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LISE-B26/pylabcontrol
build/lib/pylabcontrol/src/tools/export_default.py
https://github.com/LISE-B26/pylabcontrol/blob/67482e5157fcd1c40705e5c2cacfb93564703ed0/build/lib/pylabcontrol/src/tools/export_default.py#L170-L212
def export(target_folder, source_folders = None, class_type ='all', raise_errors = False): """ exports the existing scripts/instruments (future: probes) into folder as .b26 files Args: target_folder: target location of created .b26 script files source_folder: singel path or list of paths tha...
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exports the existing scripts/instruments (future: probes) into folder as .b26 files Args: target_folder: target location of created .b26 script files source_folder: singel path or list of paths that contains the location of python script files can also be just the name of a module class_type...
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python
train
ChristianTremblay/BAC0
BAC0/core/devices/Device.py
https://github.com/ChristianTremblay/BAC0/blob/8d95b065ea068524a08f5b0c34322ebeeba95d06/BAC0/core/devices/Device.py#L584-L594
def analog_units(self): """ Shortcut to retrieve all analog points units [Used by Bokeh trending feature] """ au = [] us = [] for each in self.points: if isinstance(each, NumericPoint): au.append(each.properties.name) u...
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Shortcut to retrieve all analog points units [Used by Bokeh trending feature]
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python
train
stevearc/dql
dql/engine.py
https://github.com/stevearc/dql/blob/e9d3aa22873076dae5ebd02e35318aa996b1e56a/dql/engine.py#L162-L167
def cloudwatch_connection(self): """ Lazy create a connection to cloudwatch """ if self._cloudwatch_connection is None: conn = self._session.create_client("cloudwatch", self.connection.region) self._cloudwatch_connection = conn return self._cloudwatch_connection
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Lazy create a connection to cloudwatch
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python
train
napalm-automation/napalm-ios
napalm_ios/ios.py
https://github.com/napalm-automation/napalm-ios/blob/7bbbc6a4d9f70a5b8cf32b7c7072a7ab437ddb81/napalm_ios/ios.py#L201-L208
def _create_tmp_file(config): """Write temp file and for use with inline config and SCP.""" tmp_dir = tempfile.gettempdir() rand_fname = py23_compat.text_type(uuid.uuid4()) filename = os.path.join(tmp_dir, rand_fname) with open(filename, 'wt') as fobj: fobj.write(conf...
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Write temp file and for use with inline config and SCP.
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python
train
nion-software/nionswift-io
nionswift_plugin/TIFF_IO/tifffile.py
https://github.com/nion-software/nionswift-io/blob/e9ae37f01faa9332c48b647f93afd5ef2166b155/nionswift_plugin/TIFF_IO/tifffile.py#L2974-L3007
def stk_metadata(self): """Return STK metadata from UIC tags as dict.""" if not self.is_stk: return None page = self.pages[0] tags = page.tags result = {} result['NumberPlanes'] = tags['UIC2tag'].count if page.description: result['PlaneDesc...
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Return STK metadata from UIC tags as dict.
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python
train
DarkEnergySurvey/ugali
ugali/analysis/results.py
https://github.com/DarkEnergySurvey/ugali/blob/21e890b4117fc810afb6fb058e8055d564f03382/ugali/analysis/results.py#L317-L332
def surfaceBrightness(abs_mag, r_physical, distance): """ Compute the average surface brightness [mag arcsec^-2] within the half-light radius abs_mag = absolute magnitude [mag] r_physical = half-light radius [kpc] distance = [kpc] The factor 2 in the c_v equation below account for half the lu...
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Compute the average surface brightness [mag arcsec^-2] within the half-light radius abs_mag = absolute magnitude [mag] r_physical = half-light radius [kpc] distance = [kpc] The factor 2 in the c_v equation below account for half the luminosity within the half-light radius. The 3600.**2 is conver...
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python
train
vsergeev/python-periphery
periphery/mmio.py
https://github.com/vsergeev/python-periphery/blob/ff4d535691a1747a76962a3d077d96d224308611/periphery/mmio.py#L245-L268
def write(self, offset, data): """Write a string of bytes to the specified `offset` in bytes, relative to the base physical address of the MMIO region. Args: offset (int, long): offset from base physical address, in bytes. data (bytes, bytearray, list): a byte array or l...
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Write a string of bytes to the specified `offset` in bytes, relative to the base physical address of the MMIO region. Args: offset (int, long): offset from base physical address, in bytes. data (bytes, bytearray, list): a byte array or list of 8-bit ...
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python
train
wrboyce/telegrambot
telegrambot/api/__init__.py
https://github.com/wrboyce/telegrambot/blob/c35ce19886df4c306a2a19851cc1f63e3066d70d/telegrambot/api/__init__.py#L178-L185
def send_chat_action(self, action, to): """ Use this method when you need to tell the user that something is happening on the bot's side. The status is set for 5 seconds or less (when a message arrives from your bot, Telegram clients clear its typing status). """ ...
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Use this method when you need to tell the user that something is happening on the bot's side. The status is set for 5 seconds or less (when a message arrives from your bot, Telegram clients clear its typing status).
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python
train
wolfhong/formic
formic/formic.py
https://github.com/wolfhong/formic/blob/0d81eb88dcbb6fa705194fc6ccf2993f4abbaa76/formic/formic.py#L237-L272
def _match_iter_generic(self, path_elements, start_at): """Implementation of match_iter for >1 self.elements""" length = len(path_elements) # If bound to start, we stop searching at the first element if self.bound_start: end = 1 else: end = length - self....
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Implementation of match_iter for >1 self.elements
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python
train
aiven/pghoard
pghoard/pghoard.py
https://github.com/aiven/pghoard/blob/2994165d4ef3ff7a5669a2527346bcbfb5b3bd8a/pghoard/pghoard.py#L346-L392
def startup_walk_for_missed_files(self): """Check xlog and xlog_incoming directories for files that receivexlog has received but not yet compressed as well as the files we have compressed but not yet uploaded and process them.""" for site in self.config["backup_sites"]: compressed_xl...
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Check xlog and xlog_incoming directories for files that receivexlog has received but not yet compressed as well as the files we have compressed but not yet uploaded and process them.
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python
train
ARMmbed/icetea
icetea_lib/tools/asserts.py
https://github.com/ARMmbed/icetea/blob/b2b97ac607429830cf7d62dae2e3903692c7c778/icetea_lib/tools/asserts.py#L191-L215
def assertJsonContains(jsonStr=None, key=None, message=None): """ Assert that jsonStr contains key. :param jsonStr: Json as string :param key: Key to look for :param message: Failure message :raises: TestStepFail if key is not in jsonStr or if loading jsonStr to a dictionary fails or if jso...
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Assert that jsonStr contains key. :param jsonStr: Json as string :param key: Key to look for :param message: Failure message :raises: TestStepFail if key is not in jsonStr or if loading jsonStr to a dictionary fails or if jsonStr is None.
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python
train
MolSSI-BSE/basis_set_exchange
basis_set_exchange/curate/compare.py
https://github.com/MolSSI-BSE/basis_set_exchange/blob/e79110aaeb65f392ed5032420322dee3336948f7/basis_set_exchange/curate/compare.py#L188-L218
def compare_ecp_pots(potential1, potential2, compare_meta=False, rel_tol=0.0): ''' Compare two ecp potentials for approximate equality (exponents/coefficients are within a tolerance) If compare_meta is True, the metadata is also compared for exact equality. ''' if potential1['angular_momentum...
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Compare two ecp potentials for approximate equality (exponents/coefficients are within a tolerance) If compare_meta is True, the metadata is also compared for exact equality.
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python
train
saltstack/salt
salt/minion.py
https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/minion.py#L2928-L2945
def destroy(self): ''' Tear down the minion ''' if self._running is False: return self._running = False if hasattr(self, 'schedule'): del self.schedule if hasattr(self, 'pub_channel') and self.pub_channel is not None: self.pub_...
