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

text stringlengths 75 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 0.18
def parse(raw_email): # type: (six.string_types) -> Tuple[six.string_types, six.string_types] """Extract email from a full address. Example: 'John Doe <jdoe+github@foo.com>' -> jdoe@foo.com >>> parse("John Doe <me+github.com@someorg.com") ('me', 'someorg.com') >>> parse(42) # doctest: +IGNOR...	[ "def", "parse", "(", "raw_email", ")", ":", "# type: (six.string_types) -> Tuple[six.string_types, six.string_types]", "if", "not", "isinstance", "(", "raw_email", ",", "six", ".", "string_types", ")", ":", "raise", "InvalidEmail", "(", "\"Invalid email: %s\"", "%", "ra...	40.533333	0.000803
def create_todo_item(self, list_id, content, party_id=None, notify=False): """ This call lets you add an item to an existing list. The item is added to the bottom of the list. If a person is responsible for the item, give their id as the party_id value. If a company is responsible, ...	[ "def", "create_todo_item", "(", "self", ",", "list_id", ",", "content", ",", "party_id", "=", "None", ",", "notify", "=", "False", ")", ":", "path", "=", "'/todos/create_item/%u'", "%", "list_id", "req", "=", "ET", ".", "Element", "(", "'request'", ")", ...	55.764706	0.002075
def _build_showstr(self, seed): """ Returns show() display string for data attribute """ output = ["%s (%s) data" % (seed, self.params['lang'])] output.append('{') maxwidth = WPToolsQuery.MAXWIDTH for item in sorted(self.data): if self.data[item] i...	[ "def", "_build_showstr", "(", "self", ",", "seed", ")", ":", "output", "=", "[", "\"%s (%s) data\"", "%", "(", "seed", ",", "self", ".", "params", "[", "'lang'", "]", ")", "]", "output", ".", "append", "(", "'{'", ")", "maxwidth", "=", "WPToolsQuery", ...	33.627907	0.001344
def bam_to_fastq_pair(in_file, target_region, pair): """Generator to convert BAM files into name, seq, qual in a region. """ space, start, end = target_region bam_file = pysam.Samfile(in_file, "rb") for read in bam_file: if (not read.is_unmapped and not read.mate_is_unmapped ...	[ "def", "bam_to_fastq_pair", "(", "in_file", ",", "target_region", ",", "pair", ")", ":", "space", ",", "start", ",", "end", "=", "target_region", "bam_file", "=", "pysam", ".", "Samfile", "(", "in_file", ",", "\"rb\"", ")", "for", "read", "in", "bam_file",...	45.789474	0.001126
def make_app(global_conf, **app_conf): """Create a WSGI application and return it ``global_conf`` The inherited configuration for this application. Normally from the [DEFAULT] section of the Paste ini file. ``app_conf`` The application's local configuration. Normally specified in ...	[ "def", "make_app", "(", "global_conf", ",", "", "", "app_conf", ")", ":", "# Configure the environment and fill conf dictionary.", "environment", ".", "load_environment", "(", "global_conf", ",", "app_conf", ")", "# Dispatch request to controllers.", "app", "=", "contro...	34.369565	0.001845
def get_object_stats(self, obj_name): """ :param obj_name: requested object name :returns: all statistics values for the requested object. """ return dict(zip(self.captions, self.statistics[obj_name]))	[ "def", "get_object_stats", "(", "self", ",", "obj_name", ")", ":", "return", "dict", "(", "zip", "(", "self", ".", "captions", ",", "self", ".", "statistics", "[", "obj_name", "]", ")", ")" ]	33.714286	0.008264
def fix_double_nodes(coor, ngroups, conns, eps): """ Detect and attempt fixing double nodes in a mesh. The double nodes are nodes having the same coordinates w.r.t. precision given by `eps`. """ n_nod, dim = coor.shape cmap = find_map( coor, nm.zeros( (0,dim) ), eps = eps, allow_double = Tr...	[ "def", "fix_double_nodes", "(", "coor", ",", "ngroups", ",", "conns", ",", "eps", ")", ":", "n_nod", ",", "dim", "=", "coor", ".", "shape", "cmap", "=", "find_map", "(", "coor", ",", "nm", ".", "zeros", "(", "(", "0", ",", "dim", ")", ")", ",", ...	31.789474	0.026506
def generate_dirlist_html(FS, filepath): """ Generate directory listing HTML Arguments: FS (FS): filesystem object to read files from filepath (str): path to generate directory listings for Keyword Arguments: list_dir (callable: list[str]): list file names in a directory ...	[ "def", "generate_dirlist_html", "(", "FS", ",", "filepath", ")", ":", "yield", "'<table class=\"dirlist\">'", "if", "filepath", "==", "'/'", ":", "filepath", "=", "''", "for", "name", "in", "FS", ".", "listdir", "(", "filepath", ")", ":", "full_path", "=", ...	30.48	0.001272
def log_exception(cls, msg): """Try to log an error message to this process's error log and the shared error log. NB: Doesn't raise (logs an error instead). """ pid = os.getpid() fatal_error_log_entry = cls._format_exception_message(msg, pid) # We care more about this log than the shared log, ...	[ "def", "log_exception", "(", "cls", ",", "msg", ")", ":", "pid", "=", "os", ".", "getpid", "(", ")", "fatal_error_log_entry", "=", "cls", ".", "_format_exception_message", "(", "msg", ",", "pid", ")", "# We care more about this log than the shared log, so write to i...	40.96	0.012405
def set_storage_container_acl(kwargs=None, storage_conn=None, call=None): ''' .. versionadded:: 2015.8.0 Set a storage container's acl CLI Example: .. code-block:: bash salt-cloud -f set_storage_container my-azure name=mycontainer name: Name of existing container. signed...	[ "def", "set_storage_container_acl", "(", "kwargs", "=", "None", ",", "storage_conn", "=", "None", ",", "call", "=", "None", ")", ":", "if", "call", "!=", "'function'", ":", "raise", "SaltCloudSystemExit", "(", "'The create_storage_container function must be called wit...	32.275	0.001504
def _render_table(data, fields=None): """ Helper to render a list of dictionaries as an HTML display object. """ return IPython.core.display.HTML(datalab.utils.commands.HtmlBuilder.render_table(data, fields))	[ "def", "_render_table", "(", "data", ",", "fields", "=", "None", ")", ":", "return", "IPython", ".", "core", ".", "display", ".", "HTML", "(", "datalab", ".", "utils", ".", "commands", ".", "HtmlBuilder", ".", "render_table", "(", "data", ",", "fields", ...	70	0.018868
def clear(self): """ 直接把现在的清空 """ if not self.timer: return # 不阻塞 try: self.timer.kill(block=False) except: pass self.timer = None	[ "def", "clear", "(", "self", ")", ":", "if", "not", "self", ".", "timer", ":", "return", "# 不阻塞", "try", ":", "self", ".", "timer", ".", "kill", "(", "block", "=", "False", ")", "except", ":", "pass", "self", ".", "timer", "=", "None" ]	16.846154	0.012987
def startswith(self, value): """ Sets the operator type to Query.Op.Startswith and sets \ the value to the inputted value. This method will only work on text \ based fields. :param value <str> :return <Query> :usage ...	[ "def", "startswith", "(", "self", ",", "value", ")", ":", "newq", "=", "self", ".", "copy", "(", ")", "newq", ".", "setOp", "(", "Query", ".", "Op", ".", "Startswith", ")", "newq", ".", "setValue", "(", "value", ")", "return", "newq" ]	31.684211	0.008065
def update_one(self, filter, update, upsert=False, bypass_document_validation=False, collation=None, array_filters=None, session=None): """Update a single document matching the filter. >>> for doc in db.test.find(): ... print(doc) ... ...	[ "def", "update_one", "(", "self", ",", "filter", ",", "update", ",", "upsert", "=", "False", ",", "bypass_document_validation", "=", "False", ",", "collation", "=", "None", ",", "array_filters", "=", "None", ",", "session", "=", "None", ")", ":", "common",...	37.507246	0.001883
def createNetwork(dataSource): """Create the Network instance. The network has a sensor region reading data from `dataSource` and passing the encoded representation to an Identity Region. :param dataSource: a RecordStream instance to get data from :returns: a Network instance ready to run """ network = ...	[ "def", "createNetwork", "(", "dataSource", ")", ":", "network", "=", "Network", "(", ")", "# Our input is sensor data from the gym file. The RecordSensor region", "# allows us to specify a file record stream as the input source via the", "# dataSource attribute.", "network", ".", "ad...	35.978723	0.016695
def readFILTERLIST(self): """ Read a length-prefixed list of FILTERs """ number = self.readUI8() return [self.readFILTER() for _ in range(number)]	[ "def", "readFILTERLIST", "(", "self", ")", ":", "number", "=", "self", ".", "readUI8", "(", ")", "return", "[", "self", ".", "readFILTER", "(", ")", "for", "_", "in", "range", "(", "number", ")", "]" ]	41.75	0.011765
def fileUpd(self, buffer=None, filename=None, ufilename=None, desc=None): """Update annotation attached file.""" CheckParent(self) return _fitz.Annot_fileUpd(self, buffer, filename, ufilename, desc)	[ "def", "fileUpd", "(", "self", ",", "buffer", "=", "None", ",", "filename", "=", "None", ",", "ufilename", "=", "None", ",", "desc", "=", "None", ")", ":", "CheckParent", "(", "self", ")", "return", "_fitz", ".", "Annot_fileUpd", "(", "self", ",", "b...	31.285714	0.013333
def keyevent_to_keyseq(self, event): """Return a QKeySequence representation of the provided QKeyEvent.""" self.keyPressEvent(event) event.accept() return self.keySequence()	[ "def", "keyevent_to_keyseq", "(", "self", ",", "event", ")", ":", "self", ".", "keyPressEvent", "(", "event", ")", "event", ".", "accept", "(", ")", "return", "self", ".", "keySequence", "(", ")" ]	41	0.009569
def get_branch_info(self): """ Retrieve branch_info from Satellite Server """ branch_info = None if os.path.exists(constants.cached_branch_info): # use cached branch info file if less than 10 minutes old # (failsafe, should be deleted at end of client run...	[ "def", "get_branch_info", "(", "self", ")", ":", "branch_info", "=", "None", "if", "os", ".", "path", ".", "exists", "(", "constants", ".", "cached_branch_info", ")", ":", "# use cached branch info file if less than 10 minutes old", "# (failsafe, should be deleted at end...	47.688889	0.002283
def as_list(func): """ A decorator used to return a JSON response of a list of model objects. It expects the decorated function to return a list of model instances. It then converts the instances to dicts and serializes them into a json response Examples: >>> @app.route...	[ "def", "as_list", "(", "func", ")", ":", "@", "wraps", "(", "func", ")", "def", "wrapper", "(", "", "args", ",", "", "", "kwargs", ")", ":", "response", "=", "func", "(", "", "args", ",", "", "", "kwargs", ")", "if", "isinstance", "(", "r...	31.434783	0.001342
def make_spo(sub, prd, obj): ''' Decorates the three given strings as a line of ntriples ''' # To establish string as a curie and expand, # we use a global curie_map(.yaml) # sub are allways uri (unless a bnode) # prd are allways uri (unless prd is 'a') # should fail loudly if curie do...	[ "def", "make_spo", "(", "sub", ",", "prd", ",", "obj", ")", ":", "# To establish string as a curie and expand,", "# we use a global curie_map(.yaml)", "# sub are allways uri (unless a bnode)", "# prd are allways uri (unless prd is 'a')", "# should fail loudly if curie does not exist", ...	32.806452	0.000955
def xmlrpc_run(self, port=24444, bind='127.0.0.1', logRequests=False): '''Run xmlrpc server''' import umsgpack from pyspider.libs.wsgi_xmlrpc import WSGIXMLRPCApplication try: from xmlrpc.client import Binary except ImportError: from xmlrpclib import Binar...	[ "def", "xmlrpc_run", "(", "self", ",", "port", "=", "24444", ",", "bind", "=", "'127.0.0.1'", ",", "logRequests", "=", "False", ")", ":", "import", "umsgpack", "from", "pyspider", ".", "libs", ".", "wsgi_xmlrpc", "import", "WSGIXMLRPCApplication", "try", ":"...	37.558824	0.00229
def _ml_t_joint(self): """ Compute the joint maximum likelihood assignment of the internal nodes positions by propagating from the tree leaves towards the root. Given the assignment of parent nodes, reconstruct the maximum-likelihood positions of the child nodes by propagating fr...	[ "def", "_ml_t_joint", "(", "self", ")", ":", "def", "_cleanup", "(", ")", ":", "for", "node", "in", "self", ".", "tree", ".", "find_clades", "(", ")", ":", "del", "node", ".", "joint_pos_Lx", "del", "node", ".", "joint_pos_Cx", "self", ".", "logger", ...	56.191304	0.010189
def rules(self, x, y): # type: (int, int) -> List[Type[Rule]] """ Get rules at specific position in the structure. :param x: X coordinate :param y: Y coordinate :return: List of rules """ return [r for r in self._field[y][x]]	[ "def", "rules", "(", "self", ",", "x", ",", "y", ")", ":", "# type: (int, int) -> List[Type[Rule]]", "return", "[", "r", "for", "r", "in", "self", ".", "_field", "[", "y", "]", "[", "x", "]", "]" ]	31.222222	0.010381
def _reset(self): """ Reset the Screen. """ self._last_start_line = 0 self._colour = None self._attr = None self._bg = None self._cur_x = None self._cur_y = None	[ "def", "_reset", "(", "self", ")", ":", "self", ".", "_last_start_line", "=", "0", "self", ".", "_colour", "=", "None", "self", ".", "_attr", "=", "None", "self", ".", "_bg", "=", "None", "self", ".", "_cur_x", "=", "None", "self", ".", "_cur_y", "...	22.4	0.008584
def plot_elements_to_ax(self, cid, ax=None, *kwargs): """Plot element data (parameter sets). If the parameter ax* is not set, then a new figure will be created with a corresponding axes. Parameters ---------- cid : int or :py:class:`numpy.ndarray` if *cid...	[ "def", "plot_elements_to_ax", "(", "self", ",", "cid", ",", "ax", "=", "None", ",", "", "", "kwargs", ")", ":", "rasterize", "=", "kwargs", ".", "get", "(", "'rasterize'", ",", "False", ")", "xmin", "=", "kwargs", ".", "get", "(", "'xmin'", ",", ...	34.210526	0.000272
