kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def miscellaneous_menu(self, value): """ Setter for self.__miscellaneous_menu attribute. :param value: Attribute value. :type value: QMenu """ if value is not None: assert type(value) is QMenu, "'{0}' attribute: '{1}' type is not 'QMenu'!".format( ...	[ "def", "miscellaneous_menu", "(", "self", ",", "value", ")", ":", "if", "value", "is", "not", "None", ":", "assert", "type", "(", "value", ")", "is", "QMenu", ",", "\"'{0}' attribute: '{1}' type is not 'QMenu'!\"", ".", "format", "(", "\"miscellaneous_menu\"", "...	32.416667	15.75
def project(self, point_cloud, round_px=True): """Projects a point cloud onto the camera image plane. Parameters ---------- point_cloud : :obj:`autolab_core.PointCloud` or :obj:`autolab_core.Point` A PointCloud or Point to project onto the camera image plane. round_...	[ "def", "project", "(", "self", ",", "point_cloud", ",", "round_px", "=", "True", ")", ":", "if", "not", "isinstance", "(", "point_cloud", ",", "PointCloud", ")", "and", "not", "(", "isinstance", "(", "point_cloud", ",", "Point", ")", "and", "point_cloud", ...	44.575	27.45
def editMeta(self, title=None, description=None): """Set metadata for photo. (flickr.photos.setMeta)""" method = 'flickr.photosets.editMeta' if title is None: title = self.title if description is None: description = self.description _dopost(m...	[ "def", "editMeta", "(", "self", ",", "title", "=", "None", ",", "description", "=", "None", ")", ":", "method", "=", "'flickr.photosets.editMeta'", "if", "title", "is", "None", ":", "title", "=", "self", ".", "title", "if", "description", "is", "None", "...	33.2	14.066667
def csp_header(csp={}): """ Decorator to include csp header on app.route wrapper """ _csp = csp_default().read() _csp.update(csp) _header = '' if 'report-only' in _csp and _csp['report-only'] is True: _header = 'Content-Security-Policy-Report-Only' else: _header = 'Content-Securit...	[ "def", "csp_header", "(", "csp", "=", "{", "}", ")", ":", "_csp", "=", "csp_default", "(", ")", ".", "read", "(", ")", "_csp", ".", "update", "(", "csp", ")", "_header", "=", "''", "if", "'report-only'", "in", "_csp", "and", "_csp", "[", "'report-o...	31.458333	15.541667
def _compute_value(power, wg): """Return the weight corresponding to single power.""" if power not in wg: p1, p2 = power # y power if p1 == 0: yy = wg[(0, -1)] wg[power] = numpy.power(yy, p2 / 2).sum() / len(yy) # x power else: xx = wg[...	[ "def", "_compute_value", "(", "power", ",", "wg", ")", ":", "if", "power", "not", "in", "wg", ":", "p1", ",", "p2", "=", "power", "# y power", "if", "p1", "==", "0", ":", "yy", "=", "wg", "[", "(", "0", ",", "-", "1", ")", "]", "wg", "[", "...	30.846154	17.615385
def send(self, data): """ Send encoded instructions to Guacamole guacd server. """ self.logger.debug('Sending data: %s' % data) self.client.sendall(data.encode())	[ "def", "send", "(", "self", ",", "data", ")", ":", "self", ".", "logger", ".", "debug", "(", "'Sending data: %s'", "%", "data", ")", "self", ".", "client", ".", "sendall", "(", "data", ".", "encode", "(", ")", ")" ]	32.833333	8.833333
def _dist_kw_arg(self, k): """ Returns a dictionary of keyword arguments for the k'th distribution. :param int k: Index of the distribution in question. :rtype: ``dict`` """ if self._dist_kw_args is not None: return { key:self._dist_kw...	[ "def", "_dist_kw_arg", "(", "self", ",", "k", ")", ":", "if", "self", ".", "_dist_kw_args", "is", "not", "None", ":", "return", "{", "key", ":", "self", ".", "_dist_kw_args", "[", "key", "]", "[", "k", ",", ":", "]", "for", "key", "in", "self", "...	28.266667	14.666667
def upgradeUserInfo1to2(oldUserInfo): """ Concatenate the I{firstName} and I{lastName} attributes from the old user info item and set the result as the I{realName} attribute of the upgraded item. """ newUserInfo = oldUserInfo.upgradeVersion( UserInfo.typeName, 1, 2, realName=oldU...	[ "def", "upgradeUserInfo1to2", "(", "oldUserInfo", ")", ":", "newUserInfo", "=", "oldUserInfo", ".", "upgradeVersion", "(", "UserInfo", ".", "typeName", ",", "1", ",", "2", ",", "realName", "=", "oldUserInfo", ".", "firstName", "+", "u\" \"", "+", "oldUserInfo"...	38.2	16.8
def epoch_rates_to_pmf(problems, epoch_rates=None): """Create a probability-mass-function based on relative epoch rates. if epoch_rates=None, then we use uniform epoch rates [1.0] * len(problems) i.e. it takes each problem the same time to go through one epoch. If epoch_rates is given, then these are the rela...	[ "def", "epoch_rates_to_pmf", "(", "problems", ",", "epoch_rates", "=", "None", ")", ":", "if", "epoch_rates", "is", "None", ":", "epoch_rates", "=", "[", "1.0", "]", "", "len", "(", "problems", ")", "example_rates", "=", "[", "epoch_rate", "", "p", "."...	35.869565	20.695652
def render_heading(self, token): """ Overrides super().render_heading; stores rendered heading first, then returns it. """ rendered = super().render_heading(token) content = self.parse_rendered_heading(rendered) if not (self.omit_title and token.level == 1 ...	[ "def", "render_heading", "(", "self", ",", "token", ")", ":", "rendered", "=", "super", "(", ")", ".", "render_heading", "(", "token", ")", "content", "=", "self", ".", "parse_rendered_heading", "(", "rendered", ")", "if", "not", "(", "self", ".", "omit_...	41.416667	13.083333
def _validate_cmds(self): """ 确保 cmd 没有重复 :return: """ cmd_list = list(self.rule_map.keys()) for bp in self.blueprints: cmd_list.extend(bp.rule_map.keys()) duplicate_cmds = (Counter(cmd_list) - Counter(set(cmd_list))).keys() assert not dupl...	[ "def", "_validate_cmds", "(", "self", ")", ":", "cmd_list", "=", "list", "(", "self", ".", "rule_map", ".", "keys", "(", ")", ")", "for", "bp", "in", "self", ".", "blueprints", ":", "cmd_list", ".", "extend", "(", "bp", ".", "rule_map", ".", "keys", ...	25.428571	21.857143
def setup(self): """ NSCF calculations should use the same FFT mesh as the one employed in the GS task (in principle, it's possible to interpolate inside Abinit but tests revealed some numerical noise Here we change the input file of the NSCF task to have the same FFT mesh. """ ...	[ "def", "setup", "(", "self", ")", ":", "for", "dep", "in", "self", ".", "deps", ":", "if", "\"DEN\"", "in", "dep", ".", "exts", ":", "parent_task", "=", "dep", ".", "node", "break", "else", ":", "raise", "RuntimeError", "(", "\"Cannot find parent node pr...	41.916667	23.583333
def stop(self): """ Stop the config change monitoring thread. """ self.observer_thread.stop() self.observer_thread.join() logging.info("Configfile watcher plugin: Stopped")	[ "def", "stop", "(", "self", ")", ":", "self", ".", "observer_thread", ".", "stop", "(", ")", "self", ".", "observer_thread", ".", "join", "(", ")", "logging", ".", "info", "(", "\"Configfile watcher plugin: Stopped\"", ")" ]	26.75	12.75
def rotation_matrix(axis, theta): """The Euler–Rodrigues formula. Return the rotation matrix associated with counterclockwise rotation about the given axis by theta radians. Parameters ---------- axis: vector to rotate around theta: rotation angle, in rad """ axis = np.asarray(axis...	[ "def", "rotation_matrix", "(", "axis", ",", "theta", ")", ":", "axis", "=", "np", ".", "asarray", "(", "axis", ")", "axis", "=", "axis", "/", "np", ".", "linalg", ".", "norm", "(", "axis", ")", "a", "=", "np", ".", "cos", "(", "theta", "/", "2"...	33.136364	16.772727
def flatten(d, key_as_tuple=True, sep='.', list_of_dicts=None, all_iters=None): """ get nested dict as flat {key:val,...}, where key is tuple/string of all nested keys Parameters ---------- d : object key_as_tuple : bool whether keys are list of nested keys or delimited string of nested...	[ "def", "flatten", "(", "d", ",", "key_as_tuple", "=", "True", ",", "sep", "=", "'.'", ",", "list_of_dicts", "=", "None", ",", "all_iters", "=", "None", ")", ":", "def", "expand", "(", "key", ",", "value", ")", ":", "if", "is_dict_like", "(", "value",...	36.906977	20.290698
def doMove(self, from_path, to_path, overwrite = False, bShareFireCopy = 'false', dummy = 56147): """Move a file. >>> nd.doMove('/Picture/flower.png', '/flower.png') :param from_path: The path to the file or folder to be moved. :param to_path: The destination path of the file or fo...	[ "def", "doMove", "(", "self", ",", "from_path", ",", "to_path", ",", "overwrite", "=", "False", ",", "bShareFireCopy", "=", "'false'", ",", "dummy", "=", "56147", ")", ":", "if", "overwrite", ":", "overwrite", "=", "'F'", "else", ":", "overwrite", "=", ...	35.965517	23.551724
def stream_reader_statements(stream_arn): """Returns statements to allow Lambda to read from a stream. Handles both DynamoDB & Kinesis streams. Automatically figures out the type of stream, and provides the correct actions from the supplied Arn. Arg: stream_arn (str): A kinesis or dynamodb str...	[ "def", "stream_reader_statements", "(", "stream_arn", ")", ":", "action_type", "=", "get_stream_action_type", "(", "stream_arn", ")", "arn_parts", "=", "stream_arn", ".", "split", "(", "\"/\"", ")", "# Cut off the last bit and replace it with a wildcard", "wildcard_arn_part...	29.971429	18.228571
def word_tokenize(sentence): """ A generator which yields tokens based on the given sentence without deleting anything. >>> context = "I love you. Please don't leave." >>> list(word_tokenize(context)) ['I', ' ', 'love', ' ', 'you', '.', ' ', 'Please', ' ', 'don', "'", 't', ' ', 'leave', '.'] "...	[ "def", "word_tokenize", "(", "sentence", ")", ":", "date_pattern", "=", "r'\\d\\d(\\d\\d)?[\\\\-]\\d\\d[\\\\-]\\d\\d(\\d\\d)?'", "number_pattern", "=", "r'[\\+-]?(\\d+\\.\\d+\|\\d{1,3},(\\d{3},)*\\d{3}\|\\d+)'", "arr_pattern", "=", "r'(?: \\w\\.){2,3}\|(?:\\A\|\\s)(?:\\w\\.){2,3}\|[A-Z]\\. [a...	47.8	26
def auto_build(self): """Auto built tool """ options = [ "-a", "--autobuild" ] if len(self.args) >= 3 and self.args[0] in options: AutoBuild(self.args[1], self.args[2:], self.meta.path).run() else: usage("")	[ "def", "auto_build", "(", "self", ")", ":", "options", "=", "[", "\"-a\"", ",", "\"--autobuild\"", "]", "if", "len", "(", "self", ".", "args", ")", ">=", "3", "and", "self", ".", "args", "[", "0", "]", "in", "options", ":", "AutoBuild", "(", "self"...	26.636364	18.727273
def snapshot(name, suffix=None, connection=None, username=None, password=None): ''' Takes a snapshot of a particular VM or by a UNIX-style wildcard. .. versionadded:: 2016.3.0 :param connection: libvirt connection URI, overriding defaults .. versionadded:: 2019.2.0 :param username: userna...	[ "def", "snapshot", "(", "name", ",", "suffix", "=", "None", ",", "connection", "=", "None", ",", "username", "=", "None", ",", "password", "=", "None", ")", ":", "return", "_virt_call", "(", "name", ",", "'snapshot'", ",", "'saved'", ",", "'Snapshot has ...	28.655172	27.689655