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Tear down the minion
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python
train
quantopian/pgcontents
pgcontents/query.py
https://github.com/quantopian/pgcontents/blob/ed36268b7917332d16868208e1e565742a8753e1/pgcontents/query.py#L256-L286
def get_directory(db, user_id, api_dirname, content): """ Return the names of all files/directories that are direct children of api_dirname. If content is False, return a bare model containing just a database-style name. """ db_dirname = from_api_dirname(api_dirname) if not _dir_exists(...
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Return the names of all files/directories that are direct children of api_dirname. If content is False, return a bare model containing just a database-style name.
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python
test
tbobm/devscripts
devscripts/logs.py
https://github.com/tbobm/devscripts/blob/beb23371ba80739afb5474766e8049ead3837925/devscripts/logs.py#L12-L49
def simple_logger(**kwargs): """ Creates a simple logger :param str name: The logger's name ('api', 'back'...) :param int base_level: Lowest level allowed to log (Default: DEBUG) :param str log_format: Logging format used for STDOUT (Default: logs.FORMAT) :param bool...
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Creates a simple logger :param str name: The logger's name ('api', 'back'...) :param int base_level: Lowest level allowed to log (Default: DEBUG) :param str log_format: Logging format used for STDOUT (Default: logs.FORMAT) :param bool should_stdout: Allows to log to stdout (...
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python
train
telefonicaid/fiware-sdc
python-sdcclient/sdcclient/client.py
https://github.com/telefonicaid/fiware-sdc/blob/d2d5f87fc574caf6bcc49594bbcb31f620ba8c51/python-sdcclient/sdcclient/client.py#L165-L173
def set_headers(self, headers): """ Set header. :param headers: Headers to be used by next request (dict) :return: None """ logger.debug("Setting headers: " + str(headers)) self.headers = headers
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Set header. :param headers: Headers to be used by next request (dict) :return: None
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python
train
bjoernricks/python-quilt
quilt/db.py
https://github.com/bjoernricks/python-quilt/blob/fae88237f601848cc34d073584d9dcb409f01777/quilt/db.py#L296-L300
def create(self): """ Creates the dirname and inserts a .version file """ if not os.path.exists(self.dirname): os.makedirs(self.dirname) self._create_version(self.version_file)
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Creates the dirname and inserts a .version file
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python
test
toidi/hadoop-yarn-api-python-client
yarn_api_client/resource_manager.py
https://github.com/toidi/hadoop-yarn-api-python-client/blob/d245bd41808879be6637acfd7460633c0c7dfdd6/yarn_api_client/resource_manager.py#L161-L172
def cluster_application(self, application_id): """ An application resource contains information about a particular application that was submitted to a cluster. :param str application_id: The application id :returns: API response object with JSON data :rtype: :py:class:`y...
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An application resource contains information about a particular application that was submitted to a cluster. :param str application_id: The application id :returns: API response object with JSON data :rtype: :py:class:`yarn_api_client.base.Response`
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python
train
arista-eosplus/pyeapi
pyeapi/eapilib.py
https://github.com/arista-eosplus/pyeapi/blob/96a74faef1fe3bd79c4e900aed29c9956a0587d6/pyeapi/eapilib.py#L308-L436
def send(self, data): """Sends the eAPI request to the destination node This method is responsible for sending an eAPI request to the destination node and returning a response based on the eAPI response object. eAPI responds to request messages with either a success message or ...
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Sends the eAPI request to the destination node This method is responsible for sending an eAPI request to the destination node and returning a response based on the eAPI response object. eAPI responds to request messages with either a success message or failure message. eAPI Re...
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python
train
ARMmbed/icetea
icetea_lib/Result.py
https://github.com/ARMmbed/icetea/blob/b2b97ac607429830cf7d62dae2e3903692c7c778/icetea_lib/Result.py#L159-L168
def build_date(self): """ get build date. :return: build date. None if not found """ # pylint: disable=len-as-condition if len(self.dutinformation) > 0 and (self.dutinformation.get(0).build is not None): return self.dutinformation.get(0).build.date re...
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get build date. :return: build date. None if not found
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python
train
andreikop/qutepart
qutepart/bookmarks.py
https://github.com/andreikop/qutepart/blob/109d76b239751318bcef06f39b2fbbf18687a40b/qutepart/bookmarks.py#L25-L36
def _createAction(self, widget, iconFileName, text, shortcut, slot): """Create QAction with given parameters and add to the widget """ icon = qutepart.getIcon(iconFileName) action = QAction(icon, text, widget) action.setShortcut(QKeySequence(shortcut)) action.setShortcutC...
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Create QAction with given parameters and add to the widget
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python
train
google/textfsm
textfsm/parser.py
https://github.com/google/textfsm/blob/63a2aaece33e07947aa80963dca99b893964633b/textfsm/parser.py#L622-L626
def _GetValue(self, name): """Returns the TextFSMValue object natching the requested name.""" for value in self.values: if value.name == name: return value
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Returns the TextFSMValue object natching the requested name.
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python
train
aarongarrett/inspyred
inspyred/ec/variators/crossovers.py
https://github.com/aarongarrett/inspyred/blob/d5976ab503cc9d51c6f586cbb7bb601a38c01128/inspyred/ec/variators/crossovers.py#L444-L493
def laplace_crossover(random, mom, dad, args): """Return the offspring of Laplace crossover on the candidates. This function performs Laplace crosssover (LX), following the implementation specified in (Deep and Thakur, "A new crossover operator for real coded genetic algorithms," Applied Mathemat...
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Return the offspring of Laplace crossover on the candidates. This function performs Laplace crosssover (LX), following the implementation specified in (Deep and Thakur, "A new crossover operator for real coded genetic algorithms," Applied Mathematics and Computation, Volume 188, Issue 1, May 200...
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python
train
Opentrons/opentrons
api/src/opentrons/system/smoothie_update.py
https://github.com/Opentrons/opentrons/blob/a7c15cc2636ecb64ab56c7edc1d8a57163aaeadf/api/src/opentrons/system/smoothie_update.py#L6-L16
def _ensure_programmer_executable(): """ Find the lpc21isp executable and ensure it is executable """ # Find the lpc21isp executable, explicitly allowing the case where it # is not executable (since that’s exactly what we’re trying to fix) updater_executable = shutil.which('lpc21isp', ...
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Find the lpc21isp executable and ensure it is executable
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python
train
doconix/django-mako-plus
django_mako_plus/template/util.py
https://github.com/doconix/django-mako-plus/blob/a90f9b4af19e5fa9f83452989cdcaed21569a181/django_mako_plus/template/util.py#L40-L170
def get_template_debug(template_name, error): ''' This structure is what Django wants when errors occur in templates. It gives the user a nice stack trace in the error page during debug. ''' # This is taken from mako.exceptions.html_error_template(), which has an issue # in Py3 where files get l...
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This structure is what Django wants when errors occur in templates. It gives the user a nice stack trace in the error page during debug.
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python
train
sorgerlab/indra
indra/sources/isi/api.py
https://github.com/sorgerlab/indra/blob/79a70415832c5702d7a820c7c9ccc8e25010124b/indra/sources/isi/api.py#L240-L264
def process_json_file(file_path, pmid=None, extra_annotations=None, add_grounding=True): """Extracts statements from the given ISI output file. Parameters ---------- file_path : str The ISI output file from which to extract statements pmid : int The PMID of the...
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Extracts statements from the given ISI output file. Parameters ---------- file_path : str The ISI output file from which to extract statements pmid : int The PMID of the document being preprocessed, or None if not specified extra_annotations : dict Extra annotations ...