def _render(self, value, format): """ Writes javascript to call momentjs function """ template = '<script>\ndocument.write(moment(\"{t}\").{f});\n</script>' return Markup(template.format(t=value, f=format))	[ "def", "_render", "(", "self", ",", "value", ",", "format", ")", ":", "template", "=", "'<script>\\ndocument.write(moment(\\\"{t}\\\").{f});\\n</script>'", "return", "Markup", "(", "template", ".", "format", "(", "t", "=", "value", ",", "f", "=", "format", ")", ...	56.75	0.008696
def _get_ipmitool_path(self, cmd='ipmitool'): """Get full path to the ipmitool command using the unix `which` command """ p = subprocess.Popen(["which", cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = p.communicate() return o...	[ "def", "_get_ipmitool_path", "(", "self", ",", "cmd", "=", "'ipmitool'", ")", ":", "p", "=", "subprocess", ".", "Popen", "(", "[", "\"which\"", ",", "cmd", "]", ",", "stdout", "=", "subprocess", ".", "PIPE", ",", "stderr", "=", "subprocess", ".", "PIPE...	40.375	0.018182
def render(jinja_template_text=None, jinja_template_function='highstate_doc.markdown_default_jinja_template', **kwargs): ''' Render highstate to a text format (default Markdown) if `jinja_template_text` is not set, `jinja_template_function` is used. jinja_template_text: jinja text that the render uses...	[ "def", "render", "(", "jinja_template_text", "=", "None", ",", "jinja_template_function", "=", "'highstate_doc.markdown_default_jinja_template'", ",", "", "", "kwargs", ")", ":", "config", "=", "_get_config", "(", "", "", "kwargs", ")", "lowstates", "=", "proc...	37.342105	0.00206
def ctype_for_encoding(self, encoding): """Return ctypes type for an encoded Objective-C type.""" if encoding in self.typecodes: return self.typecodes[encoding] elif encoding[0:1] == b'^' and encoding[1:] in self.typecodes: return POINTER(self.typecodes[encoding[1:]]) ...	[ "def", "ctype_for_encoding", "(", "self", ",", "encoding", ")", ":", "if", "encoding", "in", "self", ".", "typecodes", ":", "return", "self", ".", "typecodes", "[", "encoding", "]", "elif", "encoding", "[", "0", ":", "1", "]", "==", "b'^'", "and", "enc...	53	0.002317
def matrix_to_points(matrix, pitch, origin): """ Convert an (n,m,p) matrix into a set of points for each voxel center. Parameters ----------- matrix: (n,m,p) bool, voxel matrix pitch: float, what pitch was the voxel matrix computed with origin: (3,) float, what is the origin of the voxel ma...	[ "def", "matrix_to_points", "(", "matrix", ",", "pitch", ",", "origin", ")", ":", "indices", "=", "np", ".", "column_stack", "(", "np", ".", "nonzero", "(", "matrix", ")", ")", "points", "=", "indices_to_points", "(", "indices", "=", "indices", ",", "pitc...	30.631579	0.001667
def parse_fqscreen(self, f): """ Parse the FastQ Screen output into a 3D dict """ parsed_data = OrderedDict() reads_processed = None nohits_pct = None for l in f['f']: if l.startswith('%Hit_no_genomes:') or l.startswith('%Hit_no_libraries:'): nohits_pc...	[ "def", "parse_fqscreen", "(", "self", ",", "f", ")", ":", "parsed_data", "=", "OrderedDict", "(", ")", "reads_processed", "=", "None", "nohits_pct", "=", "None", "for", "l", "in", "f", "[", "'f'", "]", ":", "if", "l", ".", "startswith", "(", "'%Hit_no_...	61.625	0.009185
def _get_variants(data): """Retrieve variants from CWL and standard inputs for organizing variants. """ active_vs = [] if "variants" in data: variants = data["variants"] # CWL based list of variants if isinstance(variants, dict) and "samples" in variants: variants = v...	[ "def", "_get_variants", "(", "data", ")", ":", "active_vs", "=", "[", "]", "if", "\"variants\"", "in", "data", ":", "variants", "=", "data", "[", "\"variants\"", "]", "# CWL based list of variants", "if", "isinstance", "(", "variants", ",", "dict", ")", "and...	45.115385	0.000835
def equivalent_to(self, token): """ Gets all tokens which match the character and scopes of a reference token :param token: :class:`esi.models.Token` :return: :class:`esi.managers.TokenQueryset` """ return self.filter(character_id=token.character_id).require_scopes_exact(...	[ "def", "equivalent_to", "(", "self", ",", "token", ")", ":", "return", "self", ".", "filter", "(", "character_id", "=", "token", ".", "character_id", ")", ".", "require_scopes_exact", "(", "token", ".", "scopes", ".", "all", "(", ")", ")", ".", "filter",...	53.75	0.011442
def main(): """ Command-line processor. See ``--help`` for details. """ main_only_quicksetup_rootlogger(level=logging.DEBUG) parser = argparse.ArgumentParser() parser.add_argument( "--mysql", default="mysql", help="MySQL program (default=mysql)") parser.add_argument( ...	[ "def", "main", "(", ")", ":", "main_only_quicksetup_rootlogger", "(", "level", "=", "logging", ".", "DEBUG", ")", "parser", "=", "argparse", ".", "ArgumentParser", "(", ")", "parser", ".", "add_argument", "(", "\"--mysql\"", ",", "default", "=", "\"mysql\"", ...	38.532468	0.000329
def srp1(args,*kargs): """Send and receive packets at layer 2 and return only the first answer nofilter: put 1 to avoid use of bpf filters retry: if positive, how many times to resend unanswered packets if negative, how many times to retry when no more packets are answered timeout: how much time to ...	[ "def", "srp1", "(", "", "args", ",", "", "", "kargs", ")", ":", "if", "not", "\"timeout\"", "in", "kargs", ":", "kargs", "[", "\"timeout\"", "]", "=", "-", "1", "a", ",", "b", "=", "srp", "(", "", "args", ",", "", "", "kargs", ")", "if"...	39.882353	0.010086
def prep_bam_inputs(out_dir, sample, call_file, bam_file): """Prepare expected input BAM files from pre-aligned. """ base = utils.splitext_plus(os.path.basename(bam_file))[0] with open(call_file) as in_handle: for cur_hla in (x.strip() for x in in_handle): out_file = os.path.join(uti...	[ "def", "prep_bam_inputs", "(", "out_dir", ",", "sample", ",", "call_file", ",", "bam_file", ")", ":", "base", "=", "utils", ".", "splitext_plus", "(", "os", ".", "path", ".", "basename", "(", "bam_file", ")", ")", "[", "0", "]", "with", "open", "(", ...	55.181818	0.008104
def comparator(objective): """ Higher order function creating a compare function for objectives. Args: objective (cipy.algorithms.core.Objective): The objective to create a compare for. Returns: callable: Function accepting two objectives to compare. Examples: ...	[ "def", "comparator", "(", "objective", ")", ":", "if", "isinstance", "(", "objective", ",", "Minimum", ")", ":", "return", "lambda", "l", ",", "r", ":", "l", "<", "r", "else", ":", "return", "lambda", "l", ",", "r", ":", "l", ">", "r" ]	25.318182	0.00173
def detect_anomaly(self): """ Detect anomalies in the timeseries data for the submetrics specified in the config file. Identified anomalies are stored in self.anomalies as well as written to .anomalies.csv file to be used by the client charting page. Anomaly detection uses the luminol library (http://py...	[ "def", "detect_anomaly", "(", "self", ")", ":", "if", "not", "self", ".", "anomaly_detection_metrics", "or", "len", "(", "self", ".", "anomaly_detection_metrics", ")", "<=", "0", ":", "return", "for", "submetric", "in", "self", ".", "anomaly_detection_metrics", ...	54.857143	0.009386
def listen_many(*rooms): """Listen for changes in all registered listeners in all specified rooms""" rooms = set(r.conn for r in rooms) for room in rooms: room.validate_listeners() with ARBITRATOR.condition: while any(r.connected for r in rooms): ARBITRATOR.condition.wait() ...	[ "def", "listen_many", "(", "*", "rooms", ")", ":", "rooms", "=", "set", "(", "r", ".", "conn", "for", "r", "in", "rooms", ")", "for", "room", "in", "rooms", ":", "room", ".", "validate_listeners", "(", ")", "with", "ARBITRATOR", ".", "condition", ":"...	34.5	0.002353
def _make_chunk_size(self, req_size): """ Takes an allocation size as requested by the user and modifies it to be a suitable chunk size. """ size = req_size size += 2 * self._chunk_size_t_size # Two size fields size = self._chunk_min_size if size < self._chunk_min_size e...	[ "def", "_make_chunk_size", "(", "self", ",", "req_size", ")", ":", "size", "=", "req_size", "size", "+=", "2", "*", "self", ".", "_chunk_size_t_size", "# Two size fields", "size", "=", "self", ".", "_chunk_min_size", "if", "size", "<", "self", ".", "_chunk_m...	54.8	0.008977
def build_response( self, request, response, from_cache=False, cacheable_methods=None ): """ Build a response by making a request or using the cache. This will end up calling send and returning a potentially cached response """ cacheable = cacheable_methods o...	[ "def", "build_response", "(", "self", ",", "request", ",", "response", ",", "from_cache", "=", "False", ",", "cacheable_methods", "=", "None", ")", ":", "cacheable", "=", "cacheable_methods", "or", "self", ".", "cacheable_methods", "if", "not", "from_cache", "...	40.09589	0.001334
def decode_example(self, tfexample_data): """See base class for details.""" # TODO(epot): Support dynamic shape if self.shape.count(None) < 2: # Restore the shape if possible. TF Example flattened it. shape = [-1 if i is None else i for i in self.shape] tfexample_data = tf.reshape(tfexampl...	[ "def", "decode_example", "(", "self", ",", "tfexample_data", ")", ":", "# TODO(epot): Support dynamic shape", "if", "self", ".", "shape", ".", "count", "(", "None", ")", "<", "2", ":", "# Restore the shape if possible. TF Example flattened it.", "shape", "=", "[", "...	46	0.010661
def detect_language(index_page): """ Detect `languages` using `langdetect` library. Args: index_page (str): HTML content of the page you wish to analyze. Returns: obj: One :class:`.SourceString` object. """ dom = dhtmlparser.parseString(index_page) clean_content = dhtmlpar...	[ "def", "detect_language", "(", "index_page", ")", ":", "dom", "=", "dhtmlparser", ".", "parseString", "(", "index_page", ")", "clean_content", "=", "dhtmlparser", ".", "removeTags", "(", "dom", ")", "lang", "=", "None", "try", ":", "lang", "=", "langdetect",...	23.291667	0.001718
def at_index(iterable, index): # type: (Iterable[T], int) -> T """" Return the item at the index of this iterable or raises IndexError. WARNING: this will consume generators. Negative indices are allowed but be aware they will cause n items to be held in memory, where n = abs(index) ...	[ "def", "at_index", "(", "iterable", ",", "index", ")", ":", "# type: (Iterable[T], int) -> T", "try", ":", "if", "index", "<", "0", ":", "return", "deque", "(", "iterable", ",", "maxlen", "=", "abs", "(", "index", ")", ")", ".", "popleft", "(", ")", "r...	36.625	0.001664
def _init_add_goid_alt(self): ''' Add alternate GO IDs to term counts. ''' # Fill aspect_counts. Find alternate GO IDs that may not be on gocnts goid_alts = set() go2cnt_add = {} aspect_counts = self.aspect_counts gocnts = self.gocnts go2obj = ...	[ "def", "_init_add_goid_alt", "(", "self", ")", ":", "# Fill aspect_counts. Find alternate GO IDs that may not be on gocnts", "goid_alts", "=", "set", "(", ")", "go2cnt_add", "=", "{", "}", "aspect_counts", "=", "self", ".", "aspect_counts", "gocnts", "=", "self", ".",...	41.793103	0.002419
def is_worktree(cwd, user=None, password=None, output_encoding=None): ''' .. versionadded:: 2015.8.0 This function will attempt to determine if ``cwd`` is part of a worktree by checking its ``.git`` to see if it is a file containing a reference to ano...	[ "def", "is_worktree", "(", "cwd", ",", "user", "=", "None", ",", "password", "=", "None", ",", "output_encoding", "=", "None", ")", ":", "cwd", "=", "_expand_path", "(", "cwd", ",", "user", ")", "try", ":", "toplevel", "=", "_get_toplevel", "(", "cwd",...	33.771429	0.000411
def crop_frequencies(self, low=None, high=None, copy=False): """Crop this `Spectrogram` to the specified frequencies Parameters ---------- low : `float` lower frequency bound for cropped `Spectrogram` high : `float` upper frequency bound for cropped `Spec...	[ "def", "crop_frequencies", "(", "self", ",", "low", "=", "None", ",", "high", "=", "None", ",", "copy", "=", "False", ")", ":", "if", "low", "is", "not", "None", ":", "low", "=", "units", ".", "Quantity", "(", "low", ",", "self", ".", "_default_yun...	38.254902	0.001
def account(self, id): """Get :py:class:`ofxclient.Account` by section id""" if self.parser.has_section(id): return self._section_to_account(id) return None	[ "def", "account", "(", "self", ",", "id", ")", ":", "if", "self", ".", "parser", ".", "has_section", "(", "id", ")", ":", "return", "self", ".", "_section_to_account", "(", "id", ")", "return", "None" ]	37.6	0.010417
def clean(input_string, tag_dictionary=constants.SUPPORTED_TAGS): """ Sanitizes HTML. Tags not contained as keys in the tag_dictionary input are removed, and child nodes are recursively moved to parent of removed node. Attributes not contained as arguments in tag_dictionary are removed. Do...	[ "def", "clean", "(", "input_string", ",", "tag_dictionary", "=", "constants", ".", "SUPPORTED_TAGS", ")", ":", "try", ":", "assert", "isinstance", "(", "input_string", ",", "basestring", ")", "except", "AssertionError", ":", "raise", "TypeError", "root", "=", ...	45.590164	0.002464
