kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def make_body(self, resp, params, meta, content): """Construct response body in ``resp`` object using JSON serialization. Args: resp (falcon.Response): response object where to include serialized body params (dict): dictionary of parsed parameters met...	[ "def", "make_body", "(", "self", ",", "resp", ",", "params", ",", "meta", ",", "content", ")", ":", "response", "=", "{", "'meta'", ":", "meta", ",", "'content'", ":", "content", "}", "resp", ".", "content_type", "=", "'application/json'", "resp", ".", ...	34.44	21.56
def validate(document, spec): """Validate that a document meets a specification. Returns True if validation was successful, but otherwise raises a ValueError.""" if not spec: return True missing = [] for key, field in spec.iteritems(): if field.required and key not in document: ...	[ "def", "validate", "(", "document", ",", "spec", ")", ":", "if", "not", "spec", ":", "return", "True", "missing", "=", "[", "]", "for", "key", ",", "field", "in", "spec", ".", "iteritems", "(", ")", ":", "if", "field", ".", "required", "and", "key"...	38.208333	17.5
def _create_api_uri(self, *parts): """Creates fully qualified endpoint URIs. :param parts: the string parts that form the request URI """ return urljoin(self.API_URI, '/'.join(map(quote, parts)))	[ "def", "_create_api_uri", "(", "self", ",", "*", "parts", ")", ":", "return", "urljoin", "(", "self", ".", "API_URI", ",", "'/'", ".", "join", "(", "map", "(", "quote", ",", "parts", ")", ")", ")" ]	29.571429	18.142857
def _add_model(self, model_list_or_dict, core_element, model_class, model_key=None, load_meta_data=True): """Adds one model for a given core element. The method will add a model for a given core object and checks if there is a corresponding model object in the future expected model list. The me...	[ "def", "_add_model", "(", "self", ",", "model_list_or_dict", ",", "core_element", ",", "model_class", ",", "model_key", "=", "None", ",", "load_meta_data", "=", "True", ")", ":", "found_model", "=", "self", ".", "_get_future_expected_model", "(", "core_element", ...	53.310345	36.62069
def iterate(self, max_iter=150, n_rewightings=1): r"""Iterate This method calls update until either convergence criteria is met or the maximum number of iterations is reached Parameters ---------- max_iter : int, optional Maximum number of iterations (defaul...	[ "def", "iterate", "(", "self", ",", "max_iter", "=", "150", ",", "n_rewightings", "=", "1", ")", ":", "self", ".", "_run_alg", "(", "max_iter", ")", "if", "not", "isinstance", "(", "self", ".", "_reweight", ",", "type", "(", "None", ")", ")", ":", ...	30.888889	17.481481
def _formatFilterQuery(self, request=None, featureSets=[]): """ Generate a formatted sparql query with appropriate filters """ query = self._baseQuery() filters = [] if issubclass(request.__class__, protocol.SearchGenotypePhenotypeRequest): ...	[ "def", "_formatFilterQuery", "(", "self", ",", "request", "=", "None", ",", "featureSets", "=", "[", "]", ")", ":", "query", "=", "self", ".", "_baseQuery", "(", ")", "filters", "=", "[", "]", "if", "issubclass", "(", "request", ".", "__class__", ",", ...	37.6	18
def get_plain_text(self): """Returns a list""" _msg = self.message if self.message is not None else [""] msg = _msg if isinstance(_msg, list) else [_msg] line = "" if not self.line else ", line {}".format(self.line) ret = ["{} found in file '{}'{}::".format(self.type.capital...	[ "def", "get_plain_text", "(", "self", ")", ":", "_msg", "=", "self", ".", "message", "if", "self", ".", "message", "is", "not", "None", "else", "[", "\"\"", "]", "msg", "=", "_msg", "if", "isinstance", "(", "_msg", ",", "list", ")", "else", "[", "_...	45.2	19.7
def tile_to_path(self, tile): '''return full path to a tile''' return os.path.join(self.cache_path, self.service, tile.path())	[ "def", "tile_to_path", "(", "self", ",", "tile", ")", ":", "return", "os", ".", "path", ".", "join", "(", "self", ".", "cache_path", ",", "self", ".", "service", ",", "tile", ".", "path", "(", ")", ")" ]	42.666667	14
def adjust_for_triggers(self): """Remove trigger-related plugins when needed If there are no triggers defined, it's assumed the feature is disabled and all trigger-related plugins are removed. If there are triggers defined, and this is a custom base image, some trigger-...	[ "def", "adjust_for_triggers", "(", "self", ")", ":", "triggers", "=", "self", ".", "template", "[", "'spec'", "]", ".", "get", "(", "'triggers'", ",", "[", "]", ")", "remove_plugins", "=", "[", "(", "\"prebuild_plugins\"", ",", "\"check_and_set_rebuild\"", "...	38.368421	20.473684
def query_metric_stats(self, metric_type, metric_id=None, start=None, end=None, bucketDuration=None, **query_options): """ Query for metric aggregates from the server. This is called buckets in the Hawkular-Metrics documentation. :param metric_type: MetricType to be matched (required) :...	[ "def", "query_metric_stats", "(", "self", ",", "metric_type", ",", "metric_id", "=", "None", ",", "start", "=", "None", ",", "end", "=", "None", ",", "bucketDuration", "=", "None", ",", "", "", "query_options", ")", ":", "if", "start", "is", "not", "...	48.324324	28
def _parse_metafiles(self, metafile_input): """ Parses class input and verifies metadata file names. :param metafile_input: class input parameter `metafiles` :type metafile_input: str or list(str) or None :return: verified list of metadata files :rtype: list(str) ...	[ "def", "_parse_metafiles", "(", "self", ",", "metafile_input", ")", ":", "all_metafiles", "=", "AwsConstants", ".", "S2_L1C_METAFILES", "if", "self", ".", "data_source", "is", "DataSource", ".", "SENTINEL2_L1C", "else", "AwsConstants", ".", "S2_L2A_METAFILES", "if",...	48.62069	21.862069
def get_directory(request): """Get API directory as a nested list of lists.""" def get_url(url): return reverse(url, request=request) if url else url def is_active_url(path, url): return path.startswith(url) if url and path else False path = request.path directory_list = [] d...	[ "def", "get_directory", "(", "request", ")", ":", "def", "get_url", "(", "url", ")", ":", "return", "reverse", "(", "url", ",", "request", "=", "request", ")", "if", "url", "else", "url", "def", "is_active_url", "(", "path", ",", "url", ")", ":", "re...	29.146341	18.170732
def div_safe( numerator, denominator ): """ Ufunc-extension that returns 0 instead of nan when dividing numpy arrays Parameters ---------- numerator: array-like denominator: scalar or array-like that can be validly divided by the numerator returns a numpy array example: div_safe( [-1...	[ "def", "div_safe", "(", "numerator", ",", "denominator", ")", ":", "#First handle scalars", "if", "np", ".", "isscalar", "(", "numerator", ")", ":", "raise", "ValueError", "(", "\"div_safe should only be used with an array-like numerator\"", ")", "#Then numpy arrays", "...	29.153846	23.615385
def get_commits(repo_dir, old_commit, new_commit, hide_merges=True): """Find all commits between two commit SHAs.""" repo = Repo(repo_dir) commits = repo.iter_commits(rev="{0}..{1}".format(old_commit, new_commit)) if hide_merges: return [x for x in commits if not x.summary.startswith("Merge ")] ...	[ "def", "get_commits", "(", "repo_dir", ",", "old_commit", ",", "new_commit", ",", "hide_merges", "=", "True", ")", ":", "repo", "=", "Repo", "(", "repo_dir", ")", "commits", "=", "repo", ".", "iter_commits", "(", "rev", "=", "\"{0}..{1}\"", ".", "format", ...	43.875	22.25
def parse_reaction(reaction_def, default_compartment, context=None): """Parse a structured reaction definition as obtained from a YAML file Returns a ReactionEntry. """ reaction_id = reaction_def.get('id') _check_id(reaction_id, 'Reaction') reaction_props = dict(reaction_def) # Parse rea...	[ "def", "parse_reaction", "(", "reaction_def", ",", "default_compartment", ",", "context", "=", "None", ")", ":", "reaction_id", "=", "reaction_def", ".", "get", "(", "'id'", ")", "_check_id", "(", "reaction_id", ",", "'Reaction'", ")", "reaction_props", "=", "...	31.222222	16.944444
def listen_for_dweets_from(thing_name, timeout=900, key=None, session=None): """Create a real-time subscription to dweets """ url = BASE_URL + '/listen/for/dweets/from/{0}'.format(thing_name) session = session or requests.Session() if key is not None: params = {'key': key} else: ...	[ "def", "listen_for_dweets_from", "(", "thing_name", ",", "timeout", "=", "900", ",", "key", "=", "None", ",", "session", "=", "None", ")", ":", "url", "=", "BASE_URL", "+", "'/listen/for/dweets/from/{0}'", ".", "format", "(", "thing_name", ")", "session", "=...	39.619048	21.190476
def draw_beam(ax, p1, p2, width=0, beta1=None, beta2=None, format=None, kwds): r"""Draw a laser beam.""" if format is None: format = 'k-' if width == 0: x0 = [p1[0], p2[0]] y0 = [p1[1], p2[1]] ax.plot(x0, y0, format, kwds) else: a = width/2 ...	[ "def", "draw_beam", "(", "ax", ",", "p1", ",", "p2", ",", "width", "=", "0", ",", "beta1", "=", "None", ",", "beta2", "=", "None", ",", "format", "=", "None", ",", "", "", "kwds", ")", ":", "if", "format", "is", "None", ":", "format", "=", ...	127.733333	118.333333
def QA_fetch_get_sz_margin(date): """return shenzhen margin data Arguments: date {str YYYY-MM-DD} -- date format Returns: pandas.DataFrame -- res for margin data """ if date in trade_date_sse: return pd.read_excel(_sz_url.format(date)).assign(date=date).assign(sse='sz')	[ "def", "QA_fetch_get_sz_margin", "(", "date", ")", ":", "if", "date", "in", "trade_date_sse", ":", "return", "pd", ".", "read_excel", "(", "_sz_url", ".", "format", "(", "date", ")", ")", ".", "assign", "(", "date", "=", "date", ")", ".", "assign", "("...	25.5	20.583333
def run_forever(self) -> None: '''Execute the tasky/asyncio event loop until terminated.''' Log.debug('running event loop until terminated') asyncio.ensure_future(self.init()) self.loop.run_forever() self.loop.close()	[ "def", "run_forever", "(", "self", ")", "->", "None", ":", "Log", ".", "debug", "(", "'running event loop until terminated'", ")", "asyncio", ".", "ensure_future", "(", "self", ".", "init", "(", ")", ")", "self", ".", "loop", ".", "run_forever", "(", ")", ...	36	17.142857
async def get_bearer_info(self): """Get the application bearer token from client_id and client_secret.""" if self.client_id is None: raise SpotifyException(_GET_BEARER_ERR % 'client_id') elif self.client_secret is None: raise SpotifyException(_GET_BEARER_ERR % 'client_se...	[ "async", "def", "get_bearer_info", "(", "self", ")", ":", "if", "self", ".", "client_id", "is", "None", ":", "raise", "SpotifyException", "(", "_GET_BEARER_ERR", "%", "'client_id'", ")", "elif", "self", ".", "client_secret", "is", "None", ":", "raise", "Spot...	40.722222	23.722222
def unique(self, *args): """ Returns all unique values as a DataFrame. This is executing: SELECT DISTINCT <name_of_the_column_1> , <name_of_the_column_2> , <name_of_the_column_3> ... F...	[ "def", "unique", "(", "self", ",", "*", "args", ")", ":", "q", "=", "self", ".", "_query_templates", "[", "'table'", "]", "[", "'unique'", "]", ".", "format", "(", "columns", "=", "self", ".", "_format_columns", "(", "args", ")", ",", "schema", "=", ...	25.259259	20.296296
def token(self, id, kwargs): """ Retrieve a service request ID from a token. >>> Three('api.city.gov').token('12345') {'service_request_id': {'for': {'token': '12345'}}} """ data = self.get('tokens', id, kwargs) return data	[ "def", "token", "(", "self", ",", "id", ",", "", "", "kwargs", ")", ":", "data", "=", "self", ".", "get", "(", "'tokens'", ",", "id", ",", "", "", "kwargs", ")", "return", "data" ]	30.666667	12.888889
def dict_from_hdf5(dict_like, h5group): """ Load a dictionnary-like object from a h5 file group """ # Read attributes for name, value in h5group.attrs.items(): dict_like[name] = value	[ "def", "dict_from_hdf5", "(", "dict_like", ",", "h5group", ")", ":", "# Read attributes", "for", "name", ",", "value", "in", "h5group", ".", "attrs", ".", "items", "(", ")", ":", "dict_like", "[", "name", "]", "=", "value" ]	29.285714	7
def remove_binding(site, hostheader='', ipaddress='*', port=80): ''' Remove an IIS binding. Args: site (str): The IIS site name. hostheader (str): The host header of the binding. ipaddress (str): The IP address of the binding. port (int): The TCP port of the binding. Re...	[ "def", "remove_binding", "(", "site", ",", "hostheader", "=", "''", ",", "ipaddress", "=", "'*'", ",", "port", "=", "80", ")", ":", "name", "=", "_get_binding_info", "(", "hostheader", ",", "ipaddress", ",", "port", ")", "current_bindings", "=", "list_bind...	30.209302	21.744186
def getVariantAnnotationSets(self, datasetId): """ Returns the list of ReferenceSets for this server. """ # TODO this should be displayed per-variant set, not per dataset. variantAnnotationSets = [] dataset = app.backend.getDataRepository().getDataset(datasetId) f...	[ "def", "getVariantAnnotationSets", "(", "self", ",", "datasetId", ")", ":", "# TODO this should be displayed per-variant set, not per dataset.", "variantAnnotationSets", "=", "[", "]", "dataset", "=", "app", ".", "backend", ".", "getDataRepository", "(", ")", ".", "getD...	44.181818	11.272727