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python
train
multiformats/py-multibase
multibase/converters.py
https://github.com/multiformats/py-multibase/blob/8f435762b50a17f921c13b59eb0c7b9c52afc879/multibase/converters.py#L47-L51
def _chunk_with_padding(self, iterable, n, fillvalue=None): "Collect data into fixed-length chunks or blocks" # _chunk_with_padding('ABCDEFG', 3, 'x') --> ABC DEF Gxx" args = [iter(iterable)] * n return zip_longest(*args, fillvalue=fillvalue)
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Collect data into fixed-length chunks or blocks
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python
train
QualiSystems/vCenterShell
package/cloudshell/cp/vcenter/common/vcenter/vmomi_service.py
https://github.com/QualiSystems/vCenterShell/blob/e2e24cd938a92a68f4a8e6a860810d3ef72aae6d/package/cloudshell/cp/vcenter/common/vcenter/vmomi_service.py#L306-L313
def get_network_by_full_name(self, si, default_network_full_name): """ Find network by a Full Name :param default_network_full_name: <str> Full Network Name - likes 'Root/Folder/Network' :return: """ path, name = get_path_and_name(default_network_full_name) return...
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Find network by a Full Name :param default_network_full_name: <str> Full Network Name - likes 'Root/Folder/Network' :return:
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python
train
Rapptz/discord.py
discord/guild.py
https://github.com/Rapptz/discord.py/blob/05d4f7f9620ef33635d6ac965b26528e09cdaf5b/discord/guild.py#L1375-L1399
async def unban(self, user, *, reason=None): """|coro| Unbans a user from the guild. The user must meet the :class:`abc.Snowflake` abc. You must have the :attr:`~Permissions.ban_members` permission to do this. Parameters ----------- user: :class:`abc.S...
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|coro| Unbans a user from the guild. The user must meet the :class:`abc.Snowflake` abc. You must have the :attr:`~Permissions.ban_members` permission to do this. Parameters ----------- user: :class:`abc.Snowflake` The user to unban. reason:...
[ "|coro|" ]
python
train
echinopsii/net.echinopsii.ariane.community.cli.python3
ariane_clip3/injector.py
https://github.com/echinopsii/net.echinopsii.ariane.community.cli.python3/blob/0a7feddebf66fee4bef38d64f456d93a7e9fcd68/ariane_clip3/injector.py#L1103-L1112
def remove(self): """ remove the gear from the cache and stop this actor :return: """ LOGGER.debug("InjectorGearSkeleton.remove") ret = self.cached_gear_actor.remove().get() if self.actor_ref: self.stop() return ret
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remove the gear from the cache and stop this actor :return:
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python
train
salu133445/pypianoroll
pypianoroll/multitrack.py
https://github.com/salu133445/pypianoroll/blob/6224dc1e29222de2124d249acb80f3d072166917/pypianoroll/multitrack.py#L210-L253
def check_validity(self): """ Raise an error if any invalid attribute found. Raises ------ TypeError If an attribute has an invalid type. ValueError If an attribute has an invalid value (of the correct type). """ # tracks ...
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Raise an error if any invalid attribute found. Raises ------ TypeError If an attribute has an invalid type. ValueError If an attribute has an invalid value (of the correct type).
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python
train
noxdafox/clipspy
clips/classes.py
https://github.com/noxdafox/clipspy/blob/b22d71a6da821c1715d8fa00d7d75cabc09ed364/clips/classes.py#L336-L338
def superclass(self, klass): """True if the Class is a superclass of the given one.""" return bool(lib.EnvSuperclassP(self._env, self._cls, klass._cls))
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True if the Class is a superclass of the given one.
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python
train
fossasia/knittingpattern
knittingpattern/convert/image_to_knittingpattern.py
https://github.com/fossasia/knittingpattern/blob/8e608896b0ab82fea1ca9fbfa2b4ee023d8c8027/knittingpattern/convert/image_to_knittingpattern.py#L12-L64
def convert_image_to_knitting_pattern(path, colors=("white", "black")): """Load a image file such as a png bitmap of jpeg file and convert it to a :ref:`knitting pattern file <FileFormatSpecification>`. :param list colors: a list of strings that should be used as :ref:`colors <png-color>`. :param...
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Load a image file such as a png bitmap of jpeg file and convert it to a :ref:`knitting pattern file <FileFormatSpecification>`. :param list colors: a list of strings that should be used as :ref:`colors <png-color>`. :param str path: ignore this. It is fulfilled by the loeder. Example: .. co...
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python
valid
nugget/python-anthemav
anthemav/protocol.py
https://github.com/nugget/python-anthemav/blob/c3cee38f2d452c1ab1335d9885e0769ec24d5f90/anthemav/protocol.py#L157-L167
def connection_made(self, transport): """Called when asyncio.Protocol establishes the network connection.""" self.log.info('Connection established to AVR') self.transport = transport #self.transport.set_write_buffer_limits(0) limit_low, limit_high = self.transport.get_write_buff...
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Called when asyncio.Protocol establishes the network connection.
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python
train
blockstack/blockstack-core
blockstack/blockstackd.py
https://github.com/blockstack/blockstack-core/blob/1dcfdd39b152d29ce13e736a6a1a0981401a0505/blockstack/blockstackd.py#L623-L650
def get_name_record(self, name, include_expired=False, include_history=False): """ Get the whois-related info for a name (not a subdomain). Optionally include the history. Return {'status': True, 'record': rec} on success Return {'error': ...} on error """ if not ...
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Get the whois-related info for a name (not a subdomain). Optionally include the history. Return {'status': True, 'record': rec} on success Return {'error': ...} on error
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python
train
PyThaiNLP/pythainlp
pythainlp/tokenize/tcc.py
https://github.com/PyThaiNLP/pythainlp/blob/e9a300b8a99dfd1a67a955e7c06f62e4afe0fbca/pythainlp/tokenize/tcc.py#L52-L69
def tcc(text: str) -> str: """ TCC generator, generates Thai Character Clusters :param str text: text to be tokenized to character clusters :return: subword (character cluster) """ if not text or not isinstance(text, str): return "" p = 0 while p < len(text): m = PAT_TCC...
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TCC generator, generates Thai Character Clusters :param str text: text to be tokenized to character clusters :return: subword (character cluster)
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python
train
inveniosoftware/invenio-collections
invenio_collections/receivers.py
https://github.com/inveniosoftware/invenio-collections/blob/f3adca45c6d00a4dbf1f48fd501e8a68fe347f2f/invenio_collections/receivers.py#L74-L91
def get_record_collections(record, matcher): """Return list of collections to which record belongs to. :param record: Record instance. :param matcher: Function used to check if a record belongs to a collection. :return: list of collection names. """ collections = current_collections.collections...
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Return list of collections to which record belongs to. :param record: Record instance. :param matcher: Function used to check if a record belongs to a collection. :return: list of collection names.
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python
train
erikdejonge/arguments
examples/classbased.py
https://github.com/erikdejonge/arguments/blob/fc222d3989d459343a81944cabb56854014335ed/examples/classbased.py#L98-L111
def main(): """ main """ args = MainArguments() if args.tool.lower() == "tool1": args = Tool1Arguments() elif args.tool.lower() == "tool2": args = Tool2Arguments() else: print("Unknown tool", args.tool) print(args)
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main
[ "main" ]
python
train
refenv/cijoe
modules/cij/reporter.py
https://github.com/refenv/cijoe/blob/21d7b2ed4ff68e0a1457e7df2db27f6334f1a379/modules/cij/reporter.py#L165-L174
def process_tcase(tcase): """Goes through the trun and processes "run.log" """ tcase["src_content"] = src_to_html(tcase["fpath"]) tcase["log_content"] = runlogs_to_html(tcase["res_root"]) tcase["aux_list"] = aux_listing(tcase["aux_root"]) tcase["descr_short"], tcase["descr_long"] = tcase_parse_desc...
