kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def obfn_cns(self): r"""Compute constraint violation measure :math:`\\| P(\mathbf{y}) - \mathbf{y}\\|_2`. """ Y = self.obfn_gvar() return np.linalg.norm((self.Pcn(Y) - Y))	[ "def", "obfn_cns", "(", "self", ")", ":", "Y", "=", "self", ".", "obfn_gvar", "(", ")", "return", "np", ".", "linalg", ".", "norm", "(", "(", "self", ".", "Pcn", "(", "Y", ")", "-", "Y", ")", ")" ]	29.142857	13.571429
def get_account_statement( self, locale=None, from_record=None, record_count=None, item_date_range=None, include_item=None, wallet=None): """Get account statement. :param str locale: The language to be used where applicable :param int from_record: Specifies the first rec...	[ "def", "get_account_statement", "(", "self", ",", "locale", "=", "None", ",", "from_record", "=", "None", ",", "record_count", "=", "None", ",", "item_date_range", "=", "None", ",", "include_item", "=", "None", ",", "wallet", "=", "None", ")", ":", "return...	47.444444	22
def secrets_manager(*secret_names): """ Get secrets from the `AWS Secrets Manager <https://aws.amazon.com/secrets-manager/>`_. Secrets are added to a dictionary named ``secrets`` on the context object. This requires your lambda to have the ``secretsmanager:GetSecretValue`` permission for the reque...	[ "def", "secrets_manager", "(", "*", "secret_names", ")", ":", "def", "wrapper_wrapper", "(", "handler", ")", ":", "@", "wraps", "(", "handler", ")", "def", "wrapper", "(", "event", ",", "context", ")", ":", "if", "not", "hasattr", "(", "context", ",", ...	36.184211	23.236842
def _remove_dupes(self, phonetic): """Remove duplicates from a phonetic encoding list. Parameters ---------- phonetic : str A Beider-Morse phonetic encoding Returns ------- str A Beider-Morse phonetic code """ alt_string ...	[ "def", "_remove_dupes", "(", "self", ",", "phonetic", ")", ":", "alt_string", "=", "phonetic", "alt_array", "=", "alt_string", ".", "split", "(", "'\|'", ")", "result", "=", "'\|'", "for", "i", "in", "range", "(", "len", "(", "alt_array", ")", ")", ":", ...	23.375	17.708333
def s2dctmat(nfilt,ncep,freqstep): """Return the 'legacy' not-quite-DCT matrix used by Sphinx""" melcos = numpy.empty((ncep, nfilt), 'double') for i in range(0,ncep): freq = numpy.pi * float(i) / nfilt melcos[i] = numpy.cos(freq * numpy.arange(0.5, float(nfilt)+0.5, 1.0, 'double')) melco...	[ "def", "s2dctmat", "(", "nfilt", ",", "ncep", ",", "freqstep", ")", ":", "melcos", "=", "numpy", ".", "empty", "(", "(", "ncep", ",", "nfilt", ")", ",", "'double'", ")", "for", "i", "in", "range", "(", "0", ",", "ncep", ")", ":", "freq", "=", "...	44.625	13.25
def main(): """pyprf_opt_brute entry point.""" # Get list of input arguments (without first one, which is the path to the # function that is called): --NOTE: This is another way of accessing # input arguments, but since we use 'argparse' it is redundant. # lstArgs = sys.argv[1:] strWelcome = 'p...	[ "def", "main", "(", ")", ":", "# Get list of input arguments (without first one, which is the path to the", "# function that is called): --NOTE: This is another way of accessing", "# input arguments, but since we use 'argparse' it is redundant.", "# lstArgs = sys.argv[1:]", "strWelcome", "=", ...	43.938776	24.530612
def finished(experiment_name, reset=True): """ Track a conversion. :param experiment_name: Name of the experiment. :param reset: If set to `True` current user's session is reset so that they may start the test again in the future. If set to `False` the user will always see the alternat...	[ "def", "finished", "(", "experiment_name", ",", "reset", "=", "True", ")", ":", "if", "_exclude_visitor", "(", ")", ":", "return", "redis", "=", "_get_redis_connection", "(", ")", "try", ":", "experiment", "=", "Experiment", ".", "find", "(", "redis", ",",...	38.485714	17.742857
def addFASTAEditingCommandLineOptions(parser): """ Add standard FASTA editing command-line options to an argparse parser. These are options that can be used to alter FASTA records, NOT options that simply select or reject those things (for those see addFASTAFilteringCommandLineOptions). @param...	[ "def", "addFASTAEditingCommandLineOptions", "(", "parser", ")", ":", "# A mutually exclusive group for --keepSites, --keepSitesFile,", "# --removeSites, and --removeSitesFile.", "group", "=", "parser", ".", "add_mutually_exclusive_group", "(", ")", "# In the 4 options below, the 'indic...	45.976744	24.232558
def prepare_request_uri(self, uri, redirect_uri=None, scope=None, state=None, **kwargs): """Prepare the implicit grant request URI. The client constructs the request URI by adding the following parameters to the query component of the authorization endpoint URI ...	[ "def", "prepare_request_uri", "(", "self", ",", "uri", ",", "redirect_uri", "=", "None", ",", "scope", "=", "None", ",", "state", "=", "None", ",", "", "", "kwargs", ")", ":", "return", "prepare_grant_uri", "(", "uri", ",", "self", ".", "client_id", ...	62.744681	36.93617
def remove_object(self, obj): """Remove an object from the definition.""" self._objects.remove(obj) self._pairs.difference_update((obj, p) for p in self._properties)	[ "def", "remove_object", "(", "self", ",", "obj", ")", ":", "self", ".", "_objects", ".", "remove", "(", "obj", ")", "self", ".", "_pairs", ".", "difference_update", "(", "(", "obj", ",", "p", ")", "for", "p", "in", "self", ".", "_properties", ")" ]	46.5	12.75
def virtual_resource(self): """ Available on a Master Engine only. To get all virtual resources call:: engine.virtual_resource.all() :raises UnsupportedEngineFeature: master engine only :rtype: CreateCollection(VirtualResource) """ resource = create...	[ "def", "virtual_resource", "(", "self", ")", ":", "resource", "=", "create_collection", "(", "self", ".", "get_relation", "(", "'virtual_resources'", ",", "UnsupportedEngineFeature", ")", ",", "VirtualResource", ")", "resource", ".", "_load_from_engine", "(", "self"...	30	13.111111
def fast_sync_inspect_snapshot( snapshot_path ): """ Inspect a snapshot Return useful information Return {'status': True, 'signatures': ..., 'payload_size': ..., 'sig_append_offset': ..., 'hash': ...} on success Return {'error': ...} on error """ with open(snapshot_path, 'r') as f: i...	[ "def", "fast_sync_inspect_snapshot", "(", "snapshot_path", ")", ":", "with", "open", "(", "snapshot_path", ",", "'r'", ")", "as", "f", ":", "info", "=", "fast_sync_inspect", "(", "f", ")", "if", "'error'", "in", "info", ":", "log", ".", "error", "(", "\"...	37.833333	20.5
def add_arrow(self, x1, y1, x2, y2, side='left', shape='full', color='black', width=0.01, head_width=0.03, overhang=0, **kws): """add arrow supplied x, y position""" dx, dy = x2-x1, y2-y1 axes = self.axes if side == 'right': axes = self.g...	[ "def", "add_arrow", "(", "self", ",", "x1", ",", "y1", ",", "x2", ",", "y2", ",", "side", "=", "'left'", ",", "shape", "=", "'full'", ",", "color", "=", "'black'", ",", "width", "=", "0.01", ",", "head_width", "=", "0.03", ",", "overhang", "=", "...	38.733333	11.8
def add_new_init_method(obj): """ Replace the existing obj.__init__() method with a new one which calls the original one and in addition performs the following actions: (1) Finds all instances of tohu.BaseGenerator in the namespace and collects them in the dictionary `self.field_gens`. ...	[ "def", "add_new_init_method", "(", "obj", ")", ":", "orig_init", "=", "obj", ".", "__init__", "def", "new_init", "(", "self", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "logger", ".", "debug", "(", "f\"Initialising new {self}\"", ")", "# Call ori...	36.706667	23.346667
def evecs(self): """ The eigenvectors of the parameter space. This is a Dictionary of numpy.matrix Each entry in the dictionary is as described under evals. Each numpy.matrix contains the eigenvectors which, with the eigenvalues in evals, are needed to rotate the ...	[ "def", "evecs", "(", "self", ")", ":", "if", "self", ".", "_evecs", "is", "None", ":", "errMsg", "=", "\"The metric eigenvectors have not been set in the \"", "errMsg", "+=", "\"metricParameters instance.\"", "raise", "ValueError", "(", "errMsg", ")", "return", "sel...	43.357143	14.785714
def write(self, file_or_filename): """ Writes case data to file in Excel format. """ self.book = Workbook() self._write_data(None) self.book.save(file_or_filename)	[ "def", "write", "(", "self", ",", "file_or_filename", ")", ":", "self", ".", "book", "=", "Workbook", "(", ")", "self", ".", "_write_data", "(", "None", ")", "self", ".", "book", ".", "save", "(", "file_or_filename", ")" ]	33	4.333333
def generate_defect_structure(self, supercell=(1, 1, 1)): """ Returns Defective Vacancy structure, decorated with charge Args: supercell (int, [3x1], or [[]] (3x3)): supercell integer, vector, or scaling matrix """ defect_structure = self.bulk_structure.copy() ...	[ "def", "generate_defect_structure", "(", "self", ",", "supercell", "=", "(", "1", ",", "1", ",", "1", ")", ")", ":", "defect_structure", "=", "self", ".", "bulk_structure", ".", "copy", "(", ")", "defect_structure", ".", "make_supercell", "(", "supercell", ...	49.565217	23.304348
def _reflect_table(self): """Load the tables definition from the database.""" with self.db.lock: try: self._table = SQLATable(self.name, self.db.metadata, schema=self.db.schema, ...	[ "def", "_reflect_table", "(", "self", ")", ":", "with", "self", ".", "db", ".", "lock", ":", "try", ":", "self", ".", "_table", "=", "SQLATable", "(", "self", ".", "name", ",", "self", ".", "db", ".", "metadata", ",", "schema", "=", "self", ".", ...	40.5	14
def rmdir(self, pathobj): """ Removes a directory """ stat = self.stat(pathobj) if not stat.is_dir: raise OSError(20, "Not a directory: '%s'" % str(pathobj)) url = str(pathobj) + '/' text, code = self.rest_del(url, session=pathobj.session, verify=pa...	[ "def", "rmdir", "(", "self", ",", "pathobj", ")", ":", "stat", "=", "self", ".", "stat", "(", "pathobj", ")", "if", "not", "stat", ".", "is_dir", ":", "raise", "OSError", "(", "20", ",", "\"Not a directory: '%s'\"", "%", "str", "(", "pathobj", ")", "...	30.2	23
def ipv4_generate_random(total=100): """ The generator to produce random, unique IPv4 addresses that are not defined (can be looked up using ipwhois). Args: total (:obj:`int`): The total number of IPv4 addresses to generate. Yields: str: The next IPv4 address. """ count = ...	[ "def", "ipv4_generate_random", "(", "total", "=", "100", ")", ":", "count", "=", "0", "yielded", "=", "set", "(", ")", "while", "count", "<", "total", ":", "address", "=", "str", "(", "IPv4Address", "(", "random", ".", "randint", "(", "0", ",", "2", ...	24.478261	23.347826
def select_group(self, group_id): """Copy the query and add filtering by group. Example:: query = query.select_group('1234567') :type group_id: str :param group_id: The ID of a group to filter by. :rtype: :class:`Query` :returns: The new query object. ...	[ "def", "select_group", "(", "self", ",", "group_id", ")", ":", "new_query", "=", "copy", ".", "deepcopy", "(", "self", ")", "new_query", ".", "_filter", ".", "group_id", "=", "group_id", "return", "new_query" ]	26.4375	16.3125
