remove entities for a list of items.
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python
train
fermiPy/fermipy
fermipy/jobs/chain.py
https://github.com/fermiPy/fermipy/blob/9df5e7e3728307fd58c5bba36fd86783c39fbad4/fermipy/jobs/chain.py#L345-L365
def update_args(self, override_args): """Update the argument used to invoke the application Note that this will also update the dictionary of input and output files. Parameters ----------- override_args : dict dictionary passed to the links """ ...
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Update the argument used to invoke the application Note that this will also update the dictionary of input and output files. Parameters ----------- override_args : dict dictionary passed to the links
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python
train
Ouranosinc/xclim
xclim/checks.py
https://github.com/Ouranosinc/xclim/blob/2080d139188bd8de2aeca097a025c2d89d6e0e09/xclim/checks.py#L108-L118
def valid_daily_max_min_temperature(comp, units='K'): r"""Decorator to check that a computation runs on valid min and max temperature datasets.""" @wraps(comp) def func(tasmax, tasmin, **kwds): valid_daily_max_temperature(tasmax, units) valid_daily_min_temperature(tasmin, units) re...
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r"""Decorator to check that a computation runs on valid min and max temperature datasets.
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python
train
shoebot/shoebot
lib/web/BeautifulSoup.py
https://github.com/shoebot/shoebot/blob/d554c1765c1899fa25727c9fc6805d221585562b/lib/web/BeautifulSoup.py#L1398-L1416
def parse_declaration(self, i): """Treat a bogus SGML declaration as raw data. Treat a CDATA declaration as a CData object.""" j = None if self.rawdata[i:i+9] == '<![CDATA[': k = self.rawdata.find(']]>', i) if k == -1: k = len(self.rawdata) ...
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Treat a bogus SGML declaration as raw data. Treat a CDATA declaration as a CData object.
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python
valid
KelSolaar/Foundations
foundations/parsers.py
https://github.com/KelSolaar/Foundations/blob/5c141330faf09dad70a12bc321f4c564917d0a91/foundations/parsers.py#L238-L253
def namespace_splitter(self, value): """ Setter for **self.__namespace_splitter** attribute. :param value: Attribute value. :type value: unicode """ if value is not None: assert type(value) is unicode, "'{0}' attribute: '{1}' type is not 'unicode'!".format( ...
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Setter for **self.__namespace_splitter** attribute. :param value: Attribute value. :type value: unicode
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python
train
devassistant/devassistant
devassistant/dapi/dapicli.py
https://github.com/devassistant/devassistant/blob/2dbfeaa666a64127263664d18969c55d19ecc83e/devassistant/dapi/dapicli.py#L302-L319
def format_installed_dap_list(simple=False): '''Formats all installed DAPs in a human readable form to list of lines''' lines = [] if simple: for pkg in sorted(get_installed_daps()): lines.append(pkg) else: for pkg, instances in sorted(get_installed_daps_detailed().items()): ...
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Formats all installed DAPs in a human readable form to list of lines
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python
train
mozilla/treeherder
treeherder/seta/models.py
https://github.com/mozilla/treeherder/blob/cc47bdec872e5c668d0f01df89517390a164cda3/treeherder/seta/models.py#L21-L37
def adjust_jobs_priority(self, high_value_jobs, priority=1): """For every job priority determine if we need to increase or decrease the job priority Currently, high value jobs have a priority of 1 and a timeout of 0. """ # Only job priorities that don't have an expiration date (2 weeks ...
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python
train
funilrys/PyFunceble
PyFunceble/database.py
https://github.com/funilrys/PyFunceble/blob/cdf69cbde120199171f7158e1c33635753e6e2f5/PyFunceble/database.py#L270-L279
def _backup(self): """ Save the current database into the inactive-db.json file. """ if PyFunceble.CONFIGURATION["inactive_database"]: # The database subsystem is activated. # We save the current database state into the database file. Dict(PyFunceble...
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Save the current database into the inactive-db.json file.