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Goes through the trun and processes "run.log"
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python
valid
Richienb/quilt
src/quilt_lang/__init__.py
https://github.com/Richienb/quilt/blob/4a659cac66f5286ad046d54a12fd850be5606643/src/quilt_lang/__init__.py#L1135-L1197
def circleconvert(amount, currentformat, newformat): """ Convert a circle measurement. :type amount: number :param amount: The number to convert. :type currentformat: string :param currentformat: The format of the provided value. :type newformat: string :param newformat: The intended ...
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Convert a circle measurement. :type amount: number :param amount: The number to convert. :type currentformat: string :param currentformat: The format of the provided value. :type newformat: string :param newformat: The intended format of the value. >>> circleconvert(45, "radius", "diamet...
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python
train
etal/biofrills
biofrills/pairutils.py
https://github.com/etal/biofrills/blob/36684bb6c7632f96215e8b2b4ebc86640f331bcd/biofrills/pairutils.py#L83-L116
def score_pairwise(aseq, bseq): """Compute pairwise distances between two sequences (raw strings).""" assert len(aseq) == len(bseq) # Affine gap penalties -- default values from EMBOSS needle/water GAP_OPEN = -10.0 GAP_EXTEND = -0.5 GAP_CHARS = frozenset('-.') score = 0.0 in_gap = True...
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Compute pairwise distances between two sequences (raw strings).
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python
train
hydpy-dev/hydpy
hydpy/exe/commandtools.py
https://github.com/hydpy-dev/hydpy/blob/1bc6a82cf30786521d86b36e27900c6717d3348d/hydpy/exe/commandtools.py#L223-L284
def execute_scriptfunction() -> None: """Execute a HydPy script function. Function |execute_scriptfunction| is indirectly applied and explained in the documentation on module |hyd|. """ try: args_given = [] kwargs_given = {} for arg in sys.argv[1:]: if len(arg) <...
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Execute a HydPy script function. Function |execute_scriptfunction| is indirectly applied and explained in the documentation on module |hyd|.
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python
train
tariqdaouda/pyGeno
pyGeno/tools/SegmentTree.py
https://github.com/tariqdaouda/pyGeno/blob/474b1250bf78ce5c7e7c3bbbfdbad9635d5a7d14/pyGeno/tools/SegmentTree.py#L224-L229
def removeGaps(self) : """Remove all gaps between regions""" for i in range(1, len(self.children)) : if self.children[i].x1 > self.children[i-1].x2: aux_moveTree(self.children[i-1].x2-self.children[i].x1, self.children[i])
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Remove all gaps between regions
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python
train
ericpruitt/cronex
cronex/__init__.py
https://github.com/ericpruitt/cronex/blob/ff48a3a71bbcdf01cff46c0bf9376e69492c9224/cronex/__init__.py#L156-L261
def check_trigger(self, date_tuple, utc_offset=0): """ Returns boolean indicating if the trigger is active at the given time. The date tuple should be in the local time. Unless periodicities are used, utc_offset does not need to be specified. If periodicities are used, specifical...
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Returns boolean indicating if the trigger is active at the given time. The date tuple should be in the local time. Unless periodicities are used, utc_offset does not need to be specified. If periodicities are used, specifically in the hour and minutes fields, it is crucial that the utc_o...
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python
train
StorjOld/pyp2p
pyp2p/rendezvous_server.py
https://github.com/StorjOld/pyp2p/blob/7024208c3af20511496a652ff212f54c420e0464/pyp2p/rendezvous_server.py#L108-L122
def cleanup_candidates(self, node_ip): """ Removes old TCP hole punching candidates for a designated node if a certain amount of time has passed since they last connected. """ if node_ip in self.factory.candidates: old_candidates = [] for c...
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Removes old TCP hole punching candidates for a designated node if a certain amount of time has passed since they last connected.
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python
train
numenta/htmresearch
htmresearch/algorithms/apical_tiebreak_temporal_memory.py
https://github.com/numenta/htmresearch/blob/70c096b09a577ea0432c3f3bfff4442d4871b7aa/htmresearch/algorithms/apical_tiebreak_temporal_memory.py#L410-L475
def _calculateApicalLearning(self, learningCells, activeColumns, activeApicalSegments, matchingApicalSegments, apicalPotentialOverlaps): """ Calculate apical...
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Calculate apical learning for each learning cell. The set of learning cells was determined completely from basal segments. Do all apical learning on the same cells. Learn on any active segments on learning cells. For cells without active segments, learn on the best matching segment. For cells without ...
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python
train
dwavesystems/dwave-system
dwave/system/composites/embedding.py
https://github.com/dwavesystems/dwave-system/blob/86a1698f15ccd8b0ece0ed868ee49292d3f67f5b/dwave/system/composites/embedding.py#L432-L434
def _embed_state(embedding, state): """Embed a single state/sample by spreading it's values over the chains in the embedding""" return {u: state[v] for v, chain in embedding.items() for u in chain}
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Embed a single state/sample by spreading it's values over the chains in the embedding
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python
train
launchdarkly/relayCommander
relay_commander/generators.py
https://github.com/launchdarkly/relayCommander/blob/eee7fa22f04edc3854dd53c3ec2db8c599ad1e89/relay_commander/generators.py#L20-L38
def generate_relay_config(self, environments: list) -> None: """Generate ld-relay.conf file. Given a list of environments of a project, this will generate a ``ld-relay.conf`` file in the current working directory. The conf file follows the specification that is documented in the main `l...
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Generate ld-relay.conf file. Given a list of environments of a project, this will generate a ``ld-relay.conf`` file in the current working directory. The conf file follows the specification that is documented in the main `ld-relay`_ documentation. .. _ld-relay: https://github.c...
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python
train
Microsoft/azure-devops-python-api
azure-devops/azure/devops/v5_1/work_item_tracking/work_item_tracking_client.py
https://github.com/Microsoft/azure-devops-python-api/blob/4777ffda2f5052fabbaddb2abe9cb434e0cf1aa8/azure-devops/azure/devops/v5_1/work_item_tracking/work_item_tracking_client.py#L1180-L1204
def get_updates(self, id, project=None, top=None, skip=None): """GetUpdates. [Preview API] Returns a the deltas between work item revisions :param int id: :param str project: Project ID or project name :param int top: :param int skip: :rtype: [WorkItemUpdate] ...
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GetUpdates. [Preview API] Returns a the deltas between work item revisions :param int id: :param str project: Project ID or project name :param int top: :param int skip: :rtype: [WorkItemUpdate]
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python
train
wavefrontHQ/python-client
wavefront_api_client/api/webhook_api.py
https://github.com/wavefrontHQ/python-client/blob/b0f1046a8f68c2c7d69e395f7167241f224c738a/wavefront_api_client/api/webhook_api.py#L36-L56
def create_webhook(self, **kwargs): # noqa: E501 """Create a specific webhook # noqa: E501 # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.create_webhook(async_req=True) ...
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Create a specific webhook # noqa: E501 # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.create_webhook(async_req=True) >>> result = thread.get() :param async_req bo...
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python
train
phac-nml/sistr_cmd
sistr/src/writers.py
https://github.com/phac-nml/sistr_cmd/blob/4630fae72439723b354a94b94fbe76ad2f9f6295/sistr/src/writers.py#L5-L22
def listattrs(x): """Get all instance and class attributes for an object Get all instance and class attributes for an object except those that start with "__" (double underscore). __dict__ of an object only reports the instance attributes while dir() reports all of the attributes of an ob...
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Get all instance and class attributes for an object Get all instance and class attributes for an object except those that start with "__" (double underscore). __dict__ of an object only reports the instance attributes while dir() reports all of the attributes of an object including private on...
