kejian/codesearchnet-python-rebalanced · Datasets at Hugging Face

text stringlengths 75 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 0.18
def note_and_log(cls): """ This will be used as a decorator on class to activate logging and store messages in the variable cls._notes This will allow quick access to events in the web app. A note can be added to cls._notes without logging if passing the argument log=false to function note() ...	[ "def", "note_and_log", "(", "cls", ")", ":", "if", "hasattr", "(", "cls", ",", "\"DEBUG_LEVEL\"", ")", ":", "if", "cls", ".", "DEBUG_LEVEL", "==", "\"debug\"", ":", "file_level", "=", "logging", ".", "DEBUG", "console_level", "=", "logging", ".", "DEBUG", ...	31.161765	0.000686
def process_params(self, params): ''' Populates the launch data from a dictionary. Only cares about keys in the LAUNCH_DATA_PARAMETERS list, or that start with 'custom_' or 'ext_'. ''' for key, val in params.items(): if key in LAUNCH_DATA_PARAMETERS and val !=...	[ "def", "process_params", "(", "self", ",", "params", ")", ":", "for", "key", ",", "val", "in", "params", ".", "items", "(", ")", ":", "if", "key", "in", "LAUNCH_DATA_PARAMETERS", "and", "val", "!=", "'None'", ":", "if", "key", "==", "'roles'", ":", "...	42.285714	0.002203
def getMultiSeriesRegistrations(self,q_filter=Q(),name_series=False,**kwargs): ''' Use the getSeriesRegistered method above to get a list of each series the person has registered for. The return only indicates whether they are registered more than once for the same series (e.g. for keep...	[ "def", "getMultiSeriesRegistrations", "(", "self", ",", "q_filter", "=", "Q", "(", ")", ",", "name_series", "=", "False", ",", "", "", "kwargs", ")", ":", "series_registered", "=", "self", ".", "getSeriesRegistered", "(", "q_filter", ",", "distinct", "=", ...	56.333333	0.012609
def process_item(self, item): """Calculate new maximum value for each group, for "new" items only. """ group, value = item['group'], item['value'] if group in self._groups: cur_val = self._groups[group] self._groups[group] = max(cur_val, value) els...	[ "def", "process_item", "(", "self", ",", "item", ")", ":", "group", ",", "value", "=", "item", "[", "'group'", "]", ",", "item", "[", "'value'", "]", "if", "group", "in", "self", ".", "_groups", ":", "cur_val", "=", "self", ".", "_groups", "[", "gr...	44.7	0.002191
def isel_variable_and_index( name: Hashable, variable: Variable, index: pd.Index, indexers: Mapping[Any, Union[slice, Variable]], ) -> Tuple[Variable, Optional[pd.Index]]: """Index a Variable and pandas.Index together.""" if not indexers: # nothing to index return variable.copy(d...	[ "def", "isel_variable_and_index", "(", "name", ":", "Hashable", ",", "variable", ":", "Variable", ",", "index", ":", "pd", ".", "Index", ",", "indexers", ":", "Mapping", "[", "Any", ",", "Union", "[", "slice", ",", "Variable", "]", "]", ",", ")", "->",...	30.482759	0.001096
def _interpret_result(self, task): """ Interpret the result of a ping. :param task: The pinger task. The result or exception of the `task` is interpreted as follows: * :data:`None` result: positive * :class:`aioxmpp.errors.XMPPError`, ``service-unavailable``: ...	[ "def", "_interpret_result", "(", "self", ",", "task", ")", ":", "if", "task", ".", "exception", "(", ")", "is", "None", ":", "self", ".", "_on_fresh", "(", ")", "return", "exc", "=", "task", ".", "exception", "(", ")", "if", "isinstance", "(", "exc",...	34.882353	0.001641
def htmljoin(ol,sp,**kwargs): ''' ol = [1,2,3,4] htmljoin(ol,"option",outer="select") ''' if('outer' in kwargs): outer = kwargs['outer'] else: outer = "" if(outer): head = "<" + outer + ">" tail = "</" + outer + ">" else: head = ""...	[ "def", "htmljoin", "(", "ol", ",", "sp", ",", "", "", "kwargs", ")", ":", "if", "(", "'outer'", "in", "kwargs", ")", ":", "outer", "=", "kwargs", "[", "'outer'", "]", "else", ":", "outer", "=", "\"\"", "if", "(", "outer", ")", ":", "head", "=...	21.958333	0.009091
def configure_output(verbosity=0, output_levels=None, quiet=False): """ Configure verbosity level through Fabric's output managers. Provides a default mapping from verbosity levels to output types. :param verbosity: an integral verbosity level :param output_levels: an optional mapping from Fabric ...	[ "def", "configure_output", "(", "verbosity", "=", "0", ",", "output_levels", "=", "None", ",", "quiet", "=", "False", ")", ":", "verbosity", "=", "verbosity", "if", "not", "quiet", "else", "-", "1", "output_levels", "=", "output_levels", "or", "{", "\"stat...	32.675	0.002229
def setAlternateColor(self, color): """ Sets the alternate color for this node. :param color <QColor> """ color = QColor(color) if self._palette is None: self._palette = XNodePalette(self._scenePalette) self._palette.setCol...	[ "def", "setAlternateColor", "(", "self", ",", "color", ")", ":", "color", "=", "QColor", "(", "color", ")", "if", "self", ".", "_palette", "is", "None", ":", "self", ".", "_palette", "=", "XNodePalette", "(", "self", ".", "_scenePalette", ")", "self", ...	31.75	0.010204
def _setup_observers(self): """ Setup the default observers 1: pass through to parent, if present """ if self.has_parent(): self.add_observer(self._parent_, self._parent_._pass_through_notify_observers, -np.inf)	[ "def", "_setup_observers", "(", "self", ")", ":", "if", "self", ".", "has_parent", "(", ")", ":", "self", ".", "add_observer", "(", "self", ".", "_parent_", ",", "self", ".", "_parent_", ".", "_pass_through_notify_observers", ",", "-", "np", ".", "inf", ...	32.125	0.011364
def clean(self): """ Remove unused filters. """ for f in sorted(self.components.keys()): unused = not any(self.switches[a][f] for a in self.analytes) if unused: self.remove(f)	[ "def", "clean", "(", "self", ")", ":", "for", "f", "in", "sorted", "(", "self", ".", "components", ".", "keys", "(", ")", ")", ":", "unused", "=", "not", "any", "(", "self", ".", "switches", "[", "a", "]", "[", "f", "]", "for", "a", "in", "se...	30	0.008097
def bytes2fsn(data, encoding="utf-8"): """ Args: data (bytes): The data to convert encoding (`str`): encoding used for Windows Returns: `fsnative` Raises: TypeError: If no `bytes` path is passed ValueError: If decoding fails or the encoding is invalid Turns `...	[ "def", "bytes2fsn", "(", "data", ",", "encoding", "=", "\"utf-8\"", ")", ":", "if", "not", "isinstance", "(", "data", ",", "bytes", ")", ":", "raise", "TypeError", "(", "\"data needs to be bytes\"", ")", "if", "is_win", ":", "if", "encoding", "is", "None",...	30.4	0.000797
def update_actualremoterelieve_v1(self): """Constrain the actual relieve discharge to a remote location. Required control parameter: \|HighestRemoteDischarge\| Required derived parameter: \|HighestRemoteSmoothPar\| Updated flux sequence: \|ActualRemoteRelieve\| Basic equation - disco...	[ "def", "update_actualremoterelieve_v1", "(", "self", ")", ":", "con", "=", "self", ".", "parameters", ".", "control", ".", "fastaccess", "der", "=", "self", ".", "parameters", ".", "derived", ".", "fastaccess", "flu", "=", "self", ".", "sequences", ".", "f...	35.057143	0.000264
def anonymous_required(function=None, redirect_url=None): """ Decorator requiring the current user to be anonymous (not logged in). """ if not redirect_url: redirect_url = settings.LOGIN_REDIRECT_URL actual_decorator = user_passes_test( is_anonymous, login_url=redirect_url, ...	[ "def", "anonymous_required", "(", "function", "=", "None", ",", "redirect_url", "=", "None", ")", ":", "if", "not", "redirect_url", ":", "redirect_url", "=", "settings", ".", "LOGIN_REDIRECT_URL", "actual_decorator", "=", "user_passes_test", "(", "is_anonymous", "...	26.9375	0.002242
def post_event_display_settings(self, id, **data): """ POST /events/:id/display_settings/ Updates the display settings for an event. """ return self.post("/events/{0}/display_settings/".format(id), data=data)	[ "def", "post_event_display_settings", "(", "self", ",", "id", ",", "", "", "data", ")", ":", "return", "self", ".", "post", "(", "\"/events/{0}/display_settings/\"", ".", "format", "(", "id", ")", ",", "data", "=", "data", ")" ]	35.857143	0.011673
def shortlex(start, other, excludestart=False): """Yield all unions of start with other in shortlex order. >>> ['{:03b}'.format(s) for s in shortlex(0, [0b100, 0b010, 0b001])] ['000', '100', '010', '001', '110', '101', '011', '111'] >>> ', '.join(''.join(sorted(s)) ... for s in shortlex(set(), [{'...	[ "def", "shortlex", "(", "start", ",", "other", ",", "excludestart", "=", "False", ")", ":", "if", "not", "excludestart", ":", "yield", "start", "queue", "=", "collections", ".", "deque", "(", "[", "(", "start", ",", "other", ")", "]", ")", "while", "...	29.344828	0.001138
def _variants_fields(fields, exclude_fields, info_ids): """Utility function to determine which fields to extract when loading variants.""" if fields is None: # no fields specified by user # by default extract all standard and INFO fields fields = config.STANDARD_VARIANT_FIELDS + info...	[ "def", "_variants_fields", "(", "fields", ",", "exclude_fields", ",", "info_ids", ")", ":", "if", "fields", "is", "None", ":", "# no fields specified by user", "# by default extract all standard and INFO fields", "fields", "=", "config", ".", "STANDARD_VARIANT_FIELDS", "+...	45.5	0.001076
def accelerated_proximal_gradient(x, f, g, gamma, niter, callback=None, **kwargs): r"""Accelerated proximal gradient algorithm for convex optimization. The method is known as "Fast Iterative Soft-Thresholding Algorithm" (FISTA). See `[Beck2009]`_ for more information. ...	[ "def", "accelerated_proximal_gradient", "(", "x", ",", "f", ",", "g", ",", "gamma", ",", "niter", ",", "callback", "=", "None", ",", "", "", "kwargs", ")", ":", "# Get and validate input", "if", "x", "not", "in", "f", ".", "domain", ":", "raise", "Ty...	28.457447	0.000361
def down_capture(returns, factor_returns, **kwargs): """ Compute the capture ratio for periods when the benchmark return is negative Parameters ---------- returns : pd.Series or np.ndarray Returns of the strategy, noncumulative. - See full explanation in :func:`~empyrical.stats.cum_...	[ "def", "down_capture", "(", "returns", ",", "factor_returns", ",", "", "", "kwargs", ")", ":", "return", "down", "(", "returns", ",", "factor_returns", ",", "function", "=", "capture", ",", "", "", "kwargs", ")" ]	32.1875	0.000943
def saved_searches(self): """ :reference: https://developer.twitter.com/en/docs/accounts-and-users/manage-account-settings/api-reference/get-saved_searches-list """ return bind_api( api=self, path='/saved_searches/list.json', payload_type='saved_search', payload_list=...	[ "def", "saved_searches", "(", "self", ")", ":", "return", "bind_api", "(", "api", "=", "self", ",", "path", "=", "'/saved_searches/list.json'", ",", "payload_type", "=", "'saved_search'", ",", "payload_list", "=", "True", ",", "require_auth", "=", "True", ")" ...	44.75	0.008219
