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 get_languages(self): """ :calls: `GET /repos/:owner/:repo/languages <http://developer.github.com/v3/repos>`_ :rtype: dict of string to integer """ headers, data = self._requester.requestJsonAndCheck( "GET", self.url + "/languages" ) ret...	[ "def", "get_languages", "(", "self", ")", ":", "headers", ",", "data", "=", "self", ".", "_requester", ".", "requestJsonAndCheck", "(", "\"GET\"", ",", "self", ".", "url", "+", "\"/languages\"", ")", "return", "data" ]	31.9	0.009146
def time_multi_coincidence(times, slide_step=0, slop=.003, pivot='H1', fixed='L1'): """ Find multi detector concidences. Parameters ---------- times: dict of numpy.ndarrays Dictionary keyed by ifo of the times of each single detector trigger. slide_step: float ...	[ "def", "time_multi_coincidence", "(", "times", ",", "slide_step", "=", "0", ",", "slop", "=", ".003", ",", "pivot", "=", "'H1'", ",", "fixed", "=", "'L1'", ")", ":", "# pivots are used to determine standard coincidence triggers, we then", "# pair off additional detector...	41.885057	0.001609
def troutslap(rest): "Slap some(one\|thing) with a fish" slapee = rest karma.Karma.store.change(slapee, -1) return "/me slaps %s around a bit with a large trout" % slapee	[ "def", "troutslap", "(", "rest", ")", ":", "slapee", "=", "rest", "karma", ".", "Karma", ".", "store", ".", "change", "(", "slapee", ",", "-", "1", ")", "return", "\"/me slaps %s around a bit with a large trout\"", "%", "slapee" ]	33.8	0.028902
def _GceMetadataRequest(relative_url, use_metadata_ip=False): """Request the given url from the GCE metadata service.""" if use_metadata_ip: base_url = os.environ.get('GCE_METADATA_IP', '169.254.169.254') else: base_url = os.environ.get( 'GCE_METADATA_ROOT', 'metadata.google.inte...	[ "def", "_GceMetadataRequest", "(", "relative_url", ",", "use_metadata_ip", "=", "False", ")", ":", "if", "use_metadata_ip", ":", "base_url", "=", "os", ".", "environ", ".", "get", "(", "'GCE_METADATA_IP'", ",", "'169.254.169.254'", ")", "else", ":", "base_url", ...	46.315789	0.001114
def _try_reduce(self) -> Tuple[List["HdlStatement"], bool]: """ Doc on parent class :meth:`HdlStatement._try_reduce` """ io_change = False new_cases = [] for val, statements in self.cases: _statements, rank_decrease, _io_change = self._try_reduce_list( ...	[ "def", "_try_reduce", "(", "self", ")", "->", "Tuple", "[", "List", "[", "\"HdlStatement\"", "]", ",", "bool", "]", ":", "io_change", "=", "False", "new_cases", "=", "[", "]", "for", "val", ",", "statements", "in", "self", ".", "cases", ":", "_statemen...	33.891304	0.001247
def ls_handler(self, args): '''Handler for ls command''' if len(args) == 1: self.pretty_print(self.s3handler().list_buckets()) return self.validate('cmd\|s3', args) self.pretty_print(self.s3handler().s3walk(args[1]))	[ "def", "ls_handler", "(", "self", ",", "args", ")", ":", "if", "len", "(", "args", ")", "==", "1", ":", "self", ".", "pretty_print", "(", "self", ".", "s3handler", "(", ")", ".", "list_buckets", "(", ")", ")", "return", "self", ".", "validate", "("...	29.625	0.012295
def import_plugin(name): """Imports plugin python module""" path = os.path.join("plugins", name + ".py") try: with open(path, 'rb') as f: try: plugin = imp.load_module( "p_" + name, f, name + '.py', ('.py', 'rb', imp.PY_SOURCE) ...	[ "def", "import_plugin", "(", "name", ")", ":", "path", "=", "os", ".", "path", ".", "join", "(", "\"plugins\"", ",", "name", "+", "\".py\"", ")", "try", ":", "with", "open", "(", "path", ",", "'rb'", ")", "as", "f", ":", "try", ":", "plugin", "="...	36.833333	0.001471
def create_parser(parser: argparse.ArgumentParser) -> None: """ Creates the parser by setting all the possible arguments :param parser: The parser """ parser.add_argument("solidity_file", nargs="*") commands = parser.add_argument_group("commands") commands.add_argument("-g", "--graph", help...	[ "def", "create_parser", "(", "parser", ":", "argparse", ".", "ArgumentParser", ")", "->", "None", ":", "parser", ".", "add_argument", "(", "\"solidity_file\"", ",", "nargs", "=", "\"*\"", ")", "commands", "=", "parser", ".", "add_argument_group", "(", "\"comma...	30.343915	0.00152
def UpdateFlows(self, client_id_flow_id_pairs, pending_termination=db.Database.unchanged, cursor=None): """Updates flow objects in the database.""" if pending_termination == db.Database.unchanged: return serialized_termination = pending_terminati...	[ "def", "UpdateFlows", "(", "self", ",", "client_id_flow_id_pairs", ",", "pending_termination", "=", "db", ".", "Database", ".", "unchanged", ",", "cursor", "=", "None", ")", ":", "if", "pending_termination", "==", "db", ".", "Database", ".", "unchanged", ":", ...	39.777778	0.00955
def _do_unjoin_packet(self, packet, ip, port): """ React to unjoin packet - remove a client from this server :param packet: Packet from client that wants to join :type packet: paps.si.app.message.APPJoinMessage :param ip: Client ip address :type ip: unicode :para...	[ "def", "_do_unjoin_packet", "(", "self", ",", "packet", ",", "ip", ",", "port", ")", ":", "self", ".", "debug", "(", "\"()\"", ")", "device_id", "=", "packet", ".", "header", ".", "device_id", "if", "device_id", "<=", "Id", ".", "SERVER", ":", "self", ...	30.380952	0.002278
def get_cuda_visible_devices(): """Get the device IDs in the CUDA_VISIBLE_DEVICES environment variable. Returns: if CUDA_VISIBLE_DEVICES is set, this returns a list of integers with the IDs of the GPUs. If it is not set, this returns None. """ gpu_ids_str = os.environ.get("CUDA_VISI...	[ "def", "get_cuda_visible_devices", "(", ")", ":", "gpu_ids_str", "=", "os", ".", "environ", ".", "get", "(", "\"CUDA_VISIBLE_DEVICES\"", ",", "None", ")", "if", "gpu_ids_str", "is", "None", ":", "return", "None", "if", "gpu_ids_str", "==", "\"\"", ":", "retu...	29.4375	0.002058
def ToHashArray(self): """ Turn the tree into a list of hashes. Returns: list: """ hashes = set() MerkleTree.__DepthFirstSearch(self.Root, hashes) return list(hashes)	[ "def", "ToHashArray", "(", "self", ")", ":", "hashes", "=", "set", "(", ")", "MerkleTree", ".", "__DepthFirstSearch", "(", "self", ".", "Root", ",", "hashes", ")", "return", "list", "(", "hashes", ")" ]	22.6	0.008511
def drop_database(self, name_or_database, session=None): """Drop a database. Raises :class:`TypeError` if `name_or_database` is not an instance of :class:`basestring` (:class:`str` in python 3) or :class:`~pymongo.database.Database`. :Parameters: - `name_or_database`:...	[ "def", "drop_database", "(", "self", ",", "name_or_database", ",", "session", "=", "None", ")", ":", "name", "=", "name_or_database", "if", "isinstance", "(", "name", ",", "database", ".", "Database", ")", ":", "name", "=", "name", ".", "name", "if", "no...	37.860465	0.001796
def parse_value_namedinstance(self, tup_tree): """ :: <!ELEMENT VALUE.NAMEDINSTANCE (INSTANCENAME, INSTANCE)> Returns: CIMInstance object with path set (without host or namespace). """ self.check_node(tup_tree, 'VALUE.NAMEDINSTANCE') k = kids...	[ "def", "parse_value_namedinstance", "(", "self", ",", "tup_tree", ")", ":", "self", ".", "check_node", "(", "tup_tree", ",", "'VALUE.NAMEDINSTANCE'", ")", "k", "=", "kids", "(", "tup_tree", ")", "if", "len", "(", "k", ")", "!=", "2", ":", "raise", "CIMXM...	30.615385	0.002436
def _make_f_expectation(self, expr): """ Calculates :math:`<F>` in eq. 12 (see Ale et al. 2013) to calculate :math:`<F>` for EACH VARIABLE combination. :param expr: an expression :return: a column vector. Each row correspond to an element of counter. :rtype: :class:`sympy.Matrix...	[ "def", "_make_f_expectation", "(", "self", ",", "expr", ")", ":", "# compute derivatives for EACH ENTRY in COUNTER", "derives", "=", "sp", ".", "Matrix", "(", "[", "derive_expr_from_counter_entry", "(", "expr", ",", "self", ".", "__species", ",", "tuple", "(", "c"...	38.454545	0.008074
def send_dynamic_message(sender, message): """Send a dynamic message to the listeners. Dynamic messages represents a progress. Usually it will be appended to the previous messages. .. versionadded:: 3.3 :param sender: The sender. :type sender: object :param message: An instance of our ri...	[ "def", "send_dynamic_message", "(", "sender", ",", "message", ")", ":", "dispatcher", ".", "send", "(", "signal", "=", "DYNAMIC_MESSAGE_SIGNAL", ",", "sender", "=", "sender", ",", "message", "=", "message", ")" ]	25.157895	0.002016
def _get_column_boundaries(self): '''Use the guessed ends to guess the boundaries of the plain text columns. ''' # Try to figure out the most common column boundaries. ends = self._get_column_ends() if not ends: # If there aren't even any nontrivial sequences ...	[ "def", "_get_column_boundaries", "(", "self", ")", ":", "# Try to figure out the most common column boundaries.", "ends", "=", "self", ".", "_get_column_ends", "(", ")", "if", "not", "ends", ":", "# If there aren't even any nontrivial sequences of whitespace", "# dividing text,...	39.473684	0.001301
def execute_and_reset( expr, params=None, scope=None, aggcontext=None, **kwargs ): """Execute an expression against data that are bound to it. If no data are bound, raise an Exception. Notes ----- The difference between this function and :func:`~ibis.pandas.core.execute` is that this functi...	[ "def", "execute_and_reset", "(", "expr", ",", "params", "=", "None", ",", "scope", "=", "None", ",", "aggcontext", "=", "None", ",", "", "", "kwargs", ")", ":", "result", "=", "execute", "(", "expr", ",", "params", "=", "params", ",", "scope", "=",...	32.44898	0.000611
def is_empty(self): """ Test interval emptiness. :return: True if interval is empty, False otherwise. """ return ( self._lower > self._upper or (self._lower == self._upper and (self._left == OPEN or self._right == OPEN)) )	[ "def", "is_empty", "(", "self", ")", ":", "return", "(", "self", ".", "_lower", ">", "self", ".", "_upper", "or", "(", "self", ".", "_lower", "==", "self", ".", "_upper", "and", "(", "self", ".", "_left", "==", "OPEN", "or", "self", ".", "_right", ...	28.6	0.010169
def booleanized(values, min_value, max_value, hysteresis=0): """ Returns True for each item in values between min_value and max_value, and False otherwise. hysteresis can optionally be used to add `hysteresis`_ which prevents the output value rapidly flipping when the input value is fluctuat...	[ "def", "booleanized", "(", "values", ",", "min_value", ",", "max_value", ",", "hysteresis", "=", "0", ")", ":", "values", "=", "_normalize", "(", "values", ")", "if", "min_value", ">=", "max_value", ":", "raise", "ValueError", "(", "'min_value must be smaller ...	36.885246	0.001732