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python
train
xtuml/pyxtuml
bridgepoint/oal.py
https://github.com/xtuml/pyxtuml/blob/7dd9343b9a0191d1db1887ab9288d0a026608d9a/bridgepoint/oal.py#L975-L978
def t_END_WHILE(self, t): r"(?i)end[\s]+while" t.endlexpos = t.lexpos + len(t.value) return t
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r"(?i)end[\s]+while
[ "r", "(", "?i", ")", "end", "[", "\\", "s", "]", "+", "while" ]
python
test
diging/tethne
tethne/utilities.py
https://github.com/diging/tethne/blob/ba10eeb264b7a3f2dbcce71cfd5cb2d6bbf7055f/tethne/utilities.py#L184-L194
def subdict(super_dict, keys): """ Returns a subset of the super_dict with the specified keys. """ sub_dict = {} valid_keys = super_dict.keys() for key in keys: if key in valid_keys: sub_dict[key] = super_dict[key] return sub_dict
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Returns a subset of the super_dict with the specified keys.
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python
train
seequent/properties
properties/base/instance.py
https://github.com/seequent/properties/blob/096b07012fff86b0a880c8c018320c3b512751b9/properties/base/instance.py#L161-L172
def to_json(value, **kwargs): """Convert instance to JSON""" if isinstance(value, HasProperties): return value.serialize(**kwargs) try: return json.loads(json.dumps(value)) except TypeError: raise TypeError( "Cannot convert type {} to J...
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Convert instance to JSON
[ "Convert", "instance", "to", "JSON" ]
python
train
RedFantom/ttkthemes
ttkthemes/_utils.py
https://github.com/RedFantom/ttkthemes/blob/e7fc354c02faf0e3eb4842d7f44131a1c43dd299/ttkthemes/_utils.py#L18-L49
def temporary_chdir(new_dir): """ Like os.chdir(), but always restores the old working directory For example, code like this... old_curdir = os.getcwd() os.chdir('stuff') do_some_stuff() os.chdir(old_curdir) ...leaves the current working directory unchanged if do_some_...
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Like os.chdir(), but always restores the old working directory For example, code like this... old_curdir = os.getcwd() os.chdir('stuff') do_some_stuff() os.chdir(old_curdir) ...leaves the current working directory unchanged if do_some_stuff() raises an error, so it should ...
[ "Like", "os", ".", "chdir", "()", "but", "always", "restores", "the", "old", "working", "directory" ]
python
train
nion-software/nionswift-instrumentation-kit
nionswift_plugin/nion_instrumentation_ui/ScanControlPanel.py
https://github.com/nion-software/nionswift-instrumentation-kit/blob/b20c4fff17e840e8cb3d544705faf5bd05f1cbf7/nionswift_plugin/nion_instrumentation_ui/ScanControlPanel.py#L581-L590
def size_to_content(self, horizontal_padding=None, vertical_padding=None): """ Size the canvas item to the text content. """ if horizontal_padding is None: horizontal_padding = 0 if vertical_padding is None: vertical_padding = 0 self.sizing.set_fixed_size(Geome...
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Size the canvas item to the text content.
[ "Size", "the", "canvas", "item", "to", "the", "text", "content", "." ]
python
train
offu/WeRoBot
werobot/session/mysqlstorage.py
https://github.com/offu/WeRoBot/blob/fd42109105b03f9acf45ebd9dcabb9d5cff98f3c/werobot/session/mysqlstorage.py#L72-L88
def set(self, id, value): """ 根据 id 写入数据。 :param id: 要写入的 id :param value: 要写入的数据,可以是一个 ``dict`` 对象 """ value = json_dumps(value) self.conn.cursor().execute( "INSERT INTO WeRoBot (id, value) VALUES (%s,%s) \ ON DUPLICATE KEY UPDATE val...
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根据 id 写入数据。 :param id: 要写入的 id :param value: 要写入的数据,可以是一个 ``dict`` 对象
[ "根据", "id", "写入数据。" ]
python
train
boriel/zxbasic
arch/zx48k/backend/__16bit.py
https://github.com/boriel/zxbasic/blob/23b28db10e41117805bdb3c0f78543590853b132/arch/zx48k/backend/__16bit.py#L620-L634
def _ne16(ins): ''' Compares & pops top 2 operands out of the stack, and checks if the 1st operand != 2nd operand (top of the stack). Pushes 0 if False, 1 if True. 16 bit un/signed version ''' output = _16bit_oper(ins.quad[2], ins.quad[3]) output.append('or a') # Resets carry f...
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Compares & pops top 2 operands out of the stack, and checks if the 1st operand != 2nd operand (top of the stack). Pushes 0 if False, 1 if True. 16 bit un/signed version
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python
train
3DLIRIOUS/MeshLabXML
examples/shield.py
https://github.com/3DLIRIOUS/MeshLabXML/blob/177cce21e92baca500f56a932d66bd9a33257af8/examples/shield.py#L38-L130
def main(): """Run main script""" # segments = number of segments to use for circles segments = 50 # star_points = number of points (or sides) of the star star_points = 5 # star_radius = radius of circle circumscribing the star star_radius = 2 # ring_thickness = thickness of the colored ...
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Run main script
[ "Run", "main", "script" ]
python
test
zkbt/the-friendly-stars
thefriendlystars/constellations/lspm.py
https://github.com/zkbt/the-friendly-stars/blob/50d3f979e79e63c66629065c75595696dc79802e/thefriendlystars/constellations/lspm.py#L73-L105
def from_sky(cls, magnitudelimit=None): ''' Create a Constellation from a criteria search of the whole sky. Parameters ---------- magnitudelimit : float Maximum magnitude (for Ve = "estimated V"). ''' # define a query for cone search surrounding thi...
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Create a Constellation from a criteria search of the whole sky. Parameters ---------- magnitudelimit : float Maximum magnitude (for Ve = "estimated V").
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python
train
apache/spark
python/pyspark/rdd.py
https://github.com/apache/spark/blob/618d6bff71073c8c93501ab7392c3cc579730f0b/python/pyspark/rdd.py#L329-L342
def flatMap(self, f, preservesPartitioning=False): """ Return a new RDD by first applying a function to all elements of this RDD, and then flattening the results. >>> rdd = sc.parallelize([2, 3, 4]) >>> sorted(rdd.flatMap(lambda x: range(1, x)).collect()) [1, 1, 1, 2, 2,...
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Return a new RDD by first applying a function to all elements of this RDD, and then flattening the results. >>> rdd = sc.parallelize([2, 3, 4]) >>> sorted(rdd.flatMap(lambda x: range(1, x)).collect()) [1, 1, 1, 2, 2, 3] >>> sorted(rdd.flatMap(lambda x: [(x, x), (x, x)]).collect(...
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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#L799-L809
def update_dcnm_net_info(self, tenant_id, direc, vlan_id, segmentation_id): """Update the DCNM net info with allocated values of seg/vlan. """ net_dict = self.retrieve_dcnm_net_info(tenant_id, direc) if not net_dict: return None net_dict['vlan_id'...
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Update the DCNM net info with allocated values of seg/vlan.
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python
train
saltstack/salt
salt/modules/pcs.py
https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/modules/pcs.py#L306-L323
def prop_show(prop, extra_args=None, cibfile=None): ''' Show the value of a cluster property prop name of the property extra_args additional options for the pcs property command cibfile use cibfile instead of the live CIB CLI Example: .. code-block:: bash ...
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Show the value of a cluster property prop name of the property extra_args additional options for the pcs property command cibfile use cibfile instead of the live CIB CLI Example: .. code-block:: bash salt '*' pcs.prop_show cibfile='/tmp/2_node_cluster.cib' prop='n...