def make_d2p_id(self): """ Make an association id for phenotypic associations with disease that is defined by: source of association + disease + relationship + phenotype + onset + frequency :return: """ attributes = [self.onset, self.frequency] ...	[ "def", "make_d2p_id", "(", "self", ")", ":", "attributes", "=", "[", "self", ".", "onset", ",", "self", ".", "frequency", "]", "assoc_id", "=", "self", ".", "make_association_id", "(", "self", ".", "definedby", ",", "self", ".", "disease_id", ",", "self"...	28.25	22.5
def enter_maintenance_mode(self): """ Put the service in maintenance mode. @return: Reference to the completed command. @since: API v2 """ cmd = self._cmd('enterMaintenanceMode') if cmd.success: self._update(_get_service(self._get_resource_root(), self._path())) return cmd	[ "def", "enter_maintenance_mode", "(", "self", ")", ":", "cmd", "=", "self", ".", "_cmd", "(", "'enterMaintenanceMode'", ")", "if", "cmd", ".", "success", ":", "self", ".", "_update", "(", "_get_service", "(", "self", ".", "_get_resource_root", "(", ")", ",...	27.454545	14.545455
def oridam_generate_patterns(word_in,cm,ed=1,level=0,pos=0,candidates=None): """ ed = 1 by default, pos - internal variable for algorithm """ alternates = cm.get(word_in[pos],[]) if not candidates: candidates = [] assert ed <= len(word_in), 'edit distance has to be comparable to word size [ins/d...	[ "def", "oridam_generate_patterns", "(", "word_in", ",", "cm", ",", "ed", "=", "1", ",", "level", "=", "0", ",", "pos", "=", "0", ",", "candidates", "=", "None", ")", ":", "alternates", "=", "cm", ".", "get", "(", "word_in", "[", "pos", "]", ",", ...	40.758621	15.586207
def watch(directory=None, auto_clear=False, extensions=[]): """Starts a server to render the specified file or directory containing a README.""" if directory and not os.path.isdir(directory): raise ValueError('Directory not found: ' + directory) directory = os.path.abspath(directory) # Initial ...	[ "def", "watch", "(", "directory", "=", "None", ",", "auto_clear", "=", "False", ",", "extensions", "=", "[", "]", ")", ":", "if", "directory", "and", "not", "os", ".", "path", ".", "isdir", "(", "directory", ")", ":", "raise", "ValueError", "(", "'Di...	32.5	20.5
def get(self, request): """ Called after the user is redirected back to our application. Tries to: - Complete the OAuth / OAuth2 flow - Redirect the user to another view that deals with login, connecting or user creation. """ try: client ...	[ "def", "get", "(", "self", ",", "request", ")", ":", "try", ":", "client", "=", "request", ".", "session", "[", "self", ".", "get_client", "(", ")", ".", "get_session_key", "(", ")", "]", "logger", ".", "debug", "(", "\"API returned: %s\"", ",", "reque...	42.521739	21.913043
def _connected(self, transport, conn): """Login and sync the ElkM1 panel to memory.""" LOG.info("Connected to ElkM1") self._conn = conn self._transport = transport self._connection_retry_timer = 1 if url_scheme_is_secure(self._config['url']): self._conn.write_...	[ "def", "_connected", "(", "self", ",", "transport", ",", "conn", ")", ":", "LOG", ".", "info", "(", "\"Connected to ElkM1\"", ")", "self", ".", "_conn", "=", "conn", "self", ".", "_transport", "=", "transport", "self", ".", "_connection_retry_timer", "=", ...	49.25	13.166667
def parse(self, data): """ Converts a OpenVPN JSON to a NetworkX Graph object which is then returned. """ # initialize graph and list of aggregated nodes graph = self._init_graph() server = self._server_common_name # add server (central node) to graph ...	[ "def", "parse", "(", "self", ",", "data", ")", ":", "# initialize graph and list of aggregated nodes", "graph", "=", "self", ".", "_init_graph", "(", ")", "server", "=", "self", ".", "_server_common_name", "# add server (central node) to graph", "graph", ".", "add_nod...	39.511628	14.302326
def run(addr, commands, kwargs): """ Non-threaded batch command runner returning output results """ results = [] handler = VarnishHandler(addr, *kwargs) for cmd in commands: if isinstance(cmd, tuple) and len(cmd)>1: results.extend([getattr(handler, c[0].replace('.','_'))(...	[ "def", "run", "(", "addr", ",", "", "commands", ",", "", "", "kwargs", ")", ":", "results", "=", "[", "]", "handler", "=", "VarnishHandler", "(", "addr", ",", "", "*", "kwargs", ")", "for", "cmd", "in", "commands", ":", "if", "isinstance", "(",...	34.428571	18.857143
def times(self, multiplier): ''' Given an FSM and a multiplier, return the multiplied FSM. ''' if multiplier < 0: raise Exception("Can't multiply an FSM by " + repr(multiplier)) alphabet = self.alphabet # metastate is a set of iterations+states initial = {(self.initial, 0)} def final(state): '...	[ "def", "times", "(", "self", ",", "multiplier", ")", ":", "if", "multiplier", "<", "0", ":", "raise", "Exception", "(", "\"Can't multiply an FSM by \"", "+", "repr", "(", "multiplier", ")", ")", "alphabet", "=", "self", ".", "alphabet", "# metastate is a set o...	30.371429	19.8
def handle_vcf_calls(vcf_file, data, orig_items): """Prioritize VCF calls based on external annotations supplied through GEMINI. """ if not _do_prioritize(orig_items): return vcf_file else: ann_vcf = population.run_vcfanno(vcf_file, data) if ann_vcf: priority_file = _...	[ "def", "handle_vcf_calls", "(", "vcf_file", ",", "data", ",", "orig_items", ")", ":", "if", "not", "_do_prioritize", "(", "orig_items", ")", ":", "return", "vcf_file", "else", ":", "ann_vcf", "=", "population", ".", "run_vcfanno", "(", "vcf_file", ",", "data...	40.692308	17.076923
def assign_enterprise_learner_role(sender, instance, **kwargs): # pylint: disable=unused-argument """ Assign an enterprise learner role to EnterpriseCustomerUser whenever a new record is created. """ if kwargs['created'] and instance.user: enterprise_learner_role, __ = SystemWideEnterpriseRo...	[ "def", "assign_enterprise_learner_role", "(", "sender", ",", "instance", ",", "", "", "kwargs", ")", ":", "# pylint: disable=unused-argument", "if", "kwargs", "[", "'created'", "]", "and", "instance", ".", "user", ":", "enterprise_learner_role", ",", "__", "=", ...	51.8	26.4
def to_json(self, destination): """ Save a dictionnary into a JSON file. :param destination: A path to a file where we're going to write the converted dict into a JSON format. :type destination: str """ try: with open(destination, "w"...	[ "def", "to_json", "(", "self", ",", "destination", ")", ":", "try", ":", "with", "open", "(", "destination", ",", "\"w\"", ")", "as", "file", ":", "# We open the file we are going to write.", "# Note: We always overwrite the destination.", "# We save the current dictionna...	34.083333	16.138889
def TNE_metric(bpmn_graph): """ Returns the value of the TNE metric (Total Number of Events of the Model) for the BPMNDiagramGraph instance. :param bpmn_graph: an instance of BpmnDiagramGraph representing BPMN model. """ events_counts = get_events_counts(bpmn_graph) return sum( [c...	[ "def", "TNE_metric", "(", "bpmn_graph", ")", ":", "events_counts", "=", "get_events_counts", "(", "bpmn_graph", ")", "return", "sum", "(", "[", "count", "for", "_", ",", "count", "in", "events_counts", ".", "items", "(", ")", "]", ")" ]	27.461538	22.538462
def state_cpfs(self) -> List[CPF]: '''Returns list of state-fluent CPFs.''' _, cpfs = self.cpfs state_cpfs = [] for cpf in cpfs: name = utils.rename_next_state_fluent(cpf.name) if name in self.state_fluents: state_cpfs.append(cpf) state_cpf...	[ "def", "state_cpfs", "(", "self", ")", "->", "List", "[", "CPF", "]", ":", "_", ",", "cpfs", "=", "self", ".", "cpfs", "state_cpfs", "=", "[", "]", "for", "cpf", "in", "cpfs", ":", "name", "=", "utils", ".", "rename_next_state_fluent", "(", "cpf", ...	38.5	12.3
def has_permission(self, perm): """ Checks if current user (or role) has the given permission. Args: perm: Permmission code or object. Depends on the :attr:`~zengine.auth.auth_backend.AuthBackend` implementation. Returns: Boolean. """ ...	[ "def", "has_permission", "(", "self", ",", "perm", ")", ":", "return", "self", ".", "user", ".", "superuser", "or", "self", ".", "auth", ".", "has_permission", "(", "perm", ")" ]	30.916667	22.416667
def population_fraction(self): """The filtered/unfiltered ratio for cube response. This value is required for properly calculating population on a cube where a filter has been applied. Returns 1.0 for an unfiltered cube. Returns `np.nan` if the unfiltered count is zero, which would ...	[ "def", "population_fraction", "(", "self", ")", ":", "numerator", "=", "self", ".", "_cube_dict", "[", "\"result\"", "]", ".", "get", "(", "\"filtered\"", ",", "{", "}", ")", ".", "get", "(", "\"weighted_n\"", ")", "denominator", "=", "self", ".", "_cube...	43.8125	21.0625
def parse_sidebar(self, user_page): """Parses the DOM and returns user attributes in the sidebar. :type user_page: :class:`bs4.BeautifulSoup` :param user_page: MAL user page's DOM :rtype: dict :return: User attributes :raises: :class:`.InvalidUserError`, :class:`.MalformedUserPageError` "...	[ "def", "parse_sidebar", "(", "self", ",", "user_page", ")", ":", "user_info", "=", "{", "}", "# if MAL says the series doesn't exist, raise an InvalidUserError.", "error_tag", "=", "user_page", ".", "find", "(", "u'div'", ",", "{", "u'class'", ":", "u'badresult'", "...	43.991379	25.37069
def lookup_linke_turbidity(time, latitude, longitude, filepath=None, interp_turbidity=True): """ Look up the Linke Turibidity from the ``LinkeTurbidities.h5`` data file supplied with pvlib. Parameters ---------- time : pandas.DatetimeIndex latitude : float l...	[ "def", "lookup_linke_turbidity", "(", "time", ",", "latitude", ",", "longitude", ",", "filepath", "=", "None", ",", "interp_turbidity", "=", "True", ")", ":", "# The .h5 file 'LinkeTurbidities.h5' contains a single 2160 x 4320 x 12", "# matrix of type uint8 called 'LinkeTurbidi...	35.8125	24.9375
def start(self, pin, dutycycle, frequency_hz=2000): """Enable PWM output on specified pin. Set to intiial percent duty cycle value (0.0 to 100.0) and frequency (in Hz). """ if dutycycle < 0.0 or dutycycle > 100.0: raise ValueError('Invalid duty cycle value, must be between 0...	[ "def", "start", "(", "self", ",", "pin", ",", "dutycycle", ",", "frequency_hz", "=", "2000", ")", ":", "if", "dutycycle", "<", "0.0", "or", "dutycycle", ">", "100.0", ":", "raise", "ValueError", "(", "'Invalid duty cycle value, must be between 0.0 to 100.0 (inclus...	53.25	14.416667
def request_instance(vm_=None, call=None): ''' Put together all of the information necessary to request an instance on EC2, and then fire off the request the instance. Returns data about the instance ''' if call == 'function': # Technically this function may be called other ways too, bu...	[ "def", "request_instance", "(", "vm_", "=", "None", ",", "call", "=", "None", ")", ":", "if", "call", "==", "'function'", ":", "# Technically this function may be called other ways too, but it", "# definitely cannot be called with --function.", "raise", "SaltCloudSystemExit",...	37.384615	20.787879