def save(self, filehandle, destination=None, metadata=None, validate=True, catch_all_errors=False, args, *kwargs): """Saves the filehandle to the provided destination or the attached default destination. Allows passing arbitrary positional and keyword arguments to the saving mecha...	[ "def", "save", "(", "self", ",", "filehandle", ",", "destination", "=", "None", ",", "metadata", "=", "None", ",", "validate", "=", "True", ",", "catch_all_errors", "=", "False", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "destination", "=", ...	45.617647	0.001894
def _serialize(self, value, ct): """Auto-serialization of the value based upon the content-type value. :param any value: The value to serialize :param ietfparse.: The content type to serialize :rtype: str :raises: ValueError """ key = '{}/{}'.format(ct.content_t...	[ "def", "_serialize", "(", "self", ",", "value", ",", "ct", ")", ":", "key", "=", "'{}/{}'", ".", "format", "(", "ct", ".", "content_type", ",", "ct", ".", "content_subtype", ")", "if", "key", "not", "in", "self", ".", "_SERIALIZATION_MAP", ":", "raise"...	44.578947	0.002312
def do_photometry(self, image, init_guesses=None): """ Perform PSF photometry in ``image``. This method assumes that ``psf_model`` has centroids and flux parameters which will be fitted to the data provided in ``image``. A compound model, in fact a sum of ``psf_model``, ...	[ "def", "do_photometry", "(", "self", ",", "image", ",", "init_guesses", "=", "None", ")", ":", "if", "self", ".", "bkg_estimator", "is", "not", "None", ":", "image", "=", "image", "-", "self", ".", "bkg_estimator", "(", "image", ")", "if", "self", ".",...	48.233645	0.00057
def set_mode(self, mode): """ Set Vim mode to ``mode``. Supported modes: * ``normal`` * ``insert`` * ``command`` * ``visual`` * ``visual-block`` This method behave as setter-only property. Example: >>> import headlessvim ...	[ "def", "set_mode", "(", "self", ",", "mode", ")", ":", "keys", "=", "'\\033\\033'", "if", "mode", "==", "'normal'", ":", "pass", "elif", "mode", "==", "'insert'", ":", "keys", "+=", "'i'", "elif", "mode", "==", "'command'", ":", "keys", "+=", "':'", ...	24.794872	0.00199
def _decay(): """L2 weight decay loss.""" costs = [] for var in tf.trainable_variables(): if var.op.name.find('DW') > 0: costs.append(tf.nn.l2_loss(var)) return tf.add_n(costs)	[ "def", "_decay", "(", ")", ":", "costs", "=", "[", "]", "for", "var", "in", "tf", ".", "trainable_variables", "(", ")", ":", "if", "var", ".", "op", ".", "name", ".", "find", "(", "'DW'", ")", ">", "0", ":", "costs", ".", "append", "(", "tf", ...	26.857143	0.030928
def stop_server(self): """ Stop serving """ if self.api_server is not None: try: self.api_server.socket.shutdown(socket.SHUT_RDWR) except: log.warning("Failed to shut down API server socket") self.api_server.shutdown()	[ "def", "stop_server", "(", "self", ")", ":", "if", "self", ".", "api_server", "is", "not", "None", ":", "try", ":", "self", ".", "api_server", ".", "socket", ".", "shutdown", "(", "socket", ".", "SHUT_RDWR", ")", "except", ":", "log", ".", "warning", ...	28.090909	0.009404
def separate_resources(self): # type: () -> None """Move contents of resources key in internal dictionary into self.resources Returns: None """ self._separate_hdxobjects(self.resources, 'resources', 'name', hdx.data.resource.Resource)	[ "def", "separate_resources", "(", "self", ")", ":", "# type: () -> None", "self", ".", "_separate_hdxobjects", "(", "self", ".", "resources", ",", "'resources'", ",", "'name'", ",", "hdx", ".", "data", ".", "resource", ".", "Resource", ")" ]	35	0.017422
def add_classification_events(obj, events, labels, signal_label=None, weights=None, test=False): """Add classification events to a TMVA::Factory or TMVA::DataLoader from NumPy arrays. Parameters ---------- obj : TMVA::Factory or TMVA::DataLoader A TMVA::Factory or ...	[ "def", "add_classification_events", "(", "obj", ",", "events", ",", "labels", ",", "signal_label", "=", "None", ",", "weights", "=", "None", ",", "test", "=", "False", ")", ":", "if", "NEW_TMVA_API", ":", "# pragma: no cover", "if", "not", "isinstance", "(",...	45.058824	0.000766
def rank(matrix, atol=1e-13, rtol=0): """ Estimate the rank, i.e., the dimension of the column space, of a matrix. The algorithm used by this function is based on the singular value decomposition of `stoichiometry_matrix`. Parameters ---------- matrix : ndarray The matrix should be...	[ "def", "rank", "(", "matrix", ",", "atol", "=", "1e-13", ",", "rtol", "=", "0", ")", ":", "matrix", "=", "np", ".", "atleast_2d", "(", "matrix", ")", "sigma", "=", "svd", "(", "matrix", ",", "compute_uv", "=", "False", ")", "tol", "=", "max", "("...	30.533333	0.000705
def progress(self): """ Deal with next token Used to create, fillout and end groups and singles As well as just append everything else """ tokenum, value, scol = self.current.values() # Default to not appending anything just_append = False ...	[ "def", "progress", "(", "self", ")", ":", "tokenum", ",", "value", ",", "scol", "=", "self", ".", "current", ".", "values", "(", ")", "# Default to not appending anything", "just_append", "=", "False", "# Prevent from group having automatic pass given to it", "# If it...	37.10101	0.001856
def get_tan_media(self, media_type = TANMediaType2.ALL, media_class = TANMediaClass4.ALL): """Get information about TAN lists/generators. Returns tuple of fints.formals.TANUsageOption and a list of fints.formals.TANMedia4 or fints.formals.TANMedia5 objects.""" with self._get_dialog() as dialog...	[ "def", "get_tan_media", "(", "self", ",", "media_type", "=", "TANMediaType2", ".", "ALL", ",", "media_class", "=", "TANMediaClass4", ".", "ALL", ")", ":", "with", "self", ".", "_get_dialog", "(", ")", "as", "dialog", ":", "hktab", "=", "self", ".", "_fin...	40.882353	0.016878
def quick_doc(request_data): """ Worker that returns the documentation of the symbol under cursor. """ code = request_data['code'] line = request_data['line'] + 1 column = request_data['column'] path = request_data['path'] # encoding = 'utf-8' encoding = 'utf-8' script = jedi.Scr...	[ "def", "quick_doc", "(", "request_data", ")", ":", "code", "=", "request_data", "[", "'code'", "]", "line", "=", "request_data", "[", "'line'", "]", "+", "1", "column", "=", "request_data", "[", "'column'", "]", "path", "=", "request_data", "[", "'path'", ...	29.777778	0.001808
def jenkins_request_with_headers(jenkins_server, req): """ We need to get the headers in addition to the body answer to get the location from them This function uses jenkins_request method from python-jenkins library with just the return call changed :param jenkins_server: The server to query ...	[ "def", "jenkins_request_with_headers", "(", "jenkins_server", ",", "req", ")", ":", "try", ":", "response", "=", "jenkins_server", ".", "jenkins_request", "(", "req", ")", "response_body", "=", "response", ".", "content", "response_headers", "=", "response", ".", ...	43.934783	0.001452
def align_circulation_with_z(self, circulation=None): """ If the input orbit is a tube orbit, this function aligns the circulation axis with the z axis and returns a copy. Parameters ---------- circulation : array_like (optional) Array of bits that specify th...	[ "def", "align_circulation_with_z", "(", "self", ",", "circulation", "=", "None", ")", ":", "if", "circulation", "is", "None", ":", "circulation", "=", "self", ".", "circulation", "(", ")", "circulation", "=", "atleast_2d", "(", "circulation", ",", "insert_axis...	36.338235	0.011032
def correct_rytov_output(radius, sphere_index, medium_index, radius_sampling): r"""Error-correction of refractive index and radius for Rytov This method corrects the fitting results for `radius` :math:`r_\text{Ryt}` and `sphere_index` :math:`n_\text{Ryt}` obtained using :func:`qpsphere.models.rytov` us...	[ "def", "correct_rytov_output", "(", "radius", ",", "sphere_index", ",", "medium_index", ",", "radius_sampling", ")", ":", "params", "=", "get_params", "(", "radius_sampling", ")", "x", "=", "sphere_index", "/", "medium_index", "-", "1", "radius_sc", "=", "radius...	33.034483	0.000507
def _build_string_type(var, property_path=None): """ Builds schema definitions for string type values. :param var: The string type value :param List[str] property_path: The property path of the current type, defaults to None, optional :param property_path: [type], optional :return: The buil...	[ "def", "_build_string_type", "(", "var", ",", "property_path", "=", "None", ")", ":", "if", "not", "property_path", ":", "property_path", "=", "[", "]", "schema", "=", "{", "\"type\"", ":", "\"string\"", "}", "if", "is_builtin_type", "(", "var", ")", ":", ...	28.4	0.00227
def get_ddlib_feats(span, context, idxs): """ Minimalist port of generic mention features from ddlib """ if span.stable_id not in unary_ddlib_feats: unary_ddlib_feats[span.stable_id] = set() for seq_feat in _get_seq_features(context, idxs): unary_ddlib_feats[span.stable_id]...	[ "def", "get_ddlib_feats", "(", "span", ",", "context", ",", "idxs", ")", ":", "if", "span", ".", "stable_id", "not", "in", "unary_ddlib_feats", ":", "unary_ddlib_feats", "[", "span", ".", "stable_id", "]", "=", "set", "(", ")", "for", "seq_feat", "in", "...	32	0.001898
def set_secure_boot_mode(self, secure_boot_enable): """Enable/Disable secure boot on the server. Resetting the server post updating this settings is needed from the caller side to make this into effect. :param secure_boot_enable: True, if secure boot needs to be enabled f...	[ "def", "set_secure_boot_mode", "(", "self", ",", "secure_boot_enable", ")", ":", "if", "self", ".", "_is_boot_mode_uefi", "(", ")", ":", "sushy_system", "=", "self", ".", "_get_sushy_system", "(", "PROLIANT_SYSTEM_ID", ")", "try", ":", "sushy_system", ".", "secu...	49.433333	0.001323
def py_to_go_cookie(py_cookie): '''Convert a python cookie to the JSON-marshalable Go-style cookie form.''' # TODO (perhaps): # HttpOnly # Creation # LastAccess # Updated # not done properly: CanonicalHost. go_cookie = { 'Name': py_cookie.name, 'Value': py_cookie....	[ "def", "py_to_go_cookie", "(", "py_cookie", ")", ":", "# TODO (perhaps):", "# HttpOnly", "# Creation", "# LastAccess", "# Updated", "# not done properly: CanonicalHost.", "go_cookie", "=", "{", "'Name'", ":", "py_cookie", ".", "name", ",", "'Value'", ":", "py_co...	37	0.001054
def start_with(self, request): """Start the crawler using the given request. Args: request (:class:`nyawc.http.Request`): The startpoint for the crawler. """ HTTPRequestHelper.patch_with_options(request, self.__options) self.queue.add_request(request) self...	[ "def", "start_with", "(", "self", ",", "request", ")", ":", "HTTPRequestHelper", ".", "patch_with_options", "(", "request", ",", "self", ".", "__options", ")", "self", ".", "queue", ".", "add_request", "(", "request", ")", "self", ".", "__crawler_start", "("...	27.25	0.008876
def accept(self, arg1: JavaObject, arg2: JavaObject) -> None: """ >>> c = BiConsumer(lambda x,y : print(x + y)) >>> c.accept("foo", "bar") foobar """ self.lambda_function(arg1, arg2)	[ "def", "accept", "(", "self", ",", "arg1", ":", "JavaObject", ",", "arg2", ":", "JavaObject", ")", "->", "None", ":", "self", ".", "lambda_function", "(", "arg1", ",", "arg2", ")" ]	32	0.008696
def resume_service(name): """ Resume the service given by name. @warn: This method requires UAC elevation in Windows Vista and above. @note: Not all services support this. @see: L{get_services}, L{get_active_services}, L{start_service}, L{stop_service}, L{pause_ser...	[ "def", "resume_service", "(", "name", ")", ":", "with", "win32", ".", "OpenSCManager", "(", "dwDesiredAccess", "=", "win32", ".", "SC_MANAGER_CONNECT", ")", "as", "hSCManager", ":", "with", "win32", ".", "OpenService", "(", "hSCManager", ",", "name", ",", "d...	37.333333	0.011611
def HStruct_selectFields(structT, fieldsToUse): """ Select fields from structure (rest will become spacing) :param structT: HStruct type instance :param fieldsToUse: dict {name:{...}} or set of names to select, dictionary is used to select nested fields in HStruct or HUnion fields ...	[ "def", "HStruct_selectFields", "(", "structT", ",", "fieldsToUse", ")", ":", "template", "=", "[", "]", "fieldsToUse", "=", "fieldsToUse", "foundNames", "=", "set", "(", ")", "for", "f", "in", "structT", ".", "fields", ":", "name", "=", "None", "subfields"...	30.222222	0.000712
def lincr(l,cap): # to increment a list up to a max-list of 'cap' """ Simulate a counting system from an n-dimensional list. Usage: lincr(l,cap) l=list to increment, cap=max values for each list pos'n Returns: next set of values for list l, OR -1 (if overflow) """ l[0] = l[0] + 1 # e.g., [0,0,0]...	[ "def", "lincr", "(", "l", ",", "cap", ")", ":", "# to increment a list up to a max-list of 'cap'", "l", "[", "0", "]", "=", "l", "[", "0", "]", "+", "1", "# e.g., [0,0,0] --> [2,4,3] (=cap)", "for", "i", "in", "range", "(", "len", "(", "l", ")", ")", ":"...	40.066667	0.011382
def available(self, context): """ Resource availability. :param resort.engine.execution.Context context: Current execution context. """ try: if self.__available is None: encoded_name = urllib.parse.quote_plus(self.__name) status_code, msg = self.__endpoint.get( "/resources/custom-...	[ "def", "available", "(", "self", ",", "context", ")", ":", "try", ":", "if", "self", ".", "__available", "is", "None", ":", "encoded_name", "=", "urllib", ".", "parse", ".", "quote_plus", "(", "self", ".", "__name", ")", "status_code", ",", "msg", "=",...	22.5	0.057569