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python
test
brocade/pynos
pynos/versions/ver_6/ver_6_0_1/yang/brocade_system_monitor.py
https://github.com/brocade/pynos/blob/bd8a34e98f322de3fc06750827d8bbc3a0c00380/pynos/versions/ver_6/ver_6_0_1/yang/brocade_system_monitor.py#L90-L101
def system_monitor_power_alert_state(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") system_monitor = ET.SubElement(config, "system-monitor", xmlns="urn:brocade.com:mgmt:brocade-system-monitor") power = ET.SubElement(system_monitor, "power") aler...
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Auto Generated Code
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python
train
hozn/stravalib
stravalib/attributes.py
https://github.com/hozn/stravalib/blob/5500ebc39e0bf4706bb1ca4c27b25e56becaaa5f/stravalib/attributes.py#L81-L95
def unmarshal(self, v): """ Convert the value from parsed JSON structure to native python representation. By default this will leave the value as-is since the JSON parsing routines typically convert to native types. The exception may be date strings or other more complex types, ...
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python
train
ManiacalLabs/PixelWeb
pixelweb/bottle.py
https://github.com/ManiacalLabs/PixelWeb/blob/9eacbfd40a1d35011c2dcea15c303da9636c6b9e/pixelweb/bottle.py#L553-L558
def get_config(self, key, default=None): ''' Lookup a config field and return its value, first checking the route.config, then route.app.config.''' for conf in (self.config, self.app.conifg): if key in conf: return conf[key] return default
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Lookup a config field and return its value, first checking the route.config, then route.app.config.
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python
train
AltSchool/dynamic-rest
dynamic_rest/filters.py
https://github.com/AltSchool/dynamic-rest/blob/5b0338c3dd8bc638d60c3bb92645857c5b89c920/dynamic_rest/filters.py#L73-L140
def generate_query_key(self, serializer): """Get the key that can be passed to Django's filter method. To account for serialier field name rewrites, this method translates serializer field names to model field names by inspecting `serializer`. For example, a query like `filter{...
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Get the key that can be passed to Django's filter method. To account for serialier field name rewrites, this method translates serializer field names to model field names by inspecting `serializer`. For example, a query like `filter{users.events}` would be returned as `users__e...
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python
train
quantmind/pulsar
examples/chat/manage.py
https://github.com/quantmind/pulsar/blob/fee44e871954aa6ca36d00bb5a3739abfdb89b26/examples/chat/manage.py#L70-L75
def encode(self, message): '''Encode a message when publishing.''' if not isinstance(message, dict): message = {'message': message} message['time'] = time.time() return json.dumps(message)
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Encode a message when publishing.
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python
train
pyviz/holoviews
holoviews/core/data/__init__.py
https://github.com/pyviz/holoviews/blob/ae0dd2f3de448b0ca5e9065aabd6ef8d84c7e655/holoviews/core/data/__init__.py#L269-L294
def range(self, dim, data_range=True, dimension_range=True): """Return the lower and upper bounds of values along dimension. Args: dimension: The dimension to compute the range on. data_range (bool): Compute range from data values dimension_range (bool): Include Dime...
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Return the lower and upper bounds of values along dimension. Args: dimension: The dimension to compute the range on. data_range (bool): Compute range from data values dimension_range (bool): Include Dimension ranges Whether to include Dimension range and soft...
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python
train
KarchinLab/probabilistic2020
scripts/check_mutations.py
https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/scripts/check_mutations.py#L23-L35
def correct_chrom_names(chroms): """Make sure chromosome names follow UCSC chr convention.""" chrom_list = [] for chrom in chroms: # fix chrom numbering chrom = str(chrom) chrom = chrom.replace('23', 'X') chrom = chrom.replace('24', 'Y') chrom = chrom.replace('25', 'M...
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Make sure chromosome names follow UCSC chr convention.