def setup_actions(self): """ Connects slots to signals """ self.actionOpen.triggered.connect(self.on_open) self.actionNew.triggered.connect(self.on_new) self.actionSave.triggered.connect(self.on_save) self.actionSave_as.triggered.connect(self.on_save_as) self.actionQuit.t...	[ "def", "setup_actions", "(", "self", ")", ":", "self", ".", "actionOpen", ".", "triggered", ".", "connect", "(", "self", ".", "on_open", ")", "self", ".", "actionNew", ".", "triggered", ".", "connect", "(", "self", ".", "on_new", ")", "self", ".", "act...	53.666667	16.133333
def declare(self, exchange='', exchange_type='direct', virtual_host='/', passive=False, durable=False, auto_delete=False, internal=False, arguments=None): """Declare an Exchange. :param str exchange: Exchange name :param str exchange_type: Exchange type :...	[ "def", "declare", "(", "self", ",", "exchange", "=", "''", ",", "exchange_type", "=", "'direct'", ",", "virtual_host", "=", "'/'", ",", "passive", "=", "False", ",", "durable", "=", "False", ",", "auto_delete", "=", "False", ",", "internal", "=", "False"...	41.054054	16.459459
def from_rel_ref(baseURI, relative_ref): """ Return a \|PackURI\| instance containing the absolute pack URI formed by translating relative_ref onto baseURI. """ joined_uri = posixpath.join(baseURI, relative_ref) abs_uri = posixpath.abspath(joined_uri) return Pac...	[ "def", "from_rel_ref", "(", "baseURI", ",", "relative_ref", ")", ":", "joined_uri", "=", "posixpath", ".", "join", "(", "baseURI", ",", "relative_ref", ")", "abs_uri", "=", "posixpath", ".", "abspath", "(", "joined_uri", ")", "return", "PackURI", "(", "abs_u...	40.75	10.25
def extract_features(self, text): """Extracts features from a body of text. :rtype: dictionary of features """ # Feature extractor may take one or two arguments try: return self.feature_extractor(text, self.train_set) except (TypeError, AttributeError): ...	[ "def", "extract_features", "(", "self", ",", "text", ")", ":", "# Feature extractor may take one or two arguments", "try", ":", "return", "self", ".", "feature_extractor", "(", "text", ",", "self", ".", "train_set", ")", "except", "(", "TypeError", ",", "Attribute...	32.090909	15.181818
def vor_to_am(vor): r""" Given a Voronoi tessellation object from Scipy's ``spatial`` module, converts to a sparse adjacency matrix network representation in COO format. Parameters ---------- vor : Voronoi Tessellation object This object is produced by ``scipy.spatial.Voronoi`` Ret...	[ "def", "vor_to_am", "(", "vor", ")", ":", "# Create adjacency matrix in lil format for quick matrix construction", "N", "=", "vor", ".", "vertices", ".", "shape", "[", "0", "]", "rc", "=", "[", "[", "]", ",", "[", "]", "]", "for", "ij", "in", "vor", ".", ...	33.285714	17.785714
def get_environ_vars(self): """Returns a generator with all environmental vars with prefix PIP_""" for key, val in os.environ.items(): if _environ_prefix_re.search(key): yield (_environ_prefix_re.sub("", key).lower(), val)	[ "def", "get_environ_vars", "(", "self", ")", ":", "for", "key", ",", "val", "in", "os", ".", "environ", ".", "items", "(", ")", ":", "if", "_environ_prefix_re", ".", "search", "(", "key", ")", ":", "yield", "(", "_environ_prefix_re", ".", "sub", "(", ...	52.4	10
def run_calibration(self, interval, applycal): """Runs the calibration operation with the current settings :param interval: The repetition interval between stimuli presentations (seconds) :type interval: float :param applycal: Whether to apply a previous saved calibration to thi...	[ "def", "run_calibration", "(", "self", ",", "interval", ",", "applycal", ")", ":", "if", "self", ".", "selected_calibration_index", "==", "2", ":", "self", ".", "tone_calibrator", ".", "apply_calibration", "(", "applycal", ")", "self", ".", "tone_calibrator", ...	48.5	17.722222
def get_db(cls): """Return the database for the collection""" if cls._db: return getattr(cls._client, cls._db) return cls._client.get_default_database()	[ "def", "get_db", "(", "cls", ")", ":", "if", "cls", ".", "_db", ":", "return", "getattr", "(", "cls", ".", "_client", ",", "cls", ".", "_db", ")", "return", "cls", ".", "_client", ".", "get_default_database", "(", ")" ]	36.8	12.4
def _parseSimpleSelector(self, src): """simple_selector : [ namespace_selector ]? element_name? [ HASH \| class \| attrib \| pseudo ]* S* ; """ ctxsrc = src.lstrip() nsPrefix, src = self._getMatchResult(self.re_namespace_selector, src) name, src = self._getMatchResul...	[ "def", "_parseSimpleSelector", "(", "self", ",", "src", ")", ":", "ctxsrc", "=", "src", ".", "lstrip", "(", ")", "nsPrefix", ",", "src", "=", "self", ".", "_getMatchResult", "(", "self", ".", "re_namespace_selector", ",", "src", ")", "name", ",", "src", ...	38.083333	20
def manage(settingspath, root_dir, argv): """ Manage all processes """ # add settings.json to environment variables os.environ[ENV_VAR_SETTINGS] = settingspath # add root_dir os.environ[ENV_VAR_ROOT_DIR] = root_dir # get datasets list with open(settingspath) as settings_file: ...	[ "def", "manage", "(", "settingspath", ",", "root_dir", ",", "argv", ")", ":", "# add settings.json to environment variables", "os", ".", "environ", "[", "ENV_VAR_SETTINGS", "]", "=", "settingspath", "# add root_dir", "os", ".", "environ", "[", "ENV_VAR_ROOT_DIR", "]...	32.285714	9.333333
def cluster_application_state(self, application_id): """ With the application state API, you can obtain the current state of an application. :param str application_id: The application id :returns: API response object with JSON data :rtype: :py:class:`yarn_api_client.base...	[ "def", "cluster_application_state", "(", "self", ",", "application_id", ")", ":", "path", "=", "'/ws/v1/cluster/apps/{appid}/state'", ".", "format", "(", "appid", "=", "application_id", ")", "return", "self", ".", "request", "(", "path", ")" ]	35.230769	15.384615
def masked_middle_mfcc(self): """ Return the MFCC speech frames in the MIDDLE portion of the wave. :rtype: :class:`numpy.ndarray` (2D) """ begin, end = self._masked_middle_begin_end() return (self.masked_mfcc)[:, begin:end]	[ "def", "masked_middle_mfcc", "(", "self", ")", ":", "begin", ",", "end", "=", "self", ".", "_masked_middle_begin_end", "(", ")", "return", "(", "self", ".", "masked_mfcc", ")", "[", ":", ",", "begin", ":", "end", "]" ]	30.222222	8.666667
def get_transactions_xml(self, account: SEPAAccount, start_date: datetime.date = None, end_date: datetime.date = None) -> list: """ Fetches the list of transactions of a bank account in a certain timeframe as camt.052.001.02 XML files. :param account: SEPA :...	[ "def", "get_transactions_xml", "(", "self", ",", "account", ":", "SEPAAccount", ",", "start_date", ":", "datetime", ".", "date", "=", "None", ",", "end_date", ":", "datetime", ".", "date", "=", "None", ")", "->", "list", ":", "with", "self", ".", "_get_d...	41.30303	21.181818
def lookup_path(bin_name): """Calls to external binaries can't depend on $PATH """ paths = ('/usr/local/sbin/', '/usr/local/bin/', '/usr/sbin/', '/usr/bin/') for p in paths: fq_path = p + bin_name found = os.path.isfile(fq_path) and os.access(fq_path, os.X_OK) if found: ...	[ "def", "lookup_path", "(", "bin_name", ")", ":", "paths", "=", "(", "'/usr/local/sbin/'", ",", "'/usr/local/bin/'", ",", "'/usr/sbin/'", ",", "'/usr/bin/'", ")", "for", "p", "in", "paths", ":", "fq_path", "=", "p", "+", "bin_name", "found", "=", "os", ".",...	34.5	17.5
def nonblocking_input(self): '''Context manager to set the :class:`Terminal`'s input file to read in a non-blocking way. Normally, reading from :attr:`sys.stdin` blocks, which is bad if we want an interactive application that can also update information on the screen without any...	[ "def", "nonblocking_input", "(", "self", ")", ":", "# FIXME: do we handle restoring this during SIGTSTP?", "if", "hasattr", "(", "self", ".", "infile", ",", "'fileno'", ")", ":", "# Use fcntl to set stdin to non-blocking. WARNING - this is not", "# particularly portable!", "fla...	44	24.08
def is_me(self): # pragma: no cover, seems not to be used anywhere """Check if parameter name if same than name of this object TODO: is it useful? :return: true if parameter name if same than this name :rtype: bool """ logger.info("And arbiter is launched with the host...	[ "def", "is_me", "(", "self", ")", ":", "# pragma: no cover, seems not to be used anywhere", "logger", ".", "info", "(", "\"And arbiter is launched with the hostname:%s \"", "\"from an arbiter point of view of addr:%s\"", ",", "self", ".", "host_name", ",", "socket", ".", "get...	46.272727	27
def get_field_schema(name, field): """Returns a JSON Schema representation of a form field.""" field_schema = { 'type': 'string', } if field.label: field_schema['title'] = str(field.label) # force translation if field.help_text: field_schema['description'] = str(field.help...	[ "def", "get_field_schema", "(", "name", ",", "field", ")", ":", "field_schema", "=", "{", "'type'", ":", "'string'", ",", "}", "if", "field", ".", "label", ":", "field_schema", "[", "'title'", "]", "=", "str", "(", "field", ".", "label", ")", "# force ...	38.545455	17.068182
def do_pickle_ontology(filename, g=None): """ from a valid filename, generate the graph instance and pickle it too note: option to pass a pre-generated graph instance too 2015-09-17: added code to increase recursion limit if cPickle fails see http://stackoverflow.com/questions/2134706/hitting-maximum-recursion-de...	[ "def", "do_pickle_ontology", "(", "filename", ",", "g", "=", "None", ")", ":", "ONTOSPY_LOCAL_MODELS", "=", "get_home_location", "(", ")", "pickledpath", "=", "ONTOSPY_LOCAL_CACHE", "+", "\"/\"", "+", "filename", "+", "\".pickle\"", "if", "not", "g", ":", "g",...	41.133333	23.533333
def __prepare_resource(data): """Prepare the resourcepart of the JID. :Parameters: - `data`: Resourcepart of the JID :raise JIDError: if the resource name is too long. :raise pyxmpp.xmppstringprep.StringprepError: if the resourcepart fails Resourceprep preparati...	[ "def", "__prepare_resource", "(", "data", ")", ":", "if", "not", "data", ":", "return", "None", "data", "=", "unicode", "(", "data", ")", "try", ":", "resource", "=", "RESOURCEPREP", ".", "prepare", "(", "data", ")", "except", "StringprepError", ",", "er...	35.526316	16.157895
def _clean_rec_name(rec): """Clean illegal characters in input fasta file which cause problems downstream. """ out_id = [] for char in list(rec.id): if char in ALLOWED_CONTIG_NAME_CHARS: out_id.append(char) else: out_id.append("_") rec.id = "".join(out_id) ...	[ "def", "_clean_rec_name", "(", "rec", ")", ":", "out_id", "=", "[", "]", "for", "char", "in", "list", "(", "rec", ".", "id", ")", ":", "if", "char", "in", "ALLOWED_CONTIG_NAME_CHARS", ":", "out_id", ".", "append", "(", "char", ")", "else", ":", "out_...	28.75	13