def spatialDomainNoGrid(self): """ Superposition of analytical solutions without a gridded domain """ self.w = np.zeros(self.xw.shape) if self.Debug: print("w = ") print(self.w.shape) for i in range(len(self.q)): # More efficient if we have created some 0-load ...	[ "def", "spatialDomainNoGrid", "(", "self", ")", ":", "self", ".", "w", "=", "np", ".", "zeros", "(", "self", ".", "xw", ".", "shape", ")", "if", "self", ".", "Debug", ":", "print", "(", "\"w = \"", ")", "print", "(", "self", ".", "w", ".", "shape...	32.941176	0.017361
def reset (self): """ Reset all variables to default values. """ # self.url is constructed by self.build_url() out of base_url # and (base_ref or parent) as absolute and normed url. # This the real url we use when checking so it also referred to # as 'real url' ...	[ "def", "reset", "(", "self", ")", ":", "# self.url is constructed by self.build_url() out of base_url", "# and (base_ref or parent) as absolute and normed url.", "# This the real url we use when checking so it also referred to", "# as 'real url'", "self", ".", "url", "=", "None", "# a ...	36.395833	0.00223
def __get_WIOD_SEA_extension(root_path, year, data_sheet='DATA'): """ Utility function to get the extension data from the SEA file in WIOD This function is based on the structure in the WIOD_SEA_July14 file. Missing values are set to zero. The function works if the SEA file is either in path or in a s...	[ "def", "__get_WIOD_SEA_extension", "(", "root_path", ",", "year", ",", "data_sheet", "=", "'DATA'", ")", ":", "sea_ext", "=", "'.xlsx'", "sea_start", "=", "'WIOD_SEA'", "_SEA_folder", "=", "os", ".", "path", ".", "join", "(", "root_path", ",", "'SEA'", ")", ...	36.459184	0.000272
def get_log_attrs(): """Get logging attributes from the opencensus context. :rtype: :class:`LogAttrs` :return: The current span's trace ID, span ID, and sampling decision. """ try: tracer = execution_context.get_opencensus_tracer() if tracer is None: raise RuntimeError ...	[ "def", "get_log_attrs", "(", ")", ":", "try", ":", "tracer", "=", "execution_context", ".", "get_opencensus_tracer", "(", ")", "if", "tracer", "is", "None", ":", "raise", "RuntimeError", "except", "Exception", ":", "# noqa", "_meta_logger", ".", "error", "(", ...	34.731707	0.000683
def is_publication_permissible(cursor, publication_id, uuid_): """Check the given publisher of this publication given by ``publication_id`` is allowed to publish the content given by ``uuid``. """ # Check the publishing user has permission to publish cursor.execute("""\ SELECT 't'::boolean FROM ...	[ "def", "is_publication_permissible", "(", "cursor", ",", "publication_id", ",", "uuid_", ")", ":", "# Check the publishing user has permission to publish", "cursor", ".", "execute", "(", "\"\"\"\\\nSELECT 't'::boolean\nFROM\n pending_documents AS pd\n NATURAL JOIN document_acl AS acl...	26.84	0.001439
def create_html_mailto( email, subject=None, body=None, cc=None, bcc=None, link_label="%(email)s", linkattrd=None, escape_urlargd=True, escape_linkattrd=True, email_obfuscation_mode=None): """Creates a W3C compliant 'mailto' link. ...	[ "def", "create_html_mailto", "(", "email", ",", "subject", "=", "None", ",", "body", "=", "None", ",", "cc", "=", "None", ",", "bcc", "=", "None", ",", "link_label", "=", "\"%(email)s\"", ",", "linkattrd", "=", "None", ",", "escape_urlargd", "=", "True",...	38.253731	0.00057
def chown(self, path, uid, gid, dir_fd=None, follow_symlinks=None): """Set ownership of a faked file. Args: path: (str) Path to the file or directory. uid: (int) Numeric uid to set the file or directory to. gid: (int) Numeric gid to set the file or directory to. ...	[ "def", "chown", "(", "self", ",", "path", ",", "uid", ",", "gid", ",", "dir_fd", "=", "None", ",", "follow_symlinks", "=", "None", ")", ":", "if", "follow_symlinks", "is", "None", ":", "follow_symlinks", "=", "True", "elif", "sys", ".", "version_info", ...	42.219512	0.001129
def modify_attribute(self, attribute, value): """ Changes an attribute of this instance :type attribute: string :param attribute: The attribute you wish to change. AttributeName - Expected value (default) instanceType - A valid instanc...	[ "def", "modify_attribute", "(", "self", ",", "attribute", ",", "value", ")", ":", "return", "self", ".", "connection", ".", "modify_instance_attribute", "(", "self", ".", "id", ",", "attribute", ",", "value", ")" ]	43.695652	0.001947
def check_directory(self): """Check if migrations directory exists.""" exists = os.path.exists(self.directory) if not exists: logger.error("No migrations directory found. Check your path or create a migration first.") logger.error("Directory: %s" % self.directory) ...	[ "def", "check_directory", "(", "self", ")", ":", "exists", "=", "os", ".", "path", ".", "exists", "(", "self", ".", "directory", ")", "if", "not", "exists", ":", "logger", ".", "error", "(", "\"No migrations directory found. Check your path or create a migration f...	46.857143	0.008982
def update(self, friendly_name=None, description=None): """ Selectively updates Dataset information. Args: friendly_name: if not None, the new friendly name. description: if not None, the new description. Returns: """ self._get_info() if self._info: if friendly_name: ...	[ "def", "update", "(", "self", ",", "friendly_name", "=", "None", ",", "description", "=", "None", ")", ":", "self", ".", "_get_info", "(", ")", "if", "self", ".", "_info", ":", "if", "friendly_name", ":", "self", ".", "_info", "[", "'friendlyName'", "]...	26.045455	0.010101
def sr(self, multi=0): """sr([multi=1]) -> (SndRcvList, PacketList) Matches packets in the list and return ( (matched couples), (unmatched packets) )""" # noqa: E501 remain = self.res[:] sr = [] i = 0 while i < len(remain): s = remain[i] j = i ...	[ "def", "sr", "(", "self", ",", "multi", "=", "0", ")", ":", "# noqa: E501", "remain", "=", "self", ".", "res", "[", ":", "]", "sr", "=", "[", "]", "i", "=", "0", "while", "i", "<", "len", "(", "remain", ")", ":", "s", "=", "remain", "[", "i...	34.423077	0.002174
def compare(self, reference_classes: List, query_classes: List, method: Optional[SimAlgorithm] = SimAlgorithm.PHENODIGM) -> SimResult: """ Owlsim2 compare, calls compare_attribute_sets, and converts to SimResult object :return: SimResult object ...	[ "def", "compare", "(", "self", ",", "reference_classes", ":", "List", ",", "query_classes", ":", "List", ",", "method", ":", "Optional", "[", "SimAlgorithm", "]", "=", "SimAlgorithm", ".", "PHENODIGM", ")", "->", "SimResult", ":", "owlsim_results", "=", "com...	49.4	0.015905
def file_stat_for_all(self, filters=all_true): # pragma: no cover """ Find out how many files, directories and total size (Include file in it's sub-folder) it has for each folder and sub-folder. :returns: stat, a dict like ``{"directory path": { "file": number of files, "dir"...	[ "def", "file_stat_for_all", "(", "self", ",", "filters", "=", "all_true", ")", ":", "# pragma: no cover", "self", ".", "assert_is_dir_and_exists", "(", ")", "from", "collections", "import", "OrderedDict", "stat", "=", "OrderedDict", "(", ")", "stat", "[", "self"...	28.893617	0.001425
def get_balance(self): """ Get balance with provider. """ if not SMSGLOBAL_CHECK_BALANCE_COUNTRY: raise Exception('SMSGLOBAL_CHECK_BALANCE_COUNTRY setting must be set to check balance.') params = { 'user' : self.get_username(), 'password' ...	[ "def", "get_balance", "(", "self", ")", ":", "if", "not", "SMSGLOBAL_CHECK_BALANCE_COUNTRY", ":", "raise", "Exception", "(", "'SMSGLOBAL_CHECK_BALANCE_COUNTRY setting must be set to check balance.'", ")", "params", "=", "{", "'user'", ":", "self", ".", "get_username", "...	39.714286	0.014052
def cmd(send, msg, args): """Gets stats. Syntax: {command} <--high\|--low\|--userhigh\|--nick <nick>\|command> """ parser = arguments.ArgParser(args['config']) group = parser.add_mutually_exclusive_group() group.add_argument('--high', action='store_true') group.add_argument('--low', action='st...	[ "def", "cmd", "(", "send", ",", "msg", ",", "args", ")", ":", "parser", "=", "arguments", ".", "ArgParser", "(", "args", "[", "'config'", "]", ")", "group", "=", "parser", ".", "add_mutually_exclusive_group", "(", ")", "group", ".", "add_argument", "(", ...	37.74	0.001033
def kp_pan_set(self, viewer, event, data_x, data_y, msg=True): """Sets the pan position under the cursor.""" if self.canpan: self._panset(viewer, data_x, data_y, msg=msg) return True	[ "def", "kp_pan_set", "(", "self", ",", "viewer", ",", "event", ",", "data_x", ",", "data_y", ",", "msg", "=", "True", ")", ":", "if", "self", ".", "canpan", ":", "self", ".", "_panset", "(", "viewer", ",", "data_x", ",", "data_y", ",", "msg", "=", ...	42.8	0.009174
def censor(input_text): """ Returns the input string with profanity replaced with a random string of characters plucked from the censor_characters pool. """ ret = input_text words = get_words() for word in words: curse_word = re.compile(re.escape(word), re.IGNORECASE) cen = "".j...	[ "def", "censor", "(", "input_text", ")", ":", "ret", "=", "input_text", "words", "=", "get_words", "(", ")", "for", "word", "in", "words", ":", "curse_word", "=", "re", ".", "compile", "(", "re", ".", "escape", "(", "word", ")", ",", "re", ".", "IG...	33.75	0.002404
def format_sec(s): """ Format seconds in a more human readable way. It supports units down to nanoseconds. :param s: Float of seconds to format :return: String second representation, like 12.4 us """ prefixes = ["", "m", "u", "n"] unit = 0 while s < 1 and unit + 1 < len(prefixes):...	[ "def", "format_sec", "(", "s", ")", ":", "prefixes", "=", "[", "\"\"", ",", "\"m\"", ",", "\"u\"", ",", "\"n\"", "]", "unit", "=", "0", "while", "s", "<", "1", "and", "unit", "+", "1", "<", "len", "(", "prefixes", ")", ":", "s", "*=", "1000", ...	23	0.002457
def predict_quantiles(self, X, quantiles=(2.5, 97.5), Y_metadata=None, likelihood=None, kern=None): """ Get the predictive quantiles around the prediction at X :param X: The points at which to make a prediction :type X: np.ndarray (Xnew x self.input_dim) :param quantiles: tuple ...	[ "def", "predict_quantiles", "(", "self", ",", "X", ",", "quantiles", "=", "(", "2.5", ",", "97.5", ")", ",", "Y_metadata", "=", "None", ",", "likelihood", "=", "None", ",", "kern", "=", "None", ")", ":", "qs", "=", "super", "(", "WarpedGP", ",", "s...	56.266667	0.008159
def update(self, v): """Add `v` to the hash, recursively if needed.""" self.md5.update(to_bytes(str(type(v)))) if isinstance(v, string_class): self.md5.update(to_bytes(v)) elif v is None: pass elif isinstance(v, (int, float)): self.md5.update(t...	[ "def", "update", "(", "self", ",", "v", ")", ":", "self", ".", "md5", ".", "update", "(", "to_bytes", "(", "str", "(", "type", "(", "v", ")", ")", ")", ")", "if", "isinstance", "(", "v", ",", "string_class", ")", ":", "self", ".", "md5", ".", ...	32.615385	0.002291
def exactly_n(l, n=1): ''' Tests that exactly N items in an iterable are "truthy" (neither None, False, nor 0). ''' i = iter(l) return all(any(i) for j in range(n)) and not any(i)	[ "def", "exactly_n", "(", "l", ",", "n", "=", "1", ")", ":", "i", "=", "iter", "(", "l", ")", "return", "all", "(", "any", "(", "i", ")", "for", "j", "in", "range", "(", "n", ")", ")", "and", "not", "any", "(", "i", ")" ]	28.142857	0.009852
def _get_handler(self, node_id): """Get the handler of a given node.""" handler = self._get_attrs(node_id).get(self.HANDLER, self._default_handler) # Here we make sure the handler is an instance of `BasicNodeHandler` or inherited # types. While generally being bad Python practice, we st...	[ "def", "_get_handler", "(", "self", ",", "node_id", ")", ":", "handler", "=", "self", ".", "_get_attrs", "(", "node_id", ")", ".", "get", "(", "self", ".", "HANDLER", ",", "self", ".", "_default_handler", ")", "# Here we make sure the handler is an instance of `...	55.416667	0.008876
def htmlReadDoc(cur, URL, encoding, options): """parse an XML in-memory document and build a tree. """ ret = libxml2mod.htmlReadDoc(cur, URL, encoding, options) if ret is None:raise treeError('htmlReadDoc() failed') return xmlDoc(_obj=ret)	[ "def", "htmlReadDoc", "(", "cur", ",", "URL", ",", "encoding", ",", "options", ")", ":", "ret", "=", "libxml2mod", ".", "htmlReadDoc", "(", "cur", ",", "URL", ",", "encoding", ",", "options", ")", "if", "ret", "is", "None", ":", "raise", "treeError", ...	50.2	0.011765
def create_binding(site, hostheader='', ipaddress='*', port=80, protocol='http', sslflags=None): ''' Create an IIS Web Binding. .. note:: This function only validates against the binding ipaddress:port:hostheader combination, and will return True even if the bind...	[ "def", "create_binding", "(", "site", ",", "hostheader", "=", "''", ",", "ipaddress", "=", "'*'", ",", "port", "=", "80", ",", "protocol", "=", "'http'", ",", "sslflags", "=", "None", ")", ":", "protocol", "=", "six", ".", "text_type", "(", "protocol",...	36.025	0.001689
def set_params(self, **params): """Set parameters on this object Safe setter method - attributes should not be modified directly as some changes are not valid. Valid parameters: - n_jobs - random_state - verbose Invalid parameters: (these would require mo...	[ "def", "set_params", "(", "self", ",", "", "", "params", ")", ":", "if", "'knn'", "in", "params", "and", "params", "[", "'knn'", "]", "!=", "self", ".", "knn", ":", "raise", "ValueError", "(", "\"Cannot update knn. Please create a new graph\"", ")", "if", ...	38.792453	0.000949