def all_project_administrators(self): """ Get the list of project administrators :return: """ for project in self.project_list(): log.info('Processing project: {0} - {1}'.format(project.get('key'), project.get('name'))) yield { 'project_key...	[ "def", "all_project_administrators", "(", "self", ")", ":", "for", "project", "in", "self", ".", "project_list", "(", ")", ":", "log", ".", "info", "(", "'Processing project: {0} - {1}'", ".", "format", "(", "project", ".", "get", "(", "'key'", ")", ",", "...	50.166667	23
def feed_interval_get(feed_id, parameters): 'Get adaptive interval between checks for a feed.' val = cache.get(getkey( T_INTERVAL, key=feed_interval_key(feed_id, parameters) )) return val if isinstance(val, tuple) else (val, None)	[ "def", "feed_interval_get", "(", "feed_id", ",", "parameters", ")", ":", "val", "=", "cache", ".", "get", "(", "getkey", "(", "T_INTERVAL", ",", "key", "=", "feed_interval_key", "(", "feed_id", ",", "parameters", ")", ")", ")", "return", "val", "if", "is...	46.2	7.8
def get_comments_of_credit_note_per_page(self, credit_note_id, per_page=1000, page=1): """ Get comments of credit note per page :param credit_note_id: the credit note id :param per_page: How many objects per page. Default: 1000 :param page: Which page. Default: 1 :return...	[ "def", "get_comments_of_credit_note_per_page", "(", "self", ",", "credit_note_id", ",", "per_page", "=", "1000", ",", "page", "=", "1", ")", ":", "return", "self", ".", "_get_resource_per_page", "(", "resource", "=", "CREDIT_NOTE_COMMENTS", ",", "per_page", "=", ...	35.333333	14.933333
def _x2c(self, x): """ Convert windowdow coordinates to cheb coordinates [-1,1] """ return ((2 * x - self.window[1] - self.window[0]) / (self.window[1] - self.window[0]))	[ "def", "_x2c", "(", "self", ",", "x", ")", ":", "return", "(", "(", "2", "*", "x", "-", "self", ".", "window", "[", "1", "]", "-", "self", ".", "window", "[", "0", "]", ")", "/", "(", "self", ".", "window", "[", "1", "]", "-", "self", "."...	49.75	12.75
def defect_concentration(self, chemical_potentials, temperature=300, fermi_level=0.0): """ Get the defect concentration for a temperature and Fermi level. Args: temperature: the temperature in K fermi_level: the fermi level in eV (with resp...	[ "def", "defect_concentration", "(", "self", ",", "chemical_potentials", ",", "temperature", "=", "300", ",", "fermi_level", "=", "0.0", ")", ":", "n", "=", "self", ".", "multiplicity", "*", "1e24", "/", "self", ".", "defect", ".", "bulk_structure", ".", "v...	39.6875	21.8125
def get_new_header(configuration, pofile): """ Insert info about edX into the po file headers """ team = pofile.metadata.get('Language-Team', None) if not team: return TRANSIFEX_HEADER.format(configuration.TRANSIFEX_URL) return TRANSIFEX_HEADER.format(team)	[ "def", "get_new_header", "(", "configuration", ",", "pofile", ")", ":", "team", "=", "pofile", ".", "metadata", ".", "get", "(", "'Language-Team'", ",", "None", ")", "if", "not", "team", ":", "return", "TRANSIFEX_HEADER", ".", "format", "(", "configuration",...	35.25	9.5
def fetch(self, plan_id, data={}, kwargs): """" Fetch Plan for given Id Args: plan_id : Id for which Plan object has to be retrieved Returns: Plan dict for given subscription Id """ return super(Plan, self).fetch(plan_id, data, kwargs)	[ "def", "fetch", "(", "self", ",", "plan_id", ",", "data", "=", "{", "}", ",", "", "", "kwargs", ")", ":", "return", "super", "(", "Plan", ",", "self", ")", ".", "fetch", "(", "plan_id", ",", "data", ",", "", "", "kwargs", ")" ]	27.545455	18.181818
def topoSort(roots, getParents): """Return a topological sorting of nodes in a graph. roots - list of root nodes to search from getParents - function which returns the parents of a given node """ results = [] visited = set() # Use iterative version to avoid stack limits for large datasets...	[ "def", "topoSort", "(", "roots", ",", "getParents", ")", ":", "results", "=", "[", "]", "visited", "=", "set", "(", ")", "# Use iterative version to avoid stack limits for large datasets", "stack", "=", "[", "(", "node", ",", "0", ")", "for", "node", "in", "...	31.16	16
def reject(self): """Handle ESC key""" if self.controller.is_running: self.info(self.tr("Stopping..")) self.controller.is_running = False	[ "def", "reject", "(", "self", ")", ":", "if", "self", ".", "controller", ".", "is_running", ":", "self", ".", "info", "(", "self", ".", "tr", "(", "\"Stopping..\"", ")", ")", "self", ".", "controller", ".", "is_running", "=", "False" ]	28.833333	12.5
def get_window(self, window, bands=None, xsize=None, ysize=None, resampling=Resampling.cubic, masked=None, affine=None ): """Get window from raster. :param window: requested window :param bands: list of indices of requested bads, default ...	[ "def", "get_window", "(", "self", ",", "window", ",", "bands", "=", "None", ",", "xsize", "=", "None", ",", "ysize", "=", "None", ",", "resampling", "=", "Resampling", ".", "cubic", ",", "masked", "=", "None", ",", "affine", "=", "None", ")", ":", ...	49.275	26.35
def trigger(self, attr, old, new, hint=None, setter=None): ''' Trigger callbacks for ``attr`` on this object. Args: attr (str) : old (object) : new (object) : Returns: None ''' def invoke(): callbacks = self._callback...	[ "def", "trigger", "(", "self", ",", "attr", ",", "old", ",", "new", ",", "hint", "=", "None", ",", "setter", "=", "None", ")", ":", "def", "invoke", "(", ")", ":", "callbacks", "=", "self", ".", "_callbacks", ".", "get", "(", "attr", ")", "if", ...	29.333333	22.571429
def as_page(self): """ Wrap this Tag as a self-contained webpage. Create a page with the following structure: .. code-block:: html <!DOCTYPE html> <html> <head> <meta http-equiv="Content-type" content="text/htm...	[ "def", "as_page", "(", "self", ")", ":", "H", "=", "HTML", "(", ")", "utf8", "=", "H", ".", "meta", "(", "{", "'http-equiv'", ":", "'Content-type'", "}", ",", "content", "=", "\"text/html\"", ",", "charset", "=", "\"UTF-8\"", ")", "return", "H", ".",...	29.740741	14.555556
def extend(self, values): """Extend the array, appending the given values.""" self.database.run_script( 'array_extend', keys=[self.key], args=values)	[ "def", "extend", "(", "self", ",", "values", ")", ":", "self", ".", "database", ".", "run_script", "(", "'array_extend'", ",", "keys", "=", "[", "self", ".", "key", "]", ",", "args", "=", "values", ")" ]	32.666667	10.5
def _parse_qualimap_globals(table): """Retrieve metrics of interest from globals table. """ out = {} want = {"Mapped reads": _parse_num_pct, "Duplication rate": lambda k, v: {k: v}} for row in table.find_all("tr"): col, val = [x.text for x in row.find_all("td")] if col in...	[ "def", "_parse_qualimap_globals", "(", "table", ")", ":", "out", "=", "{", "}", "want", "=", "{", "\"Mapped reads\"", ":", "_parse_num_pct", ",", "\"Duplication rate\"", ":", "lambda", "k", ",", "v", ":", "{", "k", ":", "v", "}", "}", "for", "row", "in...	34.090909	10.272727
def load_raw_arrays(self, columns, start_date, end_date, assets): """ Parameters ---------- fields : list of str 'open', 'high', 'low', 'close', or 'volume' start_dt: Timestamp Beginning of the window range. end_dt: Timestamp End of the wi...	[ "def", "load_raw_arrays", "(", "self", ",", "columns", ",", "start_date", ",", "end_date", ",", "assets", ")", ":", "rolls_by_asset", "=", "{", "}", "tc", "=", "self", ".", "trading_calendar", "start_session", "=", "tc", ".", "minute_to_session_label", "(", ...	36.835443	16.278481
def tange_pth(v, temp, v0, gamma0, a, b, theta0, n, z, t_ref=300., three_r=3. * constants.R): """ calculate thermal pressure for the Tange equation :param v: unit-cell volume in A^3 :param temp: temperature in K :param v0: unit-cell volume in A^3 at 1 bar :param gamma0: Gruneisen ...	[ "def", "tange_pth", "(", "v", ",", "temp", ",", "v0", ",", "gamma0", ",", "a", ",", "b", ",", "theta0", ",", "n", ",", "z", ",", "t_ref", "=", "300.", ",", "three_r", "=", "3.", "*", "constants", ".", "R", ")", ":", "v_mol", "=", "vol_uc2mol", ...	34.818182	11.787879
def eps_from_series(self): """ Workhorse function that handles grabbing series data from csvs and requesting episodal information from RSS feeds """ csvs = [] for _, _, filenames in os.walk('./{}'.format(self.directory)): csvs.extend(filenames) series_set = set() for c in csvs: ...	[ "def", "eps_from_series", "(", "self", ")", ":", "csvs", "=", "[", "]", "for", "_", ",", "_", ",", "filenames", "in", "os", ".", "walk", "(", "'./{}'", ".", "format", "(", "self", ".", "directory", ")", ")", ":", "csvs", ".", "extend", "(", "file...	27.222222	18.037037
def setShowTerritory(self, state): """ Sets the display mode for this widget to the inputed mode. :param state \| <bool> """ if state == self._showTerritory: return self._showTerritory = state self.setDirty()	[ "def", "setShowTerritory", "(", "self", ",", "state", ")", ":", "if", "state", "==", "self", ".", "_showTerritory", ":", "return", "self", ".", "_showTerritory", "=", "state", "self", ".", "setDirty", "(", ")" ]	27.090909	12.909091
def mean(self, axis=0, args, *kwargs): """ Mean of non-NA/null values Returns ------- mean : float """ nv.validate_mean(args, kwargs) valid_vals = self._valid_sp_values sp_sum = valid_vals.sum() ct = len(valid_vals) if self._nul...	[ "def", "mean", "(", "self", ",", "axis", "=", "0", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "nv", ".", "validate_mean", "(", "args", ",", "kwargs", ")", "valid_vals", "=", "self", ".", "_valid_sp_values", "sp_sum", "=", "valid_vals", ".",...	26.444444	14.222222
def create_document(self, parent, document, retry=google.api_core.gapic_v1.method.DEFAULT, timeout=google.api_core.gapic_v1.method.DEFAULT, metadata=None): """ Creates a new document. ...	[ "def", "create_document", "(", "self", ",", "parent", ",", "document", ",", "retry", "=", "google", ".", "api_core", ".", "gapic_v1", ".", "method", ".", "DEFAULT", ",", "timeout", "=", "google", ".", "api_core", ".", "gapic_v1", ".", "method", ".", "DEF...	44.814815	23.802469
def diskdata(): """Get total disk size in GB.""" p = os.popen("/bin/df -l -P") ddata = {} tsize = 0 for line in p.readlines(): d = line.split() if ("/dev/sd" in d[0] or "/dev/hd" in d[0] or "/dev/mapper" in d[0]): tsize = tsize + int(d[1]) ddata["Disk_GB"] = int(tsize...	[ "def", "diskdata", "(", ")", ":", "p", "=", "os", ".", "popen", "(", "\"/bin/df -l -P\"", ")", "ddata", "=", "{", "}", "tsize", "=", "0", "for", "line", "in", "p", ".", "readlines", "(", ")", ":", "d", "=", "line", ".", "split", "(", ")", "if",...	29.083333	16.916667
def fire_event(self, event, args, *kwargs): """Fires a event.""" self.event_queue.append((event, args)) self.process_events()	[ "def", "fire_event", "(", "self", ",", "event", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "self", ".", "event_queue", ".", "append", "(", "(", "event", ",", "args", ")", ")", "self", ".", "process_events", "(", ")" ]	37	5.5
def get_eidos_bayesian_scorer(prior_counts=None): """Return a BayesianScorer based on Eidos curation counts.""" table = load_eidos_curation_table() subtype_counts = {'eidos': {r: [c, i] for r, c, i in zip(table['RULE'], table['Num correct'], ta...	[ "def", "get_eidos_bayesian_scorer", "(", "prior_counts", "=", "None", ")", ":", "table", "=", "load_eidos_curation_table", "(", ")", "subtype_counts", "=", "{", "'eidos'", ":", "{", "r", ":", "[", "c", ",", "i", "]", "for", "r", ",", "c", ",", "i", "in...	46.416667	17.833333
def seek(self, pos=0): """Set the stream's file pointer to pos. Negative seeking is forbidden. """ if pos - self.pos >= 0: blocks, remainder = divmod(pos - self.pos, self.bufsize) for i in range(blocks): self.read(self.bufsize) self....	[ "def", "seek", "(", "self", ",", "pos", "=", "0", ")", ":", "if", "pos", "-", "self", ".", "pos", ">=", "0", ":", "blocks", ",", "remainder", "=", "divmod", "(", "pos", "-", "self", ".", "pos", ",", "self", ".", "bufsize", ")", "for", "i", "i...	35.666667	12.833333
def url_dirname(url): """ Return the folder containing the '.json' file """ p = six.moves.urllib.parse.urlparse(url) for e in [private.FILE_EXT_JSON, private.FILE_EXT_YAML]: if p.path.endswith(e): return six.moves.urllib.parse.urlunparse( p[:2]+ (os.pa...	[ "def", "url_dirname", "(", "url", ")", ":", "p", "=", "six", ".", "moves", ".", "urllib", ".", "parse", ".", "urlparse", "(", "url", ")", "for", "e", "in", "[", "private", ".", "FILE_EXT_JSON", ",", "private", ".", "FILE_EXT_YAML", "]", ":", "if", ...	31.75	13.25
def update(table_name, fields): """ Build a update query. >>> update('foo_table', a=5, b=2) "UPDATE `foo_table` SET `a`=%(_QB_a)s, `b`=%(_QB_b)s", { '_QB_a': 5, '_QB_b': 2 } """ prefix = "UPDATE `%s` SET " % table_name sets, params = simple_expression(', ', fields) return prefix + sets,...	[ "def", "update", "(", "table_name", ",", "", "", "fields", ")", ":", "prefix", "=", "\"UPDATE `%s` SET \"", "%", "table_name", "sets", ",", "params", "=", "simple_expression", "(", "', '", ",", "", "", "fields", ")", "return", "prefix", "+", "sets", ...	35.444444	13.222222
def _count_righthand_zero_bits(number, bits): """Count the number of zero bits on the right hand side. Args: number: an integer. bits: maximum number of bits to count. Returns: The number of zero bits on the right hand side of the number. """ if number == 0: return...	[ "def", "_count_righthand_zero_bits", "(", "number", ",", "bits", ")", ":", "if", "number", "==", "0", ":", "return", "bits", "return", "min", "(", "bits", ",", "_compat_bit_length", "(", "~", "number", "&", "(", "number", "-", "1", ")", ")", ")" ]	26.928571	21.285714