def delete_acl_request(request): """Submission to remove an ACL.""" uuid_ = request.matchdict['uuid'] posted = request.json permissions = [(x['uid'], x['permission'],) for x in posted] with db_connect() as db_conn: with db_conn.cursor() as cursor: remove_acl(cursor, uuid_, permi...	[ "def", "delete_acl_request", "(", "request", ")", ":", "uuid_", "=", "request", ".", "matchdict", "[", "'uuid'", "]", "posted", "=", "request", ".", "json", "permissions", "=", "[", "(", "x", "[", "'uid'", "]", ",", "x", "[", "'permission'", "]", ",", ...	29.692308	15.384615
def parallelize(mapfunc, workers=None): ''' Parallelize the mapfunc with multithreading. mapfunc calls will be partitioned by the provided list of arguments. Each item in the list will represent one call's arguments. They can be tuples if the function takes multiple arguments, but one-tupling is not...	[ "def", "parallelize", "(", "mapfunc", ",", "workers", "=", "None", ")", ":", "workers", "=", "workers", "if", "workers", "else", "_get_default_workers", "(", ")", "def", "wrapper", "(", "args_list", ")", ":", "result", "=", "{", "}", "with", "concurrent", ...	37.617647	20.970588
def print_usage(): """ Prints usage message. """ print('Usage: ' + os.path.basename(sys.argv[0]) + ' [options] dimacs-file') print('Options:') print(' -h, --help Show this message') print(' -m, --model Print model') print(' -s, --solver SAT solver...	[ "def", "print_usage", "(", ")", ":", "print", "(", "'Usage: '", "+", "os", ".", "path", ".", "basename", "(", "sys", ".", "argv", "[", "0", "]", ")", "+", "' [options] dimacs-file'", ")", "print", "(", "'Options:'", ")", "print", "(", "' -h, --hel...	37.916667	18.75
def covariance_matrix(self,x,y,names=None,cov=None): """build a pyemu.Cov instance from GeoStruct Parameters ---------- x : (iterable of floats) x-coordinate locations y : (iterable of floats) y-coordinate locations names : (iterable of str) ...	[ "def", "covariance_matrix", "(", "self", ",", "x", ",", "y", ",", "names", "=", "None", ",", "cov", "=", "None", ")", ":", "if", "not", "isinstance", "(", "x", ",", "np", ".", "ndarray", ")", ":", "x", "=", "np", ".", "array", "(", "x", ")", ...	32.901639	19.540984
def notification_selected_sm_changed(self, model, prop_name, info): """If a new state machine is selected, make sure the tab is open""" selected_state_machine_id = self.model.selected_state_machine_id if selected_state_machine_id is None: return page_id = self.get_page_num(s...	[ "def", "notification_selected_sm_changed", "(", "self", ",", "model", ",", "prop_name", ",", "info", ")", ":", "selected_state_machine_id", "=", "self", ".", "model", ".", "selected_state_machine_id", "if", "selected_state_machine_id", "is", "None", ":", "return", "...	46.555556	23.925926
def imagetransformer_b12l_4h_b128_uncond_dr03_tpu(): """TPU config for cifar 10.""" hparams = imagetransformer_bas8l_8h_big_uncond_dr03_imgnet() update_hparams_for_tpu(hparams) hparams.batch_size = 2 hparams.num_heads = 4 # heads are expensive on tpu hparams.num_decoder_layers = 12 hparams.block_length ...	[ "def", "imagetransformer_b12l_4h_b128_uncond_dr03_tpu", "(", ")", ":", "hparams", "=", "imagetransformer_bas8l_8h_big_uncond_dr03_imgnet", "(", ")", "update_hparams_for_tpu", "(", "hparams", ")", "hparams", ".", "batch_size", "=", "2", "hparams", ".", "num_heads", "=", ...	38	10
def options(self, route: str(), callback: object()): """ Binds a OPTIONS route with the given callback :rtype: object """ self.__set_route('options', {route: callback}) return RouteMapping	[ "def", "options", "(", "self", ",", "route", ":", "str", "(", ")", ",", "callback", ":", "object", "(", ")", ")", ":", "self", ".", "__set_route", "(", "'options'", ",", "{", "route", ":", "callback", "}", ")", "return", "RouteMapping" ]	32.857143	10
def init_jvm(java_home=None, jvm_dll=None, jvm_maxmem=None, jvm_classpath=None, jvm_properties=None, jvm_options=None, config_file=None, config=None): """ Creates a configured Java virtual machine which will be used by jp...	[ "def", "init_jvm", "(", "java_home", "=", "None", ",", "jvm_dll", "=", "None", ",", "jvm_maxmem", "=", "None", ",", "jvm_classpath", "=", "None", ",", "jvm_properties", "=", "None", ",", "jvm_options", "=", "None", ",", "config_file", "=", "None", ",", "...	48.530612	26.816327
def run(scenario, magicc_version=6, **kwargs): """ Run a MAGICC scenario and return output data and (optionally) config parameters. As a reminder, putting ``out_parameters=1`` will cause MAGICC to write out its parameters into ``out/PARAMETERS.OUT`` and they will then be read into ``output.metadata...	[ "def", "run", "(", "scenario", ",", "magicc_version", "=", "6", ",", "", "", "kwargs", ")", ":", "if", "magicc_version", "==", "6", ":", "magicc_cls", "=", "MAGICC6", "elif", "magicc_version", "==", "7", ":", "magicc_cls", "=", "MAGICC7", "else", ":", ...	29.02439	24.097561
def platform_data_dir(): """ Returns path for user-specific data files Returns: PathLike : path to the data dir used by the current operating system """ if LINUX: # nocover dpath_ = os.environ.get('XDG_DATA_HOME', '~/.local/share') elif DARWIN: # nocover dpath_ = '~/L...	[ "def", "platform_data_dir", "(", ")", ":", "if", "LINUX", ":", "# nocover", "dpath_", "=", "os", ".", "environ", ".", "get", "(", "'XDG_DATA_HOME'", ",", "'~/.local/share'", ")", "elif", "DARWIN", ":", "# nocover", "dpath_", "=", "'~/Library/Application Support'...	31.352941	16.411765
def __get_query_agg_cardinality(cls, field, agg_id=None): """ Create an es_dsl aggregation object for getting the approximate count of distinct values of a field. :param field: field from which the get count of distinct values :return: a tuple with the aggregation id and es_dsl aggregat...	[ "def", "__get_query_agg_cardinality", "(", "cls", ",", "field", ",", "agg_id", "=", "None", ")", ":", "if", "not", "agg_id", ":", "agg_id", "=", "cls", ".", "AGGREGATION_ID", "query_agg", "=", "A", "(", "\"cardinality\"", ",", "field", "=", "field", ",", ...	42.8125	20.8125
def listBlockParents(self, block_name=""): """ list parents of a block """ if not block_name: msg = " DBSBlock/listBlockParents. Block_name must be provided as a string or a list. \ No wildcards allowed in block_name/s." dbsExceptionHandler('dbsExc...	[ "def", "listBlockParents", "(", "self", ",", "block_name", "=", "\"\"", ")", ":", "if", "not", "block_name", ":", "msg", "=", "\" DBSBlock/listBlockParents. Block_name must be provided as a string or a list. \\\n No wildcards allowed in block_name/s.\"", "dbsExceptio...	48.757576	23.060606
def rtgen_family(self, value): """Family setter.""" self.bytearray[self._get_slicers(0)] = bytearray(c_ubyte(value or 0))	[ "def", "rtgen_family", "(", "self", ",", "value", ")", ":", "self", ".", "bytearray", "[", "self", ".", "_get_slicers", "(", "0", ")", "]", "=", "bytearray", "(", "c_ubyte", "(", "value", "or", "0", ")", ")" ]	45	15.666667
def get_item(self, **kwargs): """ Get collection item taking into account generated queryset of parent view. This method allows working with nested resources properly. Thus an item returned by this method will belong to its parent view's queryset, thus filtering out objects that...	[ "def", "get_item", "(", "self", ",", "", "", "kwargs", ")", ":", "if", "six", ".", "callable", "(", "self", ".", "context", ")", ":", "self", ".", "reload_context", "(", "es_based", "=", "False", ",", "", "", "kwargs", ")", "objects", "=", "sel...	39.761905	20.666667
def move_right(self, keep_anchor=False, nb_chars=1): """ Moves the cursor on the right. :param keep_anchor: True to keep anchor (to select text) or False to move the anchor (no selection) :param nb_chars: Number of characters to move. """ text_cursor = self._...	[ "def", "move_right", "(", "self", ",", "keep_anchor", "=", "False", ",", "nb_chars", "=", "1", ")", ":", "text_cursor", "=", "self", ".", "_editor", ".", "textCursor", "(", ")", "text_cursor", ".", "movePosition", "(", "text_cursor", ".", "Right", ",", "...	40.692308	12.692308
def datasets(self): """Distinct datasets (``dataset``) in :class:`.models.Entry` Distinct datasets are SwissProt or/and TrEMBL :return: all distinct dataset types :rtype: list[str] """ r = self.session.query(distinct(models.Entry.dataset)).all() return [x[0] for...	[ "def", "datasets", "(", "self", ")", ":", "r", "=", "self", ".", "session", ".", "query", "(", "distinct", "(", "models", ".", "Entry", ".", "dataset", ")", ")", ".", "all", "(", ")", "return", "[", "x", "[", "0", "]", "for", "x", "in", "r", ...	31.9	16.8
def _apply_template(template, target, *, checkout, extra_context): """Apply a template to a temporary directory and then copy results to target.""" with tempfile.TemporaryDirectory() as tempdir: repo_dir = cc_main.cookiecutter( template, checkout=checkout, no_input=Tr...	[ "def", "_apply_template", "(", "template", ",", "target", ",", "*", ",", "checkout", ",", "extra_context", ")", ":", "with", "tempfile", ".", "TemporaryDirectory", "(", ")", "as", "tempdir", ":", "repo_dir", "=", "cc_main", ".", "cookiecutter", "(", "templat...	39.95	7.05
def _login(self, max_tries=2): """Logs in to Kindle Cloud Reader. Args: max_tries: The maximum number of login attempts that will be made. Raises: BrowserError: If method called when browser not at a signin URL. LoginError: If login unsuccessful after `max_tries` attempts. """ i...	[ "def", "_login", "(", "self", ",", "max_tries", "=", "2", ")", ":", "if", "not", "self", ".", "current_url", ".", "startswith", "(", "_KindleCloudReaderBrowser", ".", "_SIGNIN_URL", ")", ":", "raise", "BrowserError", "(", "'Current url \"%s\" is not a signin url (...	32.458333	21.770833
def _get_setup(self, result): """Internal method which process the results from the server.""" self.__devices = {} if ('setup' not in result.keys() or 'devices' not in result['setup'].keys()): raise Exception( "Did not find device definition.") ...	[ "def", "_get_setup", "(", "self", ",", "result", ")", ":", "self", ".", "__devices", "=", "{", "}", "if", "(", "'setup'", "not", "in", "result", ".", "keys", "(", ")", "or", "'devices'", "not", "in", "result", "[", "'setup'", "]", ".", "keys", "(",...	37.2	15.866667
def _create_options(self, items): """Helper method to create options from list, or instance. Applies preprocess method if available to create a uniform output """ return OrderedDict(map(lambda x: (x.name, x), coerce_to_list(items, self.preprocess)))	[ "def", "_create_options", "(", "self", ",", "items", ")", ":", "return", "OrderedDict", "(", "map", "(", "lambda", "x", ":", "(", "x", ".", "name", ",", "x", ")", ",", "coerce_to_list", "(", "items", ",", "self", ".", "preprocess", ")", ")", ")" ]	38.75	17.375