def get_renderers(self): """Optionally block Browsable API rendering. """ renderers = super(WithDynamicViewSetMixin, self).get_renderers() if settings.ENABLE_BROWSABLE_API is False: return [ r for r in renderers if not isinstance(r, BrowsableAPIRenderer) ]...	[ "def", "get_renderers", "(", "self", ")", ":", "renderers", "=", "super", "(", "WithDynamicViewSetMixin", ",", "self", ")", ".", "get_renderers", "(", ")", "if", "settings", ".", "ENABLE_BROWSABLE_API", "is", "False", ":", "return", "[", "r", "for", "r", "...	39.444444	20.333333
def top(self, num, key=None): """ Get the top N elements from an RDD. .. note:: This method should only be used if the resulting array is expected to be small, as all the data is loaded into the driver's memory. .. note:: It returns the list sorted in descending order. ...	[ "def", "top", "(", "self", ",", "num", ",", "key", "=", "None", ")", ":", "def", "topIterator", "(", "iterator", ")", ":", "yield", "heapq", ".", "nlargest", "(", "num", ",", "iterator", ",", "key", "=", "key", ")", "def", "merge", "(", "a", ",",...	32.869565	22.347826
def _create_entry(entry_body): ''' Adds common part of entry to a given entry body and return the whole xml. ''' updated_str = datetime.utcnow().isoformat() if datetime.utcnow().utcoffset() is None: updated_str += '+00:00' entry_start = '''<?xml version="1.0" encoding="utf-8" standalone="ye...	[ "def", "_create_entry", "(", "entry_body", ")", ":", "updated_str", "=", "datetime", ".", "utcnow", "(", ")", ".", "isoformat", "(", ")", "if", "datetime", ".", "utcnow", "(", ")", ".", "utcoffset", "(", ")", "is", "None", ":", "updated_str", "+=", "'+...	53.538462	29.538462
def _special_dbkey_maps(dbkey, ref_file): """Avoid duplicate VEP information for databases with chromosome differences like hg19/GRCh37. """ remaps = {"hg19": "GRCh37", "hg38-noalt": "hg38"} if dbkey in remaps: base_dir = os.path.normpath(os.path.join(os.path.dirname(ref_file), os....	[ "def", "_special_dbkey_maps", "(", "dbkey", ",", "ref_file", ")", ":", "remaps", "=", "{", "\"hg19\"", ":", "\"GRCh37\"", ",", "\"hg38-noalt\"", ":", "\"hg38\"", "}", "if", "dbkey", "in", "remaps", ":", "base_dir", "=", "os", ".", "path", ".", "normpath", ...	43.5	17.777778
def locate(cls): """Locates the active PEX bootstrap. :rtype: :class:`Bootstrap` """ if cls._INSTANCE is None: bootstrap_path = __file__ module_import_path = __name__.split('.') # For example, our __file__ might be requests.pex/.bootstrap/pex/bootstrap.pyc and our import # path...	[ "def", "locate", "(", "cls", ")", ":", "if", "cls", ".", "_INSTANCE", "is", "None", ":", "bootstrap_path", "=", "__file__", "module_import_path", "=", "__name__", ".", "split", "(", "'.'", ")", "# For example, our __file__ might be requests.pex/.bootstrap/pex/bootstra...	39.176471	24.176471
def quote(self) -> str: """Get a random quote. :return: Quote from movie. :Example: "Bond... James Bond." """ quotes = self._data['quotes'] return self.random.choice(quotes)	[ "def", "quote", "(", "self", ")", "->", "str", ":", "quotes", "=", "self", ".", "_data", "[", "'quotes'", "]", "return", "self", ".", "random", ".", "choice", "(", "quotes", ")" ]	22.6	13.7
def get_all_hits(self): ''' Get all HITs ''' if not self.connect_to_turk(): return False try: hits = [] paginator = self.mtc.get_paginator('list_hits') for page in paginator.paginate(): hits.extend(page['HITs']) except Excep...	[ "def", "get_all_hits", "(", "self", ")", ":", "if", "not", "self", ".", "connect_to_turk", "(", ")", ":", "return", "False", "try", ":", "hits", "=", "[", "]", "paginator", "=", "self", ".", "mtc", ".", "get_paginator", "(", "'list_hits'", ")", "for", ...	31.214286	13.642857
def model_to_json(self, object, cleanup=True): """Take a model instance and return it as a json struct""" model_name = type(object).__name__ if model_name not in self.swagger_dict['definitions']: raise ValidationError("Swagger spec has no definition for model %s" % model_name) ...	[ "def", "model_to_json", "(", "self", ",", "object", ",", "cleanup", "=", "True", ")", ":", "model_name", "=", "type", "(", "object", ")", ".", "__name__", "if", "model_name", "not", "in", "self", ".", "swagger_dict", "[", "'definitions'", "]", ":", "rais...	50.363636	17.454545
def suppress_stdout(): """ Context manager that suppresses stdout. Examples: >>> with suppress_stdout(): ... print('Test print') >>> print('test') test """ save_stdout = sys.stdout sys.stdout = DevNull() yield sys.stdout = save_stdout	[ "def", "suppress_stdout", "(", ")", ":", "save_stdout", "=", "sys", ".", "stdout", "sys", ".", "stdout", "=", "DevNull", "(", ")", "yield", "sys", ".", "stdout", "=", "save_stdout" ]	18.125	18.125
def add_root(self, id_): """Adds a root node. arg: id (osid.id.Id): the ``Id`` of the node raise: AlreadyExists - ``id`` is already in hierarchy raise: NotFound - ``id`` not found raise: NullArgument - ``id`` is ``null`` raise: OperationFailed - unable to complete...	[ "def", "add_root", "(", "self", ",", "id_", ")", ":", "if", "(", "bool", "(", "self", ".", "_rls", ".", "get_relationships_by_genus_type_for_source", "(", "id_", ",", "self", ".", "_relationship_type", ")", ".", "available", "(", ")", ")", "or", "bool", ...	47.875	23.3125
def validate(message, config): """ Return true or false if the message is signed appropriately. """ if not _validate_implementations: init(config) cfg = copy.deepcopy(config) if 'gpg_home' not in cfg: cfg['gpg_home'] = os.path.expanduser('~/.gnupg/') if 'ssldir' not in cfg: ...	[ "def", "validate", "(", "message", ",", "", "", "config", ")", ":", "if", "not", "_validate_implementations", ":", "init", "(", "", "", "config", ")", "cfg", "=", "copy", ".", "deepcopy", "(", "config", ")", "if", "'gpg_home'", "not", "in", "cfg", ...	34.605263	19.973684
def reconnect_to_broker(self): """Connect or reconnect to broker""" #print "CONNECT !" if self.client: self.poller.unregister(self.client) self.client.close() self.client = self.ctx.socket(zmq.DEALER) self.client.linger = 0 self.client.connect(self...	[ "def", "reconnect_to_broker", "(", "self", ")", ":", "#print \"CONNECT !\"", "if", "self", ".", "client", ":", "self", ".", "poller", ".", "unregister", "(", "self", ".", "client", ")", "self", ".", "client", ".", "close", "(", ")", "self", ".", "client"...	39.166667	11.5
def fromrdd(rdd, nrecords=None, shape=None, index=None, labels=None, dtype=None, ordered=False): """ Load series data from a Spark RDD. Assumes keys are tuples with increasing and unique indices, and values are 1d ndarrays. Will try to infer properties that are not explicitly provided. Paramet...	[ "def", "fromrdd", "(", "rdd", ",", "nrecords", "=", "None", ",", "shape", "=", "None", ",", "index", "=", "None", ",", "labels", "=", "None", ",", "dtype", "=", "None", ",", "ordered", "=", "False", ")", ":", "from", ".", "series", "import", "Serie...	29.283333	21.55
def render(opts, functions, states=None, proxy=None, context=None): ''' Returns the render modules ''' if context is None: context = {} pack = {'__salt__': functions, '__grains__': opts.get('grains', {}), '__context__': context} if states: pack['__states...	[ "def", "render", "(", "opts", ",", "functions", ",", "states", "=", "None", ",", "proxy", "=", "None", ",", "context", "=", "None", ")", ":", "if", "context", "is", "None", ":", "context", "=", "{", "}", "pack", "=", "{", "'__salt__'", ":", "functi...	28.757576	22.636364
def Sample(self): """Takes a sample for profiling.""" self._profiling_sample += 1 if self._profiling_sample >= self._profiling_sample_rate: if self._heapy: heap = self._heapy.heap() heap.dump(self._sample_file) self._profiling_sample = 0	[ "def", "Sample", "(", "self", ")", ":", "self", ".", "_profiling_sample", "+=", "1", "if", "self", ".", "_profiling_sample", ">=", "self", ".", "_profiling_sample_rate", ":", "if", "self", ".", "_heapy", ":", "heap", "=", "self", ".", "_heapy", ".", "hea...	27	17.1
def extract(fileobj, keywords, comment_tags, options): """Extracts translation messages from underscore template files. This method does also extract django templates. If a template does not contain any django translation tags we always fallback to underscore extraction. This is a plugin to Babel, wri...	[ "def", "extract", "(", "fileobj", ",", "keywords", ",", "comment_tags", ",", "options", ")", ":", "encoding", "=", "options", ".", "get", "(", "'encoding'", ",", "'utf-8'", ")", "original_position", "=", "fileobj", ".", "tell", "(", ")", "text", "=", "fi...	35.64	21.04
def connect(self, chip_name, speed='auto', verbose=False): """Connects the J-Link to its target. Args: self (JLink): the ``JLink`` instance chip_name (str): target chip name speed (int): connection speed, one of ``{5-12000, 'auto', 'adaptive'}`` verbose (bool): b...	[ "def", "connect", "(", "self", ",", "chip_name", ",", "speed", "=", "'auto'", ",", "verbose", "=", "False", ")", ":", "if", "verbose", ":", "self", ".", "exec_command", "(", "'EnableRemarks = 1'", ")", "# This is weird but is currently the only way to specify what t...	33.555556	21.62963
def reset(self): """Reset the instance to begin sampling from scratch""" self._sampled = [np.repeat(False, x) for x in self.sizes_] self._n_sampled = np.zeros(self.n_strata_, dtype=int)	[ "def", "reset", "(", "self", ")", ":", "self", ".", "_sampled", "=", "[", "np", ".", "repeat", "(", "False", ",", "x", ")", "for", "x", "in", "self", ".", "sizes_", "]", "self", ".", "_n_sampled", "=", "np", ".", "zeros", "(", "self", ".", "n_s...	51.5	17.75
def _add_out_streams(self, spbl): """Adds outputs to a given protobuf Bolt or Spout message""" if self.outputs is None: return # sanitize outputs and get a map <stream_id -> out fields> output_map = self._sanitize_outputs() for stream_id, out_fields in output_map.items(): out_stream = ...	[ "def", "_add_out_streams", "(", "self", ",", "spbl", ")", ":", "if", "self", ".", "outputs", "is", "None", ":", "return", "# sanitize outputs and get a map <stream_id -> out fields>", "output_map", "=", "self", ".", "_sanitize_outputs", "(", ")", "for", "stream_id",...	39.416667	19.083333
def repository_factory(vcs_type, **kw): """ Instantiate a :class:`Repository` object based on the given type and arguments. :param vcs_type: One of the strings 'bazaar', 'bzr', 'git', 'hg' or 'mercurial' or a subclass of :class:`Repository`. :param kw: The keyword arguments to :fun...	[ "def", "repository_factory", "(", "vcs_type", ",", "", "", "kw", ")", ":", "# Resolve VCS aliases to Repository subclasses.", "if", "isinstance", "(", "vcs_type", ",", "string_types", ")", ":", "vcs_type", "=", "vcs_type", ".", "lower", "(", ")", "for", "cls",...	50.266667	20