def parse(raw_email): # type: (six.string_types) -> Tuple[six.string_types, six.string_types] """Extract email from a full address. Example: 'John Doe <jdoe+github@foo.com>' -> jdoe@foo.com >>> parse("John Doe <me+github.com@someorg.com") ('me', 'someorg.com') >>> parse(42) # doctest: +IGNOR...

[ "def", "parse", "(", "raw_email", ")", ":", "# type: (six.string_types) -> Tuple[six.string_types, six.string_types]", "if", "not", "isinstance", "(", "raw_email", ",", "six", ".", "string_types", ")", ":", "raise", "InvalidEmail", "(", "\"Invalid email: %s\"", "%", "ra...

40.533333

0.000803

def create_todo_item(self, list_id, content, party_id=None, notify=False): """ This call lets you add an item to an existing list. The item is added to the bottom of the list. If a person is responsible for the item, give their id as the party_id value. If a company is responsible, ...

[ "def", "create_todo_item", "(", "self", ",", "list_id", ",", "content", ",", "party_id", "=", "None", ",", "notify", "=", "False", ")", ":", "path", "=", "'/todos/create_item/%u'", "%", "list_id", "req", "=", "ET", ".", "Element", "(", "'request'", ")", ...

55.764706

0.002075

def _build_showstr(self, seed): """ Returns show() display string for data attribute """ output = ["%s (%s) data" % (seed, self.params['lang'])] output.append('{') maxwidth = WPToolsQuery.MAXWIDTH for item in sorted(self.data): if self.data[item] i...

[ "def", "_build_showstr", "(", "self", ",", "seed", ")", ":", "output", "=", "[", "\"%s (%s) data\"", "%", "(", "seed", ",", "self", ".", "params", "[", "'lang'", "]", ")", "]", "output", ".", "append", "(", "'{'", ")", "maxwidth", "=", "WPToolsQuery", ...

33.627907

0.001344

def bam_to_fastq_pair(in_file, target_region, pair): """Generator to convert BAM files into name, seq, qual in a region. """ space, start, end = target_region bam_file = pysam.Samfile(in_file, "rb") for read in bam_file: if (not read.is_unmapped and not read.mate_is_unmapped ...

[ "def", "bam_to_fastq_pair", "(", "in_file", ",", "target_region", ",", "pair", ")", ":", "space", ",", "start", ",", "end", "=", "target_region", "bam_file", "=", "pysam", ".", "Samfile", "(", "in_file", ",", "\"rb\"", ")", "for", "read", "in", "bam_file",...

45.789474

0.001126

def make_app(global_conf, **app_conf): """Create a WSGI application and return it ``global_conf`` The inherited configuration for this application. Normally from the [DEFAULT] section of the Paste ini file. ``app_conf`` The application's local configuration. Normally specified in ...

[ "def", "make_app", "(", "global_conf", ",", "*", "*", "app_conf", ")", ":", "# Configure the environment and fill conf dictionary.", "environment", ".", "load_environment", "(", "global_conf", ",", "app_conf", ")", "# Dispatch request to controllers.", "app", "=", "contro...

34.369565

0.001845

def get_object_stats(self, obj_name): """ :param obj_name: requested object name :returns: all statistics values for the requested object. """ return dict(zip(self.captions, self.statistics[obj_name]))

[ "def", "get_object_stats", "(", "self", ",", "obj_name", ")", ":", "return", "dict", "(", "zip", "(", "self", ".", "captions", ",", "self", ".", "statistics", "[", "obj_name", "]", ")", ")" ]

33.714286

0.008264

def fix_double_nodes(coor, ngroups, conns, eps): """ Detect and attempt fixing double nodes in a mesh. The double nodes are nodes having the same coordinates w.r.t. precision given by `eps`. """ n_nod, dim = coor.shape cmap = find_map( coor, nm.zeros( (0,dim) ), eps = eps, allow_double = Tr...

[ "def", "fix_double_nodes", "(", "coor", ",", "ngroups", ",", "conns", ",", "eps", ")", ":", "n_nod", ",", "dim", "=", "coor", ".", "shape", "cmap", "=", "find_map", "(", "coor", ",", "nm", ".", "zeros", "(", "(", "0", ",", "dim", ")", ")", ",", ...

31.789474

0.026506

def generate_dirlist_html(FS, filepath): """ Generate directory listing HTML Arguments: FS (FS): filesystem object to read files from filepath (str): path to generate directory listings for Keyword Arguments: list_dir (callable: list[str]): list file names in a directory ...

[ "def", "generate_dirlist_html", "(", "FS", ",", "filepath", ")", ":", "yield", "'<table class=\"dirlist\">'", "if", "filepath", "==", "'/'", ":", "filepath", "=", "''", "for", "name", "in", "FS", ".", "listdir", "(", "filepath", ")", ":", "full_path", "=", ...

30.48

0.001272

def log_exception(cls, msg): """Try to log an error message to this process's error log and the shared error log. NB: Doesn't raise (logs an error instead). """ pid = os.getpid() fatal_error_log_entry = cls._format_exception_message(msg, pid) # We care more about this log than the shared log, ...

[ "def", "log_exception", "(", "cls", ",", "msg", ")", ":", "pid", "=", "os", ".", "getpid", "(", ")", "fatal_error_log_entry", "=", "cls", ".", "_format_exception_message", "(", "msg", ",", "pid", ")", "# We care more about this log than the shared log, so write to i...

40.96

0.012405

def set_storage_container_acl(kwargs=None, storage_conn=None, call=None): ''' .. versionadded:: 2015.8.0 Set a storage container's acl CLI Example: .. code-block:: bash salt-cloud -f set_storage_container my-azure name=mycontainer name: Name of existing container. signed...

[ "def", "set_storage_container_acl", "(", "kwargs", "=", "None", ",", "storage_conn", "=", "None", ",", "call", "=", "None", ")", ":", "if", "call", "!=", "'function'", ":", "raise", "SaltCloudSystemExit", "(", "'The create_storage_container function must be called wit...

32.275

0.001504

def _render_table(data, fields=None): """ Helper to render a list of dictionaries as an HTML display object. """ return IPython.core.display.HTML(datalab.utils.commands.HtmlBuilder.render_table(data, fields))

[ "def", "_render_table", "(", "data", ",", "fields", "=", "None", ")", ":", "return", "IPython", ".", "core", ".", "display", ".", "HTML", "(", "datalab", ".", "utils", ".", "commands", ".", "HtmlBuilder", ".", "render_table", "(", "data", ",", "fields", ...

70

0.018868

def clear(self): """ 直接把现在的清空 """ if not self.timer: return # 不阻塞 try: self.timer.kill(block=False) except: pass self.timer = None

[ "def", "clear", "(", "self", ")", ":", "if", "not", "self", ".", "timer", ":", "return", "# 不阻塞", "try", ":", "self", ".", "timer", ".", "kill", "(", "block", "=", "False", ")", "except", ":", "pass", "self", ".", "timer", "=", "None" ]

16.846154

0.012987

def startswith(self, value): """ Sets the operator type to Query.Op.Startswith and sets \ the value to the inputted value. This method will only work on text \ based fields. :param value <str> :return <Query> :usage ...

[ "def", "startswith", "(", "self", ",", "value", ")", ":", "newq", "=", "self", ".", "copy", "(", ")", "newq", ".", "setOp", "(", "Query", ".", "Op", ".", "Startswith", ")", "newq", ".", "setValue", "(", "value", ")", "return", "newq" ]

31.684211

0.008065

def update_one(self, filter, update, upsert=False, bypass_document_validation=False, collation=None, array_filters=None, session=None): """Update a single document matching the filter. >>> for doc in db.test.find(): ... print(doc) ... ...

[ "def", "update_one", "(", "self", ",", "filter", ",", "update", ",", "upsert", "=", "False", ",", "bypass_document_validation", "=", "False", ",", "collation", "=", "None", ",", "array_filters", "=", "None", ",", "session", "=", "None", ")", ":", "common",...

37.507246

0.001883

def createNetwork(dataSource): """Create the Network instance. The network has a sensor region reading data from `dataSource` and passing the encoded representation to an Identity Region. :param dataSource: a RecordStream instance to get data from :returns: a Network instance ready to run """ network = ...

[ "def", "createNetwork", "(", "dataSource", ")", ":", "network", "=", "Network", "(", ")", "# Our input is sensor data from the gym file. The RecordSensor region", "# allows us to specify a file record stream as the input source via the", "# dataSource attribute.", "network", ".", "ad...

35.978723

0.016695

def readFILTERLIST(self): """ Read a length-prefixed list of FILTERs """ number = self.readUI8() return [self.readFILTER() for _ in range(number)]

[ "def", "readFILTERLIST", "(", "self", ")", ":", "number", "=", "self", ".", "readUI8", "(", ")", "return", "[", "self", ".", "readFILTER", "(", ")", "for", "_", "in", "range", "(", "number", ")", "]" ]

41.75

0.011765

def fileUpd(self, buffer=None, filename=None, ufilename=None, desc=None): """Update annotation attached file.""" CheckParent(self) return _fitz.Annot_fileUpd(self, buffer, filename, ufilename, desc)

[ "def", "fileUpd", "(", "self", ",", "buffer", "=", "None", ",", "filename", "=", "None", ",", "ufilename", "=", "None", ",", "desc", "=", "None", ")", ":", "CheckParent", "(", "self", ")", "return", "_fitz", ".", "Annot_fileUpd", "(", "self", ",", "b...

31.285714

0.013333

def keyevent_to_keyseq(self, event): """Return a QKeySequence representation of the provided QKeyEvent.""" self.keyPressEvent(event) event.accept() return self.keySequence()

[ "def", "keyevent_to_keyseq", "(", "self", ",", "event", ")", ":", "self", ".", "keyPressEvent", "(", "event", ")", "event", ".", "accept", "(", ")", "return", "self", ".", "keySequence", "(", ")" ]

41

0.009569

def get_branch_info(self): """ Retrieve branch_info from Satellite Server """ branch_info = None if os.path.exists(constants.cached_branch_info): # use cached branch info file if less than 10 minutes old # (failsafe, should be deleted at end of client run...

[ "def", "get_branch_info", "(", "self", ")", ":", "branch_info", "=", "None", "if", "os", ".", "path", ".", "exists", "(", "constants", ".", "cached_branch_info", ")", ":", "# use cached branch info file if less than 10 minutes old", "# (failsafe, should be deleted at end...

47.688889

0.002283

def as_list(func): """ A decorator used to return a JSON response of a list of model objects. It expects the decorated function to return a list of model instances. It then converts the instances to dicts and serializes them into a json response Examples: >>> @app.route...

[ "def", "as_list", "(", "func", ")", ":", "@", "wraps", "(", "func", ")", "def", "wrapper", "(", "*", "args", ",", "*", "*", "kwargs", ")", ":", "response", "=", "func", "(", "*", "args", ",", "*", "*", "kwargs", ")", "if", "isinstance", "(", "r...

31.434783

0.001342

def make_spo(sub, prd, obj): ''' Decorates the three given strings as a line of ntriples ''' # To establish string as a curie and expand, # we use a global curie_map(.yaml) # sub are allways uri (unless a bnode) # prd are allways uri (unless prd is 'a') # should fail loudly if curie do...

[ "def", "make_spo", "(", "sub", ",", "prd", ",", "obj", ")", ":", "# To establish string as a curie and expand,", "# we use a global curie_map(.yaml)", "# sub are allways uri (unless a bnode)", "# prd are allways uri (unless prd is 'a')", "# should fail loudly if curie does not exist", ...

32.806452

0.000955

def xmlrpc_run(self, port=24444, bind='127.0.0.1', logRequests=False): '''Run xmlrpc server''' import umsgpack from pyspider.libs.wsgi_xmlrpc import WSGIXMLRPCApplication try: from xmlrpc.client import Binary except ImportError: from xmlrpclib import Binar...

[ "def", "xmlrpc_run", "(", "self", ",", "port", "=", "24444", ",", "bind", "=", "'127.0.0.1'", ",", "logRequests", "=", "False", ")", ":", "import", "umsgpack", "from", "pyspider", ".", "libs", ".", "wsgi_xmlrpc", "import", "WSGIXMLRPCApplication", "try", ":"...

37.558824

0.00229

def _ml_t_joint(self): """ Compute the joint maximum likelihood assignment of the internal nodes positions by propagating from the tree leaves towards the root. Given the assignment of parent nodes, reconstruct the maximum-likelihood positions of the child nodes by propagating fr...

[ "def", "_ml_t_joint", "(", "self", ")", ":", "def", "_cleanup", "(", ")", ":", "for", "node", "in", "self", ".", "tree", ".", "find_clades", "(", ")", ":", "del", "node", ".", "joint_pos_Lx", "del", "node", ".", "joint_pos_Cx", "self", ".", "logger", ...

56.191304

0.010189

def rules(self, x, y): # type: (int, int) -> List[Type[Rule]] """ Get rules at specific position in the structure. :param x: X coordinate :param y: Y coordinate :return: List of rules """ return [r for r in self._field[y][x]]

[ "def", "rules", "(", "self", ",", "x", ",", "y", ")", ":", "# type: (int, int) -> List[Type[Rule]]", "return", "[", "r", "for", "r", "in", "self", ".", "_field", "[", "y", "]", "[", "x", "]", "]" ]

31.222222

0.010381

def _reset(self): """ Reset the Screen. """ self._last_start_line = 0 self._colour = None self._attr = None self._bg = None self._cur_x = None self._cur_y = None

[ "def", "_reset", "(", "self", ")", ":", "self", ".", "_last_start_line", "=", "0", "self", ".", "_colour", "=", "None", "self", ".", "_attr", "=", "None", "self", ".", "_bg", "=", "None", "self", ".", "_cur_x", "=", "None", "self", ".", "_cur_y", "...

22.4

0.008584

def plot_elements_to_ax(self, cid, ax=None, **kwargs): """Plot element data (parameter sets). If the parameter *ax* is not set, then a new figure will be created with a corresponding axes. Parameters ---------- cid : int or :py:class:`numpy.ndarray` if *cid...

[ "def", "plot_elements_to_ax", "(", "self", ",", "cid", ",", "ax", "=", "None", ",", "*", "*", "kwargs", ")", ":", "rasterize", "=", "kwargs", ".", "get", "(", "'rasterize'", ",", "False", ")", "xmin", "=", "kwargs", ".", "get", "(", "'xmin'", ",", ...