def _get_demand_array_construct(self): """ Returns a construct for an array of power demand data. """ bus_no = integer.setResultsName("bus_no") s_rating = real.setResultsName("s_rating") # MVA p_direction = real.setResultsName("p_direction") # p.u. q_direction = real.setR...	[ "def", "_get_demand_array_construct", "(", "self", ")", ":", "bus_no", "=", "integer", ".", "setResultsName", "(", "\"bus_no\"", ")", "s_rating", "=", "real", ".", "setResultsName", "(", "\"s_rating\"", ")", "# MVA", "p_direction", "=", "real", ".", "setResultsN...	51.941176	22.323529
def _invokeWrite(self, fileIO, session, directory, filename, replaceParamFile): """ Invoke File Write Method on Other Files """ # Default value for instance instance = None try: # Handle case where fileIO interfaces with single file # Retrieve Fil...	[ "def", "_invokeWrite", "(", "self", ",", "fileIO", ",", "session", ",", "directory", ",", "filename", ",", "replaceParamFile", ")", ":", "# Default value for instance", "instance", "=", "None", "try", ":", "# Handle case where fileIO interfaces with single file", "# Ret...	40.585366	21.804878
def show_updates(self): """ Check installed packages for available updates on PyPI @param project_name: optional package name to check; checks every installed pacakge if none specified @type project_name: string @returns: None """ di...	[ "def", "show_updates", "(", "self", ")", ":", "dists", "=", "Distributions", "(", ")", "if", "self", ".", "project_name", ":", "#Check for a single package", "pkg_list", "=", "[", "self", ".", "project_name", "]", "else", ":", "#Check for every installed package",...	39.386364	19.704545
def _raise_server_index(self): """Round robin magic: Raises the current redis server index and returns it""" self._current_server_index = (self._current_server_index + 1) % len(self._servers) return self._current_server_index	[ "def", "_raise_server_index", "(", "self", ")", ":", "self", ".", "_current_server_index", "=", "(", "self", ".", "_current_server_index", "+", "1", ")", "%", "len", "(", "self", ".", "_servers", ")", "return", "self", ".", "_current_server_index" ]	41	23.5
def reset_downloads_folder(): ''' Clears the downloads folder. If settings.ARCHIVE_EXISTING_DOWNLOADS is set to True, archives it. ''' if os.path.exists(downloads_path) and not os.listdir(downloads_path) == []: archived_downloads_folder = os.path.join(downloads_path, '..', ...	[ "def", "reset_downloads_folder", "(", ")", ":", "if", "os", ".", "path", ".", "exists", "(", "downloads_path", ")", "and", "not", "os", ".", "listdir", "(", "downloads_path", ")", "==", "[", "]", ":", "archived_downloads_folder", "=", "os", ".", "path", ...	60.636364	23.363636
def set_generator_validation_nb(self, number): """ sets self.nb_val_samples which is used in model.fit if input is a generator :param number: :return: """ self.nb_val_samples = number diff_to_batch = number % self.get_batch_size() if diff_to_batch > 0: ...	[ "def", "set_generator_validation_nb", "(", "self", ",", "number", ")", ":", "self", ".", "nb_val_samples", "=", "number", "diff_to_batch", "=", "number", "%", "self", ".", "get_batch_size", "(", ")", "if", "diff_to_batch", ">", "0", ":", "self", ".", "nb_val...	34.466667	19.4
def fit(self, Xs=None, ys=None, Xt=None, yt=None): """Builds an optimal coupling and estimates the associated mapping from source and target sets of samples (Xs, ys) and (Xt, yt) Parameters ---------- Xs : array-like, shape (n_source_samples, n_features) The training...	[ "def", "fit", "(", "self", ",", "Xs", "=", "None", ",", "ys", "=", "None", ",", "Xt", "=", "None", ",", "yt", "=", "None", ")", ":", "# check the necessary inputs parameters are here", "if", "check_params", "(", "Xs", "=", "Xs", ",", "Xt", "=", "Xt", ...	37.625	20.107143
def make_timestamp(ts: OptTs = None) -> int: """Create zipkin timestamp in microseconds, or convert available one from second. Useful when user supplies ts from time.time() call. """ ts = ts if ts is not None else time.time() return int(ts * 1000 * 1000)	[ "def", "make_timestamp", "(", "ts", ":", "OptTs", "=", "None", ")", "->", "int", ":", "ts", "=", "ts", "if", "ts", "is", "not", "None", "else", "time", ".", "time", "(", ")", "return", "int", "(", "ts", "", "1000", "", "1000", ")" ]	44.833333	7.666667
def unlock_keychain(username): """ If the user is running via SSH, their Keychain must be unlocked first. """ if 'SSH_TTY' not in os.environ: return # Don't unlock if we've already seen this user. if username in _unlocked: return _unlocked.add(username) if sys.platform == 'da...	[ "def", "unlock_keychain", "(", "username", ")", ":", "if", "'SSH_TTY'", "not", "in", "os", ".", "environ", ":", "return", "# Don't unlock if we've already seen this user.", "if", "username", "in", "_unlocked", ":", "return", "_unlocked", ".", "add", "(", "username...	34.266667	26
def _fieldnames_to_colnames(model_cls, fieldnames): """Get the names of columns referenced by the given model fields.""" get_field = model_cls._meta.get_field fields = map(get_field, fieldnames) return {f.column for f in fields}	[ "def", "_fieldnames_to_colnames", "(", "model_cls", ",", "fieldnames", ")", ":", "get_field", "=", "model_cls", ".", "_meta", ".", "get_field", "fields", "=", "map", "(", "get_field", ",", "fieldnames", ")", "return", "{", "f", ".", "column", "for", "f", "...	51.2	4
def hook_get_results(self, changelist): """Triggered by `ChangeList.get_results()`.""" # Poor NestedSet guys they've punished themselves once chosen that approach, # and now we punish them again with all those DB hits. result_list = list(changelist.result_list) # Get children ...	[ "def", "hook_get_results", "(", "self", ",", "changelist", ")", ":", "# Poor NestedSet guys they've punished themselves once chosen that approach,", "# and now we punish them again with all those DB hits.", "result_list", "=", "list", "(", "changelist", ".", "result_list", ")", "...	38.348837	27.372093
def unpack_rgb(data, dtype=None, bitspersample=None, rescale=True): """Return array from byte string containing packed samples. Use to unpack RGB565 or RGB555 to RGB888 format. Parameters ---------- data : byte str The data to be decoded. Samples in each pixel are stored consecutively. ...	[ "def", "unpack_rgb", "(", "data", ",", "dtype", "=", "None", ",", "bitspersample", "=", "None", ",", "rescale", "=", "True", ")", ":", "if", "bitspersample", "is", "None", ":", "bitspersample", "=", "(", "5", ",", "6", ",", "5", ")", "if", "dtype", ...	35.927273	19.090909
def get_account_funds(self, wallet=None, session=None, lightweight=None): """ Get available to bet amount. :param str wallet: Name of the wallet in question :param requests.session session: Requests session object :param bool lightweight: If True will return dict not a resource ...	[ "def", "get_account_funds", "(", "self", ",", "wallet", "=", "None", ",", "session", "=", "None", ",", "lightweight", "=", "None", ")", ":", "params", "=", "clean_locals", "(", "locals", "(", ")", ")", "method", "=", "'%s%s'", "%", "(", "self", ".", ...	44.642857	21.214286
def get_parent_vault_nodes(self): """Gets the parents of this vault. return: (osid.authorization.VaultNodeList) - the parents of this vault compliance: mandatory -- This method must be implemented. """ parent_vault_nodes = [] for node in self._my_map['...	[ "def", "get_parent_vault_nodes", "(", "self", ")", ":", "parent_vault_nodes", "=", "[", "]", "for", "node", "in", "self", ".", "_my_map", "[", "'parentNodes'", "]", ":", "parent_vault_nodes", ".", "append", "(", "VaultNode", "(", "node", ".", "_my_map", ",",...	35.9375	14.375
def _compute_scaled_schoenfeld(self, X, T, E, weights, index=None): r""" Let s_k be the kth schoenfeld residuals. Then E[s_k] = 0. For tests of proportionality, we want to test if \beta_i(t) is \beta_i (constant) or not. Let V_k be the contribution to the information matrix at time t_k....	[ "def", "_compute_scaled_schoenfeld", "(", "self", ",", "X", ",", "T", ",", "E", ",", "weights", ",", "index", "=", "None", ")", ":", "n_deaths", "=", "self", ".", "event_observed", ".", "sum", "(", ")", "scaled_schoenfeld_resids", "=", "n_deaths", "*", "...	38.666667	34.185185
def annotate_image(self, request, retry=None, timeout=None): """Run image detection and annotation for an image. Example: >>> from google.cloud.vision_v1 import ImageAnnotatorClient >>> client = ImageAnnotatorClient() >>> request = { ... 'image': { ...	[ "def", "annotate_image", "(", "self", ",", "request", ",", "retry", "=", "None", ",", "timeout", "=", "None", ")", ":", "# If the image is a file handler, set the content.", "image", "=", "protobuf", ".", "get", "(", "request", ",", "\"image\"", ")", "if", "ha...	44.577778	23.244444
def get_log_events(awsclient, log_group_name, log_stream_name, start_ts=None): """Get log events for the specified log group and stream. this is used in tenkai output instance diagnostics :param log_group_name: log group name :param log_stream_name: log stream name :param start_ts: timestamp :r...	[ "def", "get_log_events", "(", "awsclient", ",", "log_group_name", ",", "log_stream_name", ",", "start_ts", "=", "None", ")", ":", "client_logs", "=", "awsclient", ".", "get_client", "(", "'logs'", ")", "request", "=", "{", "'logGroupName'", ":", "log_group_name"...	31.96	17.08
def choose(self, versions, conflict='silent'): """ Choose the highest version in the range. :param versions: Iterable of available versions. """ assert conflict in ('silent', 'warning', 'error') if not versions: raise VersionRangeMismatch('No versions to choose from') version_map = {} for version in...	[ "def", "choose", "(", "self", ",", "versions", ",", "conflict", "=", "'silent'", ")", ":", "assert", "conflict", "in", "(", "'silent'", ",", "'warning'", ",", "'error'", ")", "if", "not", "versions", ":", "raise", "VersionRangeMismatch", "(", "'No versions t...	36.605263	14.868421
def get_scratch_path(self, local_file): """Construct and return a path in the scratch area from a local file. """ (local_dirname, local_basename) = self.split_local_path(local_file) return self.construct_scratch_path(local_dirname, local_basename)	[ "def", "get_scratch_path", "(", "self", ",", "local_file", ")", ":", "(", "local_dirname", ",", "local_basename", ")", "=", "self", ".", "split_local_path", "(", "local_file", ")", "return", "self", ".", "construct_scratch_path", "(", "local_dirname", ",", "loca...	55	13.8
def skyline_empirical(self, gen=1.0, n_points = 20): ''' returns the skyline, i.e., an estimate of the inverse rate of coalesence. Here, the skyline is estimated from a sliding window average of the observed mergers, i.e., without reference to the coalescence likelihood. paramete...	[ "def", "skyline_empirical", "(", "self", ",", "gen", "=", "1.0", ",", "n_points", "=", "20", ")", ":", "mergers", "=", "self", ".", "tree_events", "[", ":", ",", "1", "]", ">", "0", "merger_tvals", "=", "self", ".", "tree_events", "[", "mergers", ","...	46.029412	25.147059
def get_queryset(self, request): """ Annote the queryset with an 'is_active' property that's true iff that row is the most recently added row for that particular set of KEY_FIELDS values. Filter the queryset to show only is_active rows by default. """ if request.GET.get(S...	[ "def", "get_queryset", "(", "self", ",", "request", ")", ":", "if", "request", ".", "GET", ".", "get", "(", "ShowHistoryFilter", ".", "parameter_name", ")", "==", "'1'", ":", "queryset", "=", "self", ".", "model", ".", "objects", ".", "with_active_flag", ...	44.933333	18.4
def installed(name, enabled=True): ''' Make sure that we have the given bundle ID or path to command installed in the assistive access panel. name The bundle ID or path to command enable Should assistive access be enabled on this application? ''' ret = {'name': name, ...	[ "def", "installed", "(", "name", ",", "enabled", "=", "True", ")", ":", "ret", "=", "{", "'name'", ":", "name", ",", "'result'", ":", "True", ",", "'comment'", ":", "''", ",", "'changes'", ":", "{", "}", "}", "is_installed", "=", "__salt__", "[", "...	27.212121	25.090909
def load_texture(self, file_path, cell_size=(256, 256)): """ Load a spritesheet texture. cell_size is the uniform size of each cell in the spritesheet. """ super(SpriteSheet, self).load_texture(file_path) self.__cell_bounds = cell_size self.__generate_cells()	[ "def", "load_texture", "(", "self", ",", "file_path", ",", "cell_size", "=", "(", "256", ",", "256", ")", ")", ":", "super", "(", "SpriteSheet", ",", "self", ")", ".", "load_texture", "(", "file_path", ")", "self", ".", "__cell_bounds", "=", "cell_size",...	38.5	9.75
def generate_set_partition_strings(n): """Generate the restricted growth strings for all of the partitions of an `n`-member set. Uses Algorithm H from page 416 of volume 4A of Knuth's `The Art of Computer Programming`. Returns the partitions in lexicographical order. Parameters ---------- ...	[ "def", "generate_set_partition_strings", "(", "n", ")", ":", "# Handle edge cases:", "if", "n", "==", "0", ":", "return", "[", "]", "elif", "n", "==", "1", ":", "return", "[", "scipy", ".", "array", "(", "[", "0", "]", ")", "]", "partitions", "=", "[...	32.490566	20.490566