def orthogonal_initialization(X,K): """ Initialize the centrodis by orthogonal_initialization. Parameters -------------------- X(data): array-like, shape= (m_samples,n_samples) K: integer number of K clusters Returns ------- centroids: array-like, shape (K,n_samples) ...	[ "def", "orthogonal_initialization", "(", "X", ",", "K", ")", ":", "N", ",", "M", "=", "X", ".", "shape", "centroids", "=", "X", "[", "np", ".", "random", ".", "randint", "(", "0", ",", "N", "-", "1", ",", "1", ")", ",", ":", "]", "data_norms", ...	44.307692	0.028887
def make_message_multipart(message): """Convert a message into a multipart message.""" if not message.is_multipart(): multipart_message = email.mime.multipart.MIMEMultipart('alternative') for header_key in set(message.keys()): # Preserve duplicate headers values = message...	[ "def", "make_message_multipart", "(", "message", ")", ":", "if", "not", "message", ".", "is_multipart", "(", ")", ":", "multipart_message", "=", "email", ".", "mime", ".", "multipart", ".", "MIMEMultipart", "(", "'alternative'", ")", "for", "header_key", "in",...	46.733333	0.001399
def _filter_schlumberger(configs): """Filter Schlumberger configurations Schlumberger configurations are selected using the following criteria: * For a given voltage dipole, there need to be at least two current injections with electrodes located on the left and the right of the voltage dipole...	[ "def", "_filter_schlumberger", "(", "configs", ")", ":", "# sort configs", "configs_sorted", "=", "np", ".", "hstack", "(", "(", "np", ".", "sort", "(", "configs", "[", ":", ",", "0", ":", "2", "]", ",", "axis", "=", "1", ")", ",", "np", ".", "sort...	30.777778	0.000389
def exp_trans(base=None, *kwargs): """ Create a exponential transform class for base* This is inverse of the log transform. Parameters ---------- base : float Base of the logarithm kwargs : dict Keyword arguments passed onto :func:`trans_new`. Should not include ...	[ "def", "exp_trans", "(", "base", "=", "None", ",", "", "", "kwargs", ")", ":", "# default to e", "if", "base", "is", "None", ":", "name", "=", "'power_e'", "base", "=", "np", ".", "exp", "(", "1", ")", "else", ":", "name", "=", "'power_{}'", ".",...	21.135135	0.001222
def ln(self, h=''): "Line Feed; default value is last cell height" self.x=self.l_margin if(isinstance(h, basestring)): self.y+=self.lasth else: self.y+=h	[ "def", "ln", "(", "self", ",", "h", "=", "''", ")", ":", "self", ".", "x", "=", "self", ".", "l_margin", "if", "(", "isinstance", "(", "h", ",", "basestring", ")", ")", ":", "self", ".", "y", "+=", "self", ".", "lasth", "else", ":", "self", "...	29	0.023923
def _pair_deltas(seq, pars): '''Add up nearest-neighbor parameters for a given sequence. :param seq: DNA sequence for which to sum nearest neighbors :type seq: str :param pars: parameter set to use :type pars: dict :returns: nearest-neighbor delta_H and delta_S sums. :rtype: tuple of floats...	[ "def", "_pair_deltas", "(", "seq", ",", "pars", ")", ":", "delta0", "=", "0", "delta1", "=", "0", "for", "i", "in", "range", "(", "len", "(", "seq", ")", "-", "1", ")", ":", "curchar", "=", "seq", "[", "i", ":", "i", "+", "2", "]", "delta0", ...	28.833333	0.001866
def _iterate_managers(connection, skip): """Iterate over instantiated managers.""" for idx, name, manager_cls in _iterate_manage_classes(skip): if name in skip: continue try: manager = manager_cls(connection=connection) except TypeError as e: click.se...	[ "def", "_iterate_managers", "(", "connection", ",", "skip", ")", ":", "for", "idx", ",", "name", ",", "manager_cls", "in", "_iterate_manage_classes", "(", "skip", ")", ":", "if", "name", "in", "skip", ":", "continue", "try", ":", "manager", "=", "manager_c...	34.25	0.00237
def FunctionalGroupColorMapping(maptype='jet', reverse=False): """Maps amino-acid functional groups to colors. Currently does not use the keyword arguments for maptype or reverse but accepts these arguments to be consistent with the other mapping functions, which all get called with these argum...	[ "def", "FunctionalGroupColorMapping", "(", "maptype", "=", "'jet'", ",", "reverse", "=", "False", ")", ":", "small_color", "=", "'#f76ab4'", "nucleophilic_color", "=", "'#ff7f00'", "hydrophobic_color", "=", "'#12ab0d'", "aromatic_color", "=", "'#84380b'", "acidic_colo...	46.166667	0.022104
def search_streams(self, query, hls=False, limit=25, offset=0): """Search for streams and return them :param query: the query string :type query: :class:`str` :param hls: If true, only return streams that have hls stream :type hls: :class:`bool` :param limit: maximum num...	[ "def", "search_streams", "(", "self", ",", "query", ",", "hls", "=", "False", ",", "limit", "=", "25", ",", "offset", "=", "0", ")", ":", "r", "=", "self", ".", "kraken_request", "(", "'GET'", ",", "'search/streams'", ",", "params", "=", "{", "'query...	42.285714	0.002203
def set_default(self_,param_name,value): """ Set the default value of param_name. Equivalent to setting param_name on the class. """ cls = self_.cls setattr(cls,param_name,value)	[ "def", "set_default", "(", "self_", ",", "param_name", ",", "value", ")", ":", "cls", "=", "self_", ".", "cls", "setattr", "(", "cls", ",", "param_name", ",", "value", ")" ]	27.5	0.026432
def _prompt(letters='yn', default=None): """ Wait for the user to type a character (and hit Enter). If the user enters one of the characters in `letters`, return that character. If the user hits Enter without entering a character, and `default` is specified, returns `default`. Otherwise, asks the...	[ "def", "_prompt", "(", "letters", "=", "'yn'", ",", "default", "=", "None", ")", ":", "while", "True", ":", "try", ":", "input_text", "=", "sys", ".", "stdin", ".", "readline", "(", ")", ".", "strip", "(", ")", "except", "KeyboardInterrupt", ":", "sy...	39.647059	0.001449
def removeBiosample(self, biosample): """ Removes the specified biosample from this repository. """ q = models.Biosample.delete().where( models.Biosample.id == biosample.getId()) q.execute()	[ "def", "removeBiosample", "(", "self", ",", "biosample", ")", ":", "q", "=", "models", ".", "Biosample", ".", "delete", "(", ")", ".", "where", "(", "models", ".", "Biosample", ".", "id", "==", "biosample", ".", "getId", "(", ")", ")", "q", ".", "e...	33.714286	0.008264
async def send_code_request(self, phone, *, force_sms=False): """ Sends a code request to the specified phone number. Args: phone (`str` \| `int`): The phone to which the code will be sent. force_sms (`bool`, optional): Whether to force se...	[ "async", "def", "send_code_request", "(", "self", ",", "phone", ",", "*", ",", "force_sms", "=", "False", ")", ":", "phone", "=", "utils", ".", "parse_phone", "(", "phone", ")", "or", "self", ".", "_phone", "phone_hash", "=", "self", ".", "_phone_code_ha...	31.657895	0.001613
def reply(self, text, loop_ms=500, max_len=None): """Reply to a string of text. If the input is not already Unicode, it will be decoded as utf-8.""" if type(text) != types.UnicodeType: # Assume that non-Unicode text is encoded as utf-8, which # should be somewhat safe in ...	[ "def", "reply", "(", "self", ",", "text", ",", "loop_ms", "=", "500", ",", "max_len", "=", "None", ")", ":", "if", "type", "(", "text", ")", "!=", "types", ".", "UnicodeType", ":", "# Assume that non-Unicode text is encoded as utf-8, which", "# should be somewha...	34.065421	0.0008
def _filter_statements(statements, agents): """Return INDRA Statements which have Agents in the given list. Only statements are returned in which all appearing Agents as in the agents list. Parameters ---------- statements : list[indra.statements.Statement] A list of INDRA Statements t...	[ "def", "_filter_statements", "(", "statements", ",", "agents", ")", ":", "filtered_statements", "=", "[", "]", "for", "s", "in", "stmts", ":", "if", "all", "(", "[", "a", "is", "not", "None", "for", "a", "in", "s", ".", "agent_list", "(", ")", "]", ...	32.791667	0.002469
def _get_struct_linestylearray(self, shape_number): """Get the values for the LINESTYLEARRAY record.""" obj = _make_object("LineStyleArray") obj.LineStyleCount = count = unpack_ui8(self._src) if count == 0xFF: obj.LineStyleCountExtended = count = unpack_ui16(self._src) ...	[ "def", "_get_struct_linestylearray", "(", "self", ",", "shape_number", ")", ":", "obj", "=", "_make_object", "(", "\"LineStyleArray\"", ")", "obj", ".", "LineStyleCount", "=", "count", "=", "unpack_ui8", "(", "self", ".", "_src", ")", "if", "count", "==", "0...	39.047619	0.00119
def query(self, query, *args, prefetch=None, timeout=None): """ make a read only query. Ideal for select statements. This method converts the query to a prepared statement and uses a cursor to return the results. So you only get so many rows at a time. This can dramatically incre...	[ "def", "query", "(", "self", ",", "query", ",", "*", "args", ",", "prefetch", "=", "None", ",", "timeout", "=", "None", ")", ":", "compiled_q", ",", "compiled_args", "=", "compile_query", "(", "query", ")", "query", ",", "args", "=", "compiled_q", ",",...	44.774194	0.00141
def _validate_importers(importers): """Validates the importers and decorates the callables with our output formatter. """ # They could have no importers, that's chill if importers is None: return None def _to_importer(priority, func): assert isinstance(priority, int), priority ...	[ "def", "_validate_importers", "(", "importers", ")", ":", "# They could have no importers, that's chill", "if", "importers", "is", "None", ":", "return", "None", "def", "_to_importer", "(", "priority", ",", "func", ")", ":", "assert", "isinstance", "(", "priority", ...	34.6	0.001876
async def delete_activity(self, context: TurnContext, conversation_reference: ConversationReference): """ Deletes an activity that was previously sent to a channel. It should be noted that not all channels support this feature. :param context: :param conversation_reference: ...	[ "async", "def", "delete_activity", "(", "self", ",", "context", ":", "TurnContext", ",", "conversation_reference", ":", "ConversationReference", ")", ":", "try", ":", "client", "=", "self", ".", "create_connector_client", "(", "conversation_reference", ".", "service...	48	0.011679
def abort(status_code, detail='', headers=None, comment=None, **kw): ''' Raise an HTTP status code, as specified. Useful for returning status codes like 401 Unauthorized or 403 Forbidden. :param status_code: The HTTP status code as an integer. :param detail: The message to send along, as a string. ...	[ "def", "abort", "(", "status_code", ",", "detail", "=", "''", ",", "headers", "=", "None", ",", "comment", "=", "None", ",", "", "", "kw", ")", ":", "# If there is a traceback, we need to catch it for a re-raise", "try", ":", "_", ",", "_", ",", "traceback...	36.172414	0.000929