34.210526

0.000272

def _render(self, value, format): """ Writes javascript to call momentjs function """ template = '<script>\ndocument.write(moment(\"{t}\").{f});\n</script>' return Markup(template.format(t=value, f=format))

[ "def", "_render", "(", "self", ",", "value", ",", "format", ")", ":", "template", "=", "'<script>\\ndocument.write(moment(\\\"{t}\\\").{f});\\n</script>'", "return", "Markup", "(", "template", ".", "format", "(", "t", "=", "value", ",", "f", "=", "format", ")", ...

56.75

0.008696

def _get_ipmitool_path(self, cmd='ipmitool'): """Get full path to the ipmitool command using the unix `which` command """ p = subprocess.Popen(["which", cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = p.communicate() return o...

[ "def", "_get_ipmitool_path", "(", "self", ",", "cmd", "=", "'ipmitool'", ")", ":", "p", "=", "subprocess", ".", "Popen", "(", "[", "\"which\"", ",", "cmd", "]", ",", "stdout", "=", "subprocess", ".", "PIPE", ",", "stderr", "=", "subprocess", ".", "PIPE...

40.375

0.018182

def render(jinja_template_text=None, jinja_template_function='highstate_doc.markdown_default_jinja_template', **kwargs): ''' Render highstate to a text format (default Markdown) if `jinja_template_text` is not set, `jinja_template_function` is used. jinja_template_text: jinja text that the render uses...

[ "def", "render", "(", "jinja_template_text", "=", "None", ",", "jinja_template_function", "=", "'highstate_doc.markdown_default_jinja_template'", ",", "*", "*", "kwargs", ")", ":", "config", "=", "_get_config", "(", "*", "*", "kwargs", ")", "lowstates", "=", "proc...

37.342105

0.00206

def ctype_for_encoding(self, encoding): """Return ctypes type for an encoded Objective-C type.""" if encoding in self.typecodes: return self.typecodes[encoding] elif encoding[0:1] == b'^' and encoding[1:] in self.typecodes: return POINTER(self.typecodes[encoding[1:]]) ...

[ "def", "ctype_for_encoding", "(", "self", ",", "encoding", ")", ":", "if", "encoding", "in", "self", ".", "typecodes", ":", "return", "self", ".", "typecodes", "[", "encoding", "]", "elif", "encoding", "[", "0", ":", "1", "]", "==", "b'^'", "and", "enc...

53

0.002317

def matrix_to_points(matrix, pitch, origin): """ Convert an (n,m,p) matrix into a set of points for each voxel center. Parameters ----------- matrix: (n,m,p) bool, voxel matrix pitch: float, what pitch was the voxel matrix computed with origin: (3,) float, what is the origin of the voxel ma...

[ "def", "matrix_to_points", "(", "matrix", ",", "pitch", ",", "origin", ")", ":", "indices", "=", "np", ".", "column_stack", "(", "np", ".", "nonzero", "(", "matrix", ")", ")", "points", "=", "indices_to_points", "(", "indices", "=", "indices", ",", "pitc...

30.631579

0.001667

def parse_fqscreen(self, f): """ Parse the FastQ Screen output into a 3D dict """ parsed_data = OrderedDict() reads_processed = None nohits_pct = None for l in f['f']: if l.startswith('%Hit_no_genomes:') or l.startswith('%Hit_no_libraries:'): nohits_pc...

[ "def", "parse_fqscreen", "(", "self", ",", "f", ")", ":", "parsed_data", "=", "OrderedDict", "(", ")", "reads_processed", "=", "None", "nohits_pct", "=", "None", "for", "l", "in", "f", "[", "'f'", "]", ":", "if", "l", ".", "startswith", "(", "'%Hit_no_...

61.625

0.009185

def _get_variants(data): """Retrieve variants from CWL and standard inputs for organizing variants. """ active_vs = [] if "variants" in data: variants = data["variants"] # CWL based list of variants if isinstance(variants, dict) and "samples" in variants: variants = v...

[ "def", "_get_variants", "(", "data", ")", ":", "active_vs", "=", "[", "]", "if", "\"variants\"", "in", "data", ":", "variants", "=", "data", "[", "\"variants\"", "]", "# CWL based list of variants", "if", "isinstance", "(", "variants", ",", "dict", ")", "and...

45.115385

0.000835

def equivalent_to(self, token): """ Gets all tokens which match the character and scopes of a reference token :param token: :class:`esi.models.Token` :return: :class:`esi.managers.TokenQueryset` """ return self.filter(character_id=token.character_id).require_scopes_exact(...

[ "def", "equivalent_to", "(", "self", ",", "token", ")", ":", "return", "self", ".", "filter", "(", "character_id", "=", "token", ".", "character_id", ")", ".", "require_scopes_exact", "(", "token", ".", "scopes", ".", "all", "(", ")", ")", ".", "filter",...

53.75

0.011442

def main(): """ Command-line processor. See ``--help`` for details. """ main_only_quicksetup_rootlogger(level=logging.DEBUG) parser = argparse.ArgumentParser() parser.add_argument( "--mysql", default="mysql", help="MySQL program (default=mysql)") parser.add_argument( ...

[ "def", "main", "(", ")", ":", "main_only_quicksetup_rootlogger", "(", "level", "=", "logging", ".", "DEBUG", ")", "parser", "=", "argparse", ".", "ArgumentParser", "(", ")", "parser", ".", "add_argument", "(", "\"--mysql\"", ",", "default", "=", "\"mysql\"", ...

38.532468

0.000329

def srp1(*args,**kargs): """Send and receive packets at layer 2 and return only the first answer nofilter: put 1 to avoid use of bpf filters retry: if positive, how many times to resend unanswered packets if negative, how many times to retry when no more packets are answered timeout: how much time to ...

[ "def", "srp1", "(", "*", "args", ",", "*", "*", "kargs", ")", ":", "if", "not", "\"timeout\"", "in", "kargs", ":", "kargs", "[", "\"timeout\"", "]", "=", "-", "1", "a", ",", "b", "=", "srp", "(", "*", "args", ",", "*", "*", "kargs", ")", "if"...

39.882353

0.010086

def prep_bam_inputs(out_dir, sample, call_file, bam_file): """Prepare expected input BAM files from pre-aligned. """ base = utils.splitext_plus(os.path.basename(bam_file))[0] with open(call_file) as in_handle: for cur_hla in (x.strip() for x in in_handle): out_file = os.path.join(uti...

[ "def", "prep_bam_inputs", "(", "out_dir", ",", "sample", ",", "call_file", ",", "bam_file", ")", ":", "base", "=", "utils", ".", "splitext_plus", "(", "os", ".", "path", ".", "basename", "(", "bam_file", ")", ")", "[", "0", "]", "with", "open", "(", ...

55.181818

0.008104

def comparator(objective): """ Higher order function creating a compare function for objectives. Args: objective (cipy.algorithms.core.Objective): The objective to create a compare for. Returns: callable: Function accepting two objectives to compare. Examples: ...

[ "def", "comparator", "(", "objective", ")", ":", "if", "isinstance", "(", "objective", ",", "Minimum", ")", ":", "return", "lambda", "l", ",", "r", ":", "l", "<", "r", "else", ":", "return", "lambda", "l", ",", "r", ":", "l", ">", "r" ]

25.318182

0.00173

def detect_anomaly(self): """ Detect anomalies in the timeseries data for the submetrics specified in the config file. Identified anomalies are stored in self.anomalies as well as written to .anomalies.csv file to be used by the client charting page. Anomaly detection uses the luminol library (http://py...

[ "def", "detect_anomaly", "(", "self", ")", ":", "if", "not", "self", ".", "anomaly_detection_metrics", "or", "len", "(", "self", ".", "anomaly_detection_metrics", ")", "<=", "0", ":", "return", "for", "submetric", "in", "self", ".", "anomaly_detection_metrics", ...

54.857143

0.009386

def listen_many(*rooms): """Listen for changes in all registered listeners in all specified rooms""" rooms = set(r.conn for r in rooms) for room in rooms: room.validate_listeners() with ARBITRATOR.condition: while any(r.connected for r in rooms): ARBITRATOR.condition.wait() ...

[ "def", "listen_many", "(", "*", "rooms", ")", ":", "rooms", "=", "set", "(", "r", ".", "conn", "for", "r", "in", "rooms", ")", "for", "room", "in", "rooms", ":", "room", ".", "validate_listeners", "(", ")", "with", "ARBITRATOR", ".", "condition", ":"...

34.5

0.002353

def _make_chunk_size(self, req_size): """ Takes an allocation size as requested by the user and modifies it to be a suitable chunk size. """ size = req_size size += 2 * self._chunk_size_t_size # Two size fields size = self._chunk_min_size if size < self._chunk_min_size e...

[ "def", "_make_chunk_size", "(", "self", ",", "req_size", ")", ":", "size", "=", "req_size", "size", "+=", "2", "*", "self", ".", "_chunk_size_t_size", "# Two size fields", "size", "=", "self", ".", "_chunk_min_size", "if", "size", "<", "self", ".", "_chunk_m...

54.8

0.008977

def build_response( self, request, response, from_cache=False, cacheable_methods=None ): """ Build a response by making a request or using the cache. This will end up calling send and returning a potentially cached response """ cacheable = cacheable_methods o...

[ "def", "build_response", "(", "self", ",", "request", ",", "response", ",", "from_cache", "=", "False", ",", "cacheable_methods", "=", "None", ")", ":", "cacheable", "=", "cacheable_methods", "or", "self", ".", "cacheable_methods", "if", "not", "from_cache", "...

40.09589

0.001334

def decode_example(self, tfexample_data): """See base class for details.""" # TODO(epot): Support dynamic shape if self.shape.count(None) < 2: # Restore the shape if possible. TF Example flattened it. shape = [-1 if i is None else i for i in self.shape] tfexample_data = tf.reshape(tfexampl...

[ "def", "decode_example", "(", "self", ",", "tfexample_data", ")", ":", "# TODO(epot): Support dynamic shape", "if", "self", ".", "shape", ".", "count", "(", "None", ")", "<", "2", ":", "# Restore the shape if possible. TF Example flattened it.", "shape", "=", "[", "...

46

0.010661

def detect_language(index_page): """ Detect `languages` using `langdetect` library. Args: index_page (str): HTML content of the page you wish to analyze. Returns: obj: One :class:`.SourceString` object. """ dom = dhtmlparser.parseString(index_page) clean_content = dhtmlpar...

[ "def", "detect_language", "(", "index_page", ")", ":", "dom", "=", "dhtmlparser", ".", "parseString", "(", "index_page", ")", "clean_content", "=", "dhtmlparser", ".", "removeTags", "(", "dom", ")", "lang", "=", "None", "try", ":", "lang", "=", "langdetect",...

23.291667

0.001718

def at_index(iterable, index): # type: (Iterable[T], int) -> T """" Return the item at the index of this iterable or raises IndexError. WARNING: this will consume generators. Negative indices are allowed but be aware they will cause n items to be held in memory, where n = abs(index) ...

[ "def", "at_index", "(", "iterable", ",", "index", ")", ":", "# type: (Iterable[T], int) -> T", "try", ":", "if", "index", "<", "0", ":", "return", "deque", "(", "iterable", ",", "maxlen", "=", "abs", "(", "index", ")", ")", ".", "popleft", "(", ")", "r...

36.625

0.001664

def _init_add_goid_alt(self): ''' Add alternate GO IDs to term counts. ''' # Fill aspect_counts. Find alternate GO IDs that may not be on gocnts goid_alts = set() go2cnt_add = {} aspect_counts = self.aspect_counts gocnts = self.gocnts go2obj = ...

[ "def", "_init_add_goid_alt", "(", "self", ")", ":", "# Fill aspect_counts. Find alternate GO IDs that may not be on gocnts", "goid_alts", "=", "set", "(", ")", "go2cnt_add", "=", "{", "}", "aspect_counts", "=", "self", ".", "aspect_counts", "gocnts", "=", "self", ".",...

41.793103

0.002419

def is_worktree(cwd, user=None, password=None, output_encoding=None): ''' .. versionadded:: 2015.8.0 This function will attempt to determine if ``cwd`` is part of a worktree by checking its ``.git`` to see if it is a file containing a reference to ano...

[ "def", "is_worktree", "(", "cwd", ",", "user", "=", "None", ",", "password", "=", "None", ",", "output_encoding", "=", "None", ")", ":", "cwd", "=", "_expand_path", "(", "cwd", ",", "user", ")", "try", ":", "toplevel", "=", "_get_toplevel", "(", "cwd",...

33.771429

0.000411

def crop_frequencies(self, low=None, high=None, copy=False): """Crop this `Spectrogram` to the specified frequencies Parameters ---------- low : `float` lower frequency bound for cropped `Spectrogram` high : `float` upper frequency bound for cropped `Spec...

[ "def", "crop_frequencies", "(", "self", ",", "low", "=", "None", ",", "high", "=", "None", ",", "copy", "=", "False", ")", ":", "if", "low", "is", "not", "None", ":", "low", "=", "units", ".", "Quantity", "(", "low", ",", "self", ".", "_default_yun...

38.254902

0.001

def account(self, id): """Get :py:class:`ofxclient.Account` by section id""" if self.parser.has_section(id): return self._section_to_account(id) return None

[ "def", "account", "(", "self", ",", "id", ")", ":", "if", "self", ".", "parser", ".", "has_section", "(", "id", ")", ":", "return", "self", ".", "_section_to_account", "(", "id", ")", "return", "None" ]

37.6

0.010417

def clean(input_string, tag_dictionary=constants.SUPPORTED_TAGS): """ Sanitizes HTML. Tags not contained as keys in the tag_dictionary input are removed, and child nodes are recursively moved to parent of removed node. Attributes not contained as arguments in tag_dictionary are removed. Do...

[ "def", "clean", "(", "input_string", ",", "tag_dictionary", "=", "constants", ".", "SUPPORTED_TAGS", ")", ":", "try", ":", "assert", "isinstance", "(", "input_string", ",", "basestring", ")", "except", "AssertionError", ":", "raise", "TypeError", "root", "=", ...

45.590164

0.002464

def save(self, filehandle, destination=None, metadata=None, validate=True, catch_all_errors=False, *args, **kwargs): """Saves the filehandle to the provided destination or the attached default destination. Allows passing arbitrary positional and keyword arguments to the saving mecha...