def pick_free_port(hostname=REDIRECT_HOST, port=0): """ Try to bind a port. Default=0 selects a free port. """ import socket s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) try: s.bind((hostname, port)) # port=0 finds an open port except OSError as e: log.warning("Could not bi...	[ "def", "pick_free_port", "(", "hostname", "=", "REDIRECT_HOST", ",", "port", "=", "0", ")", ":", "import", "socket", "s", "=", "socket", ".", "socket", "(", "socket", ".", "AF_INET", ",", "socket", ".", "SOCK_STREAM", ")", "try", ":", "s", ".", "bind",...	37.5	0.001626
def __update_upgrades_table(self, delta): """Add a new record into the upgrades information table about the applied delta Parameters ---------- delta: Delta the applied delta file""" query = """ INSERT INTO {} ( --id, version,...	[ "def", "__update_upgrades_table", "(", "self", ",", "delta", ")", ":", "query", "=", "\"\"\"\n INSERT INTO {} (\n --id,\n version,\n description,\n type,\n script,\n checksum,\n installed_by,\n --insta...	24.135135	0.002153
def cached(self, TTL=60 * 24): '''A decorator that will cache the output of the wrapped function. The key used for the cache is the function name as well as the `args` and `*kwargs` passed to the function. :param TTL: time to live in minutes .. note:: For route caching, you s...	[ "def", "cached", "(", "self", ",", "TTL", "=", "60", "*", "24", ")", ":", "def", "decorating_function", "(", "function", ")", ":", "# TODO test this method", "storage", "=", "self", ".", "get_storage", "(", "self", ".", "_function_cache_name", ",", "file_for...	42.378378	0.00187
def _find_supported_challenge(authzr, responders): """ Find a challenge combination that consists of a single challenge that the responder can satisfy. :param ~acme.messages.AuthorizationResource auth: The authorization to examine. :type responder: List[`~txacme.interfaces.IResponder`] ...	[ "def", "_find_supported_challenge", "(", "authzr", ",", "responders", ")", ":", "matches", "=", "[", "(", "responder", ",", "challbs", "[", "0", "]", ")", "for", "challbs", "in", "authzr", ".", "body", ".", "resolved_combinations", "for", "responder", "in", ...	34.296296	0.00105
def argv(args, *opts): """ Produces an argument vector from its array of arguments and keyword options. First, the options are unpacked. When the value is a ``bool``, the option is passed without an argument if it is true and skipped if it is ``false``. When the option is one of the flat built-in ...	[ "def", "argv", "(", "", "args", ",", "", "*", "opts", ")", ":", "spacer", "=", "[", "\"--\"", "]", "if", "opts", ".", "get", "(", "\"__\"", ")", "else", "[", "]", "args", "=", "[", "arg", "(", "_", ")", "for", "_", "in", "args", "]", "opt...	55.153846	0.000685
def _get_template_dirs(): """existing directories where to search for jinja2 templates. The order is important. The first found template from the first found dir wins!""" return filter(lambda x: os.path.exists(x), [ # user dir os.path.join(os.path.expanduser('~'), '.py2pack', 'templates'), ...	[ "def", "_get_template_dirs", "(", ")", ":", "return", "filter", "(", "lambda", "x", ":", "os", ".", "path", ".", "exists", "(", "x", ")", ",", "[", "# user dir", "os", ".", "path", ".", "join", "(", "os", ".", "path", ".", "expanduser", "(", "'~'",...	48.545455	0.001838
def get_spectrogram(self): """Calculate the spectrogram to be plotted This exists as a separate method to allow subclasses to override this and not the entire `get_plot` method, e.g. `Coherencegram`. This method should not apply the normalisation from `args.norm`. """ a...	[ "def", "get_spectrogram", "(", "self", ")", ":", "args", "=", "self", ".", "args", "fftlength", "=", "float", "(", "args", ".", "secpfft", ")", "overlap", "=", "fftlength", "*", "args", ".", "overlap", "self", ".", "log", "(", "2", ",", "\"Calculating ...	40.545455	0.00146
def create(cls, fpath): "Creates a `Config` from `fpath`." fpath = _expand_path(fpath) assert(fpath.suffix == '.yml') if fpath.exists(): return fpath.parent.mkdir(parents=True, exist_ok=True) with open(fpath, 'w') as yaml_file: yaml.dump(cls.DEFAULT_CONFIG, ya...	[ "def", "create", "(", "cls", ",", "fpath", ")", ":", "fpath", "=", "_expand_path", "(", "fpath", ")", "assert", "(", "fpath", ".", "suffix", "==", "'.yml'", ")", "if", "fpath", ".", "exists", "(", ")", ":", "return", "fpath", ".", "parent", ".", "m...	43.375	0.008475
def get_used_in_func(node): '''Get names, but ignore variables names to the left hand side That is to say, in case of a = b + 1 we consider b as "being accessed", while a is not. ''' if isinstance(node, ast.FunctionDef): return {node.name: get_accessed(node.body)} names = {} f...	[ "def", "get_used_in_func", "(", "node", ")", ":", "if", "isinstance", "(", "node", ",", "ast", ".", "FunctionDef", ")", ":", "return", "{", "node", ".", "name", ":", "get_accessed", "(", "node", ".", "body", ")", "}", "names", "=", "{", "}", "for", ...	34.083333	0.002381
def segment_midpoints_by_vertices(self, vertices): """ Add midpoints to any segment connected to the vertices in the list / array provided. """ segments = set() for vertex in vertices: neighbours = self.identify_vertex_neighbours(vertex) segments...	[ "def", "segment_midpoints_by_vertices", "(", "self", ",", "vertices", ")", ":", "segments", "=", "set", "(", ")", "for", "vertex", "in", "vertices", ":", "neighbours", "=", "self", ".", "identify_vertex_neighbours", "(", "vertex", ")", "segments", ".", "update...	31.176471	0.010989
def screenshot(self, filename=None): """ Take screen snapshot Args: - filename: filename where save to, optional Returns: PIL.Image object Raises: TypeError, IOError """ if self.__keep_screen: return self.__last_s...	[ "def", "screenshot", "(", "self", ",", "filename", "=", "None", ")", ":", "if", "self", ".", "__keep_screen", ":", "return", "self", ".", "__last_screen", "try", ":", "screen", "=", "self", ".", "_take_screenshot", "(", ")", "except", "IOError", ":", "# ...	28.107143	0.002457
def appendInputWithSimilarValues(inputs): """ Creates an 'one-off' record for each record in the inputs. Appends new records to the same inputs list. """ numInputs = len(inputs) for i in xrange(numInputs): input = inputs[i] for j in xrange(len(input)-1): if input[j] == 1 and input[j+1] == 0: ...	[ "def", "appendInputWithSimilarValues", "(", "inputs", ")", ":", "numInputs", "=", "len", "(", "inputs", ")", "for", "i", "in", "xrange", "(", "numInputs", ")", ":", "input", "=", "inputs", "[", "i", "]", "for", "j", "in", "xrange", "(", "len", "(", "...	31.357143	0.011062
def interpolate(self, transform, transitions=None, Y=None): """Interpolate new data onto a transformation of the graph data One of either transitions or Y should be provided Parameters ---------- transform : array-like, shape=[n_samples, n_transform_features] transiti...	[ "def", "interpolate", "(", "self", ",", "transform", ",", "transitions", "=", "None", ",", "Y", "=", "None", ")", ":", "if", "transitions", "is", "None", ":", "if", "Y", "is", "None", ":", "raise", "ValueError", "(", "\"Either `transitions` or `Y` must be pr...	34	0.001589
def soft_kill(jid, state_id=None): ''' Set up a state run to die before executing the given state id, this instructs a running state to safely exit at a given state id. This needs to pass in the jid of the running state. If a state_id is not passed then the jid referenced will be safely exited a...	[ "def", "soft_kill", "(", "jid", ",", "state_id", "=", "None", ")", ":", "minion", "=", "salt", ".", "minion", ".", "MasterMinion", "(", "__opts__", ")", "minion", ".", "functions", "[", "'state.soft_kill'", "]", "(", "jid", ",", "state_id", ")" ]	46	0.002132
def build_for_contour_tree(self, contour_tree, negate=False): """ A helper function that will reduce duplication of data by reusing the parent contour tree's parameters and data """ if self.debug: tree_type = "Join" if negate: tree_type = "Spli...	[ "def", "build_for_contour_tree", "(", "self", ",", "contour_tree", ",", "negate", "=", "False", ")", ":", "if", "self", ".", "debug", ":", "tree_type", "=", "\"Join\"", "if", "negate", ":", "tree_type", "=", "\"Split\"", "sys", ".", "stdout", ".", "write",...	32.807692	0.002278
def write_file(environ, term='bash', out_dir=None, tree_dir=None): ''' Write a tree environment file Loops over the tree environ and writes them out to a bash, tsch, or modules file Parameters: environ (dict): The tree dictionary environment term (str): The type...	[ "def", "write_file", "(", "environ", ",", "term", "=", "'bash'", ",", "out_dir", "=", "None", ",", "tree_dir", "=", "None", ")", ":", "# get the proper name, header and file extension", "name", "=", "environ", "[", "'default'", "]", "[", "'name'", "]", "header...	34.229167	0.001183
def _save_image(fig, filename, filetype='png', resolution=300): """ If filename is specified, saves the image :param str filename: Name of the file :param str filetype: Type of file :param int resolution: DPI resolution of the output figure """ if filename: fi...	[ "def", "_save_image", "(", "fig", ",", "filename", ",", "filetype", "=", "'png'", ",", "resolution", "=", "300", ")", ":", "if", "filename", ":", "filename", ",", "filetype", ",", "resolution", "=", "build_filename", "(", "filename", ",", "filetype", ",", ...	34.058824	0.001681
def inject_config(self, config, from_args): """ :param config: :type config: list :param from_args: :type from_args: dict """ # First get required values from labelStore runtime = self._get_runtime() whitelist = self._get_whitelist() #Run introspection on the libraries to retriev...	[ "def", "inject_config", "(", "self", ",", "config", ",", "from_args", ")", ":", "# First get required values from labelStore", "runtime", "=", "self", ".", "_get_runtime", "(", ")", "whitelist", "=", "self", ".", "_get_whitelist", "(", ")", "#Run introspection on th...	35.4	0.013201
def breakpoint(args): """ %prog breakpoint blastfile bedfile [options] Identify breakpoints where collinearity ends. `blastfile` contains mapping from markers (query) to scaffolds (subject). `bedfile` contains marker locations in the related species. """ from jcvi.formats.blast import bed ...	[ "def", "breakpoint", "(", "args", ")", ":", "from", "jcvi", ".", "formats", ".", "blast", "import", "bed", "from", "jcvi", ".", "utils", ".", "range", "import", "range_interleave", "p", "=", "OptionParser", "(", "breakpoint", ".", "__doc__", ")", "p", "....	38.157895	0.000672
def knapsack(p, v, cmax): """Knapsack problem: select maximum value set of items if total size not more than capacity :param p: table with size of items :param v: table with value of items :param cmax: capacity of bag :requires: number of items non-zero :returns: value optimal solution, list of...	[ "def", "knapsack", "(", "p", ",", "v", ",", "cmax", ")", ":", "n", "=", "len", "(", "p", ")", "opt", "=", "[", "[", "0", "]", "*", "(", "cmax", "+", "1", ")", "for", "_", "in", "range", "(", "n", "+", "1", ")", "]", "sel", "=", "[", "...	37.176471	0.001542