def parse_location(location): """Parse latitude and longitude from string location. Args: location (str): String to parse Returns: tuple of float: Latitude and longitude of location """ def split_dms(text, hemisphere): """Split degrees, minutes and seconds string. ...	[ "def", "parse_location", "(", "location", ")", ":", "def", "split_dms", "(", "text", ",", "hemisphere", ")", ":", "\"\"\"Split degrees, minutes and seconds string.\n\n Args:\n text (str): Text to split\n\n Returns::\n float: Decimal degrees\n \"...	31.540984	0.000504
def chainCerts(data): """ Matches and returns any certificates found except the first match. Regex code copied from L{twisted.internet.endpoints._parseSSL}. Related ticket: https://twistedmatrix.com/trac/ticket/7732 @type path: L{bytes} @param data: PEM-encoded data containing the certificates...	[ "def", "chainCerts", "(", "data", ")", ":", "matches", "=", "re", ".", "findall", "(", "r'(-----BEGIN CERTIFICATE-----\\n.+?\\n-----END CERTIFICATE-----)'", ",", "data", ",", "flags", "=", "re", ".", "DOTALL", ")", "chainCertificates", "=", "[", "Certificate", "."...	32.25	0.001506
def step(darray, args, *kwargs): """ Step plot of DataArray index against values Similar to :func:`matplotlib:matplotlib.pyplot.step` Parameters ---------- where : {'pre', 'post', 'mid'}, optional, default 'pre' Define where the steps should be placed: - 'pre': The y value is...	[ "def", "step", "(", "darray", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "if", "(", "'ls'", "in", "kwargs", ".", "keys", "(", ")", ")", "and", "(", "'linestyle'", "not", "in", "kwargs", ".", "keys", "(", ")", ")", ":", "kwargs", "[", ...	38.315789	0.00067
def validator(names_or_instance, names=None, func=None): """Specify a callback function to fire on class validation OR property set This function has two modes of operation: 1. Registering callback functions that validate Property values when they are set, before the change is saved to the HasPrope...	[ "def", "validator", "(", "names_or_instance", ",", "names", "=", "None", ",", "func", "=", "None", ")", ":", "if", "names", "is", "None", "and", "func", "is", "None", ":", "if", "callable", "(", "names_or_instance", ")", ":", "return", "ClassValidator", ...	38.973684	0.000329
def create_organizations_parser(stream): """Create an organizations parser for the given stream. Factory function that creates an organizations parser for the given stream. The stream is only used to guess the type of the required parser. :param stream: stream used to guess the type of the parser ...	[ "def", "create_organizations_parser", "(", "stream", ")", ":", "import", "sortinghat", ".", "parsing", "as", "parsing", "# First, try with default parser", "for", "p", "in", "parsing", ".", "SORTINGHAT_ORGS_PARSERS", ":", "klass", "=", "parsing", ".", "SORTINGHAT_ORGS...	30.8	0.001259
def user_config_dir(appname, roaming=True): """Return full path to the user-specific config dir for this application. "appname" is the name of application. If None, just the system directory is returned. "roaming" (boolean, default True) can be set False to not use the Windo...	[ "def", "user_config_dir", "(", "appname", ",", "roaming", "=", "True", ")", ":", "if", "WINDOWS", ":", "path", "=", "user_data_dir", "(", "appname", ",", "roaming", "=", "roaming", ")", "elif", "sys", ".", "platform", "==", "\"darwin\"", ":", "path", "="...	41.344828	0.000815
def cylindrical(cls, mag, theta, z=0): '''Returns a Vector instance from cylindircal coordinates''' return cls( mag * math.cos(theta), # X mag * math.sin(theta), # Y z # Z )	[ "def", "cylindrical", "(", "cls", ",", "mag", ",", "theta", ",", "z", "=", "0", ")", ":", "return", "cls", "(", "mag", "", "math", ".", "cos", "(", "theta", ")", ",", "# X", "mag", "", "math", ".", "sin", "(", "theta", ")", ",", "# Y", "z",...	32.857143	0.008475
def get_wildcard(self): """Return the wildcard bits notation of the netmask.""" return _convert(self._ip, notation=NM_WILDCARD, inotation=IP_DOT, _check=False, _isnm=self._isnm)	[ "def", "get_wildcard", "(", "self", ")", ":", "return", "_convert", "(", "self", ".", "_ip", ",", "notation", "=", "NM_WILDCARD", ",", "inotation", "=", "IP_DOT", ",", "_check", "=", "False", ",", "_isnm", "=", "self", ".", "_isnm", ")" ]	53.5	0.009217
def request(self, method, url, fields=None, headers=None, **urlopen_kw): """ Make a request using :meth:`urlopen` with the appropriate encoding of ``fields`` based on the ``method`` used. This is a convenience method that requires the least amount of manual effort. It can be use...	[ "def", "request", "(", "self", ",", "method", ",", "url", ",", "fields", "=", "None", ",", "headers", "=", "None", ",", "", "", "urlopen_kw", ")", ":", "method", "=", "method", ".", "upper", "(", ")", "if", "method", "in", "self", ".", "_encode_u...	48.619048	0.001921
def to_fastg(infile, outfile, circular=None): '''Writes a FASTG file in SPAdes format from input file. Currently only whether or not a sequence is circular is supported. Put circular=set of ids, or circular=filename to make those sequences circular in the output. Puts coverage=1 on all contigs''' if circular is...	[ "def", "to_fastg", "(", "infile", ",", "outfile", ",", "circular", "=", "None", ")", ":", "if", "circular", "is", "None", ":", "to_circularise", "=", "set", "(", ")", "elif", "type", "(", "circular", ")", "is", "not", "set", ":", "f", "=", "utils", ...	32.615385	0.001527
async def get_data(self): """Retrieve the data.""" url = '{}/{}'.format(self.url, 'all') try: with async_timeout.timeout(5, loop=self._loop): if self.password is None: response = await self._session.get(url) else: ...	[ "async", "def", "get_data", "(", "self", ")", ":", "url", "=", "'{}/{}'", ".", "format", "(", "self", ".", "url", ",", "'all'", ")", "try", ":", "with", "async_timeout", ".", "timeout", "(", "5", ",", "loop", "=", "self", ".", "_loop", ")", ":", ...	41.9	0.002334
def has_bad_headers(self): """ Checks for bad headers i.e. newlines in subject, sender or recipients. RFC5322 allows multiline CRLF with trailing whitespace (FWS) in headers """ headers = [self.sender, self.reply_to] + self.recipients for header in headers: if...	[ "def", "has_bad_headers", "(", "self", ")", ":", "headers", "=", "[", "self", ".", "sender", ",", "self", ".", "reply_to", "]", "+", "self", ".", "recipients", "for", "header", "in", "headers", ":", "if", "_has_newline", "(", "header", ")", ":", "retur...	38.318182	0.002315
def set_zone(timezone): ''' Unlinks, then symlinks /etc/localtime to the set timezone. The timezone is crucial to several system processes, each of which SHOULD be restarted (for instance, whatever you system uses as its cron and syslog daemons). This will not be automagically done and must be done...	[ "def", "set_zone", "(", "timezone", ")", ":", "if", "salt", ".", "utils", ".", "path", ".", "which", "(", "'timedatectl'", ")", ":", "try", ":", "__salt__", "[", "'cmd.run'", "]", "(", "'timedatectl set-timezone {0}'", ".", "format", "(", "timezone", ")", ...	33.27027	0.001972
def add_udev_trigger(self, trigger_action, subsystem): """ Subscribe to the requested udev subsystem and apply the given action. """ if self._py3_wrapper.udev_monitor.subscribe(self, trigger_action, subsystem): if trigger_action == "refresh_and_freeze": # FIXM...	[ "def", "add_udev_trigger", "(", "self", ",", "trigger_action", ",", "subsystem", ")", ":", "if", "self", ".", "_py3_wrapper", ".", "udev_monitor", ".", "subscribe", "(", "self", ",", "trigger_action", ",", "subsystem", ")", ":", "if", "trigger_action", "==", ...	55.625	0.00885
def adjustHspsForPlotting(self, titleAlignments): """ Our HSPs are about to be plotted. If we are using e-values, these need to be adjusted. @param titleAlignments: An instance of L{TitleAlignment}. """ # If we're using bit scores, there's nothing to do. if self....	[ "def", "adjustHspsForPlotting", "(", "self", ",", "titleAlignments", ")", ":", "# If we're using bit scores, there's nothing to do.", "if", "self", ".", "scoreClass", "is", "HigherIsBetterScore", ":", "return", "# Convert all e-values to high positive values, and keep track of the"...	40.372093	0.001125
def pad_to_size(data, shape, value=0.0): """ This is similar to `pad`, except you specify the final shape of the array. Parameters ---------- data : ndarray Numpy array of any dimension and type. shape : tuple Final shape of padded array. Should be tuple of length ``data.ndim``....	[ "def", "pad_to_size", "(", "data", ",", "shape", ",", "value", "=", "0.0", ")", ":", "shape", "=", "[", "data", ".", "shape", "[", "i", "]", "if", "shape", "[", "i", "]", "==", "-", "1", "else", "shape", "[", "i", "]", "for", "i", "in", "rang...	32.659091	0.000676
def try_greyscale(pixels, alpha=False, dirty_alpha=True): """ Check if flatboxed RGB `pixels` could be converted to greyscale If could - return iterator with greyscale pixels, otherwise return `False` constant """ planes = 3 + bool(alpha) res = list() apix = list() for row in pixels...	[ "def", "try_greyscale", "(", "pixels", ",", "alpha", "=", "False", ",", "dirty_alpha", "=", "True", ")", ":", "planes", "=", "3", "+", "bool", "(", "alpha", ")", "res", "=", "list", "(", ")", "apix", "=", "list", "(", ")", "for", "row", "in", "pi...	27.727273	0.001585
def check_indexes_all_same(indexes, message="Indexes are not equal."): """Check that a list of Index objects are all equal. Parameters ---------- indexes : iterable[pd.Index] Iterable of indexes to check. Raises ------ ValueError If the indexes are not all the same. """...	[ "def", "check_indexes_all_same", "(", "indexes", ",", "message", "=", "\"Indexes are not equal.\"", ")", ":", "iterator", "=", "iter", "(", "indexes", ")", "first", "=", "next", "(", "iterator", ")", "for", "other", "in", "iterator", ":", "same", "=", "(", ...	28.32	0.001366
def acceptance_prob(old_cost, new_cost, T): """annealing equation, with modifications to work towards a lower value""" #if start pos is not valid, always move if old_cost == 1e20: return 1.0 #if we have found a valid ps before, never move to nonvalid pos if new_cost == 1e20: return 0...	[ "def", "acceptance_prob", "(", "old_cost", ",", "new_cost", ",", "T", ")", ":", "#if start pos is not valid, always move", "if", "old_cost", "==", "1e20", ":", "return", "1.0", "#if we have found a valid ps before, never move to nonvalid pos", "if", "new_cost", "==", "1e2...	40.923077	0.011029
def main(): '''This is the main function of this script. The current script args are shown below :: Usage: checkplotlist [-h] [--search SEARCH] [--sortby SORTBY] [--filterby FILTERBY] [--splitout SPLITOUT] [--outprefix OUTPREFIX] [--maxkeyworke...	[ "def", "main", "(", ")", ":", "####################", "## PARSE THE ARGS ##", "####################", "aparser", "=", "argparse", ".", "ArgumentParser", "(", "epilog", "=", "PROGEPILOG", ",", "description", "=", "PROGDESC", ",", "formatter_class", "=", "argparse", "...	38.147114	0.002236