def cmd_ip_geolocation(ip_address, verbose): """Get the geolocation of an IP adddress from https://ipapi.co/. Example: \b $ habu.ip.geolocation 8.8.8.8 { "ip": "8.8.8.8", "city": "Mountain View", ... "asn": "AS15169", "org": "Google LLC" } """ if...	[ "def", "cmd_ip_geolocation", "(", "ip_address", ",", "verbose", ")", ":", "if", "verbose", ":", "logging", ".", "basicConfig", "(", "level", "=", "logging", ".", "INFO", ",", "format", "=", "'%(message)s'", ")", "print", "(", "\"Looking up %s...\"", "%", "ip...	23.296296	22.592593
def active_path(context, pattern, css=None): """ Highlight menu item based on path. Returns a css class if ``request.path`` is in given ``pattern``. :param pattern: Regex url pattern. :param css: Css class to be returned for highlighting. Return active if none set. ""...	[ "def", "active_path", "(", "context", ",", "pattern", ",", "css", "=", "None", ")", ":", "request", "=", "context", "[", "'request'", "]", "#pattern = \"^\" + pattern + \"$\"", "if", "re", ".", "search", "(", "pattern", ",", "request", ".", "path", ")", ":...	25.944444	18.055556
def prepare_encrypted_request(self, session, endpoint, message): """ Creates a prepared request to send to the server with an encrypted message and correct headers :param session: The handle of the session to prepare requests with :param endpoint: The endpoint/server to prepare ...	[ "def", "prepare_encrypted_request", "(", "self", ",", "session", ",", "endpoint", ",", "message", ")", ":", "host", "=", "urlsplit", "(", "endpoint", ")", ".", "hostname", "if", "self", ".", "protocol", "==", "'credssp'", "and", "len", "(", "message", ")",...	50.354839	26.032258
def hpforest(self, data: ['SASdata', str] = None, freq: str = None, id: str = None, input: [str, list, dict] = None, save: str = None, score: [str, bool, 'SASdata'] = True, target: [str, list, dict] = None, ...	[ "def", "hpforest", "(", "self", ",", "data", ":", "[", "'SASdata'", ",", "str", "]", "=", "None", ",", "freq", ":", "str", "=", "None", ",", "id", ":", "str", "=", "None", ",", "input", ":", "[", "str", ",", "list", ",", "dict", "]", "=", "No...	57.37037	28.481481
def from_charmm(cls, path, positions=None, forcefield=None, strict=True, **kwargs): """ Loads PSF Charmm structure from `path`. Requires `charmm_parameters`. Parameters ---------- path : str Path to PSF file forcefield : list of str Paths to Charm...	[ "def", "from_charmm", "(", "cls", ",", "path", ",", "positions", "=", "None", ",", "forcefield", "=", "None", ",", "strict", "=", "True", ",", "", "", "kwargs", ")", ":", "psf", "=", "CharmmPsfFile", "(", "path", ")", "if", "strict", "and", "forcef...	38.153846	19.923077
def init(): '''Initialise a WSGI application to be loaded by uWSGI.''' # Load values from config file config_file = os.path.realpath(os.path.join(os.getcwd(), 'swaggery.ini')) config = configparser.RawConfigParser(allow_no_value=True) config.read(config_file) log_level = config.get('application'...	[ "def", "init", "(", ")", ":", "# Load values from config file", "config_file", "=", "os", ".", "path", ".", "realpath", "(", "os", ".", "path", ".", "join", "(", "os", ".", "getcwd", "(", ")", ",", "'swaggery.ini'", ")", ")", "config", "=", "configparser...	45.882353	17.647059
def create(cls, session, record, imported=False, auto_reply=False): """Create a conversation. Please note that conversation cannot be created with more than 100 threads, if attempted the API will respond with HTTP 412. Args: session (requests.sessions.Session): Authenticate...	[ "def", "create", "(", "cls", ",", "session", ",", "record", ",", "imported", "=", "False", ",", "auto_reply", "=", "False", ")", ":", "return", "super", "(", "Conversations", ",", "cls", ")", ".", "create", "(", "session", ",", "record", ",", "imported...	45.133333	25.133333
def index(self, value, start=None, stop=None): """ Return the index of the first occurence of value. If start or stop are provided, return the smallest index such that ``s[index] == value`` and ``start <= index < stop``. """ def index_trans(pipe): len_se...	[ "def", "index", "(", "self", ",", "value", ",", "start", "=", "None", ",", "stop", "=", "None", ")", ":", "def", "index_trans", "(", "pipe", ")", ":", "len_self", ",", "normal_start", "=", "self", ".", "_normalize_index", "(", "start", "or", "0", ","...	40.947368	14.842105
def create_model(modelname, fields, indexes=None, basemodel=None, **props): """ Create model dynamically :param fields: Just format like [ {'name':name, 'type':type, ...}, ... ] type should be a string, eg. 'str', '...	[ "def", "create_model", "(", "modelname", ",", "fields", ",", "indexes", "=", "None", ",", "basemodel", "=", "None", ",", "", "", "props", ")", ":", "assert", "not", "props", "or", "isinstance", "(", "props", ",", "dict", ")", "assert", "not", "indexe...	31.103448	20.781609
def log_error(error, result): """Logs an error """ p = {'error': error, 'result':result} _log(TYPE_CODES.ERROR, p)	[ "def", "log_error", "(", "error", ",", "result", ")", ":", "p", "=", "{", "'error'", ":", "error", ",", "'result'", ":", "result", "}", "_log", "(", "TYPE_CODES", ".", "ERROR", ",", "p", ")" ]	25.2	4.6
def prefix_indent(prefix, textblock, later_prefix=' '): """ Prefix and indent all lines in textblock. prefix is a prefix string later_prefix is used on all but the first line, if it is a single character it will be repeated to match length of prefix """ textblock = te...	[ "def", "prefix_indent", "(", "prefix", ",", "textblock", ",", "later_prefix", "=", "' '", ")", ":", "textblock", "=", "textblock", ".", "split", "(", "'\\n'", ")", "line", "=", "prefix", "+", "textblock", "[", "0", "]", "+", "'\\n'", "if", "len", "(", ...	34.470588	15.647059
async def is_object_synced_to_cn(self, client, pid): """Check if object with {pid} has successfully synced to the CN. CNRead.describe() is used as it's a light-weight HTTP HEAD request. This assumes that the call is being made over a connection that has been authenticated and has read ...	[ "async", "def", "is_object_synced_to_cn", "(", "self", ",", "client", ",", "pid", ")", ":", "try", ":", "await", "client", ".", "describe", "(", "pid", ")", "except", "d1_common", ".", "types", ".", "exceptions", ".", "DataONEException", ":", "return", "Fa...	37.642857	24.142857
def cleanup(): """Close all sockets at exit""" for sck in list(Wdb._sockets): try: sck.close() except Exception: log.warn('Error in cleanup', exc_info=True)	[ "def", "cleanup", "(", ")", ":", "for", "sck", "in", "list", "(", "Wdb", ".", "_sockets", ")", ":", "try", ":", "sck", ".", "close", "(", ")", "except", "Exception", ":", "log", ".", "warn", "(", "'Error in cleanup'", ",", "exc_info", "=", "True", ...	28.285714	15.285714
def create(self, properties): """ Create and configure a storage group. The new storage group will be associated with the CPC identified by the `cpc-uri` input property. Authorization requirements: * Object-access permission to the CPC that will be associated with ...	[ "def", "create", "(", "self", ",", "properties", ")", ":", "if", "properties", "is", "None", ":", "properties", "=", "{", "}", "result", "=", "self", ".", "session", ".", "post", "(", "self", ".", "_base_uri", ",", "body", "=", "properties", ")", "# ...	36.02	21.5
def end(self, sql=None): """Commit the current transaction.""" self._transaction = False try: end = self._con.end except AttributeError: return self._con.query(sql or 'end') else: if sql: return end(sql=sql) else: ...	[ "def", "end", "(", "self", ",", "sql", "=", "None", ")", ":", "self", ".", "_transaction", "=", "False", "try", ":", "end", "=", "self", ".", "_con", ".", "end", "except", "AttributeError", ":", "return", "self", ".", "_con", ".", "query", "(", "sq...	27.916667	13.833333
def get_arguments(args): """Parse the command line.""" usage = "%(prog)s [arguments] [image files]" programs_str = ', '.join([prog.__name__ for prog in PROGRAMS]) description = "Uses "+programs_str+" if they are on the path." parser = argparse.ArgumentParser(usage=usage, description=description) ...	[ "def", "get_arguments", "(", "args", ")", ":", "usage", "=", "\"%(prog)s [arguments] [image files]\"", "programs_str", "=", "', '", ".", "join", "(", "[", "prog", ".", "__name__", "for", "prog", "in", "PROGRAMS", "]", ")", "description", "=", "\"Uses \"", "+",...	59.541667	21.072917
def main(): """ Main program entry point """ args = command_line() # TODO: Decouple Book interface and implementation query = Book( title=args.title, author=args.author, max_results=args.max, language_code=args.language, fields=('title', 'authors', 'image...	[ "def", "main", "(", ")", ":", "args", "=", "command_line", "(", ")", "# TODO: Decouple Book interface and implementation", "query", "=", "Book", "(", "title", "=", "args", ".", "title", ",", "author", "=", "args", ".", "author", ",", "max_results", "=", "arg...	27.64	20.44
def get_plugin_command(plugin_name, command_name, conn=None): """ get_specific_command function queries a specific CommandName :param plugin_name: <str> PluginName :param command_name: <str> CommandName :return: <dict> """ commands = RPX.table(plugin_name).filter( {COMMAND_NAME_KEY:...	[ "def", "get_plugin_command", "(", "plugin_name", ",", "command_name", ",", "conn", "=", "None", ")", ":", "commands", "=", "RPX", ".", "table", "(", "plugin_name", ")", ".", "filter", "(", "{", "COMMAND_NAME_KEY", ":", "command_name", "}", ")", ".", "run",...	31.5	12.928571
def shutit_method_scope(func): """Notifies the ShutIt object whenever we call a shutit module method. This allows setting values for the 'scope' of a function. """ def wrapper(self, shutit): """Wrapper to call a shutit module method, notifying the ShutIt object. """ ret = func(self, shutit) return ret retu...	[ "def", "shutit_method_scope", "(", "func", ")", ":", "def", "wrapper", "(", "self", ",", "shutit", ")", ":", "\"\"\"Wrapper to call a shutit module method, notifying the ShutIt object.\n\t\t\"\"\"", "ret", "=", "func", "(", "self", ",", "shutit", ")", "return", "ret",...	32.1	10.8
def convertloc(candsfile, candloc, memory_limit): """ For given state and location that are too bulky, calculate new location given memory_limit. """ scan, segment, candint, dmind, dtind, beamnum = candloc # set up state and find absolute integration of candidate d0 = pickle.load(open(candsfile, 'r'))...	[ "def", "convertloc", "(", "candsfile", ",", "candloc", ",", "memory_limit", ")", ":", "scan", ",", "segment", ",", "candint", ",", "dmind", ",", "dtind", ",", "beamnum", "=", "candloc", "# set up state and find absolute integration of candidate", "d0", "=", "pickl...	39.829268	21.560976