def get_progenies(p1, p2, x_linked=False, tolerance=0): """ Returns possible progenies in a trio. """ _p1 = expand_alleles(p1, tolerance=tolerance) _p2 = expand_alleles(p2, tolerance=tolerance) possible_progenies = set(tuple(sorted(x)) for x in product(_p1, _p2)) if x_linked: # Add all hemi...	[ "def", "get_progenies", "(", "p1", ",", "p2", ",", "x_linked", "=", "False", ",", "tolerance", "=", "0", ")", ":", "_p1", "=", "expand_alleles", "(", "p1", ",", "tolerance", "=", "tolerance", ")", "_p2", "=", "expand_alleles", "(", "p2", ",", "toleranc...	42.1	11.1
def _calc_bkg_bkgrms(self): """ Calculate the background and background RMS estimate in each of the meshes. Both meshes are computed at the same time here method because the filtering of both depends on the background mesh. The ``background_mesh`` and ``background_rms_m...	[ "def", "_calc_bkg_bkgrms", "(", "self", ")", ":", "if", "self", ".", "sigma_clip", "is", "not", "None", ":", "data_sigclip", "=", "self", ".", "sigma_clip", "(", "self", ".", "_mesh_data", ",", "axis", "=", "1", ")", "else", ":", "data_sigclip", "=", "...	40.185185	22.740741
def keysym_to_keycodes(self, keysym): """Look up all the keycodes that is bound to keysym. A list of tuples (keycode, index) is returned, sorted primarily on the lowest index and secondarily on the lowest keycode.""" try: # Copy the map list, reversing the arguments ...	[ "def", "keysym_to_keycodes", "(", "self", ",", "keysym", ")", ":", "try", ":", "# Copy the map list, reversing the arguments", "return", "map", "(", "lambda", "x", ":", "(", "x", "[", "1", "]", ",", "x", "[", "0", "]", ")", ",", "self", ".", "_keymap_sym...	47	15.888889
def v1_subfolder_list(request, response, kvlclient, fid): '''Retrieves a list of subfolders in a folder for the current user. The route for this endpoint is: ``GET /dossier/v1/folder/<fid>/subfolder``. (Temporarily, the "current user" can be set via the ``annotator_id`` query parameter.) The ...	[ "def", "v1_subfolder_list", "(", "request", ",", "response", ",", "kvlclient", ",", "fid", ")", ":", "fid", "=", "urllib", ".", "unquote", "(", "fid", ")", "try", ":", "return", "sorted", "(", "imap", "(", "attrgetter", "(", "'name'", ")", ",", "ifilte...	34.684211	21.736842
def words(fpth): """ ww = words(os.path.join(app_root, 'ig/helper.py')) for k, v in (ww.most_common(3)): print(k, v) :param fpth: :type fpth: :return: :rtype: """ from collections import Counter words__ = Counter() with open(fpth) as fp: for line in fp: ...	[ "def", "words", "(", "fpth", ")", ":", "from", "collections", "import", "Counter", "words__", "=", "Counter", "(", ")", "with", "open", "(", "fpth", ")", "as", "fp", ":", "for", "line", "in", "fp", ":", "words__", ".", "update", "(", "line", ".", "...	21.705882	17.352941
def create_meta_data(cls, options, args, parser): """ Override in subclass if required. """ meta_data = [] meta_data.append(('spiff_version', cls.get_version())) if options.target_engine: meta_data.append(('target_engine', options.target_engine)) if op...	[ "def", "create_meta_data", "(", "cls", ",", "options", ",", "args", ",", "parser", ")", ":", "meta_data", "=", "[", "]", "meta_data", ".", "append", "(", "(", "'spiff_version'", ",", "cls", ".", "get_version", "(", ")", ")", ")", "if", "options", ".", ...	38.166667	12.833333
async def select(**data): """ RPC method for selecting data from the database :return selected data """ try: select_data = clickhouse_queries.select_from_table(table=data['table'], query=data['query'], fields=data['fields']) return str(select_data) except ServerException as e: ...	[ "async", "def", "select", "(", "", "", "data", ")", ":", "try", ":", "select_data", "=", "clickhouse_queries", ".", "select_from_table", "(", "table", "=", "data", "[", "'table'", "]", ",", "query", "=", "data", "[", "'query'", "]", ",", "fields", "=...	29.470588	19
def flush_devices(self): """ overwrite the complete memory with zeros """ self.rom.program([0 for i in range(self.rom.size)]) self.flash.program([0 for i in range(self.flash.size)]) for i in range(self.ram.size): self.ram.write(i, 0)	[ "def", "flush_devices", "(", "self", ")", ":", "self", ".", "rom", ".", "program", "(", "[", "0", "for", "i", "in", "range", "(", "self", ".", "rom", ".", "size", ")", "]", ")", "self", ".", "flash", ".", "program", "(", "[", "0", "for", "i", ...	30.375	9.375
def _edits1(word: str) -> Set[str]: """ Return a set of words with edit distance of 1 from the input word """ splits = [(word[:i], word[i:]) for i in range(len(word) + 1)] deletes = [L + R[1:] for L, R in splits if R] transposes = [L + R[1] + R[0] + R[2:] for L, R in splits if len(R) > 1] re...	[ "def", "_edits1", "(", "word", ":", "str", ")", "->", "Set", "[", "str", "]", ":", "splits", "=", "[", "(", "word", "[", ":", "i", "]", ",", "word", "[", "i", ":", "]", ")", "for", "i", "in", "range", "(", "len", "(", "word", ")", "+", "1...	46	20.181818
def transition_matrix_non_reversible(C): """implementation of transition_matrix""" if not scipy.sparse.issparse(C): C = scipy.sparse.csr_matrix(C) rowsum = C.tocsr().sum(axis=1) # catch div by zero if np.min(rowsum) == 0.0: raise ValueError("matrix C contains rows with sum zero.") ...	[ "def", "transition_matrix_non_reversible", "(", "C", ")", ":", "if", "not", "scipy", ".", "sparse", ".", "issparse", "(", "C", ")", ":", "C", "=", "scipy", ".", "sparse", ".", "csr_matrix", "(", "C", ")", "rowsum", "=", "C", ".", "tocsr", "(", ")", ...	37.545455	8.181818
def smooth_rectangle(x, y, rec_w, rec_h, gaussian_width_x, gaussian_width_y): """ Rectangle with a solid central region, then Gaussian fall-off at the edges. """ gaussian_x_coord = abs(x)-rec_w/2.0 gaussian_y_coord = abs(y)-rec_h/2.0 box_x=np.less(gaussian_x_coord,0.0) box_y=np.less(gaussi...	[ "def", "smooth_rectangle", "(", "x", ",", "y", ",", "rec_w", ",", "rec_h", ",", "gaussian_width_x", ",", "gaussian_width_y", ")", ":", "gaussian_x_coord", "=", "abs", "(", "x", ")", "-", "rec_w", "/", "2.0", "gaussian_y_coord", "=", "abs", "(", "y", ")",...	38.95	19.65
def write(self, fb): """Write a single function benchmark. Args: fb (FunctionBenchmark): FunctionBenchmark class instance. Before passing to this, you should call ``fb.benchmark()``. """ print('[{}.{}]'.format(fb.module, fb.func.__name__), file=self.file) ...	[ "def", "write", "(", "self", ",", "fb", ")", ":", "print", "(", "'[{}.{}]'", ".", "format", "(", "fb", ".", "module", ",", "fb", ".", "func", ".", "__name__", ")", ",", "file", "=", "self", ".", "file", ")", "print", "(", "'class = {}'", ".", "fo...	47.571429	21.095238
def _assemble_agent_str(agent): """Assemble an Agent object to text.""" agent_str = agent.name # Only do the more detailed assembly for molecular agents if not isinstance(agent, ist.Agent): return agent_str # Handle mutation conditions if agent.mutations: is_generic = False ...	[ "def", "_assemble_agent_str", "(", "agent", ")", ":", "agent_str", "=", "agent", ".", "name", "# Only do the more detailed assembly for molecular agents", "if", "not", "isinstance", "(", "agent", ",", "ist", ".", "Agent", ")", ":", "return", "agent_str", "# Handle m...	38.010309	16.742268
def check_mods_docs_readme(): """ Check that all modules are listed in the YAML index at the top of docs/README.md """ docs_mods = [] readme_fn = os.path.join( os.path.dirname(config.MULTIQC_DIR), 'docs', 'README.md') if not os.path.isfile(readme_fn): if os.environ.get('TRAVIS_BUILD_DIR') ...	[ "def", "check_mods_docs_readme", "(", ")", ":", "docs_mods", "=", "[", "]", "readme_fn", "=", "os", ".", "path", ".", "join", "(", "os", ".", "path", ".", "dirname", "(", "config", ".", "MULTIQC_DIR", ")", ",", "'docs'", ",", "'README.md'", ")", "if", ...	44.058824	22.911765
def closest_common_ancestor(self, other): """ Find the common ancestor between this history node and 'other'. :param other: the PathHistory to find a common ancestor with. :return: the common ancestor SimStateHistory, or None if there isn't one """ our_history_...	[ "def", "closest_common_ancestor", "(", "self", ",", "other", ")", ":", "our_history_iter", "=", "reversed", "(", "HistoryIter", "(", "self", ")", ")", "their_history_iter", "=", "reversed", "(", "HistoryIter", "(", "other", ")", ")", "sofar", "=", "set", "("...	34.131579	15.973684
async def get_devices(self) -> List[Device]: """Get information about the users avaliable devices. Returns ------- devices : List[Device] The devices the user has available. """ data = await self.http.available_devices() return [Device(item) for item ...	[ "async", "def", "get_devices", "(", "self", ")", "->", "List", "[", "Device", "]", ":", "data", "=", "await", "self", ".", "http", ".", "available_devices", "(", ")", "return", "[", "Device", "(", "item", ")", "for", "item", "in", "data", "[", "'devi...	33	13.8
def ch_stop_time(self, channels: List[Channel]) -> int: """Return maximum time of timeslots over all channels. Args: channels: Channels over which to obtain stop time. """ intervals = list(itertools.chain(*(self._table[chan] for chan in channels ...	[ "def", "ch_stop_time", "(", "self", ",", "", "channels", ":", "List", "[", "Channel", "]", ")", "->", "int", ":", "intervals", "=", "list", "(", "itertools", ".", "chain", "(", "", "(", "self", ".", "_table", "[", "chan", "]", "for", "chan", "in"...	41.363636	22
def get_variants(self, arch=None, types=None, recursive=False): """ Return all variants of given arch and types. Supported variant types: self - include the top-level ("self") variant as well addon variant optional """ types = ...	[ "def", "get_variants", "(", "self", ",", "arch", "=", "None", ",", "types", "=", "None", ",", "recursive", "=", "False", ")", ":", "types", "=", "types", "or", "[", "]", "result", "=", "[", "]", "if", "\"self\"", "in", "types", ":", "result", ".", ...	31.259259	20.074074
def simulate(self, timepoints): """ Simulate initialised solver for the specified timepoints :param timepoints: timepoints that will be returned from simulation :return: a list of trajectories for each of the equations in the problem. """ solver = self._solver la...	[ "def", "simulate", "(", "self", ",", "timepoints", ")", ":", "solver", "=", "self", ".", "_solver", "last_timepoint", "=", "timepoints", "[", "-", "1", "]", "try", ":", "simulated_timepoints", ",", "simulated_values", "=", "solver", ".", "simulate", "(", "...	42.703704	27.740741
def table_mask(self): """ndarray, True where table margin <= min_base_size, same shape as slice.""" margin = compress_pruned( self._slice.margin( axis=None, weighted=False, include_transforms_for_dims=self._hs_dims, prune=self._...	[ "def", "table_mask", "(", "self", ")", ":", "margin", "=", "compress_pruned", "(", "self", ".", "_slice", ".", "margin", "(", "axis", "=", "None", ",", "weighted", "=", "False", ",", "include_transforms_for_dims", "=", "self", ".", "_hs_dims", ",", "prune"...	36	20.35
def deep_merge(*args): """ >>> dbt.utils.deep_merge({'a': 1, 'b': 2, 'c': 3}, {'a': 2}, {'a': 3, 'b': 1}) # noqa {'a': 3, 'b': 1, 'c': 3} """ if len(args) == 0: return None if len(args) == 1: return copy.deepcopy(args[0]) lst = list(args) last = copy.deepcopy(lst.pop(l...	[ "def", "deep_merge", "(", "*", "args", ")", ":", "if", "len", "(", "args", ")", "==", "0", ":", "return", "None", "if", "len", "(", "args", ")", "==", "1", ":", "return", "copy", ".", "deepcopy", "(", "args", "[", "0", "]", ")", "lst", "=", "...	24.466667	19.533333
def _render_attributes(self, resource): """Render the resources's attributes.""" attributes = {} attrs_to_ignore = set() for key, relationship in resource.__mapper__.relationships.items(): attrs_to_ignore.update(set( [column.name for column in relationship.lo...	[ "def", "_render_attributes", "(", "self", ",", "resource", ")", ":", "attributes", "=", "{", "}", "attrs_to_ignore", "=", "set", "(", ")", "for", "key", ",", "relationship", "in", "resource", ".", "__mapper__", ".", "relationships", ".", "items", "(", ")",...	37.15625	18.65625
def _map_sextuple_to_phenotype( self, superterm1_id, subterm1_id, quality_id, superterm2_id, subterm2_id, modifier): """ This will take the 6-part EQ-style annotation used by ZFIN and return the ZP id. Currently relies on an external mapping file, but the ...	[ "def", "_map_sextuple_to_phenotype", "(", "self", ",", "superterm1_id", ",", "subterm1_id", ",", "quality_id", ",", "superterm2_id", ",", "subterm2_id", ",", "modifier", ")", ":", "zp_id", "=", "None", "# zfin uses free-text modifiers,", "# but we need to convert them to ...	33.727273	17.181818
def update_project(self, resource_name, resource): """ Updates an entity in the data model using the given resource. Args: resource_name (string): Current name of the resource (in case the resource is getting its name changed). resource (intern.resource.b...	[ "def", "update_project", "(", "self", ",", "resource_name", ",", "resource", ")", ":", "self", ".", "project_service", ".", "set_auth", "(", "self", ".", "_token_project", ")", "return", "self", ".", "project_service", ".", "update", "(", "resource_name", ",",...	36.947368	22