def raise_for_invalid_annotation_value(self, line: str, position: int, key: str, value: str) -> None: """Raise an exception if the annotation is not defined. :raises: IllegalAnnotationValueWarning or MissingAnnotationRegexWarning """ if self._in_debug_mode: return i...	[ "def", "raise_for_invalid_annotation_value", "(", "self", ",", "line", ":", "str", ",", "position", ":", "int", ",", "key", ":", "str", ",", "value", ":", "str", ")", "->", "None", ":", "if", "self", ".", "_in_debug_mode", ":", "return", "if", "self", ...	56.125	0.009858
def check_connection_state(self): """Check the state of the connection using connection state request. This sends a CONNECTION_STATE_REQUEST. This method will only return True, if the connection is established and no error code is returned from the KNX/IP gateway """ if ...	[ "def", "check_connection_state", "(", "self", ")", ":", "if", "not", "self", ".", "connected", ":", "self", ".", "connection_state", "=", "-", "1", "return", "False", "frame", "=", "KNXIPFrame", "(", "KNXIPFrame", ".", "CONNECTIONSTATE_REQUEST", ")", "frame", ...	40.402597	0.000628
def subgroup(self, t, i): """Handle parenthesis.""" current = [] # (?flags) flags = self.get_flags(i) if flags: self.flags(flags[2:-1]) return [flags] # (?#comment) comments = self.get_comments(i) if comments: return ...	[ "def", "subgroup", "(", "self", ",", "t", ",", "i", ")", ":", "current", "=", "[", "]", "# (?flags)", "flags", "=", "self", ".", "get_flags", "(", "i", ")", "if", "flags", ":", "self", ".", "flags", "(", "flags", "[", "2", ":", "-", "1", "]", ...	22.636364	0.001925
def bam2mat(args): """ %prog bam2mat input.bam Convert bam file to .mat format, which is simply numpy 2D array. Important parameter is the resolution, which is the cell size. Small cell size lead to more fine-grained heatmap, but leads to large .mat size and slower plotting. """ import ...	[ "def", "bam2mat", "(", "args", ")", ":", "import", "pysam", "from", "jcvi", ".", "utils", ".", "cbook", "import", "percentage", "p", "=", "OptionParser", "(", "bam2mat", ".", "__doc__", ")", "p", ".", "add_option", "(", "\"--resolution\"", ",", "default", ...	33.24	0.000292
def by_population_density(self, lower=-1, upper=2 ** 31, zipcode_type=ZipcodeType.Standard, sort_by=SimpleZipcode.population_density.name, ascending=False, ...	[ "def", "by_population_density", "(", "self", ",", "lower", "=", "-", "1", ",", "upper", "=", "2", "**", "31", ",", "zipcode_type", "=", "ZipcodeType", ".", "Standard", ",", "sort_by", "=", "SimpleZipcode", ".", "population_density", ".", "name", ",", "asce...	40.666667	0.010681
def peek(self): '''Return (but do not consume) the next token At the end of input, ``None`` is returned. ''' if self.position >= len(self.tokens): return None return self.tokens[self.position]	[ "def", "peek", "(", "self", ")", ":", "if", "self", ".", "position", ">=", "len", "(", "self", ".", "tokens", ")", ":", "return", "None", "return", "self", ".", "tokens", "[", "self", ".", "position", "]" ]	23.8	0.008097
def simple_prot(x, start): """Find the first peak to the right of start""" # start must b >= 1 for i in range(start,len(x)-1): a,b,c = x[i-1], x[i], x[i+1] if b - a > 0 and b -c >= 0: return i else: return None	[ "def", "simple_prot", "(", "x", ",", "start", ")", ":", "# start must b >= 1", "for", "i", "in", "range", "(", "start", ",", "len", "(", "x", ")", "-", "1", ")", ":", "a", ",", "b", ",", "c", "=", "x", "[", "i", "-", "1", "]", ",", "x", "["...	23.181818	0.022642
def get_versions(): """ Wrap in a function to ensure that we don't run this every time a CLI command runs (yuck!) Also protects import of `requests` from issues when grabbed by setuptools. More on that inline """ # import in the func (rather than top-level scope) so that at setup time, ...	[ "def", "get_versions", "(", ")", ":", "# import in the func (rather than top-level scope) so that at setup time,", "# `requests` isn't required -- otherwise, setuptools will fail to run", "# because requests isn't installed yet.", "import", "requests", "try", ":", "version_data", "=", "r...	36.181818	0.001224
def pick_unused_port(pid=None, portserver_address=None): """A pure python implementation of PickUnusedPort. Args: pid: PID to tell the portserver to associate the reservation with. If None, the current process's PID is used. portserver_address: The address (path) of a unix domain socket ...	[ "def", "pick_unused_port", "(", "pid", "=", "None", ",", "portserver_address", "=", "None", ")", ":", "try", ":", "# Instead of `if _free_ports:` to handle the race condition.", "port", "=", "_free_ports", ".", "pop", "(", ")", "except", "KeyError", ":", "pass", "...	39.421053	0.000651
def read_config(filename): """Reads and flattens a configuration file into a single dictionary for ease of use. Works with both ``.config`` and ``.yaml`` files. Files should look like this:: search_rules: from-date: 2017-06-01 to-date: 2017-09-01 01:01 pt-rule: k...	[ "def", "read_config", "(", "filename", ")", ":", "file_type", "=", "\"yaml\"", "if", "filename", ".", "endswith", "(", "\".yaml\"", ")", "else", "\"config\"", "config", "=", "configparser", ".", "ConfigParser", "(", ")", "if", "file_type", "==", "\"yaml\"", ...	30.014286	0.000461
def _dedup(items, insensitive): ''' Deduplicate an item list, and preserve order. For case-insensitive lists, drop items if they case-insensitively match a prior item. ''' deduped = [] if insensitive: i_deduped = [] for item in items: lowered = item.lower() ...	[ "def", "_dedup", "(", "items", ",", "insensitive", ")", ":", "deduped", "=", "[", "]", "if", "insensitive", ":", "i_deduped", "=", "[", "]", "for", "item", "in", "items", ":", "lowered", "=", "item", ".", "lower", "(", ")", "if", "lowered", "not", ...	27.2	0.001776
def multi_path_generator(pathnames): """ yields (name,chunkgen) for all of the files found under the list of pathnames given. This is recursive, so directories will have their contents emitted. chunkgen is a function that can called and iterated over to obtain the contents of the file in multiple ...	[ "def", "multi_path_generator", "(", "pathnames", ")", ":", "for", "pathname", "in", "pathnames", ":", "if", "isdir", "(", "pathname", ")", ":", "for", "entry", "in", "directory_generator", "(", "pathname", ")", ":", "yield", "entry", "else", ":", "yield", ...	35.266667	0.001842
def path(self): """HTTP full path constraint. (read-only). """ path = self.__prefix if self is not self.over: path = self.over.path + path return path	[ "def", "path", "(", "self", ")", ":", "path", "=", "self", ".", "__prefix", "if", "self", "is", "not", "self", ".", "over", ":", "path", "=", "self", ".", "over", ".", "path", "+", "path", "return", "path" ]	28	0.009901
def __add_actions(self): """ Sets Component actions. """ LOGGER.debug("> Adding '{0}' Component actions.".format(self.__class__.__name__)) add_project_action = self.__engine.actions_manager.get_action( "Actions\|Umbra\|Components\|factory.script_editor\|&File\|Add Projec...	[ "def", "__add_actions", "(", "self", ")", ":", "LOGGER", ".", "debug", "(", "\"> Adding '{0}' Component actions.\"", ".", "format", "(", "self", ".", "__class__", ".", "__name__", ")", ")", "add_project_action", "=", "self", ".", "__engine", ".", "actions_manage...	53.333333	0.0086
def get_venue(self, id, **data): """ GET /venues/:id/ Returns a :format:`venue` object. """ return self.get("/venues/{0}/".format(id), data=data)	[ "def", "get_venue", "(", "self", ",", "id", ",", "", "", "data", ")", ":", "return", "self", ".", "get", "(", "\"/venues/{0}/\"", ".", "format", "(", "id", ")", ",", "data", "=", "data", ")" ]	26.857143	0.015464
def get_grounded_agent(gene_name): """Return a grounded Agent based on an HGNC symbol.""" db_refs = {'TEXT': gene_name} if gene_name in hgnc_map: gene_name = hgnc_map[gene_name] hgnc_id = hgnc_client.get_hgnc_id(gene_name) if hgnc_id: db_refs['HGNC'] = hgnc_id up_id = hgnc_cl...	[ "def", "get_grounded_agent", "(", "gene_name", ")", ":", "db_refs", "=", "{", "'TEXT'", ":", "gene_name", "}", "if", "gene_name", "in", "hgnc_map", ":", "gene_name", "=", "hgnc_map", "[", "gene_name", "]", "hgnc_id", "=", "hgnc_client", ".", "get_hgnc_id", "...	34.692308	0.00216
def add_callback(self, user_gpio, edge=RISING_EDGE, func=None): """ Calls a user supplied function (a callback) whenever the specified gpio edge is detected. user_gpio:= 0-31. edge:= EITHER_EDGE, RISING_EDGE (default), or FALLING_EDGE. func:= user supplied callback...	[ "def", "add_callback", "(", "self", ",", "user_gpio", ",", "edge", "=", "RISING_EDGE", ",", "func", "=", "None", ")", ":", "cb", "=", "Callback", "(", "self", ".", "_notify", ",", "user_gpio", ",", "edge", ",", "func", ")", "yield", "from", "self", "...	29.073171	0.001623
def endpoint_loader(request, application, model, **kwargs): """Load an AJAX endpoint. This will load either an ad-hoc endpoint or it will load up a model endpoint depending on what it finds. It first attempts to load ``model`` as if it were an ad-hoc endpoint. Alternatively, it will attempt to see if ...	[ "def", "endpoint_loader", "(", "request", ",", "application", ",", "model", ",", "", "", "kwargs", ")", ":", "if", "request", ".", "method", "!=", "\"POST\"", ":", "raise", "AJAXError", "(", "400", ",", "_", "(", "'Invalid HTTP method used.'", ")", ")", ...	30.606557	0.002076
def set_cell(self, column_family_id, column, value, timestamp=None): """Sets a value in this row. The cell is determined by the ``row_key`` of this :class:`DirectRow` and the ``column``. The ``column`` must be in an existing :class:`.ColumnFamily` (as determined by ``column_family_id``)...	[ "def", "set_cell", "(", "self", ",", "column_family_id", ",", "column", ",", "value", ",", "timestamp", "=", "None", ")", ":", "self", ".", "_set_cell", "(", "column_family_id", ",", "column", ",", "value", ",", "timestamp", "=", "timestamp", ",", "state",...	41.263158	0.001869
def load_object(path): """Return the Python object represented by dotted path.""" i = path.rfind('.') module_name, object_name = path[:i], path[i + 1:] # Load module. try: module = import_module(module_name) except ImportError: raise ImproperlyConfigured('Module %r not found' %...	[ "def", "load_object", "(", "path", ")", ":", "i", "=", "path", ".", "rfind", "(", "'.'", ")", "module_name", ",", "object_name", "=", "path", "[", ":", "i", "]", ",", "path", "[", "i", "+", "1", ":", "]", "# Load module.", "try", ":", "module", "...	37.588235	0.001527