def clean(args): """ %prog clean fastafile Remove irregular chars in FASTA seqs. """ p = OptionParser(clean.__doc__) p.add_option("--fancy", default=False, action="store_true", help="Pretty print the sequence [default: %default]") p.add_option("--canonical", default=False, ...	[ "def", "clean", "(", "args", ")", ":", "p", "=", "OptionParser", "(", "clean", ".", "__doc__", ")", "p", ".", "add_option", "(", "\"--fancy\"", ",", "default", "=", "False", ",", "action", "=", "\"store_true\"", ",", "help", "=", "\"Pretty print the sequen...	28.939394	0.001013
def create_secret( name, namespace='default', data=None, source=None, template=None, saltenv='base', **kwargs): ''' Creates the kubernetes secret as defined by the user. CLI Examples:: salt 'minion1' kubernetes.create_secret \ pas...	[ "def", "create_secret", "(", "name", ",", "namespace", "=", "'default'", ",", "data", "=", "None", ",", "source", "=", "None", ",", "template", "=", "None", ",", "saltenv", "=", "'base'", ",", "", "", "kwargs", ")", ":", "if", "source", ":", "data"...	27.339623	0.000666
def WriteClientMetadata(self, client_id, certificate=None, fleetspeak_enabled=None, first_seen=None, last_ping=None, last_clock=None, last...	[ "def", "WriteClientMetadata", "(", "self", ",", "client_id", ",", "certificate", "=", "None", ",", "fleetspeak_enabled", "=", "None", ",", "first_seen", "=", "None", ",", "last_ping", "=", "None", ",", "last_clock", "=", "None", ",", "last_ip", "=", "None", ...	27.555556	0.016553
def ask_dir(self): """ dialogue box for choosing directory """ args ['directory'] = askdirectory(**self.dir_opt) self.dir_text.set(args ['directory'])	[ "def", "ask_dir", "(", "self", ")", ":", "args", "[", "'directory'", "]", "=", "askdirectory", "(", "", "", "self", ".", "dir_opt", ")", "self", ".", "dir_text", ".", "set", "(", "args", "[", "'directory'", "]", ")" ]	26	0.062112
def hierarchical_group_items(item_list, groupids_list): """ Generalization of group_item. Convert a flast list of ids into a heirarchical dictionary. TODO: move to util_dict Reference: http://stackoverflow.com/questions/10193235/python-translate-a-table-to-a-hierarchical-dictionary Args: ...	[ "def", "hierarchical_group_items", "(", "item_list", ",", "groupids_list", ")", ":", "# Construct a defaultdict type with the appropriate number of levels", "num_groups", "=", "len", "(", "groupids_list", ")", "leaf_type", "=", "partial", "(", "defaultdict", ",", "list", ...	32.695122	0.000362
def serialize_example(transformed_json_data, features, feature_indices, target_name): """Makes an instance of data in libsvm format. Args: transformed_json_data: dict of transformed data. features: features config. feature_indices: output of feature_transforms.get_transformed_feature_indices() Retur...	[ "def", "serialize_example", "(", "transformed_json_data", ",", "features", ",", "feature_indices", ",", "target_name", ")", ":", "import", "six", "import", "tensorflow", "as", "tf", "from", "trainer", "import", "feature_transforms", "line", "=", "str", "(", "trans...	42.966667	0.012898
def process_log_event(event, context): """Lambda Entrypoint - Log Subscriber Format log events and relay to sentry (direct or sqs) """ init() # Grab the actual error log payload serialized = event['awslogs'].pop('data') data = json.loads(zlib.decompress( base64.b64decode(serialized)...	[ "def", "process_log_event", "(", "event", ",", "context", ")", ":", "init", "(", ")", "# Grab the actual error log payload", "serialized", "=", "event", "[", "'awslogs'", "]", ".", "pop", "(", "'data'", ")", "data", "=", "json", ".", "loads", "(", "zlib", ...	33.05	0.001471
def assign_value(self, comp_def, value, src_ref): """ Used by the compiler for either local or dynamic prop assignments This does the following: - Check that the property is allowed in this component - Check if the value being assigned is compatible - Assign t...	[ "def", "assign_value", "(", "self", ",", "comp_def", ",", "value", ",", "src_ref", ")", ":", "# Check if property is allowed in this component", "if", "type", "(", "comp_def", ")", "not", "in", "self", ".", "bindable_to", ":", "self", ".", "env", ".", "msg", ...	38.88	0.001004
def set_default_config(modules, params=None, yaml=None, filename=None, config=None, validate=True): """Set up global configuration for tests and noninteractive tools. `modules` is an iterable of :class:`yakonfig.Configurable` objects, or anything equivalently typed. This functio...	[ "def", "set_default_config", "(", "modules", ",", "params", "=", "None", ",", "yaml", "=", "None", ",", "filename", "=", "None", ",", "config", "=", "None", ",", "validate", "=", "True", ")", ":", "if", "params", "is", "None", ":", "params", "=", "{"...	41.5625	0.000294
def find_experiment_export(app_id): """Attempt to find a zipped export of an experiment with the ID provided and return its path. Returns None if not found. Search order: 1. local "data" subdirectory 2. user S3 bucket 3. Dallinger S3 bucket """ # Check locally first cwd...	[ "def", "find_experiment_export", "(", "app_id", ")", ":", "# Check locally first", "cwd", "=", "os", ".", "getcwd", "(", ")", "data_filename", "=", "\"{}-data.zip\"", ".", "format", "(", "app_id", ")", "path_to_data", "=", "os", ".", "path", ".", "join", "("...	28.45	0.00085
def to_timestamp(dt, timestamp): """Convert datetime to google.protobuf.Timestamp. Args: dt: a timezone naive datetime. timestamp: a google.protobuf.Timestamp to populate. Raises: TypeError: if a timezone aware datetime was provided. """ if dt.tzinfo: # this is an "aware" datetime with an ex...	[ "def", "to_timestamp", "(", "dt", ",", "timestamp", ")", ":", "if", "dt", ".", "tzinfo", ":", "# this is an \"aware\" datetime with an explicit timezone. Throw an error.", "raise", "TypeError", "(", "'Cannot store a timezone aware datetime. '", "'Convert to UTC and store the naiv...	36	0.00846
def set_widgets(self): """Set widgets on the Field Mapping step.""" on_the_fly_metadata = {} layer_purpose = self.parent.step_kw_purpose.selected_purpose() on_the_fly_metadata['layer_purpose'] = layer_purpose['key'] if layer_purpose != layer_purpose_aggregation: subca...	[ "def", "set_widgets", "(", "self", ")", ":", "on_the_fly_metadata", "=", "{", "}", "layer_purpose", "=", "self", ".", "parent", ".", "step_kw_purpose", ".", "selected_purpose", "(", ")", "on_the_fly_metadata", "[", "'layer_purpose'", "]", "=", "layer_purpose", "...	52.818182	0.001691
def connectAt(self, fromName, toName, position = None): """ Connects two layers by instantiating an instance of Connection class. Allows a position number, indicating the ordering of the connection. """ fromLayer = self.getLayer(fromName) toLayer = self.getLayer...	[ "def", "connectAt", "(", "self", ",", "fromName", ",", "toName", ",", "position", "=", "None", ")", ":", "fromLayer", "=", "self", ".", "getLayer", "(", "fromName", ")", "toLayer", "=", "self", ".", "getLayer", "(", "toName", ")", "if", "self", ".", ...	49.193548	0.009003
def get_cluster_labels(hdf5_file, N_processes): """ Returns ------- cluster_centers_indices : array of shape (n_clusters,) Indices of cluster centers labels : array of shape (n_samples,) Specify the label of the cluster to which each point has been assigned. """ wit...	[ "def", "get_cluster_labels", "(", "hdf5_file", ",", "N_processes", ")", ":", "with", "Worker", ".", "hdf5_lock", ":", "with", "tables", ".", "open_file", "(", "hdf5_file", ",", "'r+'", ")", "as", "fileh", ":", "A", "=", "fileh", ".", "root", ".", "aff_pr...	33.570093	0.017036
def wrap(x): """ Wraps an element or integer type by serializing it and base64 encoding the resulting bytes. """ # Detect the type so we can call the proper serialization routine if isinstance(x, G1Element): return _wrap(x, serializeG1) elif isinstance(x, G2Element): return...	[ "def", "wrap", "(", "x", ")", ":", "# Detect the type so we can call the proper serialization routine", "if", "isinstance", "(", "x", ",", "G1Element", ")", ":", "return", "_wrap", "(", "x", ",", "serializeG1", ")", "elif", "isinstance", "(", "x", ",", "G2Elemen...	28.153846	0.009247
def getUsrCfgFilesForPyPkg(pkgName): """ See if the user has one of their own local .cfg files for this task, such as might be created automatically during the save of a read-only package, and return their names. """ # Get the python package and it's .cfg file thePkg, theFile = findCfgFileFo...	[ "def", "getUsrCfgFilesForPyPkg", "(", "pkgName", ")", ":", "# Get the python package and it's .cfg file", "thePkg", ",", "theFile", "=", "findCfgFileForPkg", "(", "pkgName", ",", "'.cfg'", ")", "# See if the user has any of their own local .cfg files for this task", "tname", "=...	53.3	0.001845
def get_bkg_qq_data(id=None, bkg_id=None): """Get data for a quantile-quantile plot of the background data and model. id The dataset id for which to get the data; defaults if unspecified. bkg_id The identifier of the background; defaults if unspecified. Returns: An ndarray of shap...	[ "def", "get_bkg_qq_data", "(", "id", "=", "None", ",", "bkg_id", "=", "None", ")", ":", "bdata", "=", "ui", ".", "get_bkg", "(", "id", "=", "id", ",", "bkg_id", "=", "bkg_id", ")", "kev", "=", "bdata", ".", "get_x", "(", ")", "obs_data", "=", "bd...	38.409091	0.001155
def members(name, ref): """ List the members of a specific dimension or the distinct values of a given attribute. """ cube = get_cube(name) result = cube.members(ref, cuts=request.args.get('cut'), order=request.args.get('order'), page=request.args.get(...	[ "def", "members", "(", "name", ",", "ref", ")", ":", "cube", "=", "get_cube", "(", "name", ")", "result", "=", "cube", ".", "members", "(", "ref", ",", "cuts", "=", "request", ".", "args", ".", "get", "(", "'cut'", ")", ",", "order", "=", "reques...	44	0.002227
def origin(hosts): """ Return a function that returns a valid HTTP Origin or localhost if none found. """ hosts = [urlsplit(h) for h in hosts] def func(environ): if 'ISSO_CORS_ORIGIN' in environ: return environ['ISSO_CORS_ORIGIN'] if not hosts: return "...	[ "def", "origin", "(", "hosts", ")", ":", "hosts", "=", "[", "urlsplit", "(", "h", ")", "for", "h", "in", "hosts", "]", "def", "func", "(", "environ", ")", ":", "if", "'ISSO_CORS_ORIGIN'", "in", "environ", ":", "return", "environ", "[", "'ISSO_CORS_ORIG...	23.37037	0.001522