[ "Show", "the", "value", "of", "a", "cluster", "property" ]
python
train
mottosso/be
be/cli.py
https://github.com/mottosso/be/blob/0f3d4f3597c71223f616d78c6d9b2c8dffcd8a71/be/cli.py#L77-L274
def in_(ctx, topics, yes, as_, enter): """Set the current topics to `topics` Environment: BE_PROJECT: First topic BE_CWD: Current `be` working directory BE_TOPICS: Arguments to `in` BE_DEVELOPMENTDIR: Absolute path to current development directory BE_PROJECTROOT: Absolut...
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Set the current topics to `topics` Environment: BE_PROJECT: First topic BE_CWD: Current `be` working directory BE_TOPICS: Arguments to `in` BE_DEVELOPMENTDIR: Absolute path to current development directory BE_PROJECTROOT: Absolute path to current project BE_PROJECTSR...
[ "Set", "the", "current", "topics", "to", "topics" ]
python
train
marcocamma/datastorage
datastorage/datastorage.py
https://github.com/marcocamma/datastorage/blob/d88cdc08414c1c99d34d62e65fcbf807c3088a37/datastorage/datastorage.py#L158-L163
def h5ToDict(h5, readH5pyDataset=True): """ Read a hdf5 file into a dictionary """ h = h5py.File(h5, "r") ret = unwrapArray(h, recursive=True, readH5pyDataset=readH5pyDataset) if readH5pyDataset: h.close() return ret
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Read a hdf5 file into a dictionary
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python
train
ManiacalLabs/BiblioPixel
bibliopixel/project/recurse.py
https://github.com/ManiacalLabs/BiblioPixel/blob/fd97e6c651a4bbcade64733847f4eec8f7704b7c/bibliopixel/project/recurse.py#L20-L74
def recurse(desc, pre='pre_recursion', post=None, python_path=None): """ Depth first recursion through a dictionary containing type constructors The arguments pre, post and children are independently either: * None, which means to do nothing * a string, which means to use the static class method o...
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Depth first recursion through a dictionary containing type constructors The arguments pre, post and children are independently either: * None, which means to do nothing * a string, which means to use the static class method of that name on the class being constructed, or * a callable, to be call...
[ "Depth", "first", "recursion", "through", "a", "dictionary", "containing", "type", "constructors" ]
python
valid
klavinslab/coral
coral/database/_rebase.py
https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/database/_rebase.py#L15-L51
def update(self): '''Update definitions.''' # Download http://rebase.neb.com/rebase/link_withref to tmp self._tmpdir = tempfile.mkdtemp() try: self._rebase_file = self._tmpdir + '/rebase_file' print 'Downloading latest enzyme definitions' url = 'http:/...
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Update definitions.
[ "Update", "definitions", "." ]
python
train
algolia/algoliasearch-django
algoliasearch_django/models.py
https://github.com/algolia/algoliasearch-django/blob/ca219db41eb56bdd1c0389cdc1508a41698958d7/algoliasearch_django/models.py#L330-L361
def update_records(self, qs, batch_size=1000, **kwargs): """ Updates multiple records. This method is optimized for speed. It takes a QuerySet and the same arguments as QuerySet.update(). Optionnaly, you can specify the size of the batch send to Algolia with batch_size (default ...
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Updates multiple records. This method is optimized for speed. It takes a QuerySet and the same arguments as QuerySet.update(). Optionnaly, you can specify the size of the batch send to Algolia with batch_size (default to 1000). >>> from algoliasearch_django import update_records ...
[ "Updates", "multiple", "records", "." ]
python
valid
CxAalto/gtfspy
gtfspy/exports.py
https://github.com/CxAalto/gtfspy/blob/bddba4b74faae6c1b91202f19184811e326547e5/gtfspy/exports.py#L30-L44
def write_nodes(gtfs, output, fields=None): """ Parameters ---------- gtfs: gtfspy.GTFS output: str Path to the output file fields: list, optional which pieces of information to provide """ nodes = gtfs.get_table("stops") if fields is not None: nodes = nodes[f...
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Parameters ---------- gtfs: gtfspy.GTFS output: str Path to the output file fields: list, optional which pieces of information to provide
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python
valid
hydpy-dev/hydpy
hydpy/auxs/anntools.py
https://github.com/hydpy-dev/hydpy/blob/1bc6a82cf30786521d86b36e27900c6717d3348d/hydpy/auxs/anntools.py#L788-L803
def verify(self) -> None: """Raise a |RuntimeError| if the network's shape is not defined completely. >>> from hydpy import ANN >>> ANN(None).verify() Traceback (most recent call last): ... RuntimeError: The shape of the the artificial neural network \ parameter ...
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Raise a |RuntimeError| if the network's shape is not defined completely. >>> from hydpy import ANN >>> ANN(None).verify() Traceback (most recent call last): ... RuntimeError: The shape of the the artificial neural network \ parameter `ann` of element `?` has not been def...
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python
train
hsolbrig/sparql_slurper
sparql_slurper/_slurpygraph.py
https://github.com/hsolbrig/sparql_slurper/blob/9e338549337a6268d6f9c52e7fbf5b493b80cf59/sparql_slurper/_slurpygraph.py#L81-L122
def triples(self, pattern: QueryTriple): """ Return the triples that match pattern :param pattern: `(s, p, o)` tuple, with `None` as wild cards :return: Generator for resulting triples """ self.total_calls += 1 if self.graph_name is not None: gn = "?g" if not...
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Return the triples that match pattern :param pattern: `(s, p, o)` tuple, with `None` as wild cards :return: Generator for resulting triples
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python
train
widdowquinn/pyADHoRe
pyadhore/iadhore.py
https://github.com/widdowquinn/pyADHoRe/blob/b2ebbf6ae9c6afe9262eb0e3d9cf395970e38533/pyadhore/iadhore.py#L244-L259
def is_redundant_multiplicon(self, value): """ Returns True if the passed multiplicon ID is redundant, False otherwise. - value, (int) multiplicon ID """ if not hasattr(self, '_redundant_multiplicon_cache'): sql = '''SELECT id FROM multiplicons WHERE is_redun...
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Returns True if the passed multiplicon ID is redundant, False otherwise. - value, (int) multiplicon ID
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python
train
LISE-B26/pylabcontrol
build/lib/pylabcontrol/src/gui/qt_b26_widgets.py
https://github.com/LISE-B26/pylabcontrol/blob/67482e5157fcd1c40705e5c2cacfb93564703ed0/build/lib/pylabcontrol/src/gui/qt_b26_widgets.py#L183-L230
def setData(self, column, role, value): """ if value is valid sets the data to value Args: column: column of item role: role of item (see Qt doc) value: value to be set """ assert isinstance(column, int) assert isinstance(role, int) ...
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if value is valid sets the data to value Args: column: column of item role: role of item (see Qt doc) value: value to be set
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python
train
phenomecentre/isaExplorer
isaExplorer/isaExplorer.py
https://github.com/phenomecentre/isaExplorer/blob/2fc817d53b6acba46918a0db8dd2f72e5e1d785e/isaExplorer/isaExplorer.py#L158-L183
def dropStudyFromISA(studyNum, pathToISATABFile): """ This function removes a study from an ISA file Typically, you should use the exploreISA function to check the contents of the ISA file and retrieve the study number you are interested in! Warning: this function deletes the given study and all its...
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This function removes a study from an ISA file Typically, you should use the exploreISA function to check the contents of the ISA file and retrieve the study number you are interested in! Warning: this function deletes the given study and all its associated assays :param studyNum: The Study number (noti...
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python
train
acutesoftware/AIKIF
aikif/comms.py
https://github.com/acutesoftware/AIKIF/blob/fcf1582dc5f884b9a4fa7c6e20e9de9d94d21d03/aikif/comms.py#L43-L54
def delete_channel(self, channel, pwd_hash): """ adds a channel, but must have authenication """ if channel.pwd_hash == pwd_hash: self.channels.remove(channel) lg.record_process('comms.py', 'Removed channel ' + channel.name) return True else: ...