def incrementing_sleep(self, previous_attempt_number, delay_since_first_attempt_ms): """ Sleep an incremental amount of time after each attempt, starting at wait_incrementing_start and incrementing by wait_incrementing_increment """ result = self._wait_incrementing_start + (self....	[ "def", "incrementing_sleep", "(", "self", ",", "previous_attempt_number", ",", "delay_since_first_attempt_ms", ")", ":", "result", "=", "self", ".", "_wait_incrementing_start", "+", "(", "self", ".", "_wait_incrementing_increment", "*", "(", "previous_attempt_number", "...	49	0.008909
def make_folder_for_today(log_dir): """Creates the folder log_dir/yyyy/mm/dd in log_dir if it doesn't exist and returns the full path of the folder.""" now = datetime.datetime.now() sub_folders_list = ['{0:04d}'.format(now.year), '{0:02d}'.format(now.month), ...	[ "def", "make_folder_for_today", "(", "log_dir", ")", ":", "now", "=", "datetime", ".", "datetime", ".", "now", "(", ")", "sub_folders_list", "=", "[", "'{0:04d}'", ".", "format", "(", "now", ".", "year", ")", ",", "'{0:02d}'", ".", "format", "(", "now", ...	40.076923	0.001876
def show_scan_report(audio_filepaths, album_dir, r128_data): """ Display loudness scan results. """ # track loudness/peak for audio_filepath in audio_filepaths: try: loudness, peak = r128_data[audio_filepath] except KeyError: loudness, peak = "SKIPPED", "SKIPPED" else: loudness = "%....	[ "def", "show_scan_report", "(", "audio_filepaths", ",", "album_dir", ",", "r128_data", ")", ":", "# track loudness/peak", "for", "audio_filepath", "in", "audio_filepaths", ":", "try", ":", "loudness", ",", "peak", "=", "r128_data", "[", "audio_filepath", "]", "exc...	34.655172	0.017425
def get_child(self, types): """ :param types: list of requested types. :return: the first (and in most useful cases only) child of specific type(s). """ children = list(self.get_children(types)) return children[0] if any(children) else None	[ "def", "get_child", "(", "self", ",", "", "types", ")", ":", "children", "=", "list", "(", "self", ".", "get_children", "(", "", "types", ")", ")", "return", "children", "[", "0", "]", "if", "any", "(", "children", ")", "else", "None" ]	40.571429	0.010345
def phenotype_to_res_set(phenotype, resources): """ Converts a binary string to a set containing the resources indicated by the bits in the string. Inputs: phenotype - a binary string resources - a list of string indicating which resources correspond to which indices...	[ "def", "phenotype_to_res_set", "(", "phenotype", ",", "resources", ")", ":", "assert", "(", "phenotype", "[", "0", ":", "2", "]", "==", "\"0b\"", ")", "phenotype", "=", "phenotype", "[", "2", ":", "]", "# Fill in leading zeroes", "while", "len", "(", "phen...	29.72	0.001304
def create_store(self): """ Creates store object """ if self.store_class is not None: return self.store_class.load(self.client.webfinger, self) raise NotImplementedError("You need to specify PyPump.store_class or override PyPump.create_store method.")	[ "def", "create_store", "(", "self", ")", ":", "if", "self", ".", "store_class", "is", "not", "None", ":", "return", "self", ".", "store_class", ".", "load", "(", "self", ".", "client", ".", "webfinger", ",", "self", ")", "raise", "NotImplementedError", "...	47.166667	0.010417
def manual_migration(): """ Simple interactive function to pause the deployment. A manual migration can be done two different ways: Option 1: Enter y to exit the current deployment. When migration is completed run deploy again. Option 2: run the migration in a separate shell """ if env.IN...	[ "def", "manual_migration", "(", ")", ":", "if", "env", ".", "INTERACTIVITY", ":", "print", "\"A manual migration can be done two different ways:\"", "print", "\"Option 1: Enter y to exit the current deployment. When migration is completed run deploy again.\"", "print", "\"Option 2: run...	48.588235	0.009501
def get_cb_depth_set(cb_histogram, cb_cutoff): ''' Returns a set of barcodes with a minimum number of reads ''' cb_keep_set = set() if not cb_histogram: return cb_keep_set with read_cbhistogram(cb_histogram) as fh: cb_map = dict(p.strip().split() for p in fh) cb_keep_set = s...	[ "def", "get_cb_depth_set", "(", "cb_histogram", ",", "cb_cutoff", ")", ":", "cb_keep_set", "=", "set", "(", ")", "if", "not", "cb_histogram", ":", "return", "cb_keep_set", "with", "read_cbhistogram", "(", "cb_histogram", ")", "as", "fh", ":", "cb_map", "=", ...	38.769231	0.001938
def get_decimal_precision(number): """Return maximum precision of a decimal instance's fractional part. Precision is extracted from the fractional part only. """ # Copied from: https://github.com/mahmoud/boltons/pull/59 assert isinstance(number, decimal.Decimal) decimal_tuple = number.normalize(...	[ "def", "get_decimal_precision", "(", "number", ")", ":", "# Copied from: https://github.com/mahmoud/boltons/pull/59", "assert", "isinstance", "(", "number", ",", "decimal", ".", "Decimal", ")", "decimal_tuple", "=", "number", ".", "normalize", "(", ")", ".", "as_tuple...	41.5	0.002358
def convert(self, version): """convert MDF to other version Parameters ---------- version : str new mdf file version from ('2.00', '2.10', '2.14', '3.00', '3.10', '3.20', '3.30', '4.00', '4.10', '4.11'); default '4.10' Returns ------- o...	[ "def", "convert", "(", "self", ",", "version", ")", ":", "version", "=", "validate_version_argument", "(", "version", ")", "out", "=", "MDF", "(", "version", "=", "version", ")", "out", ".", "header", ".", "start_time", "=", "self", ".", "header", ".", ...	39.694118	0.001879
def option_map(self): """Map command-line options to args.""" option_map = OrderedDict() for arg in self.args.values(): for option in arg.options: option_map[option] = arg return option_map	[ "def", "option_map", "(", "self", ")", ":", "option_map", "=", "OrderedDict", "(", ")", "for", "arg", "in", "self", ".", "args", ".", "values", "(", ")", ":", "for", "option", "in", "arg", ".", "options", ":", "option_map", "[", "option", "]", "=", ...	34.714286	0.008032
def update_panel(self, panel_obj, version=None, date_obj=None): """Replace a existing gene panel with a new one Keeps the object id Args: panel_obj(dict) version(float) date_obj(datetime.datetime) Returns: updated_panel(dict) """...	[ "def", "update_panel", "(", "self", ",", "panel_obj", ",", "version", "=", "None", ",", "date_obj", "=", "None", ")", ":", "LOG", ".", "info", "(", "\"Updating panel %s\"", ",", "panel_obj", "[", "'panel_name'", "]", ")", "# update date of panel to \"today\"", ...	30.676471	0.001859
def locked_delete(self): """Delete credentials from the SQLAlchemy datastore.""" filters = {self.key_name: self.key_value} self.session.query(self.model_class).filter_by(**filters).delete()	[ "def", "locked_delete", "(", "self", ")", ":", "filters", "=", "{", "self", ".", "key_name", ":", "self", ".", "key_value", "}", "self", ".", "session", ".", "query", "(", "self", ".", "model_class", ")", ".", "filter_by", "(", "", "", "filters", "...	52.5	0.00939
def to_html(graph: BELGraph) -> str: """Render the graph as an HTML string. Common usage may involve writing to a file like: >>> from pybel.examples import sialic_acid_graph >>> with open('html_output.html', 'w') as file: ... print(to_html(sialic_acid_graph), file=file) """ context = g...	[ "def", "to_html", "(", "graph", ":", "BELGraph", ")", "->", "str", ":", "context", "=", "get_network_summary_dict", "(", "graph", ")", "summary_dict", "=", "graph", ".", "summary_dict", "(", ")", "citation_years", "=", "context", "[", "'citation_years'", "]", ...	43.296296	0.002091
def spellcheck(word, wordlist, depth = 2): """ Given a word list and a depth parameter, return all words w' in the wordlist with LevenshteinDistance(word, w') <= depth :param word: :param wordlist: >>> Dic = ['pes', 'pesse', 'pease', 'peis', 'peisse', 'pise', 'peose', 'poese', 'poisen'] >>...	[ "def", "spellcheck", "(", "word", ",", "wordlist", ",", "depth", "=", "2", ")", ":", "Aut", "=", "LevenshteinAutomaton", "(", "word", ",", "depth", "=", "depth", ")", ".", "convert_to_deterministic", "(", ")", "W", "=", "make_worlist_trie", "(", "wordlist"...	36.736842	0.009777
def find_log_dir(log_dir=None): """Returns the most suitable directory to put log files into. Args: log_dir: str\|None, if specified, the logfile(s) will be created in that directory. Otherwise if the --log_dir command-line flag is provided, the logfile will be created in that directory. Other...	[ "def", "find_log_dir", "(", "log_dir", "=", "None", ")", ":", "# Get a list of possible log dirs (will try to use them in order).", "if", "log_dir", ":", "# log_dir was explicitly specified as an arg, so use it and it alone.", "dirs", "=", "[", "log_dir", "]", "elif", "FLAGS", ...	38.68	0.0111
def _check_select(self): '''Select task to fetch & process''' while self._send_buffer: _task = self._send_buffer.pop() try: # use force=False here to prevent automatic send_buffer append and get exception self.send_task(_task, False) ex...	[ "def", "_check_select", "(", "self", ")", ":", "while", "self", ".", "_send_buffer", ":", "_task", "=", "self", ".", "_send_buffer", ".", "pop", "(", ")", "try", ":", "# use force=False here to prevent automatic send_buffer append and get exception", "self", ".", "s...	37.586538	0.002243
def cli_help(context, command_name, general_parser, command_parsers): """ Outputs help information. See :py:mod:`swiftly.cli.help` for context usage information. See :py:class:`CLIHelp` for more information. :param context: The :py:class:`swiftly.cli.context.CLIContext` to use. :param...	[ "def", "cli_help", "(", "context", ",", "command_name", ",", "general_parser", ",", "command_parsers", ")", ":", "if", "command_name", "==", "'for'", ":", "command_name", "=", "'fordo'", "with", "context", ".", "io_manager", ".", "with_stdout", "(", ")", "as",...	38.035714	0.000916
def _create_adapter_type(network_adapter, adapter_type, network_adapter_label=''): ''' Returns a vim.vm.device.VirtualEthernetCard object specifying a virtual ethernet card information network_adapter None or VirtualEthernet object adapter_type String, type...	[ "def", "_create_adapter_type", "(", "network_adapter", ",", "adapter_type", ",", "network_adapter_label", "=", "''", ")", ":", "log", ".", "trace", "(", "'Configuring virtual machine network '", "'adapter adapter_type=%s'", ",", "adapter_type", ")", "if", "adapter_type", ...	40.777778	0.001597
def _conditional_committors(source, sink, waypoint, tprob): """ Computes the conditional committors :math:`q^{ABC^+}` which are is the probability of starting in one state and visiting state B before A while also visiting state C at some point. Note that in the notation of Dickson et. al. this comp...	[ "def", "_conditional_committors", "(", "source", ",", "sink", ",", "waypoint", ",", "tprob", ")", ":", "n_states", "=", "np", ".", "shape", "(", "tprob", ")", "[", "0", "]", "forward_committors", "=", "_committors", "(", "[", "source", "]", ",", "[", "...	32.575758	0.001354