def _joint_log_likelihood(self, X): """Calculate the posterior log probability of the samples X""" check_is_fitted(self, "classes_") X = check_array(X, accept_sparse='csr') X_bin = self._transform_data(X) n_classes, n_features = self.feature_log_prob_.shape n_samples, n...	[ "def", "_joint_log_likelihood", "(", "self", ",", "X", ")", ":", "check_is_fitted", "(", "self", ",", "\"classes_\"", ")", "X", "=", "check_array", "(", "X", ",", "accept_sparse", "=", "'csr'", ")", "X_bin", "=", "self", ".", "_transform_data", "(", "X", ...	33.772727	18.318182
def SetDeviceProperties(self, object_path, properties): '''Convenience method to Set a device's properties. object_path: the device to update properties: dictionary of keys to dbus variants. If the 1.0 API is being mocked, changing this property will trigger the device's PropertiesChanged signal; ...	[ "def", "SetDeviceProperties", "(", "self", ",", "object_path", ",", "properties", ")", ":", "device", "=", "dbusmock", ".", "get_object", "(", "object_path", ")", "# set the properties", "for", "key", ",", "value", "in", "properties", ".", "items", "(", ")", ...	35.631579	21.421053
def createGenderPlot(bfile, intensities, problematic_samples, format, out_prefix): """Creates the gender plot. :param bfile: the prefix of the input binary file. :param intensities: the file containing the intensities. :param problematic_samples: the file containing the problematic...	[ "def", "createGenderPlot", "(", "bfile", ",", "intensities", ",", "problematic_samples", ",", "format", ",", "out_prefix", ")", ":", "gender_plot_options", "=", "[", "\"--bfile\"", ",", "bfile", ",", "\"--intensities\"", ",", "intensities", ",", "\"--sex-problems\""...	36.964286	18.607143
def general_neg_loglik(self, beta): """ Calculates the negative log-likelihood of the model Parameters ---------- beta : np.ndarray Contains untransformed starting values for latent variables Returns ---------- The negative logliklihood of the model ...	[ "def", "general_neg_loglik", "(", "self", ",", "beta", ")", ":", "mu", ",", "Y", "=", "self", ".", "_model", "(", "beta", ")", "parm", "=", "np", ".", "array", "(", "[", "self", ".", "latent_variables", ".", "z_list", "[", "k", "]", ".", "prior", ...	42.611111	29.111111
def on_before_transform_template(self, template_dict): """ Hook method that runs before a template gets transformed. In this method, we parse and process Globals section from the template (if present). :param dict template_dict: SAM template as a dictionary """ try: ...	[ "def", "on_before_transform_template", "(", "self", ",", "template_dict", ")", ":", "try", ":", "global_section", "=", "Globals", "(", "template_dict", ")", "except", "InvalidGlobalsSectionException", "as", "ex", ":", "raise", "InvalidDocumentException", "(", "[", "...	41.809524	22.571429
def status(name, sig=None): ''' Return the status for a service via rest_sample. If the name contains globbing, a dict mapping service name to True/False values is returned. .. versionadded:: 2015.8.0 .. versionchanged:: 2018.3.0 The service name can now be a glob (e.g. ``salt*``) ...	[ "def", "status", "(", "name", ",", "sig", "=", "None", ")", ":", "proxy_fn", "=", "'rest_sample.service_status'", "contains_globbing", "=", "bool", "(", "re", ".", "search", "(", "r'\\*\|\\?\|\\[.+\\]'", ",", "name", ")", ")", "if", "contains_globbing", ":", "...	26.547619	20.880952
def get_tkd_value(tensor_keyed_dict, tensor, allclose_kwargs=None): """ Helper function to find a value in a tensor-keyed- dictionary using an approximation to the key. This is useful if rounding errors in construction occur or hashing issues arise in tensor-keyed-dictionaries (e. g. from symme...	[ "def", "get_tkd_value", "(", "tensor_keyed_dict", ",", "tensor", ",", "allclose_kwargs", "=", "None", ")", ":", "if", "allclose_kwargs", "is", "None", ":", "allclose_kwargs", "=", "{", "}", "for", "tkey", ",", "value", "in", "tensor_keyed_dict", ".", "items", ...	39.761905	13.952381
def task_add_user(self, args, *kwargs): """Add users to the current task :returns: None :rtype: None :raises: None """ if not self.cur_task: return dialog = UserAdderDialog(task=self.cur_task) dialog.exec_() users = dialog.users ...	[ "def", "task_add_user", "(", "self", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "if", "not", "self", ".", "cur_task", ":", "return", "dialog", "=", "UserAdderDialog", "(", "task", "=", "self", ".", "cur_task", ")", "dialog", ".", "exec_", "...	28.0625	16.625
def reveal( input_image: Union[str, IO[bytes]], generator: Iterator[int], shift: int = 0, encoding: str = "UTF-8", ): """Find a message in an image (with the LSB technique). """ img = tools.open_image(input_image) img_list = list(img.getdata()) width, height = img.size buff, coun...	[ "def", "reveal", "(", "input_image", ":", "Union", "[", "str", ",", "IO", "[", "bytes", "]", "]", ",", "generator", ":", "Iterator", "[", "int", "]", ",", "shift", ":", "int", "=", "0", ",", "encoding", ":", "str", "=", "\"UTF-8\"", ",", ")", ":"...	32.285714	16.4
def flood(im, regions=None, mode='max'): r""" Floods/fills each region in an image with a single value based on the specific values in that region. The ``mode`` argument is used to determine how the value is calculated. Parameters ---------- im : array_like An ND image with isolate...	[ "def", "flood", "(", "im", ",", "regions", "=", "None", ",", "mode", "=", "'max'", ")", ":", "mask", "=", "im", ">", "0", "if", "regions", "is", "None", ":", "labels", ",", "N", "=", "spim", ".", "label", "(", "mask", ")", "else", ":", "labels"...	29.467742	20.774194
def _resume(self): # type: (Descriptor) -> int """Resume a download, if possible :param Descriptor self: this :rtype: int or None :return: verified download offset """ if self._resume_mgr is None or self._offset > 0 or self._finalized: return None ...	[ "def", "_resume", "(", "self", ")", ":", "# type: (Descriptor) -> int", "if", "self", ".", "_resume_mgr", "is", "None", "or", "self", ".", "_offset", ">", "0", "or", "self", ".", "_finalized", ":", "return", "None", "# check if path exists in resume db", "rr", ...	45.060606	14.252525
def sparse(x, rho, penalty): """ Proximal operator for the l1-norm: soft thresholding Parameters ---------- penalty : float Strength or weight on the l1-norm """ lmbda = penalty / rho return (x - lmbda) * (x >= lmbda) + (x + lmbda) * (x <= -lmbda)	[ "def", "sparse", "(", "x", ",", "rho", ",", "penalty", ")", ":", "lmbda", "=", "penalty", "/", "rho", "return", "(", "x", "-", "lmbda", ")", "", "(", "x", ">=", "lmbda", ")", "+", "(", "x", "+", "lmbda", ")", "", "(", "x", "<=", "-", "lmb...	23.166667	18.666667
def thread( mafs, species ): """ Restrict an list of alignments to a given list of species by: 1) Removing components for any other species 2) Remove any columns containing all gaps Example: >>> import bx.align.maf >>> block1 = bx.align.maf.from_string( '''...	[ "def", "thread", "(", "mafs", ",", "species", ")", ":", "for", "m", "in", "mafs", ":", "new_maf", "=", "deepcopy", "(", "m", ")", "new_components", "=", "get_components_for_species", "(", "new_maf", ",", "species", ")", "if", "new_components", ":", "remove...	44.087719	33.035088
def create_circuit_termination(circuit, interface, device, speed, xconnect_id=None, term_side='A'): ''' .. versionadded:: 2019.2.0 Terminate a circuit on an interface circuit The name of the circuit interface The name of the interface to terminate on device The name of ...	[ "def", "create_circuit_termination", "(", "circuit", ",", "interface", ",", "device", ",", "speed", ",", "xconnect_id", "=", "None", ",", "term_side", "=", "'A'", ")", ":", "nb_device", "=", "get_", "(", "'dcim'", ",", "'devices'", ",", "name", "=", "devic...	33.306122	21.795918
def _has_perm(self, permission_name, view_menu_name): """ Whether the user has this perm """ if hasattr(self, 'perms'): if (permission_name, view_menu_name) in self.perms: return True # rebuild the permissions set self._get_and_cache_perms() ...	[ "def", "_has_perm", "(", "self", ",", "permission_name", ",", "view_menu_name", ")", ":", "if", "hasattr", "(", "self", ",", "'perms'", ")", ":", "if", "(", "permission_name", ",", "view_menu_name", ")", "in", "self", ".", "perms", ":", "return", "True", ...	37.1	8.7
def scalar_pb(tag, data, description=None): """Create a scalar summary_pb2.Summary protobuf. Arguments: tag: String tag for the summary. data: A 0-dimensional `np.array` or a compatible python number type. description: Optional long-form description for this summary, as a `str`. Markdown is suppo...	[ "def", "scalar_pb", "(", "tag", ",", "data", ",", "description", "=", "None", ")", ":", "arr", "=", "np", ".", "array", "(", "data", ")", "if", "arr", ".", "shape", "!=", "(", ")", ":", "raise", "ValueError", "(", "'Expected scalar shape for tensor, got ...	37.931034	19.482759
def attach_storage(self, server, storage, storage_type, address): """ Attach a Storage object to a Server. Return a list of the server's storages. """ body = {'storage_device': {}} if storage: body['storage_device']['storage'] = str(storage) if storage_type: ...	[ "def", "attach_storage", "(", "self", ",", "server", ",", "storage", ",", "storage_type", ",", "address", ")", ":", "body", "=", "{", "'storage_device'", ":", "{", "}", "}", "if", "storage", ":", "body", "[", "'storage_device'", "]", "[", "'storage'", "]...	37.529412	22.235294
def _alerter_thread_func(self) -> None: """ Prints alerts and updates the prompt any time the prompt is showing """ self._alert_count = 0 self._next_alert_time = 0 while not self._stop_thread: # Always acquire terminal_lock before printing alerts or updating the prompt ...	[ "def", "_alerter_thread_func", "(", "self", ")", "->", "None", ":", "self", ".", "_alert_count", "=", "0", "self", ".", "_next_alert_time", "=", "0", "while", "not", "self", ".", "_stop_thread", ":", "# Always acquire terminal_lock before printing alerts or updating t...	40.15625	21.8125
def modified_lines_from_udiff(udiff): """Extract from a udiff an iterator of tuples of (start, end) line numbers.""" chunks = re.split('\n@@ [^\n]+\n', udiff)[1:] line_numbers = re.findall('@@\s[+-]\d+,\d+ \+(\d+)', udiff) line_numbers = list(map(int, line_numbers)) for c, start in zip(chunks,...	[ "def", "modified_lines_from_udiff", "(", "udiff", ")", ":", "chunks", "=", "re", ".", "split", "(", "'\\n@@ [^\\n]+\\n'", ",", "udiff", ")", "[", "1", ":", "]", "line_numbers", "=", "re", ".", "findall", "(", "'@@\\s[+-]\\d+,\\d+ \\+(\\d+)'", ",", "udiff", "...	41.8	14.933333
def create_plan(self, *, plan_code, description, interval, interval_count, max_payments_allowed, payment_attempts_delay, plan_value, plan_tax, plan_tax_return_base, currency, max_payment_attempts=None, max_pending_payments=None, trial_days=None): """ Creating a ne...	[ "def", "create_plan", "(", "self", ",", "*", ",", "plan_code", ",", "description", ",", "interval", ",", "interval_count", ",", "max_payments_allowed", ",", "payment_attempts_delay", ",", "plan_value", ",", "plan_tax", ",", "plan_tax_return_base", ",", "currency", ...	38.716049	25.259259