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python
train
wilson-eft/wilson
wilson/translate/wet.py
https://github.com/wilson-eft/wilson/blob/4164f55ff663d4f668c6e2b4575fd41562662cc9/wilson/translate/wet.py#L973-L984
def JMS_to_Fierz_nunu(C, ddll): """From JMS to semileptonic Fierz basis for Class V. `ddll` should be of the form 'sbl_enu_tau', 'dbl_munu_e' etc.""" s = dflav[ddll[0]] b = dflav[ddll[1]] l = lflav[ddll[4:ddll.find('n')]] lp = lflav[ddll[ddll.find('_',5)+1:len(ddll)]] ind = ddll.replace('l_'...
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From JMS to semileptonic Fierz basis for Class V. `ddll` should be of the form 'sbl_enu_tau', 'dbl_munu_e' etc.
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python
train
kata198/NamedAtomicLock
NamedAtomicLock/__init__.py
https://github.com/kata198/NamedAtomicLock/blob/82d480b81daf4deea926964f18bb2e47d4f30f6c/NamedAtomicLock/__init__.py#L165-L185
def __checkExpiration(self, mtime=None): ''' __checkExpiration - Check if we have expired @param mtime <int> - Optional mtime if known, otherwise will be gathered @return <bool> - True if we did expire, otherwise False ''' if not self.maxLockAge:...
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__checkExpiration - Check if we have expired @param mtime <int> - Optional mtime if known, otherwise will be gathered @return <bool> - True if we did expire, otherwise False
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python
train
futurecolors/django-geoip
django_geoip/management/ipgeobase.py
https://github.com/futurecolors/django-geoip/blob/f9eee4bcad40508089b184434b79826f842d7bd0/django_geoip/management/ipgeobase.py#L31-L39
def clear_database(self): """ Removes all geodata stored in database. Useful for development, never use on production. """ self.logger.info('Removing obsolete geoip from database...') IpRange.objects.all().delete() City.objects.all().delete() Region.objects.al...
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Removes all geodata stored in database. Useful for development, never use on production.
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python
train
manahl/arctic
arctic/store/_ndarray_store.py
https://github.com/manahl/arctic/blob/57e110b6e182dbab00e7e214dc26f7d9ec47c120/arctic/store/_ndarray_store.py#L75-L113
def _resize_with_dtype(arr, dtype): """ This function will transform arr into an array with the same type as dtype. It will do this by filling new columns with zeros (or NaNs, if it is a float column). Also, columns that are not in the new dtype will be dropped. """ structured_arrays = dtype.nam...
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This function will transform arr into an array with the same type as dtype. It will do this by filling new columns with zeros (or NaNs, if it is a float column). Also, columns that are not in the new dtype will be dropped.
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python
train
rorr73/LifeSOSpy
lifesospy/baseunit.py
https://github.com/rorr73/LifeSOSpy/blob/62360fbab2e90bf04d52b547093bdab2d4e389b4/lifesospy/baseunit.py#L539-L548
def as_dict(self) -> Dict[str, Any]: """Converts to a dict of attributes for easier serialization.""" def _on_filter(obj: Any, name: str) -> bool: # Filter out any callbacks if isinstance(obj, BaseUnit): if name.startswith('on_'): return False ...
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Converts to a dict of attributes for easier serialization.
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python
train
vaexio/vaex
packages/vaex-core/vaex/expression.py
https://github.com/vaexio/vaex/blob/a45b672f8287afca2ada8e36b74b604b9b28dd85/packages/vaex-core/vaex/expression.py#L371-L434
def value_counts(self, dropna=False, dropnull=True, ascending=False, progress=False): """Computes counts of unique values. WARNING: * If the expression/column is not categorical, it will be converted on the fly * dropna is False by default, it is True by default in pandas ...
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Computes counts of unique values. WARNING: * If the expression/column is not categorical, it will be converted on the fly * dropna is False by default, it is True by default in pandas :param dropna: when True, it will not report the missing values :param ascending: when Fa...
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python
test
SavinaRoja/PyUserInput
pykeyboard/mac.py
https://github.com/SavinaRoja/PyUserInput/blob/153c1d39b1a41b467b235fd182392d6dcbf07947/pykeyboard/mac.py#L174-L193
def _press_special_key(self, key, down): """ Helper method for special keys. Source: http://stackoverflow.com/questions/11045814/emulate-media-key-press-on-mac """ key_code = special_key_translate_table[key] ev = NSEvent.otherEventWithType_location_modifierFlags_timestamp_wind...