def note_and_log(cls): """ This will be used as a decorator on class to activate logging and store messages in the variable cls._notes This will allow quick access to events in the web app. A note can be added to cls._notes without logging if passing the argument log=false to function note() ...

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def process_params(self, params): ''' Populates the launch data from a dictionary. Only cares about keys in the LAUNCH_DATA_PARAMETERS list, or that start with 'custom_' or 'ext_'. ''' for key, val in params.items(): if key in LAUNCH_DATA_PARAMETERS and val !=...

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def getMultiSeriesRegistrations(self,q_filter=Q(),name_series=False,**kwargs): ''' Use the getSeriesRegistered method above to get a list of each series the person has registered for. The return only indicates whether they are registered more than once for the same series (e.g. for keep...

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def process_item(self, item): """Calculate new maximum value for each group, for "new" items only. """ group, value = item['group'], item['value'] if group in self._groups: cur_val = self._groups[group] self._groups[group] = max(cur_val, value) els...

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def isel_variable_and_index( name: Hashable, variable: Variable, index: pd.Index, indexers: Mapping[Any, Union[slice, Variable]], ) -> Tuple[Variable, Optional[pd.Index]]: """Index a Variable and pandas.Index together.""" if not indexers: # nothing to index return variable.copy(d...

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def _interpret_result(self, task): """ Interpret the result of a ping. :param task: The pinger task. The result or exception of the `task` is interpreted as follows: * :data:`None` result: *positive* * :class:`aioxmpp.errors.XMPPError`, ``service-unavailable``: ...

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def htmljoin(ol,sp,**kwargs): ''' ol = [1,2,3,4] htmljoin(ol,"option",outer="select") ''' if('outer' in kwargs): outer = kwargs['outer'] else: outer = "" if(outer): head = "<" + outer + ">" tail = "</" + outer + ">" else: head = ""...

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def configure_output(verbosity=0, output_levels=None, quiet=False): """ Configure verbosity level through Fabric's output managers. Provides a default mapping from verbosity levels to output types. :param verbosity: an integral verbosity level :param output_levels: an optional mapping from Fabric ...

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def setAlternateColor(self, color): """ Sets the alternate color for this node. :param color <QColor> """ color = QColor(color) if self._palette is None: self._palette = XNodePalette(self._scenePalette) self._palette.setCol...

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def _setup_observers(self): """ Setup the default observers 1: pass through to parent, if present """ if self.has_parent(): self.add_observer(self._parent_, self._parent_._pass_through_notify_observers, -np.inf)

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def clean(self): """ Remove unused filters. """ for f in sorted(self.components.keys()): unused = not any(self.switches[a][f] for a in self.analytes) if unused: self.remove(f)

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def bytes2fsn(data, encoding="utf-8"): """ Args: data (bytes): The data to convert encoding (`str`): encoding used for Windows Returns: `fsnative` Raises: TypeError: If no `bytes` path is passed ValueError: If decoding fails or the encoding is invalid Turns `...

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def anonymous_required(function=None, redirect_url=None): """ Decorator requiring the current user to be anonymous (not logged in). """ if not redirect_url: redirect_url = settings.LOGIN_REDIRECT_URL actual_decorator = user_passes_test( is_anonymous, login_url=redirect_url, ...

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def post_event_display_settings(self, id, **data): """ POST /events/:id/display_settings/ Updates the display settings for an event. """ return self.post("/events/{0}/display_settings/".format(id), data=data)

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def shortlex(start, other, excludestart=False): """Yield all unions of start with other in shortlex order. >>> ['{:03b}'.format(s) for s in shortlex(0, [0b100, 0b010, 0b001])] ['000', '100', '010', '001', '110', '101', '011', '111'] >>> ', '.join(''.join(sorted(s)) ... for s in shortlex(set(), [{'...