def do_thing(): """Execute command line cryptorito actions""" if len(sys.argv) == 5 and sys.argv[1] == "encrypt_file": encrypt_file(sys.argv[2], sys.argv[3], sys.argv[4]) elif len(sys.argv) == 4 and sys.argv[1] == "decrypt_file": decrypt_file(sys.argv[2], sys.argv[3]) elif len(sys.argv) ...	[ "def", "do_thing", "(", ")", ":", "if", "len", "(", "sys", ".", "argv", ")", "==", "5", "and", "sys", ".", "argv", "[", "1", "]", "==", "\"encrypt_file\"", ":", "encrypt_file", "(", "sys", ".", "argv", "[", "2", "]", ",", "sys", ".", "argv", "[...	43.681818	16
def subscribe(self, *events: Union[Event, Pager]) -> Callable: """Call a function in response to an event. If more than one event is given, `func` will be given as many arguments as there are events. If the pager calls notify, the decorated function will be called. Parameters ...	[ "def", "subscribe", "(", "self", ",", "*", "events", ":", "Union", "[", "Event", ",", "Pager", "]", ")", "->", "Callable", ":", "try", ":", "first_event", "=", "events", "[", "0", "]", "except", "IndexError", ":", "raise", "IndexError", "(", "'Must sub...	37.373494	19.084337
def parse_args(args): """Parse command line parameters Args: args ([str]): Command line parameters as list of strings Returns: :obj:`argparse.Namespace`: command line parameters namespace """ parser = argparse.ArgumentParser( description="Imports GramVaani data for Deep Speech" ...	[ "def", "parse_args", "(", "args", ")", ":", "parser", "=", "argparse", ".", "ArgumentParser", "(", "description", "=", "\"Imports GramVaani data for Deep Speech\"", ")", "parser", ".", "add_argument", "(", "\"--version\"", ",", "action", "=", "\"version\"", ",", "...	25.833333	18.604167
def _transform(self, Y, scan_onsets, beta, beta0, rho_e, sigma_e, rho_X, sigma2_X, rho_X0, sigma2_X0): """ Given the data Y and the response amplitudes beta and beta0 estimated in the fit step, estimate the corresponding X and X0. It is done by a forward-backward algor...	[ "def", "_transform", "(", "self", ",", "Y", ",", "scan_onsets", ",", "beta", ",", "beta0", ",", "rho_e", ",", "sigma_e", ",", "rho_X", ",", "sigma2_X", ",", "rho_X0", ",", "sigma2_X0", ")", ":", "logger", ".", "info", "(", "'Transforming new data.'", ")"...	45.730769	14.538462
def create_listeners(name, listeners, region=None, key=None, keyid=None, profile=None): ''' Create listeners on an ELB. CLI example: .. code-block:: bash salt myminion boto_elb.create_listeners myelb '[["HTTPS", "HTTP", 443, 80, "arn:aws:iam::11 11111:server-certificate/...	[ "def", "create_listeners", "(", "name", ",", "listeners", ",", "region", "=", "None", ",", "key", "=", "None", ",", "keyid", "=", "None", ",", "profile", "=", "None", ")", ":", "conn", "=", "_get_conn", "(", "region", "=", "region", ",", "key", "=", ...	36.148148	26.962963
def make_nn_funs(layer_sizes, L2_reg, noise_variance, nonlinearity=np.tanh): """These functions implement a standard multi-layer perceptron, vectorized over both training examples and weight samples.""" shapes = list(zip(layer_sizes[:-1], layer_sizes[1:])) num_weights = sum((m+1)*n for m, n in shapes) ...	[ "def", "make_nn_funs", "(", "layer_sizes", ",", "L2_reg", ",", "noise_variance", ",", "nonlinearity", "=", "np", ".", "tanh", ")", ":", "shapes", "=", "list", "(", "zip", "(", "layer_sizes", "[", ":", "-", "1", "]", ",", "layer_sizes", "[", "1", ":", ...	43.344828	14.965517
def add_prefix(self, auth, attr, args=None): """ Add a prefix and return its ID. * `auth` [BaseAuth] AAA options. * `attr` [prefix_attr] Prefix attributes. * `args` [add_prefix_args] Arguments explaining how the prefix should b...	[ "def", "add_prefix", "(", "self", ",", "auth", ",", "attr", ",", "args", "=", "None", ")", ":", "if", "args", "is", "None", ":", "args", "=", "{", "}", "self", ".", "_logger", ".", "debug", "(", "\"add_prefix called; attr: %s; args: %s\"", "%", "(", "u...	39.990148	22.433498
def heatmap(dm, partition=None, cmap=CM.Blues, fontsize=10): """ heatmap(dm, partition=None, cmap=CM.Blues, fontsize=10) Produce a 2D plot of the distance matrix, with values encoded by coloured cells. Args: partition: treeCl.Partition object - if supplied, will reorder ...	[ "def", "heatmap", "(", "dm", ",", "partition", "=", "None", ",", "cmap", "=", "CM", ".", "Blues", ",", "fontsize", "=", "10", ")", ":", "assert", "isinstance", "(", "dm", ",", "DistanceMatrix", ")", "datamax", "=", "float", "(", "np", ".", "abs", "...	31.288462	21.980769
def get_configs(self): """Load all config files and return the configobjs :returns: a list of configobjs :raises: None It always loads the coreconfig. Then it looks for all configs inside the PLUGIN_CONFIG_DIR. It will find the corresponding spec of the plugins. ...	[ "def", "get_configs", "(", "self", ")", ":", "# all loaded configs are stored in confs", "confs", "=", "[", "]", "# always load core config. it is not part of the plugin configs", "try", ":", "confs", ".", "append", "(", "iniconf", ".", "get_core_config", "(", ")", ")",...	36.065574	18.04918
def QA_indicator_BIAS(DataFrame, N1, N2, N3): '乖离率' CLOSE = DataFrame['close'] BIAS1 = (CLOSE - MA(CLOSE, N1)) / MA(CLOSE, N1) * 100 BIAS2 = (CLOSE - MA(CLOSE, N2)) / MA(CLOSE, N2) * 100 BIAS3 = (CLOSE - MA(CLOSE, N3)) / MA(CLOSE, N3) * 100 DICT = {'BIAS1': BIAS1, 'BIAS2': BIAS2, 'BIAS3': BIAS3}...	[ "def", "QA_indicator_BIAS", "(", "DataFrame", ",", "N1", ",", "N2", ",", "N3", ")", ":", "CLOSE", "=", "DataFrame", "[", "'close'", "]", "BIAS1", "=", "(", "CLOSE", "-", "MA", "(", "CLOSE", ",", "N1", ")", ")", "/", "MA", "(", "CLOSE", ",", "N1",...	38.111111	18.555556
def get_language_data(self, qid, lang, lang_data_type): """ get language data for specified qid :param qid: :param lang: language code :param lang_data_type: 'label', 'description' or 'aliases' :return: list of strings If nothing is found: If lang_data...	[ "def", "get_language_data", "(", "self", ",", "qid", ",", "lang", ",", "lang_data_type", ")", ":", "self", ".", "init_language_data", "(", "lang", ",", "lang_data_type", ")", "current_lang_data", "=", "self", ".", "loaded_langs", "[", "lang", "]", "[", "lang...	41.210526	14.894737
def set(self, oid, value, value_type=None): """ Sets a single OID value. If you do not pass value_type hnmp will try to guess the correct type. Autodetection is supported for: * int and float (as Integer, fractional part will be discarded) * IPv4 address (as IpAddress) *...	[ "def", "set", "(", "self", ",", "oid", ",", "value", ",", "value_type", "=", "None", ")", ":", "snmpsecurity", "=", "self", ".", "_get_snmp_security", "(", ")", "if", "value_type", "is", "None", ":", "if", "isinstance", "(", "value", ",", "int", ")", ...	36.636364	16.745455
def is_numeric(obj): """ This detects whether an input object is numeric or not. :param obj: object to be tested. """ try: obj+obj, obj-obj, objobj, obj*obj, obj/obj except ZeroDivisionError: return True except Exception: return False else: return True	[ "def", "is_numeric", "(", "obj", ")", ":", "try", ":", "obj", "+", "obj", ",", "obj", "-", "obj", ",", "obj", "", "obj", ",", "obj", "*", "obj", ",", "obj", "/", "obj", "except", "ZeroDivisionError", ":", "return", "True", "except", "Exception", ...	21.857143	17.857143
def to_line_string(self, closed=True): """ Convert this polygon's `exterior` to a ``LineString`` instance. Parameters ---------- closed : bool, optional Whether to close the line string, i.e. to add the first point of the `exterior` also as the last point...	[ "def", "to_line_string", "(", "self", ",", "closed", "=", "True", ")", ":", "from", "imgaug", ".", "augmentables", ".", "lines", "import", "LineString", "if", "not", "closed", "or", "len", "(", "self", ".", "exterior", ")", "<=", "1", ":", "return", "L...	36.208333	21.208333
def patched_context(module_names, *kwargs): """apply emulation patches only for a specific context :param module_names: var-args for the modules to patch, as in :func:`patch` :param local: if True, unpatching is done on every switch-out, and re-patching on every switch-in, so that they ar...	[ "def", "patched_context", "(", "", "module_names", ",", "", "*", "kwargs", ")", ":", "local", "=", "kwargs", ".", "pop", "(", "'local'", ",", "False", ")", "if", "kwargs", ":", "raise", "TypeError", "(", "\"patched_context() got an unexpected keyword \"", "+...	33.3	21.866667
def item_sectie_adapter(obj, request): """ Adapter for rendering an object of :class: `crabpy.gateway.capakey.Sectie` to json. """ return { 'id': obj.id, 'afdeling': { 'id': obj.afdeling.id, 'naam': obj.afdeling.naam, 'gemeente': { ...	[ "def", "item_sectie_adapter", "(", "obj", ",", "request", ")", ":", "return", "{", "'id'", ":", "obj", ".", "id", ",", "'afdeling'", ":", "{", "'id'", ":", "obj", ".", "afdeling", ".", "id", ",", "'naam'", ":", "obj", ".", "afdeling", ".", "naam", ...	27.333333	12.222222
def checktypes(func): """Decorator to verify arguments and return types.""" sig = inspect.signature(func) types = {} for param in sig.parameters.values(): # Iterate through function's parameters and build the list of # arguments types param_type = param.annotation if par...	[ "def", "checktypes", "(", "func", ")", ":", "sig", "=", "inspect", ".", "signature", "(", "func", ")", "types", "=", "{", "}", "for", "param", "in", "sig", ".", "parameters", ".", "values", "(", ")", ":", "# Iterate through function's parameters and build th...	42.051948	20.116883
def _pick_up_classes(modules, classnames): """ Given a list of class names to retrieve, try to fetch them from the specified list of modules and returns the list of the fetched classes. """ klasses = [] for classname in classnames: klass = None for module in modules: ...	[ "def", "_pick_up_classes", "(", "modules", ",", "classnames", ")", ":", "klasses", "=", "[", "]", "for", "classname", "in", "classnames", ":", "klass", "=", "None", "for", "module", "in", "modules", ":", "if", "hasattr", "(", "module", ",", "classname", ...	37.647059	15.294118
def get_all_subscriptions(self, server_id): """ Return all indication subscriptions in a WBEM server. This function contacts the WBEM server and retrieves the indication subscriptions by enumerating the instances of CIM class "CIM_IndicationSubscription" in the Interop namespace...	[ "def", "get_all_subscriptions", "(", "self", ",", "server_id", ")", ":", "# Validate server_id", "server", "=", "self", ".", "_get_server", "(", "server_id", ")", "return", "server", ".", "conn", ".", "EnumerateInstances", "(", "SUBSCRIPTION_CLASSNAME", ",", "name...	31.666667	25.266667