def make_body(self, resp, params, meta, content): """Construct response body in ``resp`` object using JSON serialization. Args: resp (falcon.Response): response object where to include serialized body params (dict): dictionary of parsed parameters met...

[ "def", "make_body", "(", "self", ",", "resp", ",", "params", ",", "meta", ",", "content", ")", ":", "response", "=", "{", "'meta'", ":", "meta", ",", "'content'", ":", "content", "}", "resp", ".", "content_type", "=", "'application/json'", "resp", ".", ...

34.44

21.56

def validate(document, spec): """Validate that a document meets a specification. Returns True if validation was successful, but otherwise raises a ValueError.""" if not spec: return True missing = [] for key, field in spec.iteritems(): if field.required and key not in document: ...

[ "def", "validate", "(", "document", ",", "spec", ")", ":", "if", "not", "spec", ":", "return", "True", "missing", "=", "[", "]", "for", "key", ",", "field", "in", "spec", ".", "iteritems", "(", ")", ":", "if", "field", ".", "required", "and", "key"...

38.208333

17.5

def _create_api_uri(self, *parts): """Creates fully qualified endpoint URIs. :param parts: the string parts that form the request URI """ return urljoin(self.API_URI, '/'.join(map(quote, parts)))

[ "def", "_create_api_uri", "(", "self", ",", "*", "parts", ")", ":", "return", "urljoin", "(", "self", ".", "API_URI", ",", "'/'", ".", "join", "(", "map", "(", "quote", ",", "parts", ")", ")", ")" ]

29.571429

18.142857

def _add_model(self, model_list_or_dict, core_element, model_class, model_key=None, load_meta_data=True): """Adds one model for a given core element. The method will add a model for a given core object and checks if there is a corresponding model object in the future expected model list. The me...

[ "def", "_add_model", "(", "self", ",", "model_list_or_dict", ",", "core_element", ",", "model_class", ",", "model_key", "=", "None", ",", "load_meta_data", "=", "True", ")", ":", "found_model", "=", "self", ".", "_get_future_expected_model", "(", "core_element", ...

53.310345

36.62069

def iterate(self, max_iter=150, n_rewightings=1): r"""Iterate This method calls update until either convergence criteria is met or the maximum number of iterations is reached Parameters ---------- max_iter : int, optional Maximum number of iterations (defaul...

[ "def", "iterate", "(", "self", ",", "max_iter", "=", "150", ",", "n_rewightings", "=", "1", ")", ":", "self", ".", "_run_alg", "(", "max_iter", ")", "if", "not", "isinstance", "(", "self", ".", "_reweight", ",", "type", "(", "None", ")", ")", ":", ...

30.888889

17.481481

def _formatFilterQuery(self, request=None, featureSets=[]): """ Generate a formatted sparql query with appropriate filters """ query = self._baseQuery() filters = [] if issubclass(request.__class__, protocol.SearchGenotypePhenotypeRequest): ...

[ "def", "_formatFilterQuery", "(", "self", ",", "request", "=", "None", ",", "featureSets", "=", "[", "]", ")", ":", "query", "=", "self", ".", "_baseQuery", "(", ")", "filters", "=", "[", "]", "if", "issubclass", "(", "request", ".", "__class__", ",", ...

37.6

18

def get_plain_text(self): """Returns a list""" _msg = self.message if self.message is not None else [""] msg = _msg if isinstance(_msg, list) else [_msg] line = "" if not self.line else ", line {}".format(self.line) ret = ["{} found in file '{}'{}::".format(self.type.capital...

[ "def", "get_plain_text", "(", "self", ")", ":", "_msg", "=", "self", ".", "message", "if", "self", ".", "message", "is", "not", "None", "else", "[", "\"\"", "]", "msg", "=", "_msg", "if", "isinstance", "(", "_msg", ",", "list", ")", "else", "[", "_...

45.2

19.7

def tile_to_path(self, tile): '''return full path to a tile''' return os.path.join(self.cache_path, self.service, tile.path())

[ "def", "tile_to_path", "(", "self", ",", "tile", ")", ":", "return", "os", ".", "path", ".", "join", "(", "self", ".", "cache_path", ",", "self", ".", "service", ",", "tile", ".", "path", "(", ")", ")" ]

42.666667

14

def adjust_for_triggers(self): """Remove trigger-related plugins when needed If there are no triggers defined, it's assumed the feature is disabled and all trigger-related plugins are removed. If there are triggers defined, and this is a custom base image, some trigger-...

[ "def", "adjust_for_triggers", "(", "self", ")", ":", "triggers", "=", "self", ".", "template", "[", "'spec'", "]", ".", "get", "(", "'triggers'", ",", "[", "]", ")", "remove_plugins", "=", "[", "(", "\"prebuild_plugins\"", ",", "\"check_and_set_rebuild\"", "...

38.368421

20.473684

def query_metric_stats(self, metric_type, metric_id=None, start=None, end=None, bucketDuration=None, **query_options): """ Query for metric aggregates from the server. This is called buckets in the Hawkular-Metrics documentation. :param metric_type: MetricType to be matched (required) :...

[ "def", "query_metric_stats", "(", "self", ",", "metric_type", ",", "metric_id", "=", "None", ",", "start", "=", "None", ",", "end", "=", "None", ",", "bucketDuration", "=", "None", ",", "*", "*", "query_options", ")", ":", "if", "start", "is", "not", "...

48.324324

28

def _parse_metafiles(self, metafile_input): """ Parses class input and verifies metadata file names. :param metafile_input: class input parameter `metafiles` :type metafile_input: str or list(str) or None :return: verified list of metadata files :rtype: list(str) ...

[ "def", "_parse_metafiles", "(", "self", ",", "metafile_input", ")", ":", "all_metafiles", "=", "AwsConstants", ".", "S2_L1C_METAFILES", "if", "self", ".", "data_source", "is", "DataSource", ".", "SENTINEL2_L1C", "else", "AwsConstants", ".", "S2_L2A_METAFILES", "if",...

48.62069

21.862069

def get_directory(request): """Get API directory as a nested list of lists.""" def get_url(url): return reverse(url, request=request) if url else url def is_active_url(path, url): return path.startswith(url) if url and path else False path = request.path directory_list = [] d...

[ "def", "get_directory", "(", "request", ")", ":", "def", "get_url", "(", "url", ")", ":", "return", "reverse", "(", "url", ",", "request", "=", "request", ")", "if", "url", "else", "url", "def", "is_active_url", "(", "path", ",", "url", ")", ":", "re...

29.146341

18.170732

def div_safe( numerator, denominator ): """ Ufunc-extension that returns 0 instead of nan when dividing numpy arrays Parameters ---------- numerator: array-like denominator: scalar or array-like that can be validly divided by the numerator returns a numpy array example: div_safe( [-1...

[ "def", "div_safe", "(", "numerator", ",", "denominator", ")", ":", "#First handle scalars", "if", "np", ".", "isscalar", "(", "numerator", ")", ":", "raise", "ValueError", "(", "\"div_safe should only be used with an array-like numerator\"", ")", "#Then numpy arrays", "...

29.153846

23.615385

def get_commits(repo_dir, old_commit, new_commit, hide_merges=True): """Find all commits between two commit SHAs.""" repo = Repo(repo_dir) commits = repo.iter_commits(rev="{0}..{1}".format(old_commit, new_commit)) if hide_merges: return [x for x in commits if not x.summary.startswith("Merge ")] ...

[ "def", "get_commits", "(", "repo_dir", ",", "old_commit", ",", "new_commit", ",", "hide_merges", "=", "True", ")", ":", "repo", "=", "Repo", "(", "repo_dir", ")", "commits", "=", "repo", ".", "iter_commits", "(", "rev", "=", "\"{0}..{1}\"", ".", "format", ...

43.875

22.25

def parse_reaction(reaction_def, default_compartment, context=None): """Parse a structured reaction definition as obtained from a YAML file Returns a ReactionEntry. """ reaction_id = reaction_def.get('id') _check_id(reaction_id, 'Reaction') reaction_props = dict(reaction_def) # Parse rea...

[ "def", "parse_reaction", "(", "reaction_def", ",", "default_compartment", ",", "context", "=", "None", ")", ":", "reaction_id", "=", "reaction_def", ".", "get", "(", "'id'", ")", "_check_id", "(", "reaction_id", ",", "'Reaction'", ")", "reaction_props", "=", "...

31.222222

16.944444

def listen_for_dweets_from(thing_name, timeout=900, key=None, session=None): """Create a real-time subscription to dweets """ url = BASE_URL + '/listen/for/dweets/from/{0}'.format(thing_name) session = session or requests.Session() if key is not None: params = {'key': key} else: ...

[ "def", "listen_for_dweets_from", "(", "thing_name", ",", "timeout", "=", "900", ",", "key", "=", "None", ",", "session", "=", "None", ")", ":", "url", "=", "BASE_URL", "+", "'/listen/for/dweets/from/{0}'", ".", "format", "(", "thing_name", ")", "session", "=...

39.619048

21.190476

def draw_beam(ax, p1, p2, width=0, beta1=None, beta2=None, format=None, **kwds): r"""Draw a laser beam.""" if format is None: format = 'k-' if width == 0: x0 = [p1[0], p2[0]] y0 = [p1[1], p2[1]] ax.plot(x0, y0, format, **kwds) else: a = width/2 ...

[ "def", "draw_beam", "(", "ax", ",", "p1", ",", "p2", ",", "width", "=", "0", ",", "beta1", "=", "None", ",", "beta2", "=", "None", ",", "format", "=", "None", ",", "*", "*", "kwds", ")", ":", "if", "format", "is", "None", ":", "format", "=", ...

127.733333

118.333333

def QA_fetch_get_sz_margin(date): """return shenzhen margin data Arguments: date {str YYYY-MM-DD} -- date format Returns: pandas.DataFrame -- res for margin data """ if date in trade_date_sse: return pd.read_excel(_sz_url.format(date)).assign(date=date).assign(sse='sz')

[ "def", "QA_fetch_get_sz_margin", "(", "date", ")", ":", "if", "date", "in", "trade_date_sse", ":", "return", "pd", ".", "read_excel", "(", "_sz_url", ".", "format", "(", "date", ")", ")", ".", "assign", "(", "date", "=", "date", ")", ".", "assign", "("...

25.5

20.583333

def run_forever(self) -> None: '''Execute the tasky/asyncio event loop until terminated.''' Log.debug('running event loop until terminated') asyncio.ensure_future(self.init()) self.loop.run_forever() self.loop.close()

[ "def", "run_forever", "(", "self", ")", "->", "None", ":", "Log", ".", "debug", "(", "'running event loop until terminated'", ")", "asyncio", ".", "ensure_future", "(", "self", ".", "init", "(", ")", ")", "self", ".", "loop", ".", "run_forever", "(", ")", ...

36

17.142857

async def get_bearer_info(self): """Get the application bearer token from client_id and client_secret.""" if self.client_id is None: raise SpotifyException(_GET_BEARER_ERR % 'client_id') elif self.client_secret is None: raise SpotifyException(_GET_BEARER_ERR % 'client_se...

[ "async", "def", "get_bearer_info", "(", "self", ")", ":", "if", "self", ".", "client_id", "is", "None", ":", "raise", "SpotifyException", "(", "_GET_BEARER_ERR", "%", "'client_id'", ")", "elif", "self", ".", "client_secret", "is", "None", ":", "raise", "Spot...

40.722222

23.722222

def unique(self, *args): """ Returns all unique values as a DataFrame. This is executing: SELECT DISTINCT <name_of_the_column_1> , <name_of_the_column_2> , <name_of_the_column_3> ... F...

[ "def", "unique", "(", "self", ",", "*", "args", ")", ":", "q", "=", "self", ".", "_query_templates", "[", "'table'", "]", "[", "'unique'", "]", ".", "format", "(", "columns", "=", "self", ".", "_format_columns", "(", "args", ")", ",", "schema", "=", ...

25.259259

20.296296

def token(self, id, **kwargs): """ Retrieve a service request ID from a token. >>> Three('api.city.gov').token('12345') {'service_request_id': {'for': {'token': '12345'}}} """ data = self.get('tokens', id, **kwargs) return data

[ "def", "token", "(", "self", ",", "id", ",", "*", "*", "kwargs", ")", ":", "data", "=", "self", ".", "get", "(", "'tokens'", ",", "id", ",", "*", "*", "kwargs", ")", "return", "data" ]

30.666667

12.888889

def dict_from_hdf5(dict_like, h5group): """ Load a dictionnary-like object from a h5 file group """ # Read attributes for name, value in h5group.attrs.items(): dict_like[name] = value

[ "def", "dict_from_hdf5", "(", "dict_like", ",", "h5group", ")", ":", "# Read attributes", "for", "name", ",", "value", "in", "h5group", ".", "attrs", ".", "items", "(", ")", ":", "dict_like", "[", "name", "]", "=", "value" ]

29.285714

7

def remove_binding(site, hostheader='', ipaddress='*', port=80): ''' Remove an IIS binding. Args: site (str): The IIS site name. hostheader (str): The host header of the binding. ipaddress (str): The IP address of the binding. port (int): The TCP port of the binding. Re...

[ "def", "remove_binding", "(", "site", ",", "hostheader", "=", "''", ",", "ipaddress", "=", "'*'", ",", "port", "=", "80", ")", ":", "name", "=", "_get_binding_info", "(", "hostheader", ",", "ipaddress", ",", "port", ")", "current_bindings", "=", "list_bind...

30.209302

21.744186

def getVariantAnnotationSets(self, datasetId): """ Returns the list of ReferenceSets for this server. """ # TODO this should be displayed per-variant set, not per dataset. variantAnnotationSets = [] dataset = app.backend.getDataRepository().getDataset(datasetId) f...

[ "def", "getVariantAnnotationSets", "(", "self", ",", "datasetId", ")", ":", "# TODO this should be displayed per-variant set, not per dataset.", "variantAnnotationSets", "=", "[", "]", "dataset", "=", "app", ".", "backend", ".", "getDataRepository", "(", ")", ".", "getD...

44.181818

11.272727

def all_project_administrators(self): """ Get the list of project administrators :return: """ for project in self.project_list(): log.info('Processing project: {0} - {1}'.format(project.get('key'), project.get('name'))) yield { 'project_key...

[ "def", "all_project_administrators", "(", "self", ")", ":", "for", "project", "in", "self", ".", "project_list", "(", ")", ":", "log", ".", "info", "(", "'Processing project: {0} - {1}'", ".", "format", "(", "project", ".", "get", "(", "'key'", ")", ",", "...