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def _variants_fields(fields, exclude_fields, info_ids): """Utility function to determine which fields to extract when loading variants.""" if fields is None: # no fields specified by user # by default extract all standard and INFO fields fields = config.STANDARD_VARIANT_FIELDS + info...

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def accelerated_proximal_gradient(x, f, g, gamma, niter, callback=None, **kwargs): r"""Accelerated proximal gradient algorithm for convex optimization. The method is known as "Fast Iterative Soft-Thresholding Algorithm" (FISTA). See `[Beck2009]`_ for more information. ...

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def down_capture(returns, factor_returns, **kwargs): """ Compute the capture ratio for periods when the benchmark return is negative Parameters ---------- returns : pd.Series or np.ndarray Returns of the strategy, noncumulative. - See full explanation in :func:`~empyrical.stats.cum_...

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def saved_searches(self): """ :reference: https://developer.twitter.com/en/docs/accounts-and-users/manage-account-settings/api-reference/get-saved_searches-list """ return bind_api( api=self, path='/saved_searches/list.json', payload_type='saved_search', payload_list=...

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def orthogonal_initialization(X,K): """ Initialize the centrodis by orthogonal_initialization. Parameters -------------------- X(data): array-like, shape= (m_samples,n_samples) K: integer number of K clusters Returns ------- centroids: array-like, shape (K,n_samples) ...

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def make_message_multipart(message): """Convert a message into a multipart message.""" if not message.is_multipart(): multipart_message = email.mime.multipart.MIMEMultipart('alternative') for header_key in set(message.keys()): # Preserve duplicate headers values = message...

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def _filter_schlumberger(configs): """Filter Schlumberger configurations Schlumberger configurations are selected using the following criteria: * For a given voltage dipole, there need to be at least two current injections with electrodes located on the left and the right of the voltage dipole...

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def exp_trans(base=None, **kwargs): """ Create a exponential transform class for *base* This is inverse of the log transform. Parameters ---------- base : float Base of the logarithm kwargs : dict Keyword arguments passed onto :func:`trans_new`. Should not include ...

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def ln(self, h=''): "Line Feed; default value is last cell height" self.x=self.l_margin if(isinstance(h, basestring)): self.y+=self.lasth else: self.y+=h

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def _pair_deltas(seq, pars): '''Add up nearest-neighbor parameters for a given sequence. :param seq: DNA sequence for which to sum nearest neighbors :type seq: str :param pars: parameter set to use :type pars: dict :returns: nearest-neighbor delta_H and delta_S sums. :rtype: tuple of floats...

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def _iterate_managers(connection, skip): """Iterate over instantiated managers.""" for idx, name, manager_cls in _iterate_manage_classes(skip): if name in skip: continue try: manager = manager_cls(connection=connection) except TypeError as e: click.se...

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def FunctionalGroupColorMapping(maptype='jet', reverse=False): """Maps amino-acid functional groups to colors. Currently does not use the keyword arguments for *maptype* or *reverse* but accepts these arguments to be consistent with the other mapping functions, which all get called with these argum...

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def search_streams(self, query, hls=False, limit=25, offset=0): """Search for streams and return them :param query: the query string :type query: :class:`str` :param hls: If true, only return streams that have hls stream :type hls: :class:`bool` :param limit: maximum num...

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def set_default(self_,param_name,value): """ Set the default value of param_name. Equivalent to setting param_name on the class. """ cls = self_.cls setattr(cls,param_name,value)

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def _prompt(letters='yn', default=None): """ Wait for the user to type a character (and hit Enter). If the user enters one of the characters in `letters`, return that character. If the user hits Enter without entering a character, and `default` is specified, returns `default`. Otherwise, asks the...

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def removeBiosample(self, biosample): """ Removes the specified biosample from this repository. """ q = models.Biosample.delete().where( models.Biosample.id == biosample.getId()) q.execute()

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async def send_code_request(self, phone, *, force_sms=False): """ Sends a code request to the specified phone number. Args: phone (`str` | `int`): The phone to which the code will be sent. force_sms (`bool`, optional): Whether to force se...

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def reply(self, text, loop_ms=500, max_len=None): """Reply to a string of text. If the input is not already Unicode, it will be decoded as utf-8.""" if type(text) != types.UnicodeType: # Assume that non-Unicode text is encoded as utf-8, which # should be somewhat safe in ...

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def _filter_statements(statements, agents): """Return INDRA Statements which have Agents in the given list. Only statements are returned in which all appearing Agents as in the agents list. Parameters ---------- statements : list[indra.statements.Statement] A list of INDRA Statements t...

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def _get_struct_linestylearray(self, shape_number): """Get the values for the LINESTYLEARRAY record.""" obj = _make_object("LineStyleArray") obj.LineStyleCount = count = unpack_ui8(self._src) if count == 0xFF: obj.LineStyleCountExtended = count = unpack_ui16(self._src) ...

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def query(self, query, *args, prefetch=None, timeout=None): """ make a read only query. Ideal for select statements. This method converts the query to a prepared statement and uses a cursor to return the results. So you only get so many rows at a time. This can dramatically incre...

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def _validate_importers(importers): """Validates the importers and decorates the callables with our output formatter. """ # They could have no importers, that's chill if importers is None: return None def _to_importer(priority, func): assert isinstance(priority, int), priority ...

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async def delete_activity(self, context: TurnContext, conversation_reference: ConversationReference): """ Deletes an activity that was previously sent to a channel. It should be noted that not all channels support this feature. :param context: :param conversation_reference: ...

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def abort(status_code, detail='', headers=None, comment=None, **kw): ''' Raise an HTTP status code, as specified. Useful for returning status codes like 401 Unauthorized or 403 Forbidden. :param status_code: The HTTP status code as an integer. :param detail: The message to send along, as a string. ...

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def parse_location(location): """Parse latitude and longitude from string location. Args: location (str): String to parse Returns: tuple of float: Latitude and longitude of location """ def split_dms(text, hemisphere): """Split degrees, minutes and seconds string. ...

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def chainCerts(data): """ Matches and returns any certificates found except the first match. Regex code copied from L{twisted.internet.endpoints._parseSSL}. Related ticket: https://twistedmatrix.com/trac/ticket/7732 @type path: L{bytes} @param data: PEM-encoded data containing the certificates...

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def step(darray, *args, **kwargs): """ Step plot of DataArray index against values Similar to :func:`matplotlib:matplotlib.pyplot.step` Parameters ---------- where : {'pre', 'post', 'mid'}, optional, default 'pre' Define where the steps should be placed: - 'pre': The y value is...

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def validator(names_or_instance, names=None, func=None): """Specify a callback function to fire on class validation OR property set This function has two modes of operation: 1. Registering callback functions that validate Property values when they are set, before the change is saved to the HasPrope...

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def create_organizations_parser(stream): """Create an organizations parser for the given stream. Factory function that creates an organizations parser for the given stream. The stream is only used to guess the type of the required parser. :param stream: stream used to guess the type of the parser ...

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def user_config_dir(appname, roaming=True): """Return full path to the user-specific config dir for this application. "appname" is the name of application. If None, just the system directory is returned. "roaming" (boolean, default True) can be set False to not use the Windo...

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def cylindrical(cls, mag, theta, z=0): '''Returns a Vector instance from cylindircal coordinates''' return cls( mag * math.cos(theta), # X mag * math.sin(theta), # Y z # Z )

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def get_wildcard(self): """Return the wildcard bits notation of the netmask.""" return _convert(self._ip, notation=NM_WILDCARD, inotation=IP_DOT, _check=False, _isnm=self._isnm)

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def request(self, method, url, fields=None, headers=None, **urlopen_kw): """ Make a request using :meth:`urlopen` with the appropriate encoding of ``fields`` based on the ``method`` used. This is a convenience method that requires the least amount of manual effort. It can be use...

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def to_fastg(infile, outfile, circular=None): '''Writes a FASTG file in SPAdes format from input file. Currently only whether or not a sequence is circular is supported. Put circular=set of ids, or circular=filename to make those sequences circular in the output. Puts coverage=1 on all contigs''' if circular is...

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async def get_data(self): """Retrieve the data.""" url = '{}/{}'.format(self.url, 'all') try: with async_timeout.timeout(5, loop=self._loop): if self.password is None: response = await self._session.get(url) else: ...

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def has_bad_headers(self): """ Checks for bad headers i.e. newlines in subject, sender or recipients. RFC5322 allows multiline CRLF with trailing whitespace (FWS) in headers """ headers = [self.sender, self.reply_to] + self.recipients for header in headers: if...

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def set_zone(timezone): ''' Unlinks, then symlinks /etc/localtime to the set timezone. The timezone is crucial to several system processes, each of which SHOULD be restarted (for instance, whatever you system uses as its cron and syslog daemons). This will not be automagically done and must be done...

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def add_udev_trigger(self, trigger_action, subsystem): """ Subscribe to the requested udev subsystem and apply the given action. """ if self._py3_wrapper.udev_monitor.subscribe(self, trigger_action, subsystem): if trigger_action == "refresh_and_freeze": # FIXM...

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def adjustHspsForPlotting(self, titleAlignments): """ Our HSPs are about to be plotted. If we are using e-values, these need to be adjusted. @param titleAlignments: An instance of L{TitleAlignment}. """ # If we're using bit scores, there's nothing to do. if self....

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def pad_to_size(data, shape, value=0.0): """ This is similar to `pad`, except you specify the final shape of the array. Parameters ---------- data : ndarray Numpy array of any dimension and type. shape : tuple Final shape of padded array. Should be tuple of length ``data.ndim``....

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def try_greyscale(pixels, alpha=False, dirty_alpha=True): """ Check if flatboxed RGB `pixels` could be converted to greyscale If could - return iterator with greyscale pixels, otherwise return `False` constant """ planes = 3 + bool(alpha) res = list() apix = list() for row in pixels...

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def check_indexes_all_same(indexes, message="Indexes are not equal."): """Check that a list of Index objects are all equal. Parameters ---------- indexes : iterable[pd.Index] Iterable of indexes to check. Raises ------ ValueError If the indexes are not all the same. """...