def _validate_no_null_values(self): """ Loads the tables from the gtfs object and counts the number of rows that have null values in fields that should not be null. Stores the number of null rows in warnings_container """ for table in DB_TABLE_NAMES: null_not_ok_warni...	[ "def", "_validate_no_null_values", "(", "self", ")", ":", "for", "table", "in", "DB_TABLE_NAMES", ":", "null_not_ok_warning", "=", "\"Null values in must-have columns in table {table}\"", ".", "format", "(", "table", "=", "table", ")", "null_warn_warning", "=", "\"Null ...	62.05	33.85
def scan_to_module(python_modules, module, ignore=tuple()): """ Scans `python_modules` with :py:func:`scan` and adds found providers to `module`'s :py:attr:`wiring.configuration.Module.providers`. `ignore` argument is passed through to :py:func:`scan`. """ def callback(specification, provider):...	[ "def", "scan_to_module", "(", "python_modules", ",", "module", ",", "ignore", "=", "tuple", "(", ")", ")", ":", "def", "callback", "(", "specification", ",", "provider", ")", ":", "module", ".", "providers", "[", "specification", "]", "=", "provider", "sca...	41.2	15.8
def print_to_tsplib(self, edges, tspfile, precision=0): """ See TSPlib format: <https://www.iwr.uni-heidelberg.de/groups/comopt/software/TSPLIB95/> NAME: bayg29 TYPE: TSP COMMENT: 29 Cities in Bavaria, geographical distances DIMENSION: 29 EDGE_WEIGHT_TYPE...	[ "def", "print_to_tsplib", "(", "self", ",", "edges", ",", "tspfile", ",", "precision", "=", "0", ")", ":", "fw", "=", "must_open", "(", "tspfile", ",", "\"w\"", ")", "incident", ",", "nodes", "=", "node_to_edge", "(", "edges", ",", "directed", "=", "Fa...	36.836735	16.755102
def find_cross_contamination(databases, pair, tmpdir='tmp', log='log.txt', threads=1): """ Usese mash to find out whether or not a sample has more than one genus present, indicating cross-contamination. :param databases: A databases folder, which must contain refseq.msh, a mash sketch that has one represent...	[ "def", "find_cross_contamination", "(", "databases", ",", "pair", ",", "tmpdir", "=", "'tmp'", ",", "log", "=", "'log.txt'", ",", "threads", "=", "1", ")", ":", "genera_present", "=", "list", "(", ")", "out", ",", "err", ",", "cmd", "=", "mash", ".", ...	54.138889	24.027778
def set_applications_from_meta(self, metadata, exclude=None): """ Parses meta and update or create each application :param str metadata: path or url to meta.yml :param list[str] exclude: List of application names, to exclude from meta. This might be need...	[ "def", "set_applications_from_meta", "(", "self", ",", "metadata", ",", "exclude", "=", "None", ")", ":", "if", "not", "exclude", ":", "exclude", "=", "[", "]", "if", "metadata", ".", "startswith", "(", "'http'", ")", ":", "meta", "=", "yaml", ".", "sa...	42.409091	15.863636
def build_vep_string(vep_info, vep_columns): """ Build a vep string formatted string. Take a list with vep annotations and build a new vep string Args: vep_info (list): A list with vep annotation dictionaries vep_columns (list): A list with the vep column names found in the ...	[ "def", "build_vep_string", "(", "vep_info", ",", "vep_columns", ")", ":", "logger", "=", "getLogger", "(", "__name__", ")", "logger", ".", "debug", "(", "\"Building vep string from {0}\"", ".", "format", "(", "vep_info", ")", ")", "logger", ".", "debug", "(", ...	32.448276	20.448276
def find_peaks(data, threshold, box_size=3, footprint=None, mask=None, border_width=None, npeaks=np.inf, centroid_func=None, subpixel=False, error=None, wcs=None): """ Find local peaks in an image that are above above a specified threshold value. Peaks are the maxima above...	[ "def", "find_peaks", "(", "data", ",", "threshold", ",", "box_size", "=", "3", ",", "footprint", "=", "None", ",", "mask", "=", "None", ",", "border_width", "=", "None", ",", "npeaks", "=", "np", ".", "inf", ",", "centroid_func", "=", "None", ",", "s...	40.005556	21.983333
def add_show_function(self, show_name, show_func): """ Appends a show function to the locally cached DesignDocument shows dictionary. :param show_name: Name used to identify the show function. :param show_func: Javascript show function. """ if self.get_show_funct...	[ "def", "add_show_function", "(", "self", ",", "show_name", ",", "show_func", ")", ":", "if", "self", ".", "get_show_function", "(", "show_name", ")", "is", "not", "None", ":", "raise", "CloudantArgumentError", "(", "110", ",", "show_name", ")", "self", ".", ...	37.166667	17.833333
def include(_name_or_func, args, _module=None, _default='includeme', kwargs): """ Resolve and call functions """ if callable(_name_or_func): resolved = _name_or_func else: resolved = resolve_str(_name_or_func, _module, _default) resolved(args, **kwargs)	[ "def", "include", "(", "_name_or_func", ",", "", "args", ",", "_module", "=", "None", ",", "_default", "=", "'includeme'", ",", "", "*", "kwargs", ")", ":", "if", "callable", "(", "_name_or_func", ")", ":", "resolved", "=", "_name_or_func", "else", ":"...	29.7	14.8
def issue(self, invoice_id, **kwargs): """" Issues an invoice in draft state Args: invoice_id : Id for delete the invoice Returns: Its response is the invoice entity, similar to create/update API response. Its status now would be issued. """ url =...	[ "def", "issue", "(", "self", ",", "invoice_id", ",", "", "", "kwargs", ")", ":", "url", "=", "\"{}/{}/issue\"", ".", "format", "(", "self", ".", "base_url", ",", "invoice_id", ")", "return", "self", ".", "post_url", "(", "url", ",", "{", "}", ",", ...	36.909091	19
def set_info_mapper_model(self, mapper, model): """Set the model for the info mapper :param mapper: the mapper to update :type mapper: QtGui.QDataWidgetMapper :param model: The model to set :type model: QtGui.QAbstractItemModel \| None :returns: None :rtype: None ...	[ "def", "set_info_mapper_model", "(", "self", ",", "mapper", ",", "model", ")", ":", "# nothing changed. we can return.", "# I noticed that when you set the model the very first time to None", "# it printed a message:", "# QObject::connect: Cannot connect (null)::dataChanged(QModelIndex,QMo...	46.133333	18.911111
def handle_json_GET_boundboxstops(self, params): """Return a list of up to 'limit' stops within bounding box with 'n','e' and 's','w' in the NE and SW corners. Does not handle boxes crossing longitude line 180.""" schedule = self.server.schedule n = float(params.get('n')) e = float(params.get('e...	[ "def", "handle_json_GET_boundboxstops", "(", "self", ",", "params", ")", ":", "schedule", "=", "self", ".", "server", ".", "schedule", "n", "=", "float", "(", "params", ".", "get", "(", "'n'", ")", ")", "e", "=", "float", "(", "params", ".", "get", "...	45	11.333333
def defer_sync(self, func): """ Arrange for `func()` to execute on :class:`Broker` thread, blocking the current thread until a result or exception is available. :returns: Return value of `func()`. """ latch = Latch() def wrapper(): try: ...	[ "def", "defer_sync", "(", "self", ",", "func", ")", ":", "latch", "=", "Latch", "(", ")", "def", "wrapper", "(", ")", ":", "try", ":", "latch", ".", "put", "(", "func", "(", ")", ")", "except", "Exception", ":", "latch", ".", "put", "(", "sys", ...	28.526316	15.473684
def check_for_lane_permission(self): """ One or more permissions can be associated with a lane of a workflow. In a similar way, a lane can be restricted with relation to other lanes of the workflow. This method called on lane changes and checks user has required permissi...	[ "def", "check_for_lane_permission", "(", "self", ")", ":", "# TODO: Cache lane_data in app memory", "if", "self", ".", "current", ".", "lane_permission", ":", "log", ".", "debug", "(", "\"HAS LANE PERM: %s\"", "%", "self", ".", "current", ".", "lane_permission", ")"...	43.970588	21.147059
def unpack(self, unpacker): """ unpack the contents of this instance from the values in unpacker """ (a, b, c) = unpacker.unpack_struct(_HHH) self.access_flags = a self.name_ref = b self.descriptor_ref = c self.attribs.unpack(unpacker)	[ "def", "unpack", "(", "self", ",", "unpacker", ")", ":", "(", "a", ",", "b", ",", "c", ")", "=", "unpacker", ".", "unpack_struct", "(", "_HHH", ")", "self", ".", "access_flags", "=", "a", "self", ".", "name_ref", "=", "b", "self", ".", "descriptor_...	26.454545	15.545455
def alpha_blend(self, other): """Alpha-blend this color on the other one. Args: :other: The grapefruit.Color to alpha-blend with this one. Returns: A grapefruit.Color instance which is the result of alpha-blending this color on the other one. >>> c1 = Color.from_rgb(1, 0.5, ...	[ "def", "alpha_blend", "(", "self", ",", "other", ")", ":", "# get final alpha channel", "fa", "=", "self", ".", "__a", "+", "other", ".", "__a", "-", "(", "self", ".", "__a", "*", "other", ".", "__a", ")", "# get percentage of source alpha compared to final al...	27.25	20.75
def __make_another_index(self, list_of_entries, url=False, hs_admin=False): ''' Find an index not yet used in the handle record and not reserved for any (other) special type. :param: list_of_entries: List of all entries to find which indices are used already. :pa...	[ "def", "__make_another_index", "(", "self", ",", "list_of_entries", ",", "url", "=", "False", ",", "hs_admin", "=", "False", ")", ":", "start", "=", "2", "# reserved indices:", "reserved_for_url", "=", "set", "(", "[", "1", "]", ")", "reserved_for_admin", "=...	36.4	22.1
def timesince_or_never(dt, default=None): """Call the Django ``timesince`` filter or a given default string. It returns the string default if dt is not a valid ``date`` or ``datetime`` object. When default is None, "Never" is returned. """ if default is None: default = _("Never") ...	[ "def", "timesince_or_never", "(", "dt", ",", "default", "=", "None", ")", ":", "if", "default", "is", "None", ":", "default", "=", "_", "(", "\"Never\"", ")", "if", "isinstance", "(", "dt", ",", "datetime", ".", "date", ")", ":", "return", "timesince",...	29.071429	15.857143
def render(self): """ Find {{}} tokens; resolve then replace them as described elsewhere Resolution is multi-pass: tokens may be nested to form parts of other tokens. Token search steps when resolving symbols - 1. lookups of AWS resource identifiers, such as a security group ID - 2. secure ...	[ "def", "render", "(", "self", ")", ":", "# Ensure that our symbols are clean and are not from a previous template that was rendered", "self", ".", "symbols", "=", "set", "(", ")", "# Until all symbols are resolved or it is determined that some cannot be resolved, repeat:", "go_again", ...	50.12963	22.462963
def new(self): # type: () -> None ''' A method to create a new UDF Terminating Descriptor. Parameters: None. Returns: Nothing. ''' if self._initialized: raise pycdlibexception.PyCdlibInternalError('UDF Terminating Descriptor already ...	[ "def", "new", "(", "self", ")", ":", "# type: () -> None", "if", "self", ".", "_initialized", ":", "raise", "pycdlibexception", ".", "PyCdlibInternalError", "(", "'UDF Terminating Descriptor already initialized'", ")", "self", ".", "desc_tag", "=", "UDFTag", "(", ")...	27.352941	27.235294