50.166667

23

def feed_interval_get(feed_id, parameters): 'Get adaptive interval between checks for a feed.' val = cache.get(getkey( T_INTERVAL, key=feed_interval_key(feed_id, parameters) )) return val if isinstance(val, tuple) else (val, None)

[ "def", "feed_interval_get", "(", "feed_id", ",", "parameters", ")", ":", "val", "=", "cache", ".", "get", "(", "getkey", "(", "T_INTERVAL", ",", "key", "=", "feed_interval_key", "(", "feed_id", ",", "parameters", ")", ")", ")", "return", "val", "if", "is...

46.2

7.8

def get_comments_of_credit_note_per_page(self, credit_note_id, per_page=1000, page=1): """ Get comments of credit note per page :param credit_note_id: the credit note id :param per_page: How many objects per page. Default: 1000 :param page: Which page. Default: 1 :return...

[ "def", "get_comments_of_credit_note_per_page", "(", "self", ",", "credit_note_id", ",", "per_page", "=", "1000", ",", "page", "=", "1", ")", ":", "return", "self", ".", "_get_resource_per_page", "(", "resource", "=", "CREDIT_NOTE_COMMENTS", ",", "per_page", "=", ...

35.333333

14.933333

def _x2c(self, x): """ Convert windowdow coordinates to cheb coordinates [-1,1] """ return ((2 * x - self.window[1] - self.window[0]) / (self.window[1] - self.window[0]))

[ "def", "_x2c", "(", "self", ",", "x", ")", ":", "return", "(", "(", "2", "*", "x", "-", "self", ".", "window", "[", "1", "]", "-", "self", ".", "window", "[", "0", "]", ")", "/", "(", "self", ".", "window", "[", "1", "]", "-", "self", "."...

49.75

12.75

def defect_concentration(self, chemical_potentials, temperature=300, fermi_level=0.0): """ Get the defect concentration for a temperature and Fermi level. Args: temperature: the temperature in K fermi_level: the fermi level in eV (with resp...

[ "def", "defect_concentration", "(", "self", ",", "chemical_potentials", ",", "temperature", "=", "300", ",", "fermi_level", "=", "0.0", ")", ":", "n", "=", "self", ".", "multiplicity", "*", "1e24", "/", "self", ".", "defect", ".", "bulk_structure", ".", "v...

39.6875

21.8125

def get_new_header(configuration, pofile): """ Insert info about edX into the po file headers """ team = pofile.metadata.get('Language-Team', None) if not team: return TRANSIFEX_HEADER.format(configuration.TRANSIFEX_URL) return TRANSIFEX_HEADER.format(team)

[ "def", "get_new_header", "(", "configuration", ",", "pofile", ")", ":", "team", "=", "pofile", ".", "metadata", ".", "get", "(", "'Language-Team'", ",", "None", ")", "if", "not", "team", ":", "return", "TRANSIFEX_HEADER", ".", "format", "(", "configuration",...

35.25

9.5

def fetch(self, plan_id, data={}, **kwargs): """" Fetch Plan for given Id Args: plan_id : Id for which Plan object has to be retrieved Returns: Plan dict for given subscription Id """ return super(Plan, self).fetch(plan_id, data, **kwargs)

[ "def", "fetch", "(", "self", ",", "plan_id", ",", "data", "=", "{", "}", ",", "*", "*", "kwargs", ")", ":", "return", "super", "(", "Plan", ",", "self", ")", ".", "fetch", "(", "plan_id", ",", "data", ",", "*", "*", "kwargs", ")" ]

27.545455

18.181818

def topoSort(roots, getParents): """Return a topological sorting of nodes in a graph. roots - list of root nodes to search from getParents - function which returns the parents of a given node """ results = [] visited = set() # Use iterative version to avoid stack limits for large datasets...

[ "def", "topoSort", "(", "roots", ",", "getParents", ")", ":", "results", "=", "[", "]", "visited", "=", "set", "(", ")", "# Use iterative version to avoid stack limits for large datasets", "stack", "=", "[", "(", "node", ",", "0", ")", "for", "node", "in", "...

31.16

16

def reject(self): """Handle ESC key""" if self.controller.is_running: self.info(self.tr("Stopping..")) self.controller.is_running = False

[ "def", "reject", "(", "self", ")", ":", "if", "self", ".", "controller", ".", "is_running", ":", "self", ".", "info", "(", "self", ".", "tr", "(", "\"Stopping..\"", ")", ")", "self", ".", "controller", ".", "is_running", "=", "False" ]

28.833333

12.5

def get_window(self, window, bands=None, xsize=None, ysize=None, resampling=Resampling.cubic, masked=None, affine=None ): """Get window from raster. :param window: requested window :param bands: list of indices of requested bads, default ...

[ "def", "get_window", "(", "self", ",", "window", ",", "bands", "=", "None", ",", "xsize", "=", "None", ",", "ysize", "=", "None", ",", "resampling", "=", "Resampling", ".", "cubic", ",", "masked", "=", "None", ",", "affine", "=", "None", ")", ":", ...

49.275

26.35

def trigger(self, attr, old, new, hint=None, setter=None): ''' Trigger callbacks for ``attr`` on this object. Args: attr (str) : old (object) : new (object) : Returns: None ''' def invoke(): callbacks = self._callback...

[ "def", "trigger", "(", "self", ",", "attr", ",", "old", ",", "new", ",", "hint", "=", "None", ",", "setter", "=", "None", ")", ":", "def", "invoke", "(", ")", ":", "callbacks", "=", "self", ".", "_callbacks", ".", "get", "(", "attr", ")", "if", ...

29.333333

22.571429

def as_page(self): """ Wrap this Tag as a self-contained webpage. Create a page with the following structure: .. code-block:: html <!DOCTYPE html> <html> <head> <meta http-equiv="Content-type" content="text/htm...

[ "def", "as_page", "(", "self", ")", ":", "H", "=", "HTML", "(", ")", "utf8", "=", "H", ".", "meta", "(", "{", "'http-equiv'", ":", "'Content-type'", "}", ",", "content", "=", "\"text/html\"", ",", "charset", "=", "\"UTF-8\"", ")", "return", "H", ".",...

29.740741

14.555556

def extend(self, values): """Extend the array, appending the given values.""" self.database.run_script( 'array_extend', keys=[self.key], args=values)

[ "def", "extend", "(", "self", ",", "values", ")", ":", "self", ".", "database", ".", "run_script", "(", "'array_extend'", ",", "keys", "=", "[", "self", ".", "key", "]", ",", "args", "=", "values", ")" ]

32.666667

10.5

def _parse_qualimap_globals(table): """Retrieve metrics of interest from globals table. """ out = {} want = {"Mapped reads": _parse_num_pct, "Duplication rate": lambda k, v: {k: v}} for row in table.find_all("tr"): col, val = [x.text for x in row.find_all("td")] if col in...

[ "def", "_parse_qualimap_globals", "(", "table", ")", ":", "out", "=", "{", "}", "want", "=", "{", "\"Mapped reads\"", ":", "_parse_num_pct", ",", "\"Duplication rate\"", ":", "lambda", "k", ",", "v", ":", "{", "k", ":", "v", "}", "}", "for", "row", "in...

34.090909

10.272727

def load_raw_arrays(self, columns, start_date, end_date, assets): """ Parameters ---------- fields : list of str 'open', 'high', 'low', 'close', or 'volume' start_dt: Timestamp Beginning of the window range. end_dt: Timestamp End of the wi...

[ "def", "load_raw_arrays", "(", "self", ",", "columns", ",", "start_date", ",", "end_date", ",", "assets", ")", ":", "rolls_by_asset", "=", "{", "}", "tc", "=", "self", ".", "trading_calendar", "start_session", "=", "tc", ".", "minute_to_session_label", "(", ...

36.835443

16.278481

def tange_pth(v, temp, v0, gamma0, a, b, theta0, n, z, t_ref=300., three_r=3. * constants.R): """ calculate thermal pressure for the Tange equation :param v: unit-cell volume in A^3 :param temp: temperature in K :param v0: unit-cell volume in A^3 at 1 bar :param gamma0: Gruneisen ...

[ "def", "tange_pth", "(", "v", ",", "temp", ",", "v0", ",", "gamma0", ",", "a", ",", "b", ",", "theta0", ",", "n", ",", "z", ",", "t_ref", "=", "300.", ",", "three_r", "=", "3.", "*", "constants", ".", "R", ")", ":", "v_mol", "=", "vol_uc2mol", ...

34.818182

11.787879

def eps_from_series(self): """ Workhorse function that handles grabbing series data from csvs and requesting episodal information from RSS feeds """ csvs = [] for _, _, filenames in os.walk('./{}'.format(self.directory)): csvs.extend(filenames) series_set = set() for c in csvs: ...

[ "def", "eps_from_series", "(", "self", ")", ":", "csvs", "=", "[", "]", "for", "_", ",", "_", ",", "filenames", "in", "os", ".", "walk", "(", "'./{}'", ".", "format", "(", "self", ".", "directory", ")", ")", ":", "csvs", ".", "extend", "(", "file...

27.222222

18.037037

def setShowTerritory(self, state): """ Sets the display mode for this widget to the inputed mode. :param state | <bool> """ if state == self._showTerritory: return self._showTerritory = state self.setDirty()

[ "def", "setShowTerritory", "(", "self", ",", "state", ")", ":", "if", "state", "==", "self", ".", "_showTerritory", ":", "return", "self", ".", "_showTerritory", "=", "state", "self", ".", "setDirty", "(", ")" ]

27.090909

12.909091

def mean(self, axis=0, *args, **kwargs): """ Mean of non-NA/null values Returns ------- mean : float """ nv.validate_mean(args, kwargs) valid_vals = self._valid_sp_values sp_sum = valid_vals.sum() ct = len(valid_vals) if self._nul...

[ "def", "mean", "(", "self", ",", "axis", "=", "0", ",", "*", "args", ",", "*", "*", "kwargs", ")", ":", "nv", ".", "validate_mean", "(", "args", ",", "kwargs", ")", "valid_vals", "=", "self", ".", "_valid_sp_values", "sp_sum", "=", "valid_vals", ".",...

26.444444

14.222222

def create_document(self, parent, document, retry=google.api_core.gapic_v1.method.DEFAULT, timeout=google.api_core.gapic_v1.method.DEFAULT, metadata=None): """ Creates a new document. ...

[ "def", "create_document", "(", "self", ",", "parent", ",", "document", ",", "retry", "=", "google", ".", "api_core", ".", "gapic_v1", ".", "method", ".", "DEFAULT", ",", "timeout", "=", "google", ".", "api_core", ".", "gapic_v1", ".", "method", ".", "DEF...

44.814815

23.802469

def diskdata(): """Get total disk size in GB.""" p = os.popen("/bin/df -l -P") ddata = {} tsize = 0 for line in p.readlines(): d = line.split() if ("/dev/sd" in d[0] or "/dev/hd" in d[0] or "/dev/mapper" in d[0]): tsize = tsize + int(d[1]) ddata["Disk_GB"] = int(tsize...

[ "def", "diskdata", "(", ")", ":", "p", "=", "os", ".", "popen", "(", "\"/bin/df -l -P\"", ")", "ddata", "=", "{", "}", "tsize", "=", "0", "for", "line", "in", "p", ".", "readlines", "(", ")", ":", "d", "=", "line", ".", "split", "(", ")", "if",...

29.083333

16.916667

def fire_event(self, event, *args, **kwargs): """Fires a event.""" self.event_queue.append((event, args)) self.process_events()

[ "def", "fire_event", "(", "self", ",", "event", ",", "*", "args", ",", "*", "*", "kwargs", ")", ":", "self", ".", "event_queue", ".", "append", "(", "(", "event", ",", "args", ")", ")", "self", ".", "process_events", "(", ")" ]

37

5.5

def get_eidos_bayesian_scorer(prior_counts=None): """Return a BayesianScorer based on Eidos curation counts.""" table = load_eidos_curation_table() subtype_counts = {'eidos': {r: [c, i] for r, c, i in zip(table['RULE'], table['Num correct'], ta...

[ "def", "get_eidos_bayesian_scorer", "(", "prior_counts", "=", "None", ")", ":", "table", "=", "load_eidos_curation_table", "(", ")", "subtype_counts", "=", "{", "'eidos'", ":", "{", "r", ":", "[", "c", ",", "i", "]", "for", "r", ",", "c", ",", "i", "in...

46.416667

17.833333

def seek(self, pos=0): """Set the stream's file pointer to pos. Negative seeking is forbidden. """ if pos - self.pos >= 0: blocks, remainder = divmod(pos - self.pos, self.bufsize) for i in range(blocks): self.read(self.bufsize) self....

[ "def", "seek", "(", "self", ",", "pos", "=", "0", ")", ":", "if", "pos", "-", "self", ".", "pos", ">=", "0", ":", "blocks", ",", "remainder", "=", "divmod", "(", "pos", "-", "self", ".", "pos", ",", "self", ".", "bufsize", ")", "for", "i", "i...

35.666667

12.833333

def url_dirname(url): """ Return the folder containing the '.json' file """ p = six.moves.urllib.parse.urlparse(url) for e in [private.FILE_EXT_JSON, private.FILE_EXT_YAML]: if p.path.endswith(e): return six.moves.urllib.parse.urlunparse( p[:2]+ (os.pa...

[ "def", "url_dirname", "(", "url", ")", ":", "p", "=", "six", ".", "moves", ".", "urllib", ".", "parse", ".", "urlparse", "(", "url", ")", "for", "e", "in", "[", "private", ".", "FILE_EXT_JSON", ",", "private", ".", "FILE_EXT_YAML", "]", ":", "if", ...

31.75

13.25

def update(table_name, **fields): """ Build a update query. >>> update('foo_table', a=5, b=2) "UPDATE `foo_table` SET `a`=%(_QB_a)s, `b`=%(_QB_b)s", { '_QB_a': 5, '_QB_b': 2 } """ prefix = "UPDATE `%s` SET " % table_name sets, params = simple_expression(', ', **fields) return prefix + sets,...

[ "def", "update", "(", "table_name", ",", "*", "*", "fields", ")", ":", "prefix", "=", "\"UPDATE `%s` SET \"", "%", "table_name", "sets", ",", "params", "=", "simple_expression", "(", "', '", ",", "*", "*", "fields", ")", "return", "prefix", "+", "sets", ...