[ "def", "save", "(", "self", ",", "filehandle", ",", "destination", "=", "None", ",", "metadata", "=", "None", ",", "validate", "=", "True", ",", "catch_all_errors", "=", "False", ",", "*", "args", ",", "*", "*", "kwargs", ")", ":", "destination", "=", ...

45.617647

0.001894

def _serialize(self, value, ct): """Auto-serialization of the value based upon the content-type value. :param any value: The value to serialize :param ietfparse.: The content type to serialize :rtype: str :raises: ValueError """ key = '{}/{}'.format(ct.content_t...

[ "def", "_serialize", "(", "self", ",", "value", ",", "ct", ")", ":", "key", "=", "'{}/{}'", ".", "format", "(", "ct", ".", "content_type", ",", "ct", ".", "content_subtype", ")", "if", "key", "not", "in", "self", ".", "_SERIALIZATION_MAP", ":", "raise"...

44.578947

0.002312

def do_photometry(self, image, init_guesses=None): """ Perform PSF photometry in ``image``. This method assumes that ``psf_model`` has centroids and flux parameters which will be fitted to the data provided in ``image``. A compound model, in fact a sum of ``psf_model``, ...

[ "def", "do_photometry", "(", "self", ",", "image", ",", "init_guesses", "=", "None", ")", ":", "if", "self", ".", "bkg_estimator", "is", "not", "None", ":", "image", "=", "image", "-", "self", ".", "bkg_estimator", "(", "image", ")", "if", "self", ".",...

48.233645

0.00057

def set_mode(self, mode): """ Set *Vim* mode to ``mode``. Supported modes: * ``normal`` * ``insert`` * ``command`` * ``visual`` * ``visual-block`` This method behave as setter-only property. Example: >>> import headlessvim ...

[ "def", "set_mode", "(", "self", ",", "mode", ")", ":", "keys", "=", "'\\033\\033'", "if", "mode", "==", "'normal'", ":", "pass", "elif", "mode", "==", "'insert'", ":", "keys", "+=", "'i'", "elif", "mode", "==", "'command'", ":", "keys", "+=", "':'", ...

24.794872

0.00199

def _decay(): """L2 weight decay loss.""" costs = [] for var in tf.trainable_variables(): if var.op.name.find('DW') > 0: costs.append(tf.nn.l2_loss(var)) return tf.add_n(costs)

[ "def", "_decay", "(", ")", ":", "costs", "=", "[", "]", "for", "var", "in", "tf", ".", "trainable_variables", "(", ")", ":", "if", "var", ".", "op", ".", "name", ".", "find", "(", "'DW'", ")", ">", "0", ":", "costs", ".", "append", "(", "tf", ...

26.857143

0.030928

def stop_server(self): """ Stop serving """ if self.api_server is not None: try: self.api_server.socket.shutdown(socket.SHUT_RDWR) except: log.warning("Failed to shut down API server socket") self.api_server.shutdown()

[ "def", "stop_server", "(", "self", ")", ":", "if", "self", ".", "api_server", "is", "not", "None", ":", "try", ":", "self", ".", "api_server", ".", "socket", ".", "shutdown", "(", "socket", ".", "SHUT_RDWR", ")", "except", ":", "log", ".", "warning", ...

28.090909

0.009404

def separate_resources(self): # type: () -> None """Move contents of resources key in internal dictionary into self.resources Returns: None """ self._separate_hdxobjects(self.resources, 'resources', 'name', hdx.data.resource.Resource)

[ "def", "separate_resources", "(", "self", ")", ":", "# type: () -> None", "self", ".", "_separate_hdxobjects", "(", "self", ".", "resources", ",", "'resources'", ",", "'name'", ",", "hdx", ".", "data", ".", "resource", ".", "Resource", ")" ]

35

0.017422

def add_classification_events(obj, events, labels, signal_label=None, weights=None, test=False): """Add classification events to a TMVA::Factory or TMVA::DataLoader from NumPy arrays. Parameters ---------- obj : TMVA::Factory or TMVA::DataLoader A TMVA::Factory or ...

[ "def", "add_classification_events", "(", "obj", ",", "events", ",", "labels", ",", "signal_label", "=", "None", ",", "weights", "=", "None", ",", "test", "=", "False", ")", ":", "if", "NEW_TMVA_API", ":", "# pragma: no cover", "if", "not", "isinstance", "(",...

45.058824

0.000766

def rank(matrix, atol=1e-13, rtol=0): """ Estimate the rank, i.e., the dimension of the column space, of a matrix. The algorithm used by this function is based on the singular value decomposition of `stoichiometry_matrix`. Parameters ---------- matrix : ndarray The matrix should be...

[ "def", "rank", "(", "matrix", ",", "atol", "=", "1e-13", ",", "rtol", "=", "0", ")", ":", "matrix", "=", "np", ".", "atleast_2d", "(", "matrix", ")", "sigma", "=", "svd", "(", "matrix", ",", "compute_uv", "=", "False", ")", "tol", "=", "max", "("...

30.533333

0.000705

def progress(self): """ Deal with next token Used to create, fillout and end groups and singles As well as just append everything else """ tokenum, value, scol = self.current.values() # Default to not appending anything just_append = False ...

[ "def", "progress", "(", "self", ")", ":", "tokenum", ",", "value", ",", "scol", "=", "self", ".", "current", ".", "values", "(", ")", "# Default to not appending anything", "just_append", "=", "False", "# Prevent from group having automatic pass given to it", "# If it...

37.10101

0.001856

def get_tan_media(self, media_type = TANMediaType2.ALL, media_class = TANMediaClass4.ALL): """Get information about TAN lists/generators. Returns tuple of fints.formals.TANUsageOption and a list of fints.formals.TANMedia4 or fints.formals.TANMedia5 objects.""" with self._get_dialog() as dialog...

[ "def", "get_tan_media", "(", "self", ",", "media_type", "=", "TANMediaType2", ".", "ALL", ",", "media_class", "=", "TANMediaClass4", ".", "ALL", ")", ":", "with", "self", ".", "_get_dialog", "(", ")", "as", "dialog", ":", "hktab", "=", "self", ".", "_fin...

40.882353

0.016878

def quick_doc(request_data): """ Worker that returns the documentation of the symbol under cursor. """ code = request_data['code'] line = request_data['line'] + 1 column = request_data['column'] path = request_data['path'] # encoding = 'utf-8' encoding = 'utf-8' script = jedi.Scr...

[ "def", "quick_doc", "(", "request_data", ")", ":", "code", "=", "request_data", "[", "'code'", "]", "line", "=", "request_data", "[", "'line'", "]", "+", "1", "column", "=", "request_data", "[", "'column'", "]", "path", "=", "request_data", "[", "'path'", ...

29.777778

0.001808

def jenkins_request_with_headers(jenkins_server, req): """ We need to get the headers in addition to the body answer to get the location from them This function uses jenkins_request method from python-jenkins library with just the return call changed :param jenkins_server: The server to query ...

[ "def", "jenkins_request_with_headers", "(", "jenkins_server", ",", "req", ")", ":", "try", ":", "response", "=", "jenkins_server", ".", "jenkins_request", "(", "req", ")", "response_body", "=", "response", ".", "content", "response_headers", "=", "response", ".", ...

43.934783

0.001452

def align_circulation_with_z(self, circulation=None): """ If the input orbit is a tube orbit, this function aligns the circulation axis with the z axis and returns a copy. Parameters ---------- circulation : array_like (optional) Array of bits that specify th...

[ "def", "align_circulation_with_z", "(", "self", ",", "circulation", "=", "None", ")", ":", "if", "circulation", "is", "None", ":", "circulation", "=", "self", ".", "circulation", "(", ")", "circulation", "=", "atleast_2d", "(", "circulation", ",", "insert_axis...

36.338235

0.011032

def correct_rytov_output(radius, sphere_index, medium_index, radius_sampling): r"""Error-correction of refractive index and radius for Rytov This method corrects the fitting results for `radius` :math:`r_\text{Ryt}` and `sphere_index` :math:`n_\text{Ryt}` obtained using :func:`qpsphere.models.rytov` us...

[ "def", "correct_rytov_output", "(", "radius", ",", "sphere_index", ",", "medium_index", ",", "radius_sampling", ")", ":", "params", "=", "get_params", "(", "radius_sampling", ")", "x", "=", "sphere_index", "/", "medium_index", "-", "1", "radius_sc", "=", "radius...

33.034483

0.000507

def _build_string_type(var, property_path=None): """ Builds schema definitions for string type values. :param var: The string type value :param List[str] property_path: The property path of the current type, defaults to None, optional :param property_path: [type], optional :return: The buil...

[ "def", "_build_string_type", "(", "var", ",", "property_path", "=", "None", ")", ":", "if", "not", "property_path", ":", "property_path", "=", "[", "]", "schema", "=", "{", "\"type\"", ":", "\"string\"", "}", "if", "is_builtin_type", "(", "var", ")", ":", ...

28.4

0.00227

def get_ddlib_feats(span, context, idxs): """ Minimalist port of generic mention features from ddlib """ if span.stable_id not in unary_ddlib_feats: unary_ddlib_feats[span.stable_id] = set() for seq_feat in _get_seq_features(context, idxs): unary_ddlib_feats[span.stable_id]...

[ "def", "get_ddlib_feats", "(", "span", ",", "context", ",", "idxs", ")", ":", "if", "span", ".", "stable_id", "not", "in", "unary_ddlib_feats", ":", "unary_ddlib_feats", "[", "span", ".", "stable_id", "]", "=", "set", "(", ")", "for", "seq_feat", "in", "...

32

0.001898

def set_secure_boot_mode(self, secure_boot_enable): """Enable/Disable secure boot on the server. Resetting the server post updating this settings is needed from the caller side to make this into effect. :param secure_boot_enable: True, if secure boot needs to be enabled f...

[ "def", "set_secure_boot_mode", "(", "self", ",", "secure_boot_enable", ")", ":", "if", "self", ".", "_is_boot_mode_uefi", "(", ")", ":", "sushy_system", "=", "self", ".", "_get_sushy_system", "(", "PROLIANT_SYSTEM_ID", ")", "try", ":", "sushy_system", ".", "secu...

49.433333

0.001323

def py_to_go_cookie(py_cookie): '''Convert a python cookie to the JSON-marshalable Go-style cookie form.''' # TODO (perhaps): # HttpOnly # Creation # LastAccess # Updated # not done properly: CanonicalHost. go_cookie = { 'Name': py_cookie.name, 'Value': py_cookie....

[ "def", "py_to_go_cookie", "(", "py_cookie", ")", ":", "# TODO (perhaps):", "# HttpOnly", "# Creation", "# LastAccess", "# Updated", "# not done properly: CanonicalHost.", "go_cookie", "=", "{", "'Name'", ":", "py_cookie", ".", "name", ",", "'Value'", ":", "py_co...

37

0.001054

def start_with(self, request): """Start the crawler using the given request. Args: request (:class:`nyawc.http.Request`): The startpoint for the crawler. """ HTTPRequestHelper.patch_with_options(request, self.__options) self.queue.add_request(request) self...

[ "def", "start_with", "(", "self", ",", "request", ")", ":", "HTTPRequestHelper", ".", "patch_with_options", "(", "request", ",", "self", ".", "__options", ")", "self", ".", "queue", ".", "add_request", "(", "request", ")", "self", ".", "__crawler_start", "("...

27.25

0.008876

def accept(self, arg1: JavaObject, arg2: JavaObject) -> None: """ >>> c = BiConsumer(lambda x,y : print(x + y)) >>> c.accept("foo", "bar") foobar """ self.lambda_function(arg1, arg2)

[ "def", "accept", "(", "self", ",", "arg1", ":", "JavaObject", ",", "arg2", ":", "JavaObject", ")", "->", "None", ":", "self", ".", "lambda_function", "(", "arg1", ",", "arg2", ")" ]

32

0.008696

def resume_service(name): """ Resume the service given by name. @warn: This method requires UAC elevation in Windows Vista and above. @note: Not all services support this. @see: L{get_services}, L{get_active_services}, L{start_service}, L{stop_service}, L{pause_ser...

[ "def", "resume_service", "(", "name", ")", ":", "with", "win32", ".", "OpenSCManager", "(", "dwDesiredAccess", "=", "win32", ".", "SC_MANAGER_CONNECT", ")", "as", "hSCManager", ":", "with", "win32", ".", "OpenService", "(", "hSCManager", ",", "name", ",", "d...

37.333333

0.011611

def HStruct_selectFields(structT, fieldsToUse): """ Select fields from structure (rest will become spacing) :param structT: HStruct type instance :param fieldsToUse: dict {name:{...}} or set of names to select, dictionary is used to select nested fields in HStruct or HUnion fields ...

[ "def", "HStruct_selectFields", "(", "structT", ",", "fieldsToUse", ")", ":", "template", "=", "[", "]", "fieldsToUse", "=", "fieldsToUse", "foundNames", "=", "set", "(", ")", "for", "f", "in", "structT", ".", "fields", ":", "name", "=", "None", "subfields"...

30.222222

0.000712

def lincr(l,cap): # to increment a list up to a max-list of 'cap' """ Simulate a counting system from an n-dimensional list. Usage: lincr(l,cap) l=list to increment, cap=max values for each list pos'n Returns: next set of values for list l, OR -1 (if overflow) """ l[0] = l[0] + 1 # e.g., [0,0,0]...

[ "def", "lincr", "(", "l", ",", "cap", ")", ":", "# to increment a list up to a max-list of 'cap'", "l", "[", "0", "]", "=", "l", "[", "0", "]", "+", "1", "# e.g., [0,0,0] --> [2,4,3] (=cap)", "for", "i", "in", "range", "(", "len", "(", "l", ")", ")", ":"...

40.066667

0.011382

def available(self, context): """ Resource availability. :param resort.engine.execution.Context context: Current execution context. """ try: if self.__available is None: encoded_name = urllib.parse.quote_plus(self.__name) status_code, msg = self.__endpoint.get( "/resources/custom-...

[ "def", "available", "(", "self", ",", "context", ")", ":", "try", ":", "if", "self", ".", "__available", "is", "None", ":", "encoded_name", "=", "urllib", ".", "parse", ".", "quote_plus", "(", "self", ".", "__name", ")", "status_code", ",", "msg", "=",...

22.5

0.057569

def spatialDomainNoGrid(self): """ Superposition of analytical solutions without a gridded domain """ self.w = np.zeros(self.xw.shape) if self.Debug: print("w = ") print(self.w.shape) for i in range(len(self.q)): # More efficient if we have created some 0-load ...