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Helper method for special keys. Source: http://stackoverflow.com/questions/11045814/emulate-media-key-press-on-mac
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python
train
apache/airflow
airflow/contrib/hooks/gcp_vision_hook.py
https://github.com/apache/airflow/blob/b69c686ad8a0c89b9136bb4b31767257eb7b2597/airflow/contrib/hooks/gcp_vision_hook.py#L311-L349
def create_reference_image( self, location, product_id, reference_image, reference_image_id=None, project_id=None, retry=None, timeout=None, metadata=None, ): """ For the documentation see: :py:class:`~airflow.contrib.op...
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For the documentation see: :py:class:`~airflow.contrib.operators.gcp_vision_operator.CloudVisionReferenceImageCreateOperator`
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python
test
jorisroovers/gitlint
gitlint/lint.py
https://github.com/jorisroovers/gitlint/blob/6248bd6cbc20c1be3bb6d196a5ec0425af99733b/gitlint/lint.py#L70-L96
def lint(self, commit): """ Lint the last commit in a given git context by applying all ignore, title, body and commit rules. """ LOG.debug("Linting commit %s", commit.sha or "[SHA UNKNOWN]") LOG.debug("Commit Object\n" + ustr(commit)) # Apply config rules for rule in self.confi...
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Lint the last commit in a given git context by applying all ignore, title, body and commit rules.
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python
train
ipfs/py-ipfs-api
ipfsapi/client.py
https://github.com/ipfs/py-ipfs-api/blob/7574dad04877b45dbe4ad321dcfa9e880eb2d90c/ipfsapi/client.py#L1775-L1803
def log_level(self, subsystem, level, **kwargs): r"""Changes the logging output of a running daemon. .. code-block:: python >>> c.log_level("path", "info") {'Message': "Changed log level of 'path' to 'info'\n"} Parameters ---------- subsystem : str ...
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r"""Changes the logging output of a running daemon. .. code-block:: python >>> c.log_level("path", "info") {'Message': "Changed log level of 'path' to 'info'\n"} Parameters ---------- subsystem : str The subsystem logging identifier (Use ``"all"`` f...
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python
train
tilezen/tilequeue
tilequeue/query/rawr.py
https://github.com/tilezen/tilequeue/blob/d7b9484ab92e246eb2773949c784ebb37c731e28/tilequeue/query/rawr.py#L616-L632
def _orient(shape): """ The Shapely version of the orient function appears to only work on Polygons, and fails on MultiPolygons. This is a quick wrapper to allow orienting of either. """ assert shape.geom_type in ('Polygon', 'MultiPolygon') if shape.geom_type == 'Polygon': return o...
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The Shapely version of the orient function appears to only work on Polygons, and fails on MultiPolygons. This is a quick wrapper to allow orienting of either.
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python
train
openstack/networking-cisco
networking_cisco/apps/saf/server/services/firewall/native/fabric_setup_base.py
https://github.com/openstack/networking-cisco/blob/aa58a30aec25b86f9aa5952b0863045975debfa9/networking_cisco/apps/saf/server/services/firewall/native/fabric_setup_base.py#L870-L880
def update_subnet_db_info(self, tenant_id, direc, net_id, subnet_id): """Update the subnet DB with Net and Subnet ID, given the subnet. """ subnet_dict = self.retrieve_dcnm_subnet_info(tenant_id, direc) if not subnet_dict: LOG.error("Subnet dict not found for tenant %s", tenant_id) ...
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Update the subnet DB with Net and Subnet ID, given the subnet.
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python
train
vsudilov/flask-consulate
flask_consulate/consul.py
https://github.com/vsudilov/flask-consulate/blob/514f8754e7186f960237ed2836206993d5d3d3b6/flask_consulate/consul.py#L78-L109
def apply_remote_config(self, namespace=None): """ Applies all config values defined in consul's kv store to self.app. There is no guarantee that these values will not be overwritten later elsewhere. :param namespace: kv namespace/directory. Defaults to DEFAULT_...