def obfn_cns(self): r"""Compute constraint violation measure :math:`\| P(\mathbf{y}) - \mathbf{y}\|_2`. """ Y = self.obfn_gvar() return np.linalg.norm((self.Pcn(Y) - Y))

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29.142857

13.571429

def get_account_statement( self, locale=None, from_record=None, record_count=None, item_date_range=None, include_item=None, wallet=None): """Get account statement. :param str locale: The language to be used where applicable :param int from_record: Specifies the first rec...

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47.444444

22

def secrets_manager(*secret_names): """ Get secrets from the `AWS Secrets Manager <https://aws.amazon.com/secrets-manager/>`_. Secrets are added to a dictionary named ``secrets`` on the context object. This requires your lambda to have the ``secretsmanager:GetSecretValue`` permission for the reque...

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36.184211

23.236842

def _remove_dupes(self, phonetic): """Remove duplicates from a phonetic encoding list. Parameters ---------- phonetic : str A Beider-Morse phonetic encoding Returns ------- str A Beider-Morse phonetic code """ alt_string ...

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23.375

17.708333

def s2dctmat(nfilt,ncep,freqstep): """Return the 'legacy' not-quite-DCT matrix used by Sphinx""" melcos = numpy.empty((ncep, nfilt), 'double') for i in range(0,ncep): freq = numpy.pi * float(i) / nfilt melcos[i] = numpy.cos(freq * numpy.arange(0.5, float(nfilt)+0.5, 1.0, 'double')) melco...

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44.625

13.25

def main(): """pyprf_opt_brute entry point.""" # Get list of input arguments (without first one, which is the path to the # function that is called): --NOTE: This is another way of accessing # input arguments, but since we use 'argparse' it is redundant. # lstArgs = sys.argv[1:] strWelcome = 'p...

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43.938776

24.530612

def finished(experiment_name, reset=True): """ Track a conversion. :param experiment_name: Name of the experiment. :param reset: If set to `True` current user's session is reset so that they may start the test again in the future. If set to `False` the user will always see the alternat...

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38.485714

17.742857

def addFASTAEditingCommandLineOptions(parser): """ Add standard FASTA editing command-line options to an argparse parser. These are options that can be used to alter FASTA records, NOT options that simply select or reject those things (for those see addFASTAFilteringCommandLineOptions). @param...

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45.976744

24.232558

def prepare_request_uri(self, uri, redirect_uri=None, scope=None, state=None, **kwargs): """Prepare the implicit grant request URI. The client constructs the request URI by adding the following parameters to the query component of the authorization endpoint URI ...

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62.744681

36.93617

def remove_object(self, obj): """Remove an object from the definition.""" self._objects.remove(obj) self._pairs.difference_update((obj, p) for p in self._properties)

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46.5

12.75

def virtual_resource(self): """ Available on a Master Engine only. To get all virtual resources call:: engine.virtual_resource.all() :raises UnsupportedEngineFeature: master engine only :rtype: CreateCollection(VirtualResource) """ resource = create...

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30

13.111111

def fast_sync_inspect_snapshot( snapshot_path ): """ Inspect a snapshot Return useful information Return {'status': True, 'signatures': ..., 'payload_size': ..., 'sig_append_offset': ..., 'hash': ...} on success Return {'error': ...} on error """ with open(snapshot_path, 'r') as f: i...

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37.833333

20.5

def add_arrow(self, x1, y1, x2, y2, side='left', shape='full', color='black', width=0.01, head_width=0.03, overhang=0, **kws): """add arrow supplied x, y position""" dx, dy = x2-x1, y2-y1 axes = self.axes if side == 'right': axes = self.g...

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38.733333

11.8

def add_new_init_method(obj): """ Replace the existing obj.__init__() method with a new one which calls the original one and in addition performs the following actions: (1) Finds all instances of tohu.BaseGenerator in the namespace and collects them in the dictionary `self.field_gens`. ...

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36.706667

23.346667

def evecs(self): """ The eigenvectors of the parameter space. This is a Dictionary of numpy.matrix Each entry in the dictionary is as described under evals. Each numpy.matrix contains the eigenvectors which, with the eigenvalues in evals, are needed to rotate the ...

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43.357143

14.785714

def write(self, file_or_filename): """ Writes case data to file in Excel format. """ self.book = Workbook() self._write_data(None) self.book.save(file_or_filename)

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33

4.333333

def generate_defect_structure(self, supercell=(1, 1, 1)): """ Returns Defective Vacancy structure, decorated with charge Args: supercell (int, [3x1], or [[]] (3x3)): supercell integer, vector, or scaling matrix """ defect_structure = self.bulk_structure.copy() ...

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49.565217

23.304348

def _reflect_table(self): """Load the tables definition from the database.""" with self.db.lock: try: self._table = SQLATable(self.name, self.db.metadata, schema=self.db.schema, ...

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40.5

14

def rmdir(self, pathobj): """ Removes a directory """ stat = self.stat(pathobj) if not stat.is_dir: raise OSError(20, "Not a directory: '%s'" % str(pathobj)) url = str(pathobj) + '/' text, code = self.rest_del(url, session=pathobj.session, verify=pa...