35.444444

13.222222

def _count_righthand_zero_bits(number, bits): """Count the number of zero bits on the right hand side. Args: number: an integer. bits: maximum number of bits to count. Returns: The number of zero bits on the right hand side of the number. """ if number == 0: return...

[ "def", "_count_righthand_zero_bits", "(", "number", ",", "bits", ")", ":", "if", "number", "==", "0", ":", "return", "bits", "return", "min", "(", "bits", ",", "_compat_bit_length", "(", "~", "number", "&", "(", "number", "-", "1", ")", ")", ")" ]

26.928571

21.285714

def _get_demand_array_construct(self): """ Returns a construct for an array of power demand data. """ bus_no = integer.setResultsName("bus_no") s_rating = real.setResultsName("s_rating") # MVA p_direction = real.setResultsName("p_direction") # p.u. q_direction = real.setR...

[ "def", "_get_demand_array_construct", "(", "self", ")", ":", "bus_no", "=", "integer", ".", "setResultsName", "(", "\"bus_no\"", ")", "s_rating", "=", "real", ".", "setResultsName", "(", "\"s_rating\"", ")", "# MVA", "p_direction", "=", "real", ".", "setResultsN...

51.941176

22.323529

def _invokeWrite(self, fileIO, session, directory, filename, replaceParamFile): """ Invoke File Write Method on Other Files """ # Default value for instance instance = None try: # Handle case where fileIO interfaces with single file # Retrieve Fil...

[ "def", "_invokeWrite", "(", "self", ",", "fileIO", ",", "session", ",", "directory", ",", "filename", ",", "replaceParamFile", ")", ":", "# Default value for instance", "instance", "=", "None", "try", ":", "# Handle case where fileIO interfaces with single file", "# Ret...

40.585366

21.804878

def show_updates(self): """ Check installed packages for available updates on PyPI @param project_name: optional package name to check; checks every installed pacakge if none specified @type project_name: string @returns: None """ di...

[ "def", "show_updates", "(", "self", ")", ":", "dists", "=", "Distributions", "(", ")", "if", "self", ".", "project_name", ":", "#Check for a single package", "pkg_list", "=", "[", "self", ".", "project_name", "]", "else", ":", "#Check for every installed package",...

39.386364

19.704545

def _raise_server_index(self): """Round robin magic: Raises the current redis server index and returns it""" self._current_server_index = (self._current_server_index + 1) % len(self._servers) return self._current_server_index

[ "def", "_raise_server_index", "(", "self", ")", ":", "self", ".", "_current_server_index", "=", "(", "self", ".", "_current_server_index", "+", "1", ")", "%", "len", "(", "self", ".", "_servers", ")", "return", "self", ".", "_current_server_index" ]

41

23.5

def reset_downloads_folder(): ''' Clears the downloads folder. If settings.ARCHIVE_EXISTING_DOWNLOADS is set to True, archives it. ''' if os.path.exists(downloads_path) and not os.listdir(downloads_path) == []: archived_downloads_folder = os.path.join(downloads_path, '..', ...

[ "def", "reset_downloads_folder", "(", ")", ":", "if", "os", ".", "path", ".", "exists", "(", "downloads_path", ")", "and", "not", "os", ".", "listdir", "(", "downloads_path", ")", "==", "[", "]", ":", "archived_downloads_folder", "=", "os", ".", "path", ...

60.636364

23.363636

def set_generator_validation_nb(self, number): """ sets self.nb_val_samples which is used in model.fit if input is a generator :param number: :return: """ self.nb_val_samples = number diff_to_batch = number % self.get_batch_size() if diff_to_batch > 0: ...

[ "def", "set_generator_validation_nb", "(", "self", ",", "number", ")", ":", "self", ".", "nb_val_samples", "=", "number", "diff_to_batch", "=", "number", "%", "self", ".", "get_batch_size", "(", ")", "if", "diff_to_batch", ">", "0", ":", "self", ".", "nb_val...

34.466667

19.4

def fit(self, Xs=None, ys=None, Xt=None, yt=None): """Builds an optimal coupling and estimates the associated mapping from source and target sets of samples (Xs, ys) and (Xt, yt) Parameters ---------- Xs : array-like, shape (n_source_samples, n_features) The training...

[ "def", "fit", "(", "self", ",", "Xs", "=", "None", ",", "ys", "=", "None", ",", "Xt", "=", "None", ",", "yt", "=", "None", ")", ":", "# check the necessary inputs parameters are here", "if", "check_params", "(", "Xs", "=", "Xs", ",", "Xt", "=", "Xt", ...

37.625

20.107143

def make_timestamp(ts: OptTs = None) -> int: """Create zipkin timestamp in microseconds, or convert available one from second. Useful when user supplies ts from time.time() call. """ ts = ts if ts is not None else time.time() return int(ts * 1000 * 1000)

[ "def", "make_timestamp", "(", "ts", ":", "OptTs", "=", "None", ")", "->", "int", ":", "ts", "=", "ts", "if", "ts", "is", "not", "None", "else", "time", ".", "time", "(", ")", "return", "int", "(", "ts", "*", "1000", "*", "1000", ")" ]

44.833333

7.666667

def unlock_keychain(username): """ If the user is running via SSH, their Keychain must be unlocked first. """ if 'SSH_TTY' not in os.environ: return # Don't unlock if we've already seen this user. if username in _unlocked: return _unlocked.add(username) if sys.platform == 'da...

[ "def", "unlock_keychain", "(", "username", ")", ":", "if", "'SSH_TTY'", "not", "in", "os", ".", "environ", ":", "return", "# Don't unlock if we've already seen this user.", "if", "username", "in", "_unlocked", ":", "return", "_unlocked", ".", "add", "(", "username...

34.266667

26

def _fieldnames_to_colnames(model_cls, fieldnames): """Get the names of columns referenced by the given model fields.""" get_field = model_cls._meta.get_field fields = map(get_field, fieldnames) return {f.column for f in fields}

[ "def", "_fieldnames_to_colnames", "(", "model_cls", ",", "fieldnames", ")", ":", "get_field", "=", "model_cls", ".", "_meta", ".", "get_field", "fields", "=", "map", "(", "get_field", ",", "fieldnames", ")", "return", "{", "f", ".", "column", "for", "f", "...

51.2

4

def hook_get_results(self, changelist): """Triggered by `ChangeList.get_results()`.""" # Poor NestedSet guys they've punished themselves once chosen that approach, # and now we punish them again with all those DB hits. result_list = list(changelist.result_list) # Get children ...

[ "def", "hook_get_results", "(", "self", ",", "changelist", ")", ":", "# Poor NestedSet guys they've punished themselves once chosen that approach,", "# and now we punish them again with all those DB hits.", "result_list", "=", "list", "(", "changelist", ".", "result_list", ")", "...

38.348837

27.372093

def unpack_rgb(data, dtype=None, bitspersample=None, rescale=True): """Return array from byte string containing packed samples. Use to unpack RGB565 or RGB555 to RGB888 format. Parameters ---------- data : byte str The data to be decoded. Samples in each pixel are stored consecutively. ...

[ "def", "unpack_rgb", "(", "data", ",", "dtype", "=", "None", ",", "bitspersample", "=", "None", ",", "rescale", "=", "True", ")", ":", "if", "bitspersample", "is", "None", ":", "bitspersample", "=", "(", "5", ",", "6", ",", "5", ")", "if", "dtype", ...

35.927273

19.090909

def get_account_funds(self, wallet=None, session=None, lightweight=None): """ Get available to bet amount. :param str wallet: Name of the wallet in question :param requests.session session: Requests session object :param bool lightweight: If True will return dict not a resource ...

[ "def", "get_account_funds", "(", "self", ",", "wallet", "=", "None", ",", "session", "=", "None", ",", "lightweight", "=", "None", ")", ":", "params", "=", "clean_locals", "(", "locals", "(", ")", ")", "method", "=", "'%s%s'", "%", "(", "self", ".", ...

44.642857

21.214286

def get_parent_vault_nodes(self): """Gets the parents of this vault. return: (osid.authorization.VaultNodeList) - the parents of this vault *compliance: mandatory -- This method must be implemented.* """ parent_vault_nodes = [] for node in self._my_map['...

[ "def", "get_parent_vault_nodes", "(", "self", ")", ":", "parent_vault_nodes", "=", "[", "]", "for", "node", "in", "self", ".", "_my_map", "[", "'parentNodes'", "]", ":", "parent_vault_nodes", ".", "append", "(", "VaultNode", "(", "node", ".", "_my_map", ",",...

35.9375

14.375

def _compute_scaled_schoenfeld(self, X, T, E, weights, index=None): r""" Let s_k be the kth schoenfeld residuals. Then E[s_k] = 0. For tests of proportionality, we want to test if \beta_i(t) is \beta_i (constant) or not. Let V_k be the contribution to the information matrix at time t_k....

[ "def", "_compute_scaled_schoenfeld", "(", "self", ",", "X", ",", "T", ",", "E", ",", "weights", ",", "index", "=", "None", ")", ":", "n_deaths", "=", "self", ".", "event_observed", ".", "sum", "(", ")", "scaled_schoenfeld_resids", "=", "n_deaths", "*", "...

38.666667

34.185185

def annotate_image(self, request, retry=None, timeout=None): """Run image detection and annotation for an image. Example: >>> from google.cloud.vision_v1 import ImageAnnotatorClient >>> client = ImageAnnotatorClient() >>> request = { ... 'image': { ...

[ "def", "annotate_image", "(", "self", ",", "request", ",", "retry", "=", "None", ",", "timeout", "=", "None", ")", ":", "# If the image is a file handler, set the content.", "image", "=", "protobuf", ".", "get", "(", "request", ",", "\"image\"", ")", "if", "ha...

44.577778

23.244444

def get_log_events(awsclient, log_group_name, log_stream_name, start_ts=None): """Get log events for the specified log group and stream. this is used in tenkai output instance diagnostics :param log_group_name: log group name :param log_stream_name: log stream name :param start_ts: timestamp :r...

[ "def", "get_log_events", "(", "awsclient", ",", "log_group_name", ",", "log_stream_name", ",", "start_ts", "=", "None", ")", ":", "client_logs", "=", "awsclient", ".", "get_client", "(", "'logs'", ")", "request", "=", "{", "'logGroupName'", ":", "log_group_name"...

31.96

17.08

def choose(self, versions, conflict='silent'): """ Choose the highest version in the range. :param versions: Iterable of available versions. """ assert conflict in ('silent', 'warning', 'error') if not versions: raise VersionRangeMismatch('No versions to choose from') version_map = {} for version in...

[ "def", "choose", "(", "self", ",", "versions", ",", "conflict", "=", "'silent'", ")", ":", "assert", "conflict", "in", "(", "'silent'", ",", "'warning'", ",", "'error'", ")", "if", "not", "versions", ":", "raise", "VersionRangeMismatch", "(", "'No versions t...

36.605263

14.868421

def get_scratch_path(self, local_file): """Construct and return a path in the scratch area from a local file. """ (local_dirname, local_basename) = self.split_local_path(local_file) return self.construct_scratch_path(local_dirname, local_basename)

[ "def", "get_scratch_path", "(", "self", ",", "local_file", ")", ":", "(", "local_dirname", ",", "local_basename", ")", "=", "self", ".", "split_local_path", "(", "local_file", ")", "return", "self", ".", "construct_scratch_path", "(", "local_dirname", ",", "loca...

55

13.8

def skyline_empirical(self, gen=1.0, n_points = 20): ''' returns the skyline, i.e., an estimate of the inverse rate of coalesence. Here, the skyline is estimated from a sliding window average of the observed mergers, i.e., without reference to the coalescence likelihood. paramete...

[ "def", "skyline_empirical", "(", "self", ",", "gen", "=", "1.0", ",", "n_points", "=", "20", ")", ":", "mergers", "=", "self", ".", "tree_events", "[", ":", ",", "1", "]", ">", "0", "merger_tvals", "=", "self", ".", "tree_events", "[", "mergers", ","...

46.029412

25.147059

def get_queryset(self, request): """ Annote the queryset with an 'is_active' property that's true iff that row is the most recently added row for that particular set of KEY_FIELDS values. Filter the queryset to show only is_active rows by default. """ if request.GET.get(S...

[ "def", "get_queryset", "(", "self", ",", "request", ")", ":", "if", "request", ".", "GET", ".", "get", "(", "ShowHistoryFilter", ".", "parameter_name", ")", "==", "'1'", ":", "queryset", "=", "self", ".", "model", ".", "objects", ".", "with_active_flag", ...

44.933333

18.4

def installed(name, enabled=True): ''' Make sure that we have the given bundle ID or path to command installed in the assistive access panel. name The bundle ID or path to command enable Should assistive access be enabled on this application? ''' ret = {'name': name, ...

[ "def", "installed", "(", "name", ",", "enabled", "=", "True", ")", ":", "ret", "=", "{", "'name'", ":", "name", ",", "'result'", ":", "True", ",", "'comment'", ":", "''", ",", "'changes'", ":", "{", "}", "}", "is_installed", "=", "__salt__", "[", "...

27.212121

25.090909

def load_texture(self, file_path, cell_size=(256, 256)): """ Load a spritesheet texture. cell_size is the uniform size of each cell in the spritesheet. """ super(SpriteSheet, self).load_texture(file_path) self.__cell_bounds = cell_size self.__generate_cells()

[ "def", "load_texture", "(", "self", ",", "file_path", ",", "cell_size", "=", "(", "256", ",", "256", ")", ")", ":", "super", "(", "SpriteSheet", ",", "self", ")", ".", "load_texture", "(", "file_path", ")", "self", ".", "__cell_bounds", "=", "cell_size",...

38.5

9.75

def generate_set_partition_strings(n): """Generate the restricted growth strings for all of the partitions of an `n`-member set. Uses Algorithm H from page 416 of volume 4A of Knuth's `The Art of Computer Programming`. Returns the partitions in lexicographical order. Parameters ---------- ...

[ "def", "generate_set_partition_strings", "(", "n", ")", ":", "# Handle edge cases:", "if", "n", "==", "0", ":", "return", "[", "]", "elif", "n", "==", "1", ":", "return", "[", "scipy", ".", "array", "(", "[", "0", "]", ")", "]", "partitions", "=", "[...