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Applies all config values defined in consul's kv store to self.app. There is no guarantee that these values will not be overwritten later elsewhere. :param namespace: kv namespace/directory. Defaults to DEFAULT_KV_NAMESPACE :return: None
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python
train
materialsproject/pymatgen
pymatgen/symmetry/analyzer.py
https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/symmetry/analyzer.py#L1151-L1187
def _find_spherical_axes(self): """ Looks for R5, R4, R3 and R2 axes in spherical top molecules. Point group T molecules have only one unique 3-fold and one unique 2-fold axis. O molecules have one unique 4, 3 and 2-fold axes. I molecules have a unique 5-fold axis. """ ...
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Looks for R5, R4, R3 and R2 axes in spherical top molecules. Point group T molecules have only one unique 3-fold and one unique 2-fold axis. O molecules have one unique 4, 3 and 2-fold axes. I molecules have a unique 5-fold axis.
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python
train
zsethna/OLGA
olga/generation_probability.py
https://github.com/zsethna/OLGA/blob/e825c333f0f9a4eb02132e0bcf86f0dca9123114/olga/generation_probability.py#L377-L470
def format_usage_masks(self, V_usage_mask_in, J_usage_mask_in, print_warnings = True): """Format raw usage masks into lists of indices. Usage masks allows the Pgen computation to be conditioned on the V and J gene/allele identities. The inputted masks are lists of strings, or a si...
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Format raw usage masks into lists of indices. Usage masks allows the Pgen computation to be conditioned on the V and J gene/allele identities. The inputted masks are lists of strings, or a single string, of the names of the genes or alleles to be conditioned on. The default mask ...
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python
train
blockstack/blockstack-core
blockstack/lib/client.py
https://github.com/blockstack/blockstack-core/blob/1dcfdd39b152d29ce13e736a6a1a0981401a0505/blockstack/lib/client.py#L648-L717
def get_atlas_peers(hostport, timeout=30, my_hostport=None, proxy=None): """ Get an atlas peer's neighbors. Return {'status': True, 'peers': [peers]} on success. Return {'error': ...} on error """ assert hostport or proxy, 'need either hostport or proxy' peers_schema = { 'type': 'o...
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Get an atlas peer's neighbors. Return {'status': True, 'peers': [peers]} on success. Return {'error': ...} on error
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python
train
jor-/util
util/cache/memory.py
https://github.com/jor-/util/blob/0eb0be84430f88885f4d48335596ca8881f85587/util/cache/memory.py#L35-L51
def attribute_dependend_key(key_function, *dependencies): """Return a cache key for the specified hashable arguments with additional dependent arguments.""" def dependend_key_function(self, *args, **kwargs): key = hash_key(*args, **kwargs) if len(dependencies) > 0: dependec...
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Return a cache key for the specified hashable arguments with additional dependent arguments.
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python
train
juju/charm-helpers
charmhelpers/contrib/hardening/host/checks/minimize_access.py
https://github.com/juju/charm-helpers/blob/aa785c40c3b7a8c69dbfbc7921d6b9f30142e171/charmhelpers/contrib/hardening/host/checks/minimize_access.py#L22-L50
def get_audits(): """Get OS hardening access audits. :returns: dictionary of audits """ audits = [] settings = utils.get_settings('os') # Remove write permissions from $PATH folders for all regular users. # This prevents changing system-wide commands from normal users. path_folders = ...
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Get OS hardening access audits. :returns: dictionary of audits
[ "Get", "OS", "hardening", "access", "audits", "." ]
python
train
siemens/django-dingos
dingos/import_handling.py
https://github.com/siemens/django-dingos/blob/7154f75b06d2538568e2f2455a76f3d0db0b7d70/dingos/import_handling.py#L318-L766
def xml_import(self, xml_fname=None, xml_content=None, ns_mapping=None, embedded_predicate=None, id_and_revision_extractor=None, extract_empty_embedded=False, keep_attrs_in_created_refere...