def miscellaneous_menu(self, value): """ Setter for **self.__miscellaneous_menu** attribute. :param value: Attribute value. :type value: QMenu """ if value is not None: assert type(value) is QMenu, "'{0}' attribute: '{1}' type is not 'QMenu'!".format( ...

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32.416667

15.75

def project(self, point_cloud, round_px=True): """Projects a point cloud onto the camera image plane. Parameters ---------- point_cloud : :obj:`autolab_core.PointCloud` or :obj:`autolab_core.Point` A PointCloud or Point to project onto the camera image plane. round_...

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def editMeta(self, title=None, description=None): """Set metadata for photo. (flickr.photos.setMeta)""" method = 'flickr.photosets.editMeta' if title is None: title = self.title if description is None: description = self.description _dopost(m...

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33.2

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def csp_header(csp={}): """ Decorator to include csp header on app.route wrapper """ _csp = csp_default().read() _csp.update(csp) _header = '' if 'report-only' in _csp and _csp['report-only'] is True: _header = 'Content-Security-Policy-Report-Only' else: _header = 'Content-Securit...

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31.458333

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def _compute_value(power, wg): """Return the weight corresponding to single power.""" if power not in wg: p1, p2 = power # y power if p1 == 0: yy = wg[(0, -1)] wg[power] = numpy.power(yy, p2 / 2).sum() / len(yy) # x power else: xx = wg[...

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30.846154

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def send(self, data): """ Send encoded instructions to Guacamole guacd server. """ self.logger.debug('Sending data: %s' % data) self.client.sendall(data.encode())

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32.833333

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def _dist_kw_arg(self, k): """ Returns a dictionary of keyword arguments for the k'th distribution. :param int k: Index of the distribution in question. :rtype: ``dict`` """ if self._dist_kw_args is not None: return { key:self._dist_kw...

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28.266667

14.666667

def upgradeUserInfo1to2(oldUserInfo): """ Concatenate the I{firstName} and I{lastName} attributes from the old user info item and set the result as the I{realName} attribute of the upgraded item. """ newUserInfo = oldUserInfo.upgradeVersion( UserInfo.typeName, 1, 2, realName=oldU...

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38.2

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def epoch_rates_to_pmf(problems, epoch_rates=None): """Create a probability-mass-function based on relative epoch rates. if epoch_rates=None, then we use uniform epoch rates [1.0] * len(problems) i.e. it takes each problem the same time to go through one epoch. If epoch_rates is given, then these are the rela...

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35.869565

20.695652

def render_heading(self, token): """ Overrides super().render_heading; stores rendered heading first, then returns it. """ rendered = super().render_heading(token) content = self.parse_rendered_heading(rendered) if not (self.omit_title and token.level == 1 ...

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def _validate_cmds(self): """ 确保 cmd 没有重复 :return: """ cmd_list = list(self.rule_map.keys()) for bp in self.blueprints: cmd_list.extend(bp.rule_map.keys()) duplicate_cmds = (Counter(cmd_list) - Counter(set(cmd_list))).keys() assert not dupl...

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25.428571

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def setup(self): """ NSCF calculations should use the same FFT mesh as the one employed in the GS task (in principle, it's possible to interpolate inside Abinit but tests revealed some numerical noise Here we change the input file of the NSCF task to have the same FFT mesh. """ ...

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41.916667

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def stop(self): """ Stop the config change monitoring thread. """ self.observer_thread.stop() self.observer_thread.join() logging.info("Configfile watcher plugin: Stopped")

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26.75

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def rotation_matrix(axis, theta): """The Euler–Rodrigues formula. Return the rotation matrix associated with counterclockwise rotation about the given axis by theta radians. Parameters ---------- axis: vector to rotate around theta: rotation angle, in rad """ axis = np.asarray(axis...

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33.136364

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def flatten(d, key_as_tuple=True, sep='.', list_of_dicts=None, all_iters=None): """ get nested dict as flat {key:val,...}, where key is tuple/string of all nested keys Parameters ---------- d : object key_as_tuple : bool whether keys are list of nested keys or delimited string of nested...

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36.906977

20.290698

def doMove(self, from_path, to_path, overwrite = False, bShareFireCopy = 'false', dummy = 56147): """Move a file. >>> nd.doMove('/Picture/flower.png', '/flower.png') :param from_path: The path to the file or folder to be moved. :param to_path: The destination path of the file or fo...

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35.965517

23.551724

def stream_reader_statements(stream_arn): """Returns statements to allow Lambda to read from a stream. Handles both DynamoDB & Kinesis streams. Automatically figures out the type of stream, and provides the correct actions from the supplied Arn. Arg: stream_arn (str): A kinesis or dynamodb str...

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29.971429

18.228571

def word_tokenize(sentence): """ A generator which yields tokens based on the given sentence without deleting anything. >>> context = "I love you. Please don't leave." >>> list(word_tokenize(context)) ['I', ' ', 'love', ' ', 'you', '.', ' ', 'Please', ' ', 'don', "'", 't', ' ', 'leave', '.'] "...