[ "def", "spatialDomainNoGrid", "(", "self", ")", ":", "self", ".", "w", "=", "np", ".", "zeros", "(", "self", ".", "xw", ".", "shape", ")", "if", "self", ".", "Debug", ":", "print", "(", "\"w = \"", ")", "print", "(", "self", ".", "w", ".", "shape...

32.941176

0.017361

def reset (self): """ Reset all variables to default values. """ # self.url is constructed by self.build_url() out of base_url # and (base_ref or parent) as absolute and normed url. # This the real url we use when checking so it also referred to # as 'real url' ...

[ "def", "reset", "(", "self", ")", ":", "# self.url is constructed by self.build_url() out of base_url", "# and (base_ref or parent) as absolute and normed url.", "# This the real url we use when checking so it also referred to", "# as 'real url'", "self", ".", "url", "=", "None", "# a ...

36.395833

0.00223

def __get_WIOD_SEA_extension(root_path, year, data_sheet='DATA'): """ Utility function to get the extension data from the SEA file in WIOD This function is based on the structure in the WIOD_SEA_July14 file. Missing values are set to zero. The function works if the SEA file is either in path or in a s...

[ "def", "__get_WIOD_SEA_extension", "(", "root_path", ",", "year", ",", "data_sheet", "=", "'DATA'", ")", ":", "sea_ext", "=", "'.xlsx'", "sea_start", "=", "'WIOD_SEA'", "_SEA_folder", "=", "os", ".", "path", ".", "join", "(", "root_path", ",", "'SEA'", ")", ...

36.459184

0.000272

def get_log_attrs(): """Get logging attributes from the opencensus context. :rtype: :class:`LogAttrs` :return: The current span's trace ID, span ID, and sampling decision. """ try: tracer = execution_context.get_opencensus_tracer() if tracer is None: raise RuntimeError ...

[ "def", "get_log_attrs", "(", ")", ":", "try", ":", "tracer", "=", "execution_context", ".", "get_opencensus_tracer", "(", ")", "if", "tracer", "is", "None", ":", "raise", "RuntimeError", "except", "Exception", ":", "# noqa", "_meta_logger", ".", "error", "(", ...

34.731707

0.000683

def is_publication_permissible(cursor, publication_id, uuid_): """Check the given publisher of this publication given by ``publication_id`` is allowed to publish the content given by ``uuid``. """ # Check the publishing user has permission to publish cursor.execute("""\ SELECT 't'::boolean FROM ...

[ "def", "is_publication_permissible", "(", "cursor", ",", "publication_id", ",", "uuid_", ")", ":", "# Check the publishing user has permission to publish", "cursor", ".", "execute", "(", "\"\"\"\\\nSELECT 't'::boolean\nFROM\n pending_documents AS pd\n NATURAL JOIN document_acl AS acl...

26.84

0.001439

def create_html_mailto( email, subject=None, body=None, cc=None, bcc=None, link_label="%(email)s", linkattrd=None, escape_urlargd=True, escape_linkattrd=True, email_obfuscation_mode=None): """Creates a W3C compliant 'mailto' link. ...

[ "def", "create_html_mailto", "(", "email", ",", "subject", "=", "None", ",", "body", "=", "None", ",", "cc", "=", "None", ",", "bcc", "=", "None", ",", "link_label", "=", "\"%(email)s\"", ",", "linkattrd", "=", "None", ",", "escape_urlargd", "=", "True",...

38.253731

0.00057

def chown(self, path, uid, gid, dir_fd=None, follow_symlinks=None): """Set ownership of a faked file. Args: path: (str) Path to the file or directory. uid: (int) Numeric uid to set the file or directory to. gid: (int) Numeric gid to set the file or directory to. ...

[ "def", "chown", "(", "self", ",", "path", ",", "uid", ",", "gid", ",", "dir_fd", "=", "None", ",", "follow_symlinks", "=", "None", ")", ":", "if", "follow_symlinks", "is", "None", ":", "follow_symlinks", "=", "True", "elif", "sys", ".", "version_info", ...

42.219512

0.001129

def modify_attribute(self, attribute, value): """ Changes an attribute of this instance :type attribute: string :param attribute: The attribute you wish to change. AttributeName - Expected value (default) instanceType - A valid instanc...

[ "def", "modify_attribute", "(", "self", ",", "attribute", ",", "value", ")", ":", "return", "self", ".", "connection", ".", "modify_instance_attribute", "(", "self", ".", "id", ",", "attribute", ",", "value", ")" ]

43.695652

0.001947

def check_directory(self): """Check if migrations directory exists.""" exists = os.path.exists(self.directory) if not exists: logger.error("No migrations directory found. Check your path or create a migration first.") logger.error("Directory: %s" % self.directory) ...

[ "def", "check_directory", "(", "self", ")", ":", "exists", "=", "os", ".", "path", ".", "exists", "(", "self", ".", "directory", ")", "if", "not", "exists", ":", "logger", ".", "error", "(", "\"No migrations directory found. Check your path or create a migration f...

46.857143

0.008982

def update(self, friendly_name=None, description=None): """ Selectively updates Dataset information. Args: friendly_name: if not None, the new friendly name. description: if not None, the new description. Returns: """ self._get_info() if self._info: if friendly_name: ...

[ "def", "update", "(", "self", ",", "friendly_name", "=", "None", ",", "description", "=", "None", ")", ":", "self", ".", "_get_info", "(", ")", "if", "self", ".", "_info", ":", "if", "friendly_name", ":", "self", ".", "_info", "[", "'friendlyName'", "]...

26.045455

0.010101

def sr(self, multi=0): """sr([multi=1]) -> (SndRcvList, PacketList) Matches packets in the list and return ( (matched couples), (unmatched packets) )""" # noqa: E501 remain = self.res[:] sr = [] i = 0 while i < len(remain): s = remain[i] j = i ...

[ "def", "sr", "(", "self", ",", "multi", "=", "0", ")", ":", "# noqa: E501", "remain", "=", "self", ".", "res", "[", ":", "]", "sr", "=", "[", "]", "i", "=", "0", "while", "i", "<", "len", "(", "remain", ")", ":", "s", "=", "remain", "[", "i...

34.423077

0.002174

def compare(self, reference_classes: List, query_classes: List, method: Optional[SimAlgorithm] = SimAlgorithm.PHENODIGM) -> SimResult: """ Owlsim2 compare, calls compare_attribute_sets, and converts to SimResult object :return: SimResult object ...

[ "def", "compare", "(", "self", ",", "reference_classes", ":", "List", ",", "query_classes", ":", "List", ",", "method", ":", "Optional", "[", "SimAlgorithm", "]", "=", "SimAlgorithm", ".", "PHENODIGM", ")", "->", "SimResult", ":", "owlsim_results", "=", "com...

49.4

0.015905

def file_stat_for_all(self, filters=all_true): # pragma: no cover """ Find out how many files, directories and total size (Include file in it's sub-folder) it has for each folder and sub-folder. :returns: stat, a dict like ``{"directory path": { "file": number of files, "dir"...

[ "def", "file_stat_for_all", "(", "self", ",", "filters", "=", "all_true", ")", ":", "# pragma: no cover", "self", ".", "assert_is_dir_and_exists", "(", ")", "from", "collections", "import", "OrderedDict", "stat", "=", "OrderedDict", "(", ")", "stat", "[", "self"...

28.893617

0.001425

def get_balance(self): """ Get balance with provider. """ if not SMSGLOBAL_CHECK_BALANCE_COUNTRY: raise Exception('SMSGLOBAL_CHECK_BALANCE_COUNTRY setting must be set to check balance.') params = { 'user' : self.get_username(), 'password' ...

[ "def", "get_balance", "(", "self", ")", ":", "if", "not", "SMSGLOBAL_CHECK_BALANCE_COUNTRY", ":", "raise", "Exception", "(", "'SMSGLOBAL_CHECK_BALANCE_COUNTRY setting must be set to check balance.'", ")", "params", "=", "{", "'user'", ":", "self", ".", "get_username", "...

39.714286

0.014052

def cmd(send, msg, args): """Gets stats. Syntax: {command} <--high|--low|--userhigh|--nick <nick>|command> """ parser = arguments.ArgParser(args['config']) group = parser.add_mutually_exclusive_group() group.add_argument('--high', action='store_true') group.add_argument('--low', action='st...

[ "def", "cmd", "(", "send", ",", "msg", ",", "args", ")", ":", "parser", "=", "arguments", ".", "ArgParser", "(", "args", "[", "'config'", "]", ")", "group", "=", "parser", ".", "add_mutually_exclusive_group", "(", ")", "group", ".", "add_argument", "(", ...

37.74

0.001033

def kp_pan_set(self, viewer, event, data_x, data_y, msg=True): """Sets the pan position under the cursor.""" if self.canpan: self._panset(viewer, data_x, data_y, msg=msg) return True

[ "def", "kp_pan_set", "(", "self", ",", "viewer", ",", "event", ",", "data_x", ",", "data_y", ",", "msg", "=", "True", ")", ":", "if", "self", ".", "canpan", ":", "self", ".", "_panset", "(", "viewer", ",", "data_x", ",", "data_y", ",", "msg", "=", ...

42.8

0.009174

def censor(input_text): """ Returns the input string with profanity replaced with a random string of characters plucked from the censor_characters pool. """ ret = input_text words = get_words() for word in words: curse_word = re.compile(re.escape(word), re.IGNORECASE) cen = "".j...

[ "def", "censor", "(", "input_text", ")", ":", "ret", "=", "input_text", "words", "=", "get_words", "(", ")", "for", "word", "in", "words", ":", "curse_word", "=", "re", ".", "compile", "(", "re", ".", "escape", "(", "word", ")", ",", "re", ".", "IG...

33.75

0.002404

def format_sec(s): """ Format seconds in a more human readable way. It supports units down to nanoseconds. :param s: Float of seconds to format :return: String second representation, like 12.4 us """ prefixes = ["", "m", "u", "n"] unit = 0 while s < 1 and unit + 1 < len(prefixes):...

[ "def", "format_sec", "(", "s", ")", ":", "prefixes", "=", "[", "\"\"", ",", "\"m\"", ",", "\"u\"", ",", "\"n\"", "]", "unit", "=", "0", "while", "s", "<", "1", "and", "unit", "+", "1", "<", "len", "(", "prefixes", ")", ":", "s", "*=", "1000", ...

23

0.002457

def predict_quantiles(self, X, quantiles=(2.5, 97.5), Y_metadata=None, likelihood=None, kern=None): """ Get the predictive quantiles around the prediction at X :param X: The points at which to make a prediction :type X: np.ndarray (Xnew x self.input_dim) :param quantiles: tuple ...

[ "def", "predict_quantiles", "(", "self", ",", "X", ",", "quantiles", "=", "(", "2.5", ",", "97.5", ")", ",", "Y_metadata", "=", "None", ",", "likelihood", "=", "None", ",", "kern", "=", "None", ")", ":", "qs", "=", "super", "(", "WarpedGP", ",", "s...

56.266667

0.008159

def update(self, v): """Add `v` to the hash, recursively if needed.""" self.md5.update(to_bytes(str(type(v)))) if isinstance(v, string_class): self.md5.update(to_bytes(v)) elif v is None: pass elif isinstance(v, (int, float)): self.md5.update(t...

[ "def", "update", "(", "self", ",", "v", ")", ":", "self", ".", "md5", ".", "update", "(", "to_bytes", "(", "str", "(", "type", "(", "v", ")", ")", ")", ")", "if", "isinstance", "(", "v", ",", "string_class", ")", ":", "self", ".", "md5", ".", ...

32.615385

0.002291

def exactly_n(l, n=1): ''' Tests that exactly N items in an iterable are "truthy" (neither None, False, nor 0). ''' i = iter(l) return all(any(i) for j in range(n)) and not any(i)

[ "def", "exactly_n", "(", "l", ",", "n", "=", "1", ")", ":", "i", "=", "iter", "(", "l", ")", "return", "all", "(", "any", "(", "i", ")", "for", "j", "in", "range", "(", "n", ")", ")", "and", "not", "any", "(", "i", ")" ]

28.142857

0.009852

def _get_handler(self, node_id): """Get the handler of a given node.""" handler = self._get_attrs(node_id).get(self.HANDLER, self._default_handler) # Here we make sure the handler is an instance of `BasicNodeHandler` or inherited # types. While generally being bad Python practice, we st...

[ "def", "_get_handler", "(", "self", ",", "node_id", ")", ":", "handler", "=", "self", ".", "_get_attrs", "(", "node_id", ")", ".", "get", "(", "self", ".", "HANDLER", ",", "self", ".", "_default_handler", ")", "# Here we make sure the handler is an instance of `...

55.416667

0.008876

def htmlReadDoc(cur, URL, encoding, options): """parse an XML in-memory document and build a tree. """ ret = libxml2mod.htmlReadDoc(cur, URL, encoding, options) if ret is None:raise treeError('htmlReadDoc() failed') return xmlDoc(_obj=ret)

[ "def", "htmlReadDoc", "(", "cur", ",", "URL", ",", "encoding", ",", "options", ")", ":", "ret", "=", "libxml2mod", ".", "htmlReadDoc", "(", "cur", ",", "URL", ",", "encoding", ",", "options", ")", "if", "ret", "is", "None", ":", "raise", "treeError", ...

50.2

0.011765

def create_binding(site, hostheader='', ipaddress='*', port=80, protocol='http', sslflags=None): ''' Create an IIS Web Binding. .. note:: This function only validates against the binding ipaddress:port:hostheader combination, and will return True even if the bind...

[ "def", "create_binding", "(", "site", ",", "hostheader", "=", "''", ",", "ipaddress", "=", "'*'", ",", "port", "=", "80", ",", "protocol", "=", "'http'", ",", "sslflags", "=", "None", ")", ":", "protocol", "=", "six", ".", "text_type", "(", "protocol",...

36.025

0.001689

def set_params(self, **params): """Set parameters on this object Safe setter method - attributes should not be modified directly as some changes are not valid. Valid parameters: - n_jobs - random_state - verbose Invalid parameters: (these would require mo...

[ "def", "set_params", "(", "self", ",", "*", "*", "params", ")", ":", "if", "'knn'", "in", "params", "and", "params", "[", "'knn'", "]", "!=", "self", ".", "knn", ":", "raise", "ValueError", "(", "\"Cannot update knn. Please create a new graph\"", ")", "if", ...

38.792453

0.000949