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This is the generic XML import function for dingos. Its parameters are as follows: - xml_fname: Filename of the XML file to be read - xml_content: Alternatively, the xml_content can be provided as string or as XMLNode (i.e., a piece of XML that has already been parsed) - ns_ma...
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python
train
safarijv/sbo-selenium
sbo_selenium/management/commands/selenium.py
https://github.com/safarijv/sbo-selenium/blob/16539f1b17cda18270033db3b64ab25bc05c5664/sbo_selenium/management/commands/selenium.py#L67-L71
def clean(): """Clear out any old screenshots""" screenshot_dir = settings.SELENIUM_SCREENSHOT_DIR if screenshot_dir and os.path.isdir(screenshot_dir): rmtree(screenshot_dir, ignore_errors=True)
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Clear out any old screenshots
[ "Clear", "out", "any", "old", "screenshots" ]
python
train
soravux/scoop
examples/dependency/sortingnetwork.py
https://github.com/soravux/scoop/blob/d391dfa62f47e49d48328ee9cf08aa114256fd33/examples/dependency/sortingnetwork.py#L88-L116
def draw(self): """Return an ASCII representation of the network.""" str_wires = [["-"]*7 * self.depth] str_wires[0][0] = "0" str_wires[0][1] = " o" str_spaces = [] for i in range(1, self.dimension): str_wires.append(["-"]*7 * self.depth) str_spac...
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Return an ASCII representation of the network.
[ "Return", "an", "ASCII", "representation", "of", "the", "network", "." ]
python
train
numenta/htmresearch
htmresearch/frameworks/layers/object_machine_factory.py
https://github.com/numenta/htmresearch/blob/70c096b09a577ea0432c3f3bfff4442d4871b7aa/htmresearch/frameworks/layers/object_machine_factory.py#L62-L76
def createObjectMachine(machineType, **kwargs): """ Return an object machine of the appropriate type. @param machineType (str) A supported ObjectMachine type @param kwargs (dict) Constructor argument for the class that will be instantiated. Keyword parameters specific to each...
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Return an object machine of the appropriate type. @param machineType (str) A supported ObjectMachine type @param kwargs (dict) Constructor argument for the class that will be instantiated. Keyword parameters specific to each model type should be passed...
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python
train
bloomreach/s4cmd
s4cmd.py
https://github.com/bloomreach/s4cmd/blob/bb51075bf43703e7cd95aa39288cf7732ec13a6d/s4cmd.py#L1208-L1223
def conditional(self, result, obj): '''Check all file item with given conditions.''' fileonly = (self.opt.last_modified_before is not None) or (self.opt.last_modified_after is not None) if obj['is_dir']: if not fileonly: result.append(obj) return if (self.opt.last_modified_before i...
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Check all file item with given conditions.
[ "Check", "all", "file", "item", "with", "given", "conditions", "." ]
python
test
google/openhtf
openhtf/util/data.py
https://github.com/google/openhtf/blob/655e85df7134db7bdf8f8fdd6ff9a6bf932e7b09/openhtf/util/data.py#L42-L47
def pprint_diff(first, second, first_name='first', second_name='second'): """Compare the pprint representation of two objects and yield diff lines.""" return difflib.unified_diff( pprint.pformat(first).splitlines(), pprint.pformat(second).splitlines(), fromfile=first_name, tofile=second_name, line...
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Compare the pprint representation of two objects and yield diff lines.
[ "Compare", "the", "pprint", "representation", "of", "two", "objects", "and", "yield", "diff", "lines", "." ]
python
train
mitsei/dlkit
dlkit/handcar/repository/objects.py
https://github.com/mitsei/dlkit/blob/445f968a175d61c8d92c0f617a3c17dc1dc7c584/dlkit/handcar/repository/objects.py#L837-L858
def set_distribute_compositions(self, distribute_comps=None): """Sets the distribution rights. This sets distribute verbatim to ``true``. :param distribute_comps: right to distribute modifications :type distribute_comps: ``boolean`` :raise: ``InvalidArgument`` -- ``distribute_c...