32.490566

20.490566

def get_progenies(p1, p2, x_linked=False, tolerance=0): """ Returns possible progenies in a trio. """ _p1 = expand_alleles(p1, tolerance=tolerance) _p2 = expand_alleles(p2, tolerance=tolerance) possible_progenies = set(tuple(sorted(x)) for x in product(_p1, _p2)) if x_linked: # Add all hemi...

[ "def", "get_progenies", "(", "p1", ",", "p2", ",", "x_linked", "=", "False", ",", "tolerance", "=", "0", ")", ":", "_p1", "=", "expand_alleles", "(", "p1", ",", "tolerance", "=", "tolerance", ")", "_p2", "=", "expand_alleles", "(", "p2", ",", "toleranc...

42.1

11.1

def _calc_bkg_bkgrms(self): """ Calculate the background and background RMS estimate in each of the meshes. Both meshes are computed at the same time here method because the filtering of both depends on the background mesh. The ``background_mesh`` and ``background_rms_m...

[ "def", "_calc_bkg_bkgrms", "(", "self", ")", ":", "if", "self", ".", "sigma_clip", "is", "not", "None", ":", "data_sigclip", "=", "self", ".", "sigma_clip", "(", "self", ".", "_mesh_data", ",", "axis", "=", "1", ")", "else", ":", "data_sigclip", "=", "...

40.185185

22.740741

def keysym_to_keycodes(self, keysym): """Look up all the keycodes that is bound to keysym. A list of tuples (keycode, index) is returned, sorted primarily on the lowest index and secondarily on the lowest keycode.""" try: # Copy the map list, reversing the arguments ...

[ "def", "keysym_to_keycodes", "(", "self", ",", "keysym", ")", ":", "try", ":", "# Copy the map list, reversing the arguments", "return", "map", "(", "lambda", "x", ":", "(", "x", "[", "1", "]", ",", "x", "[", "0", "]", ")", ",", "self", ".", "_keymap_sym...

47

15.888889

def v1_subfolder_list(request, response, kvlclient, fid): '''Retrieves a list of subfolders in a folder for the current user. The route for this endpoint is: ``GET /dossier/v1/folder/<fid>/subfolder``. (Temporarily, the "current user" can be set via the ``annotator_id`` query parameter.) The ...

[ "def", "v1_subfolder_list", "(", "request", ",", "response", ",", "kvlclient", ",", "fid", ")", ":", "fid", "=", "urllib", ".", "unquote", "(", "fid", ")", "try", ":", "return", "sorted", "(", "imap", "(", "attrgetter", "(", "'name'", ")", ",", "ifilte...

34.684211

21.736842

def words(fpth): """ ww = words(os.path.join(app_root, 'ig/helper.py')) for k, v in (ww.most_common(3)): print(k, v) :param fpth: :type fpth: :return: :rtype: """ from collections import Counter words__ = Counter() with open(fpth) as fp: for line in fp: ...

[ "def", "words", "(", "fpth", ")", ":", "from", "collections", "import", "Counter", "words__", "=", "Counter", "(", ")", "with", "open", "(", "fpth", ")", "as", "fp", ":", "for", "line", "in", "fp", ":", "words__", ".", "update", "(", "line", ".", "...

21.705882

17.352941

def create_meta_data(cls, options, args, parser): """ Override in subclass if required. """ meta_data = [] meta_data.append(('spiff_version', cls.get_version())) if options.target_engine: meta_data.append(('target_engine', options.target_engine)) if op...

[ "def", "create_meta_data", "(", "cls", ",", "options", ",", "args", ",", "parser", ")", ":", "meta_data", "=", "[", "]", "meta_data", ".", "append", "(", "(", "'spiff_version'", ",", "cls", ".", "get_version", "(", ")", ")", ")", "if", "options", ".", ...

38.166667

12.833333

async def select(**data): """ RPC method for selecting data from the database :return selected data """ try: select_data = clickhouse_queries.select_from_table(table=data['table'], query=data['query'], fields=data['fields']) return str(select_data) except ServerException as e: ...

[ "async", "def", "select", "(", "*", "*", "data", ")", ":", "try", ":", "select_data", "=", "clickhouse_queries", ".", "select_from_table", "(", "table", "=", "data", "[", "'table'", "]", ",", "query", "=", "data", "[", "'query'", "]", ",", "fields", "=...

29.470588

19

def flush_devices(self): """ overwrite the complete memory with zeros """ self.rom.program([0 for i in range(self.rom.size)]) self.flash.program([0 for i in range(self.flash.size)]) for i in range(self.ram.size): self.ram.write(i, 0)

[ "def", "flush_devices", "(", "self", ")", ":", "self", ".", "rom", ".", "program", "(", "[", "0", "for", "i", "in", "range", "(", "self", ".", "rom", ".", "size", ")", "]", ")", "self", ".", "flash", ".", "program", "(", "[", "0", "for", "i", ...

30.375

9.375

def _edits1(word: str) -> Set[str]: """ Return a set of words with edit distance of 1 from the input word """ splits = [(word[:i], word[i:]) for i in range(len(word) + 1)] deletes = [L + R[1:] for L, R in splits if R] transposes = [L + R[1] + R[0] + R[2:] for L, R in splits if len(R) > 1] re...

[ "def", "_edits1", "(", "word", ":", "str", ")", "->", "Set", "[", "str", "]", ":", "splits", "=", "[", "(", "word", "[", ":", "i", "]", ",", "word", "[", "i", ":", "]", ")", "for", "i", "in", "range", "(", "len", "(", "word", ")", "+", "1...

46

20.181818

def transition_matrix_non_reversible(C): """implementation of transition_matrix""" if not scipy.sparse.issparse(C): C = scipy.sparse.csr_matrix(C) rowsum = C.tocsr().sum(axis=1) # catch div by zero if np.min(rowsum) == 0.0: raise ValueError("matrix C contains rows with sum zero.") ...

[ "def", "transition_matrix_non_reversible", "(", "C", ")", ":", "if", "not", "scipy", ".", "sparse", ".", "issparse", "(", "C", ")", ":", "C", "=", "scipy", ".", "sparse", ".", "csr_matrix", "(", "C", ")", "rowsum", "=", "C", ".", "tocsr", "(", ")", ...

37.545455

8.181818

def smooth_rectangle(x, y, rec_w, rec_h, gaussian_width_x, gaussian_width_y): """ Rectangle with a solid central region, then Gaussian fall-off at the edges. """ gaussian_x_coord = abs(x)-rec_w/2.0 gaussian_y_coord = abs(y)-rec_h/2.0 box_x=np.less(gaussian_x_coord,0.0) box_y=np.less(gaussi...

[ "def", "smooth_rectangle", "(", "x", ",", "y", ",", "rec_w", ",", "rec_h", ",", "gaussian_width_x", ",", "gaussian_width_y", ")", ":", "gaussian_x_coord", "=", "abs", "(", "x", ")", "-", "rec_w", "/", "2.0", "gaussian_y_coord", "=", "abs", "(", "y", ")",...

38.95

19.65

def write(self, fb): """Write a single function benchmark. Args: fb (FunctionBenchmark): FunctionBenchmark class instance. Before passing to this, you should call ``fb.benchmark()``. """ print('[{}.{}]'.format(fb.module, fb.func.__name__), file=self.file) ...

[ "def", "write", "(", "self", ",", "fb", ")", ":", "print", "(", "'[{}.{}]'", ".", "format", "(", "fb", ".", "module", ",", "fb", ".", "func", ".", "__name__", ")", ",", "file", "=", "self", ".", "file", ")", "print", "(", "'class = {}'", ".", "fo...

47.571429

21.095238

def _assemble_agent_str(agent): """Assemble an Agent object to text.""" agent_str = agent.name # Only do the more detailed assembly for molecular agents if not isinstance(agent, ist.Agent): return agent_str # Handle mutation conditions if agent.mutations: is_generic = False ...

[ "def", "_assemble_agent_str", "(", "agent", ")", ":", "agent_str", "=", "agent", ".", "name", "# Only do the more detailed assembly for molecular agents", "if", "not", "isinstance", "(", "agent", ",", "ist", ".", "Agent", ")", ":", "return", "agent_str", "# Handle m...

38.010309

16.742268

def check_mods_docs_readme(): """ Check that all modules are listed in the YAML index at the top of docs/README.md """ docs_mods = [] readme_fn = os.path.join( os.path.dirname(config.MULTIQC_DIR), 'docs', 'README.md') if not os.path.isfile(readme_fn): if os.environ.get('TRAVIS_BUILD_DIR') ...

[ "def", "check_mods_docs_readme", "(", ")", ":", "docs_mods", "=", "[", "]", "readme_fn", "=", "os", ".", "path", ".", "join", "(", "os", ".", "path", ".", "dirname", "(", "config", ".", "MULTIQC_DIR", ")", ",", "'docs'", ",", "'README.md'", ")", "if", ...

44.058824

22.911765

def closest_common_ancestor(self, other): """ Find the common ancestor between this history node and 'other'. :param other: the PathHistory to find a common ancestor with. :return: the common ancestor SimStateHistory, or None if there isn't one """ our_history_...

[ "def", "closest_common_ancestor", "(", "self", ",", "other", ")", ":", "our_history_iter", "=", "reversed", "(", "HistoryIter", "(", "self", ")", ")", "their_history_iter", "=", "reversed", "(", "HistoryIter", "(", "other", ")", ")", "sofar", "=", "set", "("...

34.131579

15.973684

async def get_devices(self) -> List[Device]: """Get information about the users avaliable devices. Returns ------- devices : List[Device] The devices the user has available. """ data = await self.http.available_devices() return [Device(item) for item ...

[ "async", "def", "get_devices", "(", "self", ")", "->", "List", "[", "Device", "]", ":", "data", "=", "await", "self", ".", "http", ".", "available_devices", "(", ")", "return", "[", "Device", "(", "item", ")", "for", "item", "in", "data", "[", "'devi...

33

13.8

def ch_stop_time(self, *channels: List[Channel]) -> int: """Return maximum time of timeslots over all channels. Args: *channels: Channels over which to obtain stop time. """ intervals = list(itertools.chain(*(self._table[chan] for chan in channels ...

[ "def", "ch_stop_time", "(", "self", ",", "*", "channels", ":", "List", "[", "Channel", "]", ")", "->", "int", ":", "intervals", "=", "list", "(", "itertools", ".", "chain", "(", "*", "(", "self", ".", "_table", "[", "chan", "]", "for", "chan", "in"...

41.363636

22

def get_variants(self, arch=None, types=None, recursive=False): """ Return all variants of given arch and types. Supported variant types: self - include the top-level ("self") variant as well addon variant optional """ types = ...

[ "def", "get_variants", "(", "self", ",", "arch", "=", "None", ",", "types", "=", "None", ",", "recursive", "=", "False", ")", ":", "types", "=", "types", "or", "[", "]", "result", "=", "[", "]", "if", "\"self\"", "in", "types", ":", "result", ".", ...

31.259259

20.074074

def simulate(self, timepoints): """ Simulate initialised solver for the specified timepoints :param timepoints: timepoints that will be returned from simulation :return: a list of trajectories for each of the equations in the problem. """ solver = self._solver la...

[ "def", "simulate", "(", "self", ",", "timepoints", ")", ":", "solver", "=", "self", ".", "_solver", "last_timepoint", "=", "timepoints", "[", "-", "1", "]", "try", ":", "simulated_timepoints", ",", "simulated_values", "=", "solver", ".", "simulate", "(", "...

42.703704

27.740741

def table_mask(self): """ndarray, True where table margin <= min_base_size, same shape as slice.""" margin = compress_pruned( self._slice.margin( axis=None, weighted=False, include_transforms_for_dims=self._hs_dims, prune=self._...

[ "def", "table_mask", "(", "self", ")", ":", "margin", "=", "compress_pruned", "(", "self", ".", "_slice", ".", "margin", "(", "axis", "=", "None", ",", "weighted", "=", "False", ",", "include_transforms_for_dims", "=", "self", ".", "_hs_dims", ",", "prune"...

36

20.35

def deep_merge(*args): """ >>> dbt.utils.deep_merge({'a': 1, 'b': 2, 'c': 3}, {'a': 2}, {'a': 3, 'b': 1}) # noqa {'a': 3, 'b': 1, 'c': 3} """ if len(args) == 0: return None if len(args) == 1: return copy.deepcopy(args[0]) lst = list(args) last = copy.deepcopy(lst.pop(l...

[ "def", "deep_merge", "(", "*", "args", ")", ":", "if", "len", "(", "args", ")", "==", "0", ":", "return", "None", "if", "len", "(", "args", ")", "==", "1", ":", "return", "copy", ".", "deepcopy", "(", "args", "[", "0", "]", ")", "lst", "=", "...

24.466667

19.533333

def _render_attributes(self, resource): """Render the resources's attributes.""" attributes = {} attrs_to_ignore = set() for key, relationship in resource.__mapper__.relationships.items(): attrs_to_ignore.update(set( [column.name for column in relationship.lo...

[ "def", "_render_attributes", "(", "self", ",", "resource", ")", ":", "attributes", "=", "{", "}", "attrs_to_ignore", "=", "set", "(", ")", "for", "key", ",", "relationship", "in", "resource", ".", "__mapper__", ".", "relationships", ".", "items", "(", ")",...

37.15625

18.65625

def _map_sextuple_to_phenotype( self, superterm1_id, subterm1_id, quality_id, superterm2_id, subterm2_id, modifier): """ This will take the 6-part EQ-style annotation used by ZFIN and return the ZP id. Currently relies on an external mapping file, but the ...

[ "def", "_map_sextuple_to_phenotype", "(", "self", ",", "superterm1_id", ",", "subterm1_id", ",", "quality_id", ",", "superterm2_id", ",", "subterm2_id", ",", "modifier", ")", ":", "zp_id", "=", "None", "# zfin uses free-text modifiers,", "# but we need to convert them to ...

33.727273

17.181818

def update_project(self, resource_name, resource): """ Updates an entity in the data model using the given resource. Args: resource_name (string): Current name of the resource (in case the resource is getting its name changed). resource (intern.resource.b...

[ "def", "update_project", "(", "self", ",", "resource_name", ",", "resource", ")", ":", "self", ".", "project_service", ".", "set_auth", "(", "self", ".", "_token_project", ")", "return", "self", ".", "project_service", ".", "update", "(", "resource_name", ",",...

36.947368

22