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30.2

23

def ipv4_generate_random(total=100): """ The generator to produce random, unique IPv4 addresses that are not defined (can be looked up using ipwhois). Args: total (:obj:`int`): The total number of IPv4 addresses to generate. Yields: str: The next IPv4 address. """ count = ...

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24.478261

23.347826

def select_group(self, group_id): """Copy the query and add filtering by group. Example:: query = query.select_group('1234567') :type group_id: str :param group_id: The ID of a group to filter by. :rtype: :class:`Query` :returns: The new query object. ...

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26.4375

16.3125

def get_renderers(self): """Optionally block Browsable API rendering. """ renderers = super(WithDynamicViewSetMixin, self).get_renderers() if settings.ENABLE_BROWSABLE_API is False: return [ r for r in renderers if not isinstance(r, BrowsableAPIRenderer) ]...

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39.444444

20.333333

def top(self, num, key=None): """ Get the top N elements from an RDD. .. note:: This method should only be used if the resulting array is expected to be small, as all the data is loaded into the driver's memory. .. note:: It returns the list sorted in descending order. ...

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32.869565

22.347826

def _create_entry(entry_body): ''' Adds common part of entry to a given entry body and return the whole xml. ''' updated_str = datetime.utcnow().isoformat() if datetime.utcnow().utcoffset() is None: updated_str += '+00:00' entry_start = '''<?xml version="1.0" encoding="utf-8" standalone="ye...

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53.538462

29.538462

def _special_dbkey_maps(dbkey, ref_file): """Avoid duplicate VEP information for databases with chromosome differences like hg19/GRCh37. """ remaps = {"hg19": "GRCh37", "hg38-noalt": "hg38"} if dbkey in remaps: base_dir = os.path.normpath(os.path.join(os.path.dirname(ref_file), os....

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43.5

17.777778

def locate(cls): """Locates the active PEX bootstrap. :rtype: :class:`Bootstrap` """ if cls._INSTANCE is None: bootstrap_path = __file__ module_import_path = __name__.split('.') # For example, our __file__ might be requests.pex/.bootstrap/pex/bootstrap.pyc and our import # path...

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39.176471

24.176471

def quote(self) -> str: """Get a random quote. :return: Quote from movie. :Example: "Bond... James Bond." """ quotes = self._data['quotes'] return self.random.choice(quotes)

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22.6

13.7

def get_all_hits(self): ''' Get all HITs ''' if not self.connect_to_turk(): return False try: hits = [] paginator = self.mtc.get_paginator('list_hits') for page in paginator.paginate(): hits.extend(page['HITs']) except Excep...

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def model_to_json(self, object, cleanup=True): """Take a model instance and return it as a json struct""" model_name = type(object).__name__ if model_name not in self.swagger_dict['definitions']: raise ValidationError("Swagger spec has no definition for model %s" % model_name) ...

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def suppress_stdout(): """ Context manager that suppresses stdout. Examples: >>> with suppress_stdout(): ... print('Test print') >>> print('test') test """ save_stdout = sys.stdout sys.stdout = DevNull() yield sys.stdout = save_stdout

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def add_root(self, id_): """Adds a root node. arg: id (osid.id.Id): the ``Id`` of the node raise: AlreadyExists - ``id`` is already in hierarchy raise: NotFound - ``id`` not found raise: NullArgument - ``id`` is ``null`` raise: OperationFailed - unable to complete...

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def validate(message, **config): """ Return true or false if the message is signed appropriately. """ if not _validate_implementations: init(**config) cfg = copy.deepcopy(config) if 'gpg_home' not in cfg: cfg['gpg_home'] = os.path.expanduser('~/.gnupg/') if 'ssldir' not in cfg: ...

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def reconnect_to_broker(self): """Connect or reconnect to broker""" #print "CONNECT !" if self.client: self.poller.unregister(self.client) self.client.close() self.client = self.ctx.socket(zmq.DEALER) self.client.linger = 0 self.client.connect(self...

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def fromrdd(rdd, nrecords=None, shape=None, index=None, labels=None, dtype=None, ordered=False): """ Load series data from a Spark RDD. Assumes keys are tuples with increasing and unique indices, and values are 1d ndarrays. Will try to infer properties that are not explicitly provided. Paramet...

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def render(opts, functions, states=None, proxy=None, context=None): ''' Returns the render modules ''' if context is None: context = {} pack = {'__salt__': functions, '__grains__': opts.get('grains', {}), '__context__': context} if states: pack['__states...

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def Sample(self): """Takes a sample for profiling.""" self._profiling_sample += 1 if self._profiling_sample >= self._profiling_sample_rate: if self._heapy: heap = self._heapy.heap() heap.dump(self._sample_file) self._profiling_sample = 0

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def extract(fileobj, keywords, comment_tags, options): """Extracts translation messages from underscore template files. This method does also extract django templates. If a template does not contain any django translation tags we always fallback to underscore extraction. This is a plugin to Babel, wri...

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def connect(self, chip_name, speed='auto', verbose=False): """Connects the J-Link to its target. Args: self (JLink): the ``JLink`` instance chip_name (str): target chip name speed (int): connection speed, one of ``{5-12000, 'auto', 'adaptive'}`` verbose (bool): b...

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def reset(self): """Reset the instance to begin sampling from scratch""" self._sampled = [np.repeat(False, x) for x in self.sizes_] self._n_sampled = np.zeros(self.n_strata_, dtype=int)

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def _add_out_streams(self, spbl): """Adds outputs to a given protobuf Bolt or Spout message""" if self.outputs is None: return # sanitize outputs and get a map <stream_id -> out fields> output_map = self._sanitize_outputs() for stream_id, out_fields in output_map.items(): out_stream = ...

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def repository_factory(vcs_type, **kw): """ Instantiate a :class:`Repository` object based on the given type and arguments. :param vcs_type: One of the strings 'bazaar', 'bzr', 'git', 'hg' or 'mercurial' or a subclass of :class:`Repository`. :param kw: The keyword arguments to :fun...

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def _joint_log_likelihood(self, X): """Calculate the posterior log probability of the samples X""" check_is_fitted(self, "classes_") X = check_array(X, accept_sparse='csr') X_bin = self._transform_data(X) n_classes, n_features = self.feature_log_prob_.shape n_samples, n...

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def SetDeviceProperties(self, object_path, properties): '''Convenience method to Set a device's properties. object_path: the device to update properties: dictionary of keys to dbus variants. If the 1.0 API is being mocked, changing this property will trigger the device's PropertiesChanged signal; ...

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def createGenderPlot(bfile, intensities, problematic_samples, format, out_prefix): """Creates the gender plot. :param bfile: the prefix of the input binary file. :param intensities: the file containing the intensities. :param problematic_samples: the file containing the problematic...

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def general_neg_loglik(self, beta): """ Calculates the negative log-likelihood of the model Parameters ---------- beta : np.ndarray Contains untransformed starting values for latent variables Returns ---------- The negative logliklihood of the model ...

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def on_before_transform_template(self, template_dict): """ Hook method that runs before a template gets transformed. In this method, we parse and process Globals section from the template (if present). :param dict template_dict: SAM template as a dictionary """ try: ...

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def status(name, sig=None): ''' Return the status for a service via rest_sample. If the name contains globbing, a dict mapping service name to True/False values is returned. .. versionadded:: 2015.8.0 .. versionchanged:: 2018.3.0 The service name can now be a glob (e.g. ``salt*``) ...

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def get_tkd_value(tensor_keyed_dict, tensor, allclose_kwargs=None): """ Helper function to find a value in a tensor-keyed- dictionary using an approximation to the key. This is useful if rounding errors in construction occur or hashing issues arise in tensor-keyed-dictionaries (e. g. from symme...

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def task_add_user(self, *args, **kwargs): """Add users to the current task :returns: None :rtype: None :raises: None """ if not self.cur_task: return dialog = UserAdderDialog(task=self.cur_task) dialog.exec_() users = dialog.users ...

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def reveal( input_image: Union[str, IO[bytes]], generator: Iterator[int], shift: int = 0, encoding: str = "UTF-8", ): """Find a message in an image (with the LSB technique). """ img = tools.open_image(input_image) img_list = list(img.getdata()) width, height = img.size buff, coun...

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32.285714

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def flood(im, regions=None, mode='max'): r""" Floods/fills each region in an image with a single value based on the specific values in that region. The ``mode`` argument is used to determine how the value is calculated. Parameters ---------- im : array_like An ND image with isolate...

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def _resume(self): # type: (Descriptor) -> int """Resume a download, if possible :param Descriptor self: this :rtype: int or None :return: verified download offset """ if self._resume_mgr is None or self._offset > 0 or self._finalized: return None ...

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def sparse(x, rho, penalty): """ Proximal operator for the l1-norm: soft thresholding Parameters ---------- penalty : float Strength or weight on the l1-norm """ lmbda = penalty / rho return (x - lmbda) * (x >= lmbda) + (x + lmbda) * (x <= -lmbda)

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def thread( mafs, species ): """ Restrict an list of alignments to a given list of species by: 1) Removing components for any other species 2) Remove any columns containing all gaps Example: >>> import bx.align.maf >>> block1 = bx.align.maf.from_string( '''...

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def create_circuit_termination(circuit, interface, device, speed, xconnect_id=None, term_side='A'): ''' .. versionadded:: 2019.2.0 Terminate a circuit on an interface circuit The name of the circuit interface The name of the interface to terminate on device The name of ...

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def _has_perm(self, permission_name, view_menu_name): """ Whether the user has this perm """ if hasattr(self, 'perms'): if (permission_name, view_menu_name) in self.perms: return True # rebuild the permissions set self._get_and_cache_perms() ...

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def scalar_pb(tag, data, description=None): """Create a scalar summary_pb2.Summary protobuf. Arguments: tag: String tag for the summary. data: A 0-dimensional `np.array` or a compatible python number type. description: Optional long-form description for this summary, as a `str`. Markdown is suppo...

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def attach_storage(self, server, storage, storage_type, address): """ Attach a Storage object to a Server. Return a list of the server's storages. """ body = {'storage_device': {}} if storage: body['storage_device']['storage'] = str(storage) if storage_type: ...

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def _alerter_thread_func(self) -> None: """ Prints alerts and updates the prompt any time the prompt is showing """ self._alert_count = 0 self._next_alert_time = 0 while not self._stop_thread: # Always acquire terminal_lock before printing alerts or updating the prompt ...

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def modified_lines_from_udiff(udiff): """Extract from a udiff an iterator of tuples of (start, end) line numbers.""" chunks = re.split('\n@@ [^\n]+\n', udiff)[1:] line_numbers = re.findall('@@\s[+-]\d+,\d+ \+(\d+)', udiff) line_numbers = list(map(int, line_numbers)) for c, start in zip(chunks,...