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adds a channel, but must have authenication
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python
train
Pajinek/vhm
server/apps/xmlrpc/utils/vhlib_server.py
https://github.com/Pajinek/vhm/blob/e323e99855fd5c40fd61fba87c2646a1165505ed/server/apps/xmlrpc/utils/vhlib_server.py#L45-L53
def check_size_all(self): """ Get size of homedir and update data on the server """ result = self.rpc_srv.get_all_account(self.token) print "debug: %s" % result for it in result: size = getFolderSize(it["path"]) result = self.rpc_srv.set_account_si...
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Get size of homedir and update data on the server
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python
train
ScottDuckworth/python-anyvcs
anyvcs/hg.py
https://github.com/ScottDuckworth/python-anyvcs/blob/9eb09defbc6b7c99d373fad53cbf8fc81b637923/anyvcs/hg.py#L79-L83
def create(cls, path): """Create a new repository""" cmd = [HG, 'init', path] subprocess.check_call(cmd) return cls(path)
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Create a new repository
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python
train
skorch-dev/skorch
skorch/net.py
https://github.com/skorch-dev/skorch/blob/5b9b8b7b7712cb6e5aaa759d9608ea6269d5bcd3/skorch/net.py#L387-L431
def initialize_callbacks(self): """Initializes all callbacks and save the result in the ``callbacks_`` attribute. Both ``default_callbacks`` and ``callbacks`` are used (in that order). Callbacks may either be initialized or not, and if they don't have a name, the name is inferre...
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Initializes all callbacks and save the result in the ``callbacks_`` attribute. Both ``default_callbacks`` and ``callbacks`` are used (in that order). Callbacks may either be initialized or not, and if they don't have a name, the name is inferred from the class name. The ``initia...
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python
train
apple/turicreate
src/unity/python/turicreate/toolkits/topic_model/topic_model.py
https://github.com/apple/turicreate/blob/74514c3f99e25b46f22c6e02977fe3da69221c2e/src/unity/python/turicreate/toolkits/topic_model/topic_model.py#L396-L428
def _training_stats(self): """ Return a dictionary of statistics collected during creation of the model. These statistics are also available with the ``get`` method and are described in more detail in that method's documentation. Returns ------- out : dict ...
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Return a dictionary of statistics collected during creation of the model. These statistics are also available with the ``get`` method and are described in more detail in that method's documentation. Returns ------- out : dict Dictionary of statistics compiled during ...
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python
train
google/grr
grr/client/grr_response_client/comms.py
https://github.com/google/grr/blob/5cef4e8e2f0d5df43ea4877e9c798e0bf60bfe74/grr/client/grr_response_client/comms.py#L1358-L1363
def SavePrivateKey(self, private_key): """Store the new private key on disk.""" self.private_key = private_key config.CONFIG.Set("Client.private_key", self.private_key.SerializeToString()) config.CONFIG.Write()
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Store the new private key on disk.
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python
train
mjirik/io3d
io3d/dcmreaddata.py
https://github.com/mjirik/io3d/blob/ccaf3e378dcc967f2565d477fc27583fd0f61fcc/io3d/dcmreaddata.py#L645-L656
def print_series_info(self, series_info, minimal_series_number=1): """ Print series_info from dcmdirstats """ strinfo = '' if len(series_info) > minimal_series_number: for serie_number in series_info.keys(): strl = get_one_serie_info(series_info, serie...
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Print series_info from dcmdirstats
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python
train
PRIArobotics/HedgehogUtils
hedgehog/utils/__init__.py
https://github.com/PRIArobotics/HedgehogUtils/blob/cc368df270288c870cc66d707696ccb62823ca9c/hedgehog/utils/__init__.py#L21-L103
def coroutine(func): """ A decorator to wrap a generator function into a callable interface. >>> @coroutine ... def sum(count): ... sum = 0 ... for _ in range(0, count): ... # note that generator arguments are passed as a tuple, hence `num, = ...` instead...
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python
train
bcbio/bcbio-nextgen
bcbio/ngsalign/minimap2.py
https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/ngsalign/minimap2.py#L10-L42
def align(fastq_file, pair_file, index_dir, names, align_dir, data): """Perform piped alignment of fastq input files, generating sorted, deduplicated BAM. """ umi_ext = "-cumi" if "umi_bam" in data else "" out_file = os.path.join(align_dir, "{0}-sort{1}.bam".format(dd.get_sample_name(data), umi_ext)) ...
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Perform piped alignment of fastq input files, generating sorted, deduplicated BAM.
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python
train
KeplerGO/K2fov
K2fov/K2findCampaigns.py
https://github.com/KeplerGO/K2fov/blob/fb122b35687340e0357cba9e0dd47b3be0760693/K2fov/K2findCampaigns.py#L49-L86
def findCampaignsByName(target): """Returns a list of the campaigns that cover a given target. Parameters ---------- target : str Name of the celestial object. Returns ------- campaigns : list of int A list of the campaigns that cover the given target name. ra, dec : f...
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Returns a list of the campaigns that cover a given target. Parameters ---------- target : str Name of the celestial object. Returns ------- campaigns : list of int A list of the campaigns that cover the given target name. ra, dec : float, float Resolved coordinates...
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python
train
JNRowe/upoints
upoints/utils.py
https://github.com/JNRowe/upoints/blob/1e4b7a53ed2a06cd854523d54c36aabdccea3830/upoints/utils.py#L206-L228
def prepare_xml_read(data, objectify=False): """Prepare various input types for XML parsing. Args: data (iter): Data to read objectify (bool): Parse using lxml's objectify data binding Returns: etree.ElementTree: Tree suitable for parsing Raises: TypeError: Invalid val...
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Prepare various input types for XML parsing. Args: data (iter): Data to read objectify (bool): Parse using lxml's objectify data binding Returns: etree.ElementTree: Tree suitable for parsing Raises: TypeError: Invalid value for data
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python
train
BlueBrain/NeuroM
neurom/check/neuron_checks.py
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L128-L147
def has_all_nonzero_segment_lengths(neuron, threshold=0.0): '''Check presence of neuron segments with length not above threshold Arguments: neuron(Neuron): The neuron object to test threshold(float): value above which a segment length is considered to be non-zero Returns: C...
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Check presence of neuron segments with length not above threshold Arguments: neuron(Neuron): The neuron object to test threshold(float): value above which a segment length is considered to be non-zero Returns: CheckResult with result including list of (section_id, segment_id) ...
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python
train
crossbario/txaio
txaio/aio.py
https://github.com/crossbario/txaio/blob/29c77ff1210cabd4cc03f16f34672612e7eef704/txaio/aio.py#L452-L474
def make_batched_timer(self, bucket_seconds, chunk_size=100): """ Creates and returns an object implementing :class:`txaio.IBatchedTimer`. :param bucket_seconds: the number of seconds in each bucket. That is, a value of 5 means that any timeout within a 5 second ...
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Creates and returns an object implementing :class:`txaio.IBatchedTimer`. :param bucket_seconds: the number of seconds in each bucket. That is, a value of 5 means that any timeout within a 5 second window will be in the same bucket, and get notified at the same time. ...
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python
train
manns/pyspread
pyspread/src/gui/_gui_interfaces.py
https://github.com/manns/pyspread/blob/0e2fd44c2e0f06605efc3058c20a43a8c1f9e7e0/pyspread/src/gui/_gui_interfaces.py#L132-L165
def get_filepath_findex_from_user(self, wildcard, message, style, filterindex=0): """Opens a file dialog and returns filepath and filterindex Parameters ---------- wildcard: String \tWildcard string for file dialog message: String ...