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def acceptance_prob(old_cost, new_cost, T): """annealing equation, with modifications to work towards a lower value""" #if start pos is not valid, always move if old_cost == 1e20: return 1.0 #if we have found a valid ps before, never move to nonvalid pos if new_cost == 1e20: return 0...

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def main(): '''This is the main function of this script. The current script args are shown below :: Usage: checkplotlist [-h] [--search SEARCH] [--sortby SORTBY] [--filterby FILTERBY] [--splitout SPLITOUT] [--outprefix OUTPREFIX] [--maxkeyworke...

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def raise_for_invalid_annotation_value(self, line: str, position: int, key: str, value: str) -> None: """Raise an exception if the annotation is not defined. :raises: IllegalAnnotationValueWarning or MissingAnnotationRegexWarning """ if self._in_debug_mode: return i...

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def check_connection_state(self): """Check the state of the connection using connection state request. This sends a CONNECTION_STATE_REQUEST. This method will only return True, if the connection is established and no error code is returned from the KNX/IP gateway """ if ...

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def subgroup(self, t, i): """Handle parenthesis.""" current = [] # (?flags) flags = self.get_flags(i) if flags: self.flags(flags[2:-1]) return [flags] # (?#comment) comments = self.get_comments(i) if comments: return ...

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def bam2mat(args): """ %prog bam2mat input.bam Convert bam file to .mat format, which is simply numpy 2D array. Important parameter is the resolution, which is the cell size. Small cell size lead to more fine-grained heatmap, but leads to large .mat size and slower plotting. """ import ...

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def by_population_density(self, lower=-1, upper=2 ** 31, zipcode_type=ZipcodeType.Standard, sort_by=SimpleZipcode.population_density.name, ascending=False, ...

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def peek(self): '''Return (but do not consume) the next token At the end of input, ``None`` is returned. ''' if self.position >= len(self.tokens): return None return self.tokens[self.position]

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def simple_prot(x, start): """Find the first peak to the right of start""" # start must b >= 1 for i in range(start,len(x)-1): a,b,c = x[i-1], x[i], x[i+1] if b - a > 0 and b -c >= 0: return i else: return None

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def get_versions(): """ Wrap in a function to ensure that we don't run this every time a CLI command runs (yuck!) Also protects import of `requests` from issues when grabbed by setuptools. More on that inline """ # import in the func (rather than top-level scope) so that at setup time, ...

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def pick_unused_port(pid=None, portserver_address=None): """A pure python implementation of PickUnusedPort. Args: pid: PID to tell the portserver to associate the reservation with. If None, the current process's PID is used. portserver_address: The address (path) of a unix domain socket ...

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def read_config(filename): """Reads and flattens a configuration file into a single dictionary for ease of use. Works with both ``.config`` and ``.yaml`` files. Files should look like this:: search_rules: from-date: 2017-06-01 to-date: 2017-09-01 01:01 pt-rule: k...

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def _dedup(items, insensitive): ''' Deduplicate an item list, and preserve order. For case-insensitive lists, drop items if they case-insensitively match a prior item. ''' deduped = [] if insensitive: i_deduped = [] for item in items: lowered = item.lower() ...

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def multi_path_generator(pathnames): """ yields (name,chunkgen) for all of the files found under the list of pathnames given. This is recursive, so directories will have their contents emitted. chunkgen is a function that can called and iterated over to obtain the contents of the file in multiple ...

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def path(self): """HTTP full path constraint. (read-only). """ path = self.__prefix if self is not self.over: path = self.over.path + path return path

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def __add_actions(self): """ Sets Component actions. """ LOGGER.debug("> Adding '{0}' Component actions.".format(self.__class__.__name__)) add_project_action = self.__engine.actions_manager.get_action( "Actions|Umbra|Components|factory.script_editor|&File|Add Projec...

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def get_venue(self, id, **data): """ GET /venues/:id/ Returns a :format:`venue` object. """ return self.get("/venues/{0}/".format(id), data=data)

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def get_grounded_agent(gene_name): """Return a grounded Agent based on an HGNC symbol.""" db_refs = {'TEXT': gene_name} if gene_name in hgnc_map: gene_name = hgnc_map[gene_name] hgnc_id = hgnc_client.get_hgnc_id(gene_name) if hgnc_id: db_refs['HGNC'] = hgnc_id up_id = hgnc_cl...

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def add_callback(self, user_gpio, edge=RISING_EDGE, func=None): """ Calls a user supplied function (a callback) whenever the specified gpio edge is detected. user_gpio:= 0-31. edge:= EITHER_EDGE, RISING_EDGE (default), or FALLING_EDGE. func:= user supplied callback...

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def endpoint_loader(request, application, model, **kwargs): """Load an AJAX endpoint. This will load either an ad-hoc endpoint or it will load up a model endpoint depending on what it finds. It first attempts to load ``model`` as if it were an ad-hoc endpoint. Alternatively, it will attempt to see if ...

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def set_cell(self, column_family_id, column, value, timestamp=None): """Sets a value in this row. The cell is determined by the ``row_key`` of this :class:`DirectRow` and the ``column``. The ``column`` must be in an existing :class:`.ColumnFamily` (as determined by ``column_family_id``)...

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def load_object(path): """Return the Python object represented by dotted *path*.""" i = path.rfind('.') module_name, object_name = path[:i], path[i + 1:] # Load module. try: module = import_module(module_name) except ImportError: raise ImproperlyConfigured('Module %r not found' %...

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def incrementing_sleep(self, previous_attempt_number, delay_since_first_attempt_ms): """ Sleep an incremental amount of time after each attempt, starting at wait_incrementing_start and incrementing by wait_incrementing_increment """ result = self._wait_incrementing_start + (self....

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def make_folder_for_today(log_dir): """Creates the folder log_dir/yyyy/mm/dd in log_dir if it doesn't exist and returns the full path of the folder.""" now = datetime.datetime.now() sub_folders_list = ['{0:04d}'.format(now.year), '{0:02d}'.format(now.month), ...

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def show_scan_report(audio_filepaths, album_dir, r128_data): """ Display loudness scan results. """ # track loudness/peak for audio_filepath in audio_filepaths: try: loudness, peak = r128_data[audio_filepath] except KeyError: loudness, peak = "SKIPPED", "SKIPPED" else: loudness = "%....

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def get_child(self, *types): """ :param types: list of requested types. :return: the first (and in most useful cases only) child of specific type(s). """ children = list(self.get_children(*types)) return children[0] if any(children) else None

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def phenotype_to_res_set(phenotype, resources): """ Converts a binary string to a set containing the resources indicated by the bits in the string. Inputs: phenotype - a binary string resources - a list of string indicating which resources correspond to which indices...

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def create_store(self): """ Creates store object """ if self.store_class is not None: return self.store_class.load(self.client.webfinger, self) raise NotImplementedError("You need to specify PyPump.store_class or override PyPump.create_store method.")

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def manual_migration(): """ Simple interactive function to pause the deployment. A manual migration can be done two different ways: Option 1: Enter y to exit the current deployment. When migration is completed run deploy again. Option 2: run the migration in a separate shell """ if env.IN...

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def get_cb_depth_set(cb_histogram, cb_cutoff): ''' Returns a set of barcodes with a minimum number of reads ''' cb_keep_set = set() if not cb_histogram: return cb_keep_set with read_cbhistogram(cb_histogram) as fh: cb_map = dict(p.strip().split() for p in fh) cb_keep_set = s...

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def get_decimal_precision(number): """Return maximum precision of a decimal instance's fractional part. Precision is extracted from the fractional part only. """ # Copied from: https://github.com/mahmoud/boltons/pull/59 assert isinstance(number, decimal.Decimal) decimal_tuple = number.normalize(...

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def convert(self, version): """convert *MDF* to other version Parameters ---------- version : str new mdf file version from ('2.00', '2.10', '2.14', '3.00', '3.10', '3.20', '3.30', '4.00', '4.10', '4.11'); default '4.10' Returns ------- o...

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def option_map(self): """Map command-line options to args.""" option_map = OrderedDict() for arg in self.args.values(): for option in arg.options: option_map[option] = arg return option_map

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def update_panel(self, panel_obj, version=None, date_obj=None): """Replace a existing gene panel with a new one Keeps the object id Args: panel_obj(dict) version(float) date_obj(datetime.datetime) Returns: updated_panel(dict) """...

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def locked_delete(self): """Delete credentials from the SQLAlchemy datastore.""" filters = {self.key_name: self.key_value} self.session.query(self.model_class).filter_by(**filters).delete()

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def to_html(graph: BELGraph) -> str: """Render the graph as an HTML string. Common usage may involve writing to a file like: >>> from pybel.examples import sialic_acid_graph >>> with open('html_output.html', 'w') as file: ... print(to_html(sialic_acid_graph), file=file) """ context = g...

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def spellcheck(word, wordlist, depth = 2): """ Given a word list and a depth parameter, return all words w' in the wordlist with LevenshteinDistance(word, w') <= depth :param word: :param wordlist: >>> Dic = ['pes', 'pesse', 'pease', 'peis', 'peisse', 'pise', 'peose', 'poese', 'poisen'] >>...

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def find_log_dir(log_dir=None): """Returns the most suitable directory to put log files into. Args: log_dir: str|None, if specified, the logfile(s) will be created in that directory. Otherwise if the --log_dir command-line flag is provided, the logfile will be created in that directory. Other...

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def _check_select(self): '''Select task to fetch & process''' while self._send_buffer: _task = self._send_buffer.pop() try: # use force=False here to prevent automatic send_buffer append and get exception self.send_task(_task, False) ex...

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def cli_help(context, command_name, general_parser, command_parsers): """ Outputs help information. See :py:mod:`swiftly.cli.help` for context usage information. See :py:class:`CLIHelp` for more information. :param context: The :py:class:`swiftly.cli.context.CLIContext` to use. :param...

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def _create_adapter_type(network_adapter, adapter_type, network_adapter_label=''): ''' Returns a vim.vm.device.VirtualEthernetCard object specifying a virtual ethernet card information network_adapter None or VirtualEthernet object adapter_type String, type...

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def _conditional_committors(source, sink, waypoint, tprob): """ Computes the conditional committors :math:`q^{ABC^+}` which are is the probability of starting in one state and visiting state B before A while also visiting state C at some point. Note that in the notation of Dickson et. al. this comp...

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