def models_list(self, api_url=None, offset=0, limit=-1, properties=None): """Get list of model resources from a SCO-API. Parameters ---------- api_url : string, optional Base Url of the SCO-API. Uses default API if argument not present. offset : int, optional ...	[ "def", "models_list", "(", "self", ",", "api_url", "=", "None", ",", "offset", "=", "0", ",", "limit", "=", "-", "1", ",", "properties", "=", "None", ")", ":", "# Get subject listing Url for given SCO-API and return the retrieved", "# resource listing", "return", ...	35.25	0.001972
def read_table(fstream): """ Read a likwid table info from the text stream. Args: fstream: Likwid's filestream. Returns (dict(str: str)): A dict containing likwid's table info as key/value pairs. """ pos = fstream.tell() line = fstream.readline().strip() fragments = lin...	[ "def", "read_table", "(", "fstream", ")", ":", "pos", "=", "fstream", ".", "tell", "(", ")", "line", "=", "fstream", ".", "readline", "(", ")", ".", "strip", "(", ")", "fragments", "=", "line", ".", "split", "(", "\",\"", ")", "fragments", "=", "["...	27.081081	0.000963
def ne(self, other, ranks=None): """ Compares the card against another card, ``other``, and checks whether the card is not equal to ``other``, based on the given rank dict. :arg Card other: The second Card to compare. :arg dict ranks: The ranks to refer t...	[ "def", "ne", "(", "self", ",", "other", ",", "ranks", "=", "None", ")", ":", "ranks", "=", "ranks", "or", "DEFAULT_RANKS", "if", "isinstance", "(", "other", ",", "Card", ")", ":", "if", "ranks", ".", "get", "(", "\"suits\"", ")", ":", "return", "("...	31.518519	0.002281
def get_nanopubstore_start_dt(url: str): """Get last start_dt recorded for getting new nanopub ID's""" hostname = urllib.parse.urlsplit(url)[1] start_dates_doc = state_mgmt.get(start_dates_doc_key) if start_dates_doc and start_dates_doc.get("start_dates"): date = [ dt["start_dt"] ...	[ "def", "get_nanopubstore_start_dt", "(", "url", ":", "str", ")", ":", "hostname", "=", "urllib", ".", "parse", ".", "urlsplit", "(", "url", ")", "[", "1", "]", "start_dates_doc", "=", "state_mgmt", ".", "get", "(", "start_dates_doc_key", ")", "if", "start_...	33.470588	0.001709
def _z(self, x): """Standardize input `x` to a unit normal.""" with tf.name_scope("standardize"): return (x - self.loc) / self.scale	[ "def", "_z", "(", "self", ",", "x", ")", ":", "with", "tf", ".", "name_scope", "(", "\"standardize\"", ")", ":", "return", "(", "x", "-", "self", ".", "loc", ")", "/", "self", ".", "scale" ]	35.75	0.013699
def hide(self, fromQtmacs: bool=False): """ Overloaded ``hide()`` function to avoid calling it accidentally. This method is a (weak) security mechanism to prevent programmers from using the ``hide`` method as originally intended by Qt, ie. to hide a window. However, in Q...	[ "def", "hide", "(", "self", ",", "fromQtmacs", ":", "bool", "=", "False", ")", ":", "if", "not", "fromQtmacs", ":", "# Log a warning message if someone tries to call the", "# native hide() method.", "msg", "=", "(", "'hide() command for applet <b>{}</b> ignored. Use '", "...	41.204082	0.001935
def run_script(self, filename, wdir, args, debug, post_mortem, current_client, clear_variables): """Run script in current or dedicated client""" norm = lambda text: remove_backslashes(to_text_string(text)) # Run Cython files in a dedicated console is_cython = os...	[ "def", "run_script", "(", "self", ",", "filename", ",", "wdir", ",", "args", ",", "debug", ",", "post_mortem", ",", "current_client", ",", "clear_variables", ")", ":", "norm", "=", "lambda", "text", ":", "remove_backslashes", "(", "to_text_string", "(", "tex...	43.625	0.002179
def start(self): """Start performing the action.""" self.status = 'pending' self.thing.action_notify(self) self.perform_action() self.finish()	[ "def", "start", "(", "self", ")", ":", "self", ".", "status", "=", "'pending'", "self", ".", "thing", ".", "action_notify", "(", "self", ")", "self", ".", "perform_action", "(", ")", "self", ".", "finish", "(", ")" ]	29.5	0.010989
def populate_items(self, request): '''populate and returns filtered items''' self._items = self.get_items(request) return self.items	[ "def", "populate_items", "(", "self", ",", "request", ")", ":", "self", ".", "_items", "=", "self", ".", "get_items", "(", "request", ")", "return", "self", ".", "items" ]	38.25	0.012821
def send(self, url, data, headers): """ Spawn an async request to a remote webserver. """ eventlet.spawn(self._send_payload, (url, data, headers))	[ "def", "send", "(", "self", ",", "url", ",", "data", ",", "headers", ")", ":", "eventlet", ".", "spawn", "(", "self", ".", "_send_payload", ",", "(", "url", ",", "data", ",", "headers", ")", ")" ]	34.8	0.011236
def _availableResultsFraction( self ): """Private method to return the fraction of results available, as a real number between 0 and 1. This does not update the results fetched from the cluster. :returns: the fraction of available results""" tr = self.notebook().numberOfResults() + self...	[ "def", "_availableResultsFraction", "(", "self", ")", ":", "tr", "=", "self", ".", "notebook", "(", ")", ".", "numberOfResults", "(", ")", "+", "self", ".", "notebook", "(", ")", ".", "numberOfPendingResults", "(", ")", "if", "tr", "==", "0", ":", "ret...	46.8	0.014675
def get(self, args, kw): """Load the configuration if necessary and forward the call to the parent.""" if not self._loaded: self.load_config() return super(FedmsgConfig, self).get(args, **kw)	[ "def", "get", "(", "self", ",", "", "args", ",", "", "", "kw", ")", ":", "if", "not", "self", ".", "_loaded", ":", "self", ".", "load_config", "(", ")", "return", "super", "(", "FedmsgConfig", ",", "self", ")", ".", "get", "(", "", "args", ...	45.4	0.012987
def set_identifier(self, uid): """ Sets unique id for this epub :Args: - uid: Value of unique identifier for this book """ self.uid = uid self.set_unique_metadata('DC', 'identifier', self.uid, {'id': self.IDENTIFIER_ID})	[ "def", "set_identifier", "(", "self", ",", "uid", ")", ":", "self", ".", "uid", "=", "uid", "self", ".", "set_unique_metadata", "(", "'DC'", ",", "'identifier'", ",", "self", ".", "uid", ",", "{", "'id'", ":", "self", ".", "IDENTIFIER_ID", "}", ")" ]	24.636364	0.010676
def settings_and_attributes(self): """Return a combined dictionary of setting values and attribute values.""" attrs = self.setting_values() attrs.update(self.__dict__) skip = ["_instance_settings", "aliases"] for a in skip: del attrs[a] return attrs	[ "def", "settings_and_attributes", "(", "self", ")", ":", "attrs", "=", "self", ".", "setting_values", "(", ")", "attrs", ".", "update", "(", "self", ".", "__dict__", ")", "skip", "=", "[", "\"_instance_settings\"", ",", "\"aliases\"", "]", "for", "a", "in"...	37.75	0.009709
def mendelian_errors2(args): """ %prog mendelian_errors2 Trios.summary.csv Plot Mendelian errors as calculated by mendelian(). File `Trios.summary.csv` looks like: Name,Motif,Inheritance,N_Correct,N_Error,N_missing,ErrorRate [N_Error / (N_Correct + N_Error))] DM1,CTG,AD,790,12,0,1.5% DM2,C...	[ "def", "mendelian_errors2", "(", "args", ")", ":", "p", "=", "OptionParser", "(", "mendelian_errors2", ".", "__doc__", ")", "opts", ",", "args", ",", "iopts", "=", "p", ".", "set_image_options", "(", "args", ",", "figsize", "=", "\"7x7\"", ",", "format", ...	31.304348	0.001795
def parseFile(filename): """parse an XML file and build a tree. Automatic support for ZLIB/Compress compressed document is provided by default if found at compile-time. """ ret = libxml2mod.xmlParseFile(filename) if ret is None:raise parserError('xmlParseFile() failed') return xmlDoc(_obj=r...	[ "def", "parseFile", "(", "filename", ")", ":", "ret", "=", "libxml2mod", ".", "xmlParseFile", "(", "filename", ")", "if", "ret", "is", "None", ":", "raise", "parserError", "(", "'xmlParseFile() failed'", ")", "return", "xmlDoc", "(", "_obj", "=", "ret", ")...	45.285714	0.009288
def print_param_values(self_): """Print the values of all this object's Parameters.""" self = self_.self for name,val in self.param.get_param_values(): print('%s.%s = %s' % (self.name,name,val))	[ "def", "print_param_values", "(", "self_", ")", ":", "self", "=", "self_", ".", "self", "for", "name", ",", "val", "in", "self", ".", "param", ".", "get_param_values", "(", ")", ":", "print", "(", "'%s.%s = %s'", "%", "(", "self", ".", "name", ",", "...	45.2	0.021739
def _exit_gracefully(self, signum, frame): """ Helper method to clean up DAG file processors to avoid leaving orphan processes. """ self.log.info("Exiting gracefully upon receiving signal %s", signum) self.terminate() self.end() self.log.debug("Finished terminatin...	[ "def", "_exit_gracefully", "(", "self", ",", "signum", ",", "frame", ")", ":", "self", ".", "log", ".", "info", "(", "\"Exiting gracefully upon receiving signal %s\"", ",", "signum", ")", "self", ".", "terminate", "(", ")", "self", ".", "end", "(", ")", "s...	39.777778	0.008197
def matchItem(self, item): ''' [OPTIONAL] Attempts to find the specified item and returns an item that describes the same object although it's specific properties may be different. For example, a contact whose name is an identical match, but whose telephone number has changed would return the ma...	[ "def", "matchItem", "(", "self", ",", "item", ")", ":", "for", "match", "in", "self", ".", "getAllItems", "(", ")", ":", "if", "cmp", "(", "match", ",", "item", ")", "==", "0", ":", "return", "match", "return", "None" ]	40.59375	0.001504
def inspect_phone(self, gps_lat_long = [137.0000,100.0000], moving = False, move_dist_2_mn = 4, on_charge = True, screen_saver = False): """ FUNCTION STUB - TODO The intention is to get data from the mobile in the format: gps_lat = 137.000 gps_lng = 100.00...	[ "def", "inspect_phone", "(", "self", ",", "gps_lat_long", "=", "[", "137.0000", ",", "100.0000", "]", ",", "moving", "=", "False", ",", "move_dist_2_mn", "=", "4", ",", "on_charge", "=", "True", ",", "screen_saver", "=", "False", ")", ":", "self", ".", ...	39.44186	0.011507
def receive_trial_result(self, parameter_id, parameters, value): """ Record an observation of the objective function Parameters ---------- parameter_id : int parameters : dict value : dict/float if value is dict, it should have "default" key. ...	[ "def", "receive_trial_result", "(", "self", ",", "parameter_id", ",", "parameters", ",", "value", ")", ":", "reward", "=", "extract_scalar_reward", "(", "value", ")", "# restore the paramsters contains '_index'", "if", "parameter_id", "not", "in", "self", ".", "tota...	33.181818	0.001597
def build_extra_headers(request, proxyMode, orgaMode, currentOrga): """Build the list of extra headers""" things_to_add = {} # If in proxymode, add needed infos to headers if proxyMode: # User for prop in settings.PIAPI_USERDATA: if hasattr(request.user, prop): ...	[ "def", "build_extra_headers", "(", "request", ",", "proxyMode", ",", "orgaMode", ",", "currentOrga", ")", ":", "things_to_add", "=", "{", "}", "# If in proxymode, add needed infos to headers", "if", "proxyMode", ":", "# User", "for", "prop", "in", "settings", ".", ...	40.205882	0.002143