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def create_plan(self, *, plan_code, description, interval, interval_count, max_payments_allowed, payment_attempts_delay, plan_value, plan_tax, plan_tax_return_base, currency, max_payment_attempts=None, max_pending_payments=None, trial_days=None): """ Creating a ne...

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def do_thing(): """Execute command line cryptorito actions""" if len(sys.argv) == 5 and sys.argv[1] == "encrypt_file": encrypt_file(sys.argv[2], sys.argv[3], sys.argv[4]) elif len(sys.argv) == 4 and sys.argv[1] == "decrypt_file": decrypt_file(sys.argv[2], sys.argv[3]) elif len(sys.argv) ...

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def subscribe(self, *events: Union[Event, Pager]) -> Callable: """Call a function in response to an event. If more than one event is given, `func` will be given as many arguments as there are events. If the pager calls notify, the decorated function will be called. Parameters ...

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def parse_args(args): """Parse command line parameters Args: args ([str]): Command line parameters as list of strings Returns: :obj:`argparse.Namespace`: command line parameters namespace """ parser = argparse.ArgumentParser( description="Imports GramVaani data for Deep Speech" ...

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def _transform(self, Y, scan_onsets, beta, beta0, rho_e, sigma_e, rho_X, sigma2_X, rho_X0, sigma2_X0): """ Given the data Y and the response amplitudes beta and beta0 estimated in the fit step, estimate the corresponding X and X0. It is done by a forward-backward algor...

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def create_listeners(name, listeners, region=None, key=None, keyid=None, profile=None): ''' Create listeners on an ELB. CLI example: .. code-block:: bash salt myminion boto_elb.create_listeners myelb '[["HTTPS", "HTTP", 443, 80, "arn:aws:iam::11 11111:server-certificate/...

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def make_nn_funs(layer_sizes, L2_reg, noise_variance, nonlinearity=np.tanh): """These functions implement a standard multi-layer perceptron, vectorized over both training examples and weight samples.""" shapes = list(zip(layer_sizes[:-1], layer_sizes[1:])) num_weights = sum((m+1)*n for m, n in shapes) ...

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def add_prefix(self, auth, attr, args=None): """ Add a prefix and return its ID. * `auth` [BaseAuth] AAA options. * `attr` [prefix_attr] Prefix attributes. * `args` [add_prefix_args] Arguments explaining how the prefix should b...

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def heatmap(dm, partition=None, cmap=CM.Blues, fontsize=10): """ heatmap(dm, partition=None, cmap=CM.Blues, fontsize=10) Produce a 2D plot of the distance matrix, with values encoded by coloured cells. Args: partition: treeCl.Partition object - if supplied, will reorder ...

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def get_configs(self): """Load all config files and return the configobjs :returns: a list of configobjs :raises: None It always loads the coreconfig. Then it looks for all configs inside the PLUGIN_CONFIG_DIR. It will find the corresponding spec of the plugins. ...

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def QA_indicator_BIAS(DataFrame, N1, N2, N3): '乖离率' CLOSE = DataFrame['close'] BIAS1 = (CLOSE - MA(CLOSE, N1)) / MA(CLOSE, N1) * 100 BIAS2 = (CLOSE - MA(CLOSE, N2)) / MA(CLOSE, N2) * 100 BIAS3 = (CLOSE - MA(CLOSE, N3)) / MA(CLOSE, N3) * 100 DICT = {'BIAS1': BIAS1, 'BIAS2': BIAS2, 'BIAS3': BIAS3}...

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def get_language_data(self, qid, lang, lang_data_type): """ get language data for specified qid :param qid: :param lang: language code :param lang_data_type: 'label', 'description' or 'aliases' :return: list of strings If nothing is found: If lang_data...

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def set(self, oid, value, value_type=None): """ Sets a single OID value. If you do not pass value_type hnmp will try to guess the correct type. Autodetection is supported for: * int and float (as Integer, fractional part will be discarded) * IPv4 address (as IpAddress) *...

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def is_numeric(obj): """ This detects whether an input object is numeric or not. :param obj: object to be tested. """ try: obj+obj, obj-obj, obj*obj, obj**obj, obj/obj except ZeroDivisionError: return True except Exception: return False else: return True

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def to_line_string(self, closed=True): """ Convert this polygon's `exterior` to a ``LineString`` instance. Parameters ---------- closed : bool, optional Whether to close the line string, i.e. to add the first point of the `exterior` also as the last point...

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def patched_context(*module_names, **kwargs): """apply emulation patches only for a specific context :param module_names: var-args for the modules to patch, as in :func:`patch` :param local: if True, unpatching is done on every switch-out, and re-patching on every switch-in, so that they ar...

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def item_sectie_adapter(obj, request): """ Adapter for rendering an object of :class: `crabpy.gateway.capakey.Sectie` to json. """ return { 'id': obj.id, 'afdeling': { 'id': obj.afdeling.id, 'naam': obj.afdeling.naam, 'gemeente': { ...

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def checktypes(func): """Decorator to verify arguments and return types.""" sig = inspect.signature(func) types = {} for param in sig.parameters.values(): # Iterate through function's parameters and build the list of # arguments types param_type = param.annotation if par...

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def _pick_up_classes(modules, classnames): """ Given a list of class names to retrieve, try to fetch them from the specified list of modules and returns the list of the fetched classes. """ klasses = [] for classname in classnames: klass = None for module in modules: ...

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def get_all_subscriptions(self, server_id): """ Return all indication subscriptions in a WBEM server. This function contacts the WBEM server and retrieves the indication subscriptions by enumerating the instances of CIM class "CIM_IndicationSubscription" in the Interop namespace...

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def _validate_no_null_values(self): """ Loads the tables from the gtfs object and counts the number of rows that have null values in fields that should not be null. Stores the number of null rows in warnings_container """ for table in DB_TABLE_NAMES: null_not_ok_warni...

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def scan_to_module(python_modules, module, ignore=tuple()): """ Scans `python_modules` with :py:func:`scan` and adds found providers to `module`'s :py:attr:`wiring.configuration.Module.providers`. `ignore` argument is passed through to :py:func:`scan`. """ def callback(specification, provider):...

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def print_to_tsplib(self, edges, tspfile, precision=0): """ See TSPlib format: <https://www.iwr.uni-heidelberg.de/groups/comopt/software/TSPLIB95/> NAME: bayg29 TYPE: TSP COMMENT: 29 Cities in Bavaria, geographical distances DIMENSION: 29 EDGE_WEIGHT_TYPE...

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def find_cross_contamination(databases, pair, tmpdir='tmp', log='log.txt', threads=1): """ Usese mash to find out whether or not a sample has more than one genus present, indicating cross-contamination. :param databases: A databases folder, which must contain refseq.msh, a mash sketch that has one represent...

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def set_applications_from_meta(self, metadata, exclude=None): """ Parses meta and update or create each application :param str metadata: path or url to meta.yml :param list[str] exclude: List of application names, to exclude from meta. This might be need...

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def build_vep_string(vep_info, vep_columns): """ Build a vep string formatted string. Take a list with vep annotations and build a new vep string Args: vep_info (list): A list with vep annotation dictionaries vep_columns (list): A list with the vep column names found in the ...

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def find_peaks(data, threshold, box_size=3, footprint=None, mask=None, border_width=None, npeaks=np.inf, centroid_func=None, subpixel=False, error=None, wcs=None): """ Find local peaks in an image that are above above a specified threshold value. Peaks are the maxima above...

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def add_show_function(self, show_name, show_func): """ Appends a show function to the locally cached DesignDocument shows dictionary. :param show_name: Name used to identify the show function. :param show_func: Javascript show function. """ if self.get_show_funct...

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def include(_name_or_func, *args, _module=None, _default='includeme', **kwargs): """ Resolve and call functions """ if callable(_name_or_func): resolved = _name_or_func else: resolved = resolve_str(_name_or_func, _module, _default) resolved(*args, **kwargs)

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def issue(self, invoice_id, **kwargs): """" Issues an invoice in draft state Args: invoice_id : Id for delete the invoice Returns: Its response is the invoice entity, similar to create/update API response. Its status now would be issued. """ url =...

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def set_info_mapper_model(self, mapper, model): """Set the model for the info mapper :param mapper: the mapper to update :type mapper: QtGui.QDataWidgetMapper :param model: The model to set :type model: QtGui.QAbstractItemModel | None :returns: None :rtype: None ...

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def handle_json_GET_boundboxstops(self, params): """Return a list of up to 'limit' stops within bounding box with 'n','e' and 's','w' in the NE and SW corners. Does not handle boxes crossing longitude line 180.""" schedule = self.server.schedule n = float(params.get('n')) e = float(params.get('e...

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def defer_sync(self, func): """ Arrange for `func()` to execute on :class:`Broker` thread, blocking the current thread until a result or exception is available. :returns: Return value of `func()`. """ latch = Latch() def wrapper(): try: ...

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def check_for_lane_permission(self): """ One or more permissions can be associated with a lane of a workflow. In a similar way, a lane can be restricted with relation to other lanes of the workflow. This method called on lane changes and checks user has required permissi...

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def unpack(self, unpacker): """ unpack the contents of this instance from the values in unpacker """ (a, b, c) = unpacker.unpack_struct(_HHH) self.access_flags = a self.name_ref = b self.descriptor_ref = c self.attribs.unpack(unpacker)

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def alpha_blend(self, other): """Alpha-blend this color on the other one. Args: :other: The grapefruit.Color to alpha-blend with this one. Returns: A grapefruit.Color instance which is the result of alpha-blending this color on the other one. >>> c1 = Color.from_rgb(1, 0.5, ...

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def __make_another_index(self, list_of_entries, url=False, hs_admin=False): ''' Find an index not yet used in the handle record and not reserved for any (other) special type. :param: list_of_entries: List of all entries to find which indices are used already. :pa...

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def timesince_or_never(dt, default=None): """Call the Django ``timesince`` filter or a given default string. It returns the string *default* if *dt* is not a valid ``date`` or ``datetime`` object. When *default* is None, "Never" is returned. """ if default is None: default = _("Never") ...

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def render(self): """ Find {{}} tokens; resolve then replace them as described elsewhere Resolution is multi-pass: tokens may be nested to form parts of other tokens. Token search steps when resolving symbols - 1. lookups of AWS resource identifiers, such as a security group ID - 2. secure ...

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def new(self): # type: () -> None ''' A method to create a new UDF Terminating Descriptor. Parameters: None. Returns: Nothing. ''' if self._initialized: raise pycdlibexception.PyCdlibInternalError('UDF Terminating Descriptor already ...

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