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Opens a file dialog and returns filepath and filterindex Parameters ---------- wildcard: String \tWildcard string for file dialog message: String \tMessage in the file dialog style: Integer \tDialog style, e. g. wx.OPEN | wx.CHANGE_DIR filterindex...
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python
train
NLeSC/noodles
noodles/lib/utility.py
https://github.com/NLeSC/noodles/blob/3759e24e6e54a3a1a364431309dbb1061f617c04/noodles/lib/utility.py#L111-L128
def inverse_deep_map(f, root): """Sibling to |deep_map|. Recursively maps objects in a nested structure of ``list`` and ``dict`` objects. Where |deep_map| starts at the top, |inverse_deep_map| starts at the bottom. First, if `root` is a ``list`` or ``dict``, its contents are |inverse_deep_map|ed. Then a...
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Sibling to |deep_map|. Recursively maps objects in a nested structure of ``list`` and ``dict`` objects. Where |deep_map| starts at the top, |inverse_deep_map| starts at the bottom. First, if `root` is a ``list`` or ``dict``, its contents are |inverse_deep_map|ed. Then at the end, the entire object is pa...
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python
train
mitsei/dlkit
dlkit/handcar/type/managers.py
https://github.com/mitsei/dlkit/blob/445f968a175d61c8d92c0f617a3c17dc1dc7c584/dlkit/handcar/type/managers.py#L72-L93
def get_type_admin_session(self): """Gets the OsidSession associated with the type admin service. return: (osid.type.TypeAdminSession) - a TypeAdminSession raise: OperationFailed - unable to complete request raise: Unimplemented - supports_type_admin() is false compliance: opt...
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Gets the OsidSession associated with the type admin service. return: (osid.type.TypeAdminSession) - a TypeAdminSession raise: OperationFailed - unable to complete request raise: Unimplemented - supports_type_admin() is false compliance: optional - This method must be implemented if ...
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python
train
6809/MC6809
MC6809/components/memory.py
https://github.com/6809/MC6809/blob/6ba2f5106df46689017b5d0b6d84d43b7ee6a240/MC6809/components/memory.py#L311-L315
def get(self, start, end): """ used in unittests """ return [self.read_byte(addr) for addr in range(start, end)]
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used in unittests
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python
train
saltstack/salt
salt/utils/openstack/neutron.py
https://github.com/saltstack/salt/blob/e8541fd6e744ab0df786c0f76102e41631f45d46/salt/utils/openstack/neutron.py#L411-L420
def create_subnet(self, network, cidr, name=None, ip_version=4): ''' Creates a new subnet ''' net_id = self._find_network_id(network) body = {'cidr': cidr, 'ip_version': ip_version, 'network_id': net_id, 'name': name} return...
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Creates a new subnet
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python
train
tensorflow/tensorboard
tensorboard/program.py
https://github.com/tensorflow/tensorboard/blob/8e5f497b48e40f2a774f85416b8a35ac0693c35e/tensorboard/program.py#L149-L199
def configure(self, argv=('',), **kwargs): """Configures TensorBoard behavior via flags. This method will populate the "flags" property with an argparse.Namespace representing flag values parsed from the provided argv list, overridden by explicit flags from remaining keyword arguments. Args: ...
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Configures TensorBoard behavior via flags. This method will populate the "flags" property with an argparse.Namespace representing flag values parsed from the provided argv list, overridden by explicit flags from remaining keyword arguments. Args: argv: Can be set to CLI args equivalent to sys.ar...
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python
train
yougov/mongo-connector
mongo_connector/doc_managers/mongo_doc_manager.py
https://github.com/yougov/mongo-connector/blob/557cafd4b54c848cd54ef28a258391a154650cb4/mongo_connector/doc_managers/mongo_doc_manager.py#L115-L124
def _meta_collections(self): """Provides the meta collections currently being used """ if self.use_single_meta_collection: yield self.meta_collection_name else: for name in self.meta_database.collection_names( include_system_collections=False ...
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Provides the meta collections currently being used
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python
train
pyGrowler/Growler
growler/http/parser.py
https://github.com/pyGrowler/Growler/blob/90c923ff204f28b86a01d741224987a22f69540f/growler/http/parser.py#L280-L303
def determine_newline(data): """ Looks for a newline character in bytestring parameter 'data'. Currently only looks for strings '\r\n', '\n'. If '\n' is found at the first position of the string, this raises an exception. Parameters: data (bytes): The data to...
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Looks for a newline character in bytestring parameter 'data'. Currently only looks for strings '\r\n', '\n'. If '\n' is found at the first position of the string, this raises an exception. Parameters: data (bytes): The data to be searched Returns: None: ...
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python
train
Kane610/axis
axis/rtsp.py
https://github.com/Kane610/axis/blob/b2b44ce595c7b722b5e13eabcab7b91f048e1808/axis/rtsp.py#L63-L68
def stop(self): """Stop session.""" if self.transport: self.transport.write(self.method.TEARDOWN().encode()) self.transport.close() self.rtp.stop()
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Stop session.
[ "Stop", "session", "." ]
python
train
tomekwojcik/flask-htauth
flask_htauth/extension.py
https://github.com/tomekwojcik/flask-htauth/blob/bb89bee3fa7d88de3147ae338048624e01de710b/flask_htauth/extension.py#L81-L109
def authenticated(viewfunc): """Decorate **viewfunc** with this decorator to require HTTP auth on the view.""" @wraps(viewfunc) def wrapper(*args, **kwargs): ctx = stack.top if ctx and hasattr(ctx, 'htauth'): auth_header = request.headers.get('Authorization', None) ...
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Decorate **viewfunc** with this decorator to require HTTP auth on the view.
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python
train
twilio/twilio-python
twilio/rest/voice/v1/dialing_permissions/country/__init__.py
https://github.com/twilio/twilio-python/blob/c867895f55dcc29f522e6e8b8868d0d18483132f/twilio/rest/voice/v1/dialing_permissions/country/__init__.py#L115-L156
def page(self, iso_code=values.unset, continent=values.unset, country_code=values.unset, low_risk_numbers_enabled=values.unset, high_risk_special_numbers_enabled=values.unset, high_risk_tollfraud_numbers_enabled=values.unset, page_token=values.unset, page_number=value...
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Retrieve a single page of CountryInstance records from the API. Request is executed immediately :param unicode iso_code: Filter to retrieve the country permissions by specifying the ISO country code :param unicode continent: Filter to retrieve the country permissions by specifying the continent...
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python
train
pywbem/pywbem
pywbem/cim_obj.py
https://github.com/pywbem/pywbem/blob/e54ecb82c2211e289a268567443d60fdd489f1e4/pywbem/cim_obj.py#L705-L760
def mofval(value, indent=MOF_INDENT, maxline=MAX_MOF_LINE, line_pos=0, end_space=0): """ Low level function that returns the MOF representation of a non-string value (i.e. a value that cannot not be split into multiple parts, for example a numeric or boolean value). If the MOF representa...
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Low level function that returns the MOF representation of a non-string value (i.e. a value that cannot not be split into multiple parts, for example a numeric or boolean value). If the MOF representation of the value does not fit into the remaining space of the current line, it is put into a new line, ...
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python
train
NuGrid/NuGridPy
nugridpy/nugridse.py
https://github.com/NuGrid/NuGridPy/blob/eee8047446e398be77362d82c1d8b3310054fab0/nugridpy/nugridse.py#L779-L855
def ernst_table_exporter(self, cycle, outfname='table_out', sheetname='Sheet 1'): """ This routine takes NuGrid data (model output) for a given cycle and writes it into an Excel sheet. This is one format as requested by Ernst Zinner in June 2013 (thr...
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This routine takes NuGrid data (model output) for a given cycle and writes it into an Excel sheet. This is one format as requested by Ernst Zinner in June 2013 (through Marco). If you want all radioactive isotopes, start from the restart file. Empty columns are not written out and ...
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python
train