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Sets the distribution rights. This sets distribute verbatim to ``true``. :param distribute_comps: right to distribute modifications :type distribute_comps: ``boolean`` :raise: ``InvalidArgument`` -- ``distribute_comps`` is invalid :raise: ``NoAccess`` -- authorization failure ...
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python
train
mfitzp/padua
padua/visualize.py
https://github.com/mfitzp/padua/blob/8b14bf4d2f895da6aea5d7885d409315bd303ec6/padua/visualize.py#L1495-L1605
def kegg_pathway(df, pathway, a, b=None, ids_from="Proteins", cmap=cm.PuOr_r, is_log2=False, fillna=None, z_score=1): """ Visualize data on a kegg pathway. :param df: :param pathway: :param a: :param b: :param ids_from: :param cmap: :param is_log2: :param fillna: :param z_s...
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Visualize data on a kegg pathway. :param df: :param pathway: :param a: :param b: :param ids_from: :param cmap: :param is_log2: :param fillna: :param z_score: :return:
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python
train
archman/beamline
beamline/ui/myappframe.py
https://github.com/archman/beamline/blob/417bc5dc13e754bc89d246427984590fced64d07/beamline/ui/myappframe.py#L752-L764
def pack_found_items(self, s_text, target): """ pack up found items for search ctrl :param target: treectrl obj :param s_text: text to search, lower case return list of found items """ all_children = self.all_children all_text = [target.GetItemText(i)....
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pack up found items for search ctrl :param target: treectrl obj :param s_text: text to search, lower case return list of found items
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python
train
tjkessler/PyGenetics
pygenetics/selection_functions.py
https://github.com/tjkessler/PyGenetics/blob/b78ee6393605d6e85d2279fb05f3983f5833df40/pygenetics/selection_functions.py#L10-L23
def minimize_best_n(Members): ''' Orders population members from lowest fitness to highest fitness Args: Members (list): list of PyGenetics Member objects Returns: lsit: ordered lsit of Members, from highest fitness to lowest fitness ''' return(list(reversed(sorted( Me...
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Orders population members from lowest fitness to highest fitness Args: Members (list): list of PyGenetics Member objects Returns: lsit: ordered lsit of Members, from highest fitness to lowest fitness
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python
test
sdispater/cachy
cachy/tagged_cache.py
https://github.com/sdispater/cachy/blob/ee4b044d6aafa80125730a00b1f679a7bd852b8a/cachy/tagged_cache.py#L153-L179
def remember(self, key, minutes, callback): """ Get an item from the cache, or store the default value. :param key: The cache key :type key: str :param minutes: The lifetime in minutes of the cached value :type minutes: int or datetime :param callback: The defa...
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Get an item from the cache, or store the default value. :param key: The cache key :type key: str :param minutes: The lifetime in minutes of the cached value :type minutes: int or datetime :param callback: The default function :type callback: mixed :rtype: mixe...
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python
train
liftoff/pyminifier
pyminifier/minification.py
https://github.com/liftoff/pyminifier/blob/087ea7b0c8c964f1f907c3f350f5ce281798db86/pyminifier/minification.py#L401-L419
def minify(tokens, options): """ Performs minification on *tokens* according to the values in *options* """ # Remove comments remove_comments(tokens) # Remove docstrings remove_docstrings(tokens) result = token_utils.untokenize(tokens) # Minify our input script result = multiline...
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Performs minification on *tokens* according to the values in *options*
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python
train
fastai/fastai
fastai/vision/gan.py
https://github.com/fastai/fastai/blob/9fb84a5cdefe5a766cdb792b8f5d8971737b7e67/fastai/vision/gan.py#L219-L223
def from_learners(cls, learn_gen:Learner, learn_crit:Learner, switcher:Callback=None, weights_gen:Tuple[float,float]=None, **learn_kwargs): "Create a GAN from `learn_gen` and `learn_crit`." losses = gan_loss_from_func(learn_gen.loss_func, learn_crit.loss_func, weights_gen=weights_g...
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Create a GAN from `learn_gen` and `learn_crit`.
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python
train