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47.8

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def auto_build(self): """Auto built tool """ options = [ "-a", "--autobuild" ] if len(self.args) >= 3 and self.args[0] in options: AutoBuild(self.args[1], self.args[2:], self.meta.path).run() else: usage("")

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26.636364

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def snapshot(name, suffix=None, connection=None, username=None, password=None): ''' Takes a snapshot of a particular VM or by a UNIX-style wildcard. .. versionadded:: 2016.3.0 :param connection: libvirt connection URI, overriding defaults .. versionadded:: 2019.2.0 :param username: userna...

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28.655172

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def make_d2p_id(self): """ Make an association id for phenotypic associations with disease that is defined by: source of association + disease + relationship + phenotype + onset + frequency :return: """ attributes = [self.onset, self.frequency] ...

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28.25

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def enter_maintenance_mode(self): """ Put the service in maintenance mode. @return: Reference to the completed command. @since: API v2 """ cmd = self._cmd('enterMaintenanceMode') if cmd.success: self._update(_get_service(self._get_resource_root(), self._path())) return cmd

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27.454545

14.545455

def oridam_generate_patterns(word_in,cm,ed=1,level=0,pos=0,candidates=None): """ ed = 1 by default, pos - internal variable for algorithm """ alternates = cm.get(word_in[pos],[]) if not candidates: candidates = [] assert ed <= len(word_in), 'edit distance has to be comparable to word size [ins/d...

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40.758621

15.586207

def watch(directory=None, auto_clear=False, extensions=[]): """Starts a server to render the specified file or directory containing a README.""" if directory and not os.path.isdir(directory): raise ValueError('Directory not found: ' + directory) directory = os.path.abspath(directory) # Initial ...

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32.5

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def get(self, request): """ Called after the user is redirected back to our application. Tries to: - Complete the OAuth / OAuth2 flow - Redirect the user to another view that deals with login, connecting or user creation. """ try: client ...

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42.521739

21.913043

def _connected(self, transport, conn): """Login and sync the ElkM1 panel to memory.""" LOG.info("Connected to ElkM1") self._conn = conn self._transport = transport self._connection_retry_timer = 1 if url_scheme_is_secure(self._config['url']): self._conn.write_...

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49.25

13.166667

def parse(self, data): """ Converts a OpenVPN JSON to a NetworkX Graph object which is then returned. """ # initialize graph and list of aggregated nodes graph = self._init_graph() server = self._server_common_name # add server (central node) to graph ...

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39.511628

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def run(addr, *commands, **kwargs): """ Non-threaded batch command runner returning output results """ results = [] handler = VarnishHandler(addr, **kwargs) for cmd in commands: if isinstance(cmd, tuple) and len(cmd)>1: results.extend([getattr(handler, c[0].replace('.','_'))(...

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def times(self, multiplier): ''' Given an FSM and a multiplier, return the multiplied FSM. ''' if multiplier < 0: raise Exception("Can't multiply an FSM by " + repr(multiplier)) alphabet = self.alphabet # metastate is a set of iterations+states initial = {(self.initial, 0)} def final(state): '...

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def handle_vcf_calls(vcf_file, data, orig_items): """Prioritize VCF calls based on external annotations supplied through GEMINI. """ if not _do_prioritize(orig_items): return vcf_file else: ann_vcf = population.run_vcfanno(vcf_file, data) if ann_vcf: priority_file = _...

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def assign_enterprise_learner_role(sender, instance, **kwargs): # pylint: disable=unused-argument """ Assign an enterprise learner role to EnterpriseCustomerUser whenever a new record is created. """ if kwargs['created'] and instance.user: enterprise_learner_role, __ = SystemWideEnterpriseRo...

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def to_json(self, destination): """ Save a dictionnary into a JSON file. :param destination: A path to a file where we're going to write the converted dict into a JSON format. :type destination: str """ try: with open(destination, "w"...

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def TNE_metric(bpmn_graph): """ Returns the value of the TNE metric (Total Number of Events of the Model) for the BPMNDiagramGraph instance. :param bpmn_graph: an instance of BpmnDiagramGraph representing BPMN model. """ events_counts = get_events_counts(bpmn_graph) return sum( [c...

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def state_cpfs(self) -> List[CPF]: '''Returns list of state-fluent CPFs.''' _, cpfs = self.cpfs state_cpfs = [] for cpf in cpfs: name = utils.rename_next_state_fluent(cpf.name) if name in self.state_fluents: state_cpfs.append(cpf) state_cpf...

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def has_permission(self, perm): """ Checks if current user (or role) has the given permission. Args: perm: Permmission code or object. Depends on the :attr:`~zengine.auth.auth_backend.AuthBackend` implementation. Returns: Boolean. """ ...

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def population_fraction(self): """The filtered/unfiltered ratio for cube response. This value is required for properly calculating population on a cube where a filter has been applied. Returns 1.0 for an unfiltered cube. Returns `np.nan` if the unfiltered count is zero, which would ...

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def parse_sidebar(self, user_page): """Parses the DOM and returns user attributes in the sidebar. :type user_page: :class:`bs4.BeautifulSoup` :param user_page: MAL user page's DOM :rtype: dict :return: User attributes :raises: :class:`.InvalidUserError`, :class:`.MalformedUserPageError` "...

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def lookup_linke_turbidity(time, latitude, longitude, filepath=None, interp_turbidity=True): """ Look up the Linke Turibidity from the ``LinkeTurbidities.h5`` data file supplied with pvlib. Parameters ---------- time : pandas.DatetimeIndex latitude : float l...

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35.8125

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def start(self, pin, dutycycle, frequency_hz=2000): """Enable PWM output on specified pin. Set to intiial percent duty cycle value (0.0 to 100.0) and frequency (in Hz). """ if dutycycle < 0.0 or dutycycle > 100.0: raise ValueError('Invalid duty cycle value, must be between 0...

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def request_instance(vm_=None, call=None): ''' Put together all of the information necessary to request an instance on EC2, and then fire off the request the instance. Returns data about the instance ''' if call == 'function': # Technically this function may be called other ways too, bu...

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def setup_actions(self): """ Connects slots to signals """ self.actionOpen.triggered.connect(self.on_open) self.actionNew.triggered.connect(self.on_new) self.actionSave.triggered.connect(self.on_save) self.actionSave_as.triggered.connect(self.on_save_as) self.actionQuit.t...

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def declare(self, exchange='', exchange_type='direct', virtual_host='/', passive=False, durable=False, auto_delete=False, internal=False, arguments=None): """Declare an Exchange. :param str exchange: Exchange name :param str exchange_type: Exchange type :...

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def from_rel_ref(baseURI, relative_ref): """ Return a |PackURI| instance containing the absolute pack URI formed by translating *relative_ref* onto *baseURI*. """ joined_uri = posixpath.join(baseURI, relative_ref) abs_uri = posixpath.abspath(joined_uri) return Pac...

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def extract_features(self, text): """Extracts features from a body of text. :rtype: dictionary of features """ # Feature extractor may take one or two arguments try: return self.feature_extractor(text, self.train_set) except (TypeError, AttributeError): ...

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def vor_to_am(vor): r""" Given a Voronoi tessellation object from Scipy's ``spatial`` module, converts to a sparse adjacency matrix network representation in COO format. Parameters ---------- vor : Voronoi Tessellation object This object is produced by ``scipy.spatial.Voronoi`` Ret...

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def get_environ_vars(self): """Returns a generator with all environmental vars with prefix PIP_""" for key, val in os.environ.items(): if _environ_prefix_re.search(key): yield (_environ_prefix_re.sub("", key).lower(), val)

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def run_calibration(self, interval, applycal): """Runs the calibration operation with the current settings :param interval: The repetition interval between stimuli presentations (seconds) :type interval: float :param applycal: Whether to apply a previous saved calibration to thi...

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48.5

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def get_db(cls): """Return the database for the collection""" if cls._db: return getattr(cls._client, cls._db) return cls._client.get_default_database()

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36.8

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def _parseSimpleSelector(self, src): """simple_selector : [ namespace_selector ]? element_name? [ HASH | class | attrib | pseudo ]* S* ; """ ctxsrc = src.lstrip() nsPrefix, src = self._getMatchResult(self.re_namespace_selector, src) name, src = self._getMatchResul...

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38.083333

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def manage(settingspath, root_dir, argv): """ Manage all processes """ # add settings.json to environment variables os.environ[ENV_VAR_SETTINGS] = settingspath # add root_dir os.environ[ENV_VAR_ROOT_DIR] = root_dir # get datasets list with open(settingspath) as settings_file: ...

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32.285714

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def cluster_application_state(self, application_id): """ With the application state API, you can obtain the current state of an application. :param str application_id: The application id :returns: API response object with JSON data :rtype: :py:class:`yarn_api_client.base...

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35.230769

15.384615

def masked_middle_mfcc(self): """ Return the MFCC speech frames in the MIDDLE portion of the wave. :rtype: :class:`numpy.ndarray` (2D) """ begin, end = self._masked_middle_begin_end() return (self.masked_mfcc)[:, begin:end]

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30.222222

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def get_transactions_xml(self, account: SEPAAccount, start_date: datetime.date = None, end_date: datetime.date = None) -> list: """ Fetches the list of transactions of a bank account in a certain timeframe as camt.052.001.02 XML files. :param account: SEPA :...

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41.30303

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def lookup_path(bin_name): """Calls to external binaries can't depend on $PATH """ paths = ('/usr/local/sbin/', '/usr/local/bin/', '/usr/sbin/', '/usr/bin/') for p in paths: fq_path = p + bin_name found = os.path.isfile(fq_path) and os.access(fq_path, os.X_OK) if found: ...

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34.5

17.5

def nonblocking_input(self): '''Context manager to set the :class:`Terminal`'s input file to read in a non-blocking way. Normally, reading from :attr:`sys.stdin` blocks, which is bad if we want an interactive application that can also update information on the screen without any...

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44

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def is_me(self): # pragma: no cover, seems not to be used anywhere """Check if parameter name if same than name of this object TODO: is it useful? :return: true if parameter name if same than this name :rtype: bool """ logger.info("And arbiter is launched with the host...

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46.272727

27

def get_field_schema(name, field): """Returns a JSON Schema representation of a form field.""" field_schema = { 'type': 'string', } if field.label: field_schema['title'] = str(field.label) # force translation if field.help_text: field_schema['description'] = str(field.help...

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38.545455

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def do_pickle_ontology(filename, g=None): """ from a valid filename, generate the graph instance and pickle it too note: option to pass a pre-generated graph instance too 2015-09-17: added code to increase recursion limit if cPickle fails see http://stackoverflow.com/questions/2134706/hitting-maximum-recursion-de...