def to_subject_id(s): ''' to_subject_id(s) coerces the given string or number into an integer subject id. If s is not a valid subejct id, raises an exception. ''' if not pimms.is_number(s) and not pimms.is_str(s): raise ValueError('invalid type for subject id: %s' % str(type(s))) if pi...	[ "def", "to_subject_id", "(", "s", ")", ":", "if", "not", "pimms", ".", "is_number", "(", "s", ")", "and", "not", "pimms", ".", "is_str", "(", "s", ")", ":", "raise", "ValueError", "(", "'invalid type for subject id: %s'", "%", "str", "(", "type", "(", ...	39.6	0.009868
def create_more_container_files(sourceDir, suffix, maxElements, containers, containers2): """Creates additional files for the individual MPL-containers.""" # Create files for each MPL-container with 20 to 'maxElements' elements # which will be used during generation. for container in containers: ...	[ "def", "create_more_container_files", "(", "sourceDir", ",", "suffix", ",", "maxElements", ",", "containers", ",", "containers2", ")", ":", "# Create files for each MPL-container with 20 to 'maxElements' elements", "# which will be used during generation.", "for", "container", "i...	63.151515	0.012287
def logging_level(level): """ Temporarily modify param's logging level. """ level = level.upper() levels = [DEBUG, INFO, WARNING, ERROR, CRITICAL, VERBOSE] level_names = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL', 'VERBOSE'] if level not in level_names: raise Exception("Level ...	[ "def", "logging_level", "(", "level", ")", ":", "level", "=", "level", ".", "upper", "(", ")", "levels", "=", "[", "DEBUG", ",", "INFO", ",", "WARNING", ",", "ERROR", ",", "CRITICAL", ",", "VERBOSE", "]", "level_names", "=", "[", "'DEBUG'", ",", "'IN...	31.5	0.001712
def byte_str(s="", encoding="utf-8", input_encoding="utf-8", errors="strict"): """ Returns a byte string version of 's', encoded as specified in 'encoding'. Accepts str & unicode objects, interpreting non-unicode strings as byte strings encoded using the given input encoding. """ assert isinst...	[ "def", "byte_str", "(", "s", "=", "\"\"", ",", "encoding", "=", "\"utf-8\"", ",", "input_encoding", "=", "\"utf-8\"", ",", "errors", "=", "\"strict\"", ")", ":", "assert", "isinstance", "(", "s", ",", "basestring", ")", "if", "isinstance", "(", "s", ",",...	37.571429	0.001855
def add_logging_level(name, value, method_name=None): ''' Comprehensively adds a new logging level to the ``logging`` module and the currently configured logging class. Derived from: https://stackoverflow.com/a/35804945/450917 ''' if not method_name: method_name = name.lower() ...	[ "def", "add_logging_level", "(", "name", ",", "value", ",", "method_name", "=", "None", ")", ":", "if", "not", "method_name", ":", "method_name", "=", "name", ".", "lower", "(", ")", "# set levels", "logging", ".", "addLevelName", "(", "value", ",", "name"...	37.866667	0.000858
def get_plan_from_dual(alpha, beta, C, regul): """ Retrieve optimal transportation plan from optimal dual potentials. Parameters ---------- alpha: array, shape = len(a) beta: array, shape = len(b) Optimal dual potentials. C: array, shape = len(a) x len(b) Ground cost matrix....	[ "def", "get_plan_from_dual", "(", "alpha", ",", "beta", ",", "C", ",", "regul", ")", ":", "X", "=", "alpha", "[", ":", ",", "np", ".", "newaxis", "]", "+", "beta", "-", "C", "return", "regul", ".", "delta_Omega", "(", "X", ")", "[", "1", "]" ]	26.952381	0.001706
def decode_lazy(rlp, sedes=None, **sedes_kwargs): """Decode an RLP encoded object in a lazy fashion. If the encoded object is a bytestring, this function acts similar to :func:`rlp.decode`. If it is a list however, a :class:`LazyList` is returned instead. This object will decode the string lazily, avoi...	[ "def", "decode_lazy", "(", "rlp", ",", "sedes", "=", "None", ",", "", "", "sedes_kwargs", ")", ":", "item", ",", "end", "=", "consume_item_lazy", "(", "rlp", ",", "0", ")", "if", "end", "!=", "len", "(", "rlp", ")", ":", "raise", "DecodingError", ...	46.5	0.001859
def set_sampling_strategies(self, filter, strategy_and_params): """Set sampling strategy for the sensors of all the group's clients. Only sensors that match the specified filter are considered. See the `KATCPResource.set_sampling_strategies` docstring for parameter definitions and more ...	[ "def", "set_sampling_strategies", "(", "self", ",", "filter", ",", "strategy_and_params", ")", ":", "futures_dict", "=", "{", "}", "for", "res_obj", "in", "self", ".", "clients", ":", "futures_dict", "[", "res_obj", ".", "name", "]", "=", "res_obj", ".", "...	45.4	0.002157
def close(self): """Close the pool by closing and removing all of the connections""" for cid in list(self.connections.keys()): self.remove(self.connections[cid].handle) LOGGER.debug('Pool %s closed', self.id)	[ "def", "close", "(", "self", ")", ":", "for", "cid", "in", "list", "(", "self", ".", "connections", ".", "keys", "(", ")", ")", ":", "self", ".", "remove", "(", "self", ".", "connections", "[", "cid", "]", ".", "handle", ")", "LOGGER", ".", "debu...	48	0.008197
def calculate_solidity(labels,indexes=None): """Calculate the area of each label divided by the area of its convex hull labels - a label matrix indexes - the indexes of the labels to measure """ if indexes is not None: """ Convert to compat 32bit integer """ indexes = np.array(i...	[ "def", "calculate_solidity", "(", "labels", ",", "indexes", "=", "None", ")", ":", "if", "indexes", "is", "not", "None", ":", "\"\"\" Convert to compat 32bit integer \"\"\"", "indexes", "=", "np", ".", "array", "(", "indexes", ",", "dtype", "=", "np", ".", "...	41.416667	0.011811
def declare_dict(self): """Return declared sections, terms and synonyms as a dict""" # Run the parser, if it has not been run yet. if not self.root: for _ in self: pass return { 'sections': self._declared_sections, 'terms': self._declared_terms, ...	[ "def", "declare_dict", "(", "self", ")", ":", "# Run the parser, if it has not been run yet.", "if", "not", "self", ".", "root", ":", "for", "_", "in", "self", ":", "pass", "return", "{", "'sections'", ":", "self", ".", "_declared_sections", ",", "'terms'", ":...	32	0.008287
def Poll(generator=None, condition=None, interval=None, timeout=None): """Periodically calls generator function until a condition is satisfied.""" if not generator: raise ValueError("generator has to be a lambda") if not condition: raise ValueError("condition has to be a lambda") if interval is None:...	[ "def", "Poll", "(", "generator", "=", "None", ",", "condition", "=", "None", ",", "interval", "=", "None", ",", "timeout", "=", "None", ")", ":", "if", "not", "generator", ":", "raise", "ValueError", "(", "\"generator has to be a lambda\"", ")", "if", "not...	27.115385	0.013699
def _get_bokeh_chart(self, x_field, y_field, chart_type, label, opts, style, options={}, **kwargs): """ Get a Bokeh chart object """ if isinstance(x_field, list): kdims = x_field else: kdims = [x_field] if isinstance(y_fiel...	[ "def", "_get_bokeh_chart", "(", "self", ",", "x_field", ",", "y_field", ",", "chart_type", ",", "label", ",", "opts", ",", "style", ",", "options", "=", "{", "}", ",", "", "", "kwargs", ")", ":", "if", "isinstance", "(", "x_field", ",", "list", ")"...	36.607143	0.002375
def _perform_version(self, version): """Inner method for version upgrade. Not intended for standalone use. This method performs the actual version upgrade with all the pre, post operations and addons upgrades. :param version: The migration version to upgrade to :type version: I...	[ "def", "_perform_version", "(", "self", ",", "version", ")", ":", "if", "version", ".", "is_noop", "(", ")", ":", "self", ".", "log", "(", "u'version {} is a noop'", ".", "format", "(", "version", ".", "number", ")", ")", "else", ":", "self", ".", "log...	43.103448	0.001565
def request(self, method: str, url: StrOrURL, kwargs: Any) -> '_RequestContextManager': """Perform HTTP request.""" return _RequestContextManager(self._request(method, url, kwargs))	[ "def", "request", "(", "self", ",", "method", ":", "str", ",", "url", ":", "StrOrURL", ",", "", "", "kwargs", ":", "Any", ")", "->", "'_RequestContextManager'", ":", "return", "_RequestContextManager", "(", "self", ".", "_request", "(", "method", ",", ...	40.666667	0.02008
def WriteToFD(self, fd): """Write out the updated configuration to the fd.""" if self.writeback: self.writeback.SaveDataToFD(self.writeback_data, fd) else: raise RuntimeError("Attempting to write a configuration without a " "writeback location.")	[ "def", "WriteToFD", "(", "self", ",", "fd", ")", ":", "if", "self", ".", "writeback", ":", "self", ".", "writeback", ".", "SaveDataToFD", "(", "self", ".", "writeback_data", ",", "fd", ")", "else", ":", "raise", "RuntimeError", "(", "\"Attempting to write ...	41.285714	0.010169
def update(self, language=values.unset, tagged_text=values.unset, source_channel=values.unset): """ Update the SampleInstance :param unicode language: The ISO language-country string that specifies the language used for the sample :param unicode tagged_text: The text exam...	[ "def", "update", "(", "self", ",", "language", "=", "values", ".", "unset", ",", "tagged_text", "=", "values", ".", "unset", ",", "source_channel", "=", "values", ".", "unset", ")", ":", "return", "self", ".", "_proxy", ".", "update", "(", "language", ...	53.384615	0.009915
def hdf5_cache(filepath=None, parent=None, group=None, names=None, typed=False, hashed_key=False, **h5dcreate_kwargs): """HDF5 cache decorator. Parameters ---------- filepath : string, optional Path to HDF5 file. If None a temporary file name will be used. parent : string, op...	[ "def", "hdf5_cache", "(", "filepath", "=", "None", ",", "parent", "=", "None", ",", "group", "=", "None", ",", "names", "=", "None", ",", "typed", "=", "False", ",", "hashed_key", "=", "False", ",", "", "", "h5dcreate_kwargs", ")", ":", "# initialise...	31.420168	0.000259
def call_functions_parallel(worker_defs): """Call specified functions in parallel. :param worker_defs: Each positional argument can be either of a function to be called or a tuple which consists of a function, a list of positional arguments) and keyword arguments (optional). If you ne...	[ "def", "call_functions_parallel", "(", "*", "worker_defs", ")", ":", "# TODO(amotoki): Needs to figure out what max_workers can be specified.", "# According to e0ne, the apache default configuration in devstack allows", "# only 10 threads. What happens if max_worker=11 is specified?", "max_work...	50.272727	0.000591

def get_languages(self): """ :calls: `GET /repos/:owner/:repo/languages <http://developer.github.com/v3/repos>`_ :rtype: dict of string to integer """ headers, data = self._requester.requestJsonAndCheck( "GET", self.url + "/languages" ) ret...

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def time_multi_coincidence(times, slide_step=0, slop=.003, pivot='H1', fixed='L1'): """ Find multi detector concidences. Parameters ---------- times: dict of numpy.ndarrays Dictionary keyed by ifo of the times of each single detector trigger. slide_step: float ...

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def troutslap(rest): "Slap some(one|thing) with a fish" slapee = rest karma.Karma.store.change(slapee, -1) return "/me slaps %s around a bit with a large trout" % slapee

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def _GceMetadataRequest(relative_url, use_metadata_ip=False): """Request the given url from the GCE metadata service.""" if use_metadata_ip: base_url = os.environ.get('GCE_METADATA_IP', '169.254.169.254') else: base_url = os.environ.get( 'GCE_METADATA_ROOT', 'metadata.google.inte...

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def _try_reduce(self) -> Tuple[List["HdlStatement"], bool]: """ Doc on parent class :meth:`HdlStatement._try_reduce` """ io_change = False new_cases = [] for val, statements in self.cases: _statements, rank_decrease, _io_change = self._try_reduce_list( ...

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def ls_handler(self, args): '''Handler for ls command''' if len(args) == 1: self.pretty_print(self.s3handler().list_buckets()) return self.validate('cmd|s3', args) self.pretty_print(self.s3handler().s3walk(args[1]))

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def import_plugin(name): """Imports plugin python module""" path = os.path.join("plugins", name + ".py") try: with open(path, 'rb') as f: try: plugin = imp.load_module( "p_" + name, f, name + '.py', ('.py', 'rb', imp.PY_SOURCE) ...

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def create_parser(parser: argparse.ArgumentParser) -> None: """ Creates the parser by setting all the possible arguments :param parser: The parser """ parser.add_argument("solidity_file", nargs="*") commands = parser.add_argument_group("commands") commands.add_argument("-g", "--graph", help...

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def UpdateFlows(self, client_id_flow_id_pairs, pending_termination=db.Database.unchanged, cursor=None): """Updates flow objects in the database.""" if pending_termination == db.Database.unchanged: return serialized_termination = pending_terminati...

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def _do_unjoin_packet(self, packet, ip, port): """ React to unjoin packet - remove a client from this server :param packet: Packet from client that wants to join :type packet: paps.si.app.message.APPJoinMessage :param ip: Client ip address :type ip: unicode :para...

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def get_cuda_visible_devices(): """Get the device IDs in the CUDA_VISIBLE_DEVICES environment variable. Returns: if CUDA_VISIBLE_DEVICES is set, this returns a list of integers with the IDs of the GPUs. If it is not set, this returns None. """ gpu_ids_str = os.environ.get("CUDA_VISI...

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def ToHashArray(self): """ Turn the tree into a list of hashes. Returns: list: """ hashes = set() MerkleTree.__DepthFirstSearch(self.Root, hashes) return list(hashes)

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def drop_database(self, name_or_database, session=None): """Drop a database. Raises :class:`TypeError` if `name_or_database` is not an instance of :class:`basestring` (:class:`str` in python 3) or :class:`~pymongo.database.Database`. :Parameters: - `name_or_database`:...

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def parse_value_namedinstance(self, tup_tree): """ :: <!ELEMENT VALUE.NAMEDINSTANCE (INSTANCENAME, INSTANCE)> Returns: CIMInstance object with path set (without host or namespace). """ self.check_node(tup_tree, 'VALUE.NAMEDINSTANCE') k = kids...

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def _make_f_expectation(self, expr): """ Calculates :math:`<F>` in eq. 12 (see Ale et al. 2013) to calculate :math:`<F>` for EACH VARIABLE combination. :param expr: an expression :return: a column vector. Each row correspond to an element of counter. :rtype: :class:`sympy.Matrix...

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def send_dynamic_message(sender, message): """Send a dynamic message to the listeners. Dynamic messages represents a progress. Usually it will be appended to the previous messages. .. versionadded:: 3.3 :param sender: The sender. :type sender: object :param message: An instance of our ri...

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def _get_column_boundaries(self): '''Use the guessed ends to guess the boundaries of the plain text columns. ''' # Try to figure out the most common column boundaries. ends = self._get_column_ends() if not ends: # If there aren't even any nontrivial sequences ...

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def execute_and_reset( expr, params=None, scope=None, aggcontext=None, **kwargs ): """Execute an expression against data that are bound to it. If no data are bound, raise an Exception. Notes ----- The difference between this function and :func:`~ibis.pandas.core.execute` is that this functi...

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def is_empty(self): """ Test interval emptiness. :return: True if interval is empty, False otherwise. """ return ( self._lower > self._upper or (self._lower == self._upper and (self._left == OPEN or self._right == OPEN)) )

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def booleanized(values, min_value, max_value, hysteresis=0): """ Returns True for each item in *values* between *min_value* and *max_value*, and False otherwise. *hysteresis* can optionally be used to add `hysteresis`_ which prevents the output value rapidly flipping when the input value is fluctuat...

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def pick_free_port(hostname=REDIRECT_HOST, port=0): """ Try to bind a port. Default=0 selects a free port. """ import socket s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) try: s.bind((hostname, port)) # port=0 finds an open port except OSError as e: log.warning("Could not bi...

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def __update_upgrades_table(self, delta): """Add a new record into the upgrades information table about the applied delta Parameters ---------- delta: Delta the applied delta file""" query = """ INSERT INTO {} ( --id, version,...

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def cached(self, TTL=60 * 24): '''A decorator that will cache the output of the wrapped function. The key used for the cache is the function name as well as the `*args` and `**kwargs` passed to the function. :param TTL: time to live in minutes .. note:: For route caching, you s...

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def _find_supported_challenge(authzr, responders): """ Find a challenge combination that consists of a single challenge that the responder can satisfy. :param ~acme.messages.AuthorizationResource auth: The authorization to examine. :type responder: List[`~txacme.interfaces.IResponder`] ...

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def argv(*args, **opts): """ Produces an argument vector from its array of arguments and keyword options. First, the options are unpacked. When the value is a ``bool``, the option is passed without an argument if it is true and skipped if it is ``false``. When the option is one of the flat built-in ...

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def _get_template_dirs(): """existing directories where to search for jinja2 templates. The order is important. The first found template from the first found dir wins!""" return filter(lambda x: os.path.exists(x), [ # user dir os.path.join(os.path.expanduser('~'), '.py2pack', 'templates'), ...

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def get_spectrogram(self): """Calculate the spectrogram to be plotted This exists as a separate method to allow subclasses to override this and not the entire `get_plot` method, e.g. `Coherencegram`. This method should not apply the normalisation from `args.norm`. """ a...

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def create(cls, fpath): "Creates a `Config` from `fpath`." fpath = _expand_path(fpath) assert(fpath.suffix == '.yml') if fpath.exists(): return fpath.parent.mkdir(parents=True, exist_ok=True) with open(fpath, 'w') as yaml_file: yaml.dump(cls.DEFAULT_CONFIG, ya...

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def get_used_in_func(node): '''Get names, but ignore variables names to the left hand side That is to say, in case of a = b + 1 we consider b as "being accessed", while a is not. ''' if isinstance(node, ast.FunctionDef): return {node.name: get_accessed(node.body)} names = {} f...

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def segment_midpoints_by_vertices(self, vertices): """ Add midpoints to any segment connected to the vertices in the list / array provided. """ segments = set() for vertex in vertices: neighbours = self.identify_vertex_neighbours(vertex) segments...

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def screenshot(self, filename=None): """ Take screen snapshot Args: - filename: filename where save to, optional Returns: PIL.Image object Raises: TypeError, IOError """ if self.__keep_screen: return self.__last_s...

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def appendInputWithSimilarValues(inputs): """ Creates an 'one-off' record for each record in the inputs. Appends new records to the same inputs list. """ numInputs = len(inputs) for i in xrange(numInputs): input = inputs[i] for j in xrange(len(input)-1): if input[j] == 1 and input[j+1] == 0: ...

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def interpolate(self, transform, transitions=None, Y=None): """Interpolate new data onto a transformation of the graph data One of either transitions or Y should be provided Parameters ---------- transform : array-like, shape=[n_samples, n_transform_features] transiti...

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def soft_kill(jid, state_id=None): ''' Set up a state run to die before executing the given state id, this instructs a running state to safely exit at a given state id. This needs to pass in the jid of the running state. If a state_id is not passed then the jid referenced will be safely exited a...

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def build_for_contour_tree(self, contour_tree, negate=False): """ A helper function that will reduce duplication of data by reusing the parent contour tree's parameters and data """ if self.debug: tree_type = "Join" if negate: tree_type = "Spli...

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def write_file(environ, term='bash', out_dir=None, tree_dir=None): ''' Write a tree environment file Loops over the tree environ and writes them out to a bash, tsch, or modules file Parameters: environ (dict): The tree dictionary environment term (str): The type...

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def _save_image(fig, filename, filetype='png', resolution=300): """ If filename is specified, saves the image :param str filename: Name of the file :param str filetype: Type of file :param int resolution: DPI resolution of the output figure """ if filename: fi...

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def inject_config(self, config, from_args): """ :param config: :type config: list :param from_args: :type from_args: dict """ # First get required values from labelStore runtime = self._get_runtime() whitelist = self._get_whitelist() #Run introspection on the libraries to retriev...

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def breakpoint(args): """ %prog breakpoint blastfile bedfile [options] Identify breakpoints where collinearity ends. `blastfile` contains mapping from markers (query) to scaffolds (subject). `bedfile` contains marker locations in the related species. """ from jcvi.formats.blast import bed ...

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def knapsack(p, v, cmax): """Knapsack problem: select maximum value set of items if total size not more than capacity :param p: table with size of items :param v: table with value of items :param cmax: capacity of bag :requires: number of items non-zero :returns: value optimal solution, list of...

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def clean(args): """ %prog clean fastafile Remove irregular chars in FASTA seqs. """ p = OptionParser(clean.__doc__) p.add_option("--fancy", default=False, action="store_true", help="Pretty print the sequence [default: %default]") p.add_option("--canonical", default=False, ...

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def create_secret( name, namespace='default', data=None, source=None, template=None, saltenv='base', **kwargs): ''' Creates the kubernetes secret as defined by the user. CLI Examples:: salt 'minion1' kubernetes.create_secret \ pas...

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def WriteClientMetadata(self, client_id, certificate=None, fleetspeak_enabled=None, first_seen=None, last_ping=None, last_clock=None, last...

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def ask_dir(self): """ dialogue box for choosing directory """ args ['directory'] = askdirectory(**self.dir_opt) self.dir_text.set(args ['directory'])

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def hierarchical_group_items(item_list, groupids_list): """ Generalization of group_item. Convert a flast list of ids into a heirarchical dictionary. TODO: move to util_dict Reference: http://stackoverflow.com/questions/10193235/python-translate-a-table-to-a-hierarchical-dictionary Args: ...

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def serialize_example(transformed_json_data, features, feature_indices, target_name): """Makes an instance of data in libsvm format. Args: transformed_json_data: dict of transformed data. features: features config. feature_indices: output of feature_transforms.get_transformed_feature_indices() Retur...

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def process_log_event(event, context): """Lambda Entrypoint - Log Subscriber Format log events and relay to sentry (direct or sqs) """ init() # Grab the actual error log payload serialized = event['awslogs'].pop('data') data = json.loads(zlib.decompress( base64.b64decode(serialized)...

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def assign_value(self, comp_def, value, src_ref): """ Used by the compiler for either local or dynamic prop assignments This does the following: - Check that the property is allowed in this component - Check if the value being assigned is compatible - Assign t...

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def set_default_config(modules, params=None, yaml=None, filename=None, config=None, validate=True): """Set up global configuration for tests and noninteractive tools. `modules` is an iterable of :class:`yakonfig.Configurable` objects, or anything equivalently typed. This functio...

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def find_experiment_export(app_id): """Attempt to find a zipped export of an experiment with the ID provided and return its path. Returns None if not found. Search order: 1. local "data" subdirectory 2. user S3 bucket 3. Dallinger S3 bucket """ # Check locally first cwd...

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def to_timestamp(dt, timestamp): """Convert datetime to google.protobuf.Timestamp. Args: dt: a timezone naive datetime. timestamp: a google.protobuf.Timestamp to populate. Raises: TypeError: if a timezone aware datetime was provided. """ if dt.tzinfo: # this is an "aware" datetime with an ex...

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def set_widgets(self): """Set widgets on the Field Mapping step.""" on_the_fly_metadata = {} layer_purpose = self.parent.step_kw_purpose.selected_purpose() on_the_fly_metadata['layer_purpose'] = layer_purpose['key'] if layer_purpose != layer_purpose_aggregation: subca...

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def connectAt(self, fromName, toName, position = None): """ Connects two layers by instantiating an instance of Connection class. Allows a position number, indicating the ordering of the connection. """ fromLayer = self.getLayer(fromName) toLayer = self.getLayer...

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def get_cluster_labels(hdf5_file, N_processes): """ Returns ------- cluster_centers_indices : array of shape (n_clusters,) Indices of cluster centers labels : array of shape (n_samples,) Specify the label of the cluster to which each point has been assigned. """ wit...

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def wrap(x): """ Wraps an element or integer type by serializing it and base64 encoding the resulting bytes. """ # Detect the type so we can call the proper serialization routine if isinstance(x, G1Element): return _wrap(x, serializeG1) elif isinstance(x, G2Element): return...

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def getUsrCfgFilesForPyPkg(pkgName): """ See if the user has one of their own local .cfg files for this task, such as might be created automatically during the save of a read-only package, and return their names. """ # Get the python package and it's .cfg file thePkg, theFile = findCfgFileFo...

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def get_bkg_qq_data(id=None, bkg_id=None): """Get data for a quantile-quantile plot of the background data and model. *id* The dataset id for which to get the data; defaults if unspecified. *bkg_id* The identifier of the background; defaults if unspecified. Returns: An ndarray of shap...

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def members(name, ref): """ List the members of a specific dimension or the distinct values of a given attribute. """ cube = get_cube(name) result = cube.members(ref, cuts=request.args.get('cut'), order=request.args.get('order'), page=request.args.get(...

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def origin(hosts): """ Return a function that returns a valid HTTP Origin or localhost if none found. """ hosts = [urlsplit(h) for h in hosts] def func(environ): if 'ISSO_CORS_ORIGIN' in environ: return environ['ISSO_CORS_ORIGIN'] if not hosts: return "...

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def models_list(self, api_url=None, offset=0, limit=-1, properties=None): """Get list of model resources from a SCO-API. Parameters ---------- api_url : string, optional Base Url of the SCO-API. Uses default API if argument not present. offset : int, optional ...

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def read_table(fstream): """ Read a likwid table info from the text stream. Args: fstream: Likwid's filestream. Returns (dict(str: str)): A dict containing likwid's table info as key/value pairs. """ pos = fstream.tell() line = fstream.readline().strip() fragments = lin...

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def ne(self, other, ranks=None): """ Compares the card against another card, ``other``, and checks whether the card is not equal to ``other``, based on the given rank dict. :arg Card other: The second Card to compare. :arg dict ranks: The ranks to refer t...

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def get_nanopubstore_start_dt(url: str): """Get last start_dt recorded for getting new nanopub ID's""" hostname = urllib.parse.urlsplit(url)[1