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41.133333

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def __prepare_resource(data): """Prepare the resourcepart of the JID. :Parameters: - `data`: Resourcepart of the JID :raise JIDError: if the resource name is too long. :raise pyxmpp.xmppstringprep.StringprepError: if the resourcepart fails Resourceprep preparati...

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35.526316

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def _clean_rec_name(rec): """Clean illegal characters in input fasta file which cause problems downstream. """ out_id = [] for char in list(rec.id): if char in ALLOWED_CONTIG_NAME_CHARS: out_id.append(char) else: out_id.append("_") rec.id = "".join(out_id) ...

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28.75

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def delete_acl_request(request): """Submission to remove an ACL.""" uuid_ = request.matchdict['uuid'] posted = request.json permissions = [(x['uid'], x['permission'],) for x in posted] with db_connect() as db_conn: with db_conn.cursor() as cursor: remove_acl(cursor, uuid_, permi...

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29.692308

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def parallelize(mapfunc, workers=None): ''' Parallelize the mapfunc with multithreading. mapfunc calls will be partitioned by the provided list of arguments. Each item in the list will represent one call's arguments. They can be tuples if the function takes multiple arguments, but one-tupling is not...

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37.617647

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def print_usage(): """ Prints usage message. """ print('Usage: ' + os.path.basename(sys.argv[0]) + ' [options] dimacs-file') print('Options:') print(' -h, --help Show this message') print(' -m, --model Print model') print(' -s, --solver SAT solver...

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37.916667

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def covariance_matrix(self,x,y,names=None,cov=None): """build a pyemu.Cov instance from GeoStruct Parameters ---------- x : (iterable of floats) x-coordinate locations y : (iterable of floats) y-coordinate locations names : (iterable of str) ...

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32.901639

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def notification_selected_sm_changed(self, model, prop_name, info): """If a new state machine is selected, make sure the tab is open""" selected_state_machine_id = self.model.selected_state_machine_id if selected_state_machine_id is None: return page_id = self.get_page_num(s...

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46.555556

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def imagetransformer_b12l_4h_b128_uncond_dr03_tpu(): """TPU config for cifar 10.""" hparams = imagetransformer_bas8l_8h_big_uncond_dr03_imgnet() update_hparams_for_tpu(hparams) hparams.batch_size = 2 hparams.num_heads = 4 # heads are expensive on tpu hparams.num_decoder_layers = 12 hparams.block_length ...

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38

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def options(self, route: str(), callback: object()): """ Binds a OPTIONS route with the given callback :rtype: object """ self.__set_route('options', {route: callback}) return RouteMapping

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def init_jvm(java_home=None, jvm_dll=None, jvm_maxmem=None, jvm_classpath=None, jvm_properties=None, jvm_options=None, config_file=None, config=None): """ Creates a configured Java virtual machine which will be used by jp...

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48.530612

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def run(scenario, magicc_version=6, **kwargs): """ Run a MAGICC scenario and return output data and (optionally) config parameters. As a reminder, putting ``out_parameters=1`` will cause MAGICC to write out its parameters into ``out/PARAMETERS.OUT`` and they will then be read into ``output.metadata...

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def platform_data_dir(): """ Returns path for user-specific data files Returns: PathLike : path to the data dir used by the current operating system """ if LINUX: # nocover dpath_ = os.environ.get('XDG_DATA_HOME', '~/.local/share') elif DARWIN: # nocover dpath_ = '~/L...

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def __get_query_agg_cardinality(cls, field, agg_id=None): """ Create an es_dsl aggregation object for getting the approximate count of distinct values of a field. :param field: field from which the get count of distinct values :return: a tuple with the aggregation id and es_dsl aggregat...

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def listBlockParents(self, block_name=""): """ list parents of a block """ if not block_name: msg = " DBSBlock/listBlockParents. Block_name must be provided as a string or a list. \ No wildcards allowed in block_name/s." dbsExceptionHandler('dbsExc...

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def rtgen_family(self, value): """Family setter.""" self.bytearray[self._get_slicers(0)] = bytearray(c_ubyte(value or 0))

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def get_item(self, **kwargs): """ Get collection item taking into account generated queryset of parent view. This method allows working with nested resources properly. Thus an item returned by this method will belong to its parent view's queryset, thus filtering out objects that...

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def move_right(self, keep_anchor=False, nb_chars=1): """ Moves the cursor on the right. :param keep_anchor: True to keep anchor (to select text) or False to move the anchor (no selection) :param nb_chars: Number of characters to move. """ text_cursor = self._...

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def datasets(self): """Distinct datasets (``dataset``) in :class:`.models.Entry` Distinct datasets are SwissProt or/and TrEMBL :return: all distinct dataset types :rtype: list[str] """ r = self.session.query(distinct(models.Entry.dataset)).all() return [x[0] for...

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31.9

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def _apply_template(template, target, *, checkout, extra_context): """Apply a template to a temporary directory and then copy results to target.""" with tempfile.TemporaryDirectory() as tempdir: repo_dir = cc_main.cookiecutter( template, checkout=checkout, no_input=Tr...

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def _login(self, max_tries=2): """Logs in to Kindle Cloud Reader. Args: max_tries: The maximum number of login attempts that will be made. Raises: BrowserError: If method called when browser not at a signin URL. LoginError: If login unsuccessful after `max_tries` attempts. """ i...

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32.458333

21.770833

def _get_setup(self, result): """Internal method which process the results from the server.""" self.__devices = {} if ('setup' not in result.keys() or 'devices' not in result['setup'].keys()): raise Exception( "Did not find device definition.") ...

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def _create_options(self, items): """Helper method to create options from list, or instance. Applies preprocess method if available to create a uniform output """ return OrderedDict(map(lambda x: (x.name, x), coerce_to_list(items, self.preprocess)))

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38.75

17.375

def cmd_ip_geolocation(ip_address, verbose): """Get the geolocation of an IP adddress from https://ipapi.co/. Example: \b $ habu.ip.geolocation 8.8.8.8 { "ip": "8.8.8.8", "city": "Mountain View", ... "asn": "AS15169", "org": "Google LLC" } """ if...

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23.296296

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def active_path(context, pattern, css=None): """ Highlight menu item based on path. Returns a css class if ``request.path`` is in given ``pattern``. :param pattern: Regex url pattern. :param css: Css class to be returned for highlighting. Return active if none set. ""...

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25.944444

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def prepare_encrypted_request(self, session, endpoint, message): """ Creates a prepared request to send to the server with an encrypted message and correct headers :param session: The handle of the session to prepare requests with :param endpoint: The endpoint/server to prepare ...

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def hpforest(self, data: ['SASdata', str] = None, freq: str = None, id: str = None, input: [str, list, dict] = None, save: str = None, score: [str, bool, 'SASdata'] = True, target: [str, list, dict] = None, ...

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57.37037

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def from_charmm(cls, path, positions=None, forcefield=None, strict=True, **kwargs): """ Loads PSF Charmm structure from `path`. Requires `charmm_parameters`. Parameters ---------- path : str Path to PSF file forcefield : list of str Paths to Charm...

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38.153846

19.923077

def init(): '''Initialise a WSGI application to be loaded by uWSGI.''' # Load values from config file config_file = os.path.realpath(os.path.join(os.getcwd(), 'swaggery.ini')) config = configparser.RawConfigParser(allow_no_value=True) config.read(config_file) log_level = config.get('application'...

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45.882353

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def create(cls, session, record, imported=False, auto_reply=False): """Create a conversation. Please note that conversation cannot be created with more than 100 threads, if attempted the API will respond with HTTP 412. Args: session (requests.sessions.Session): Authenticate...

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def index(self, value, start=None, stop=None): """ Return the index of the first occurence of *value*. If *start* or *stop* are provided, return the smallest index such that ``s[index] == value`` and ``start <= index < stop``. """ def index_trans(pipe): len_se...

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40.947368

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def create_model(modelname, fields, indexes=None, basemodel=None, **props): """ Create model dynamically :param fields: Just format like [ {'name':name, 'type':type, ...}, ... ] type should be a string, eg. 'str', '...

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def log_error(error, result): """Logs an error """ p = {'error': error, 'result':result} _log(TYPE_CODES.ERROR, p)

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25.2

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def prefix_indent(prefix, textblock, later_prefix=' '): """ Prefix and indent all lines in *textblock*. *prefix* is a prefix string *later_prefix* is used on all but the first line, if it is a single character it will be repeated to match length of *prefix* """ textblock = te...

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async def is_object_synced_to_cn(self, client, pid): """Check if object with {pid} has successfully synced to the CN. CNRead.describe() is used as it's a light-weight HTTP HEAD request. This assumes that the call is being made over a connection that has been authenticated and has read ...

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def cleanup(): """Close all sockets at exit""" for sck in list(Wdb._sockets): try: sck.close() except Exception: log.warn('Error in cleanup', exc_info=True)

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def create(self, properties): """ Create and configure a storage group. The new storage group will be associated with the CPC identified by the `cpc-uri` input property. Authorization requirements: * Object-access permission to the CPC that will be associated with ...

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36.02

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def end(self, sql=None): """Commit the current transaction.""" self._transaction = False try: end = self._con.end except AttributeError: return self._con.query(sql or 'end') else: if sql: return end(sql=sql) else: ...

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def get_arguments(args): """Parse the command line.""" usage = "%(prog)s [arguments] [image files]" programs_str = ', '.join([prog.__name__ for prog in PROGRAMS]) description = "Uses "+programs_str+" if they are on the path." parser = argparse.ArgumentParser(usage=usage, description=description) ...

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def main(): """ Main program entry point """ args = command_line() # TODO: Decouple Book interface and implementation query = Book( title=args.title, author=args.author, max_results=args.max, language_code=args.language, fields=('title', 'authors', 'image...

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def get_plugin_command(plugin_name, command_name, conn=None): """ get_specific_command function queries a specific CommandName :param plugin_name: <str> PluginName :param command_name: <str> CommandName :return: <dict> """ commands = RPX.table(plugin_name).filter( {COMMAND_NAME_KEY:...

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def shutit_method_scope(func): """Notifies the ShutIt object whenever we call a shutit module method. This allows setting values for the 'scope' of a function. """ def wrapper(self, shutit): """Wrapper to call a shutit module method, notifying the ShutIt object. """ ret = func(self, shutit) return ret retu...

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32.1

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def convertloc(candsfile, candloc, memory_limit): """ For given state and location that are too bulky, calculate new location given memory_limit. """ scan, segment, candint, dmind, dtind, beamnum = candloc # set up state and find absolute integration of candidate d0 = pickle.load(open(candsfile, 'r'))...

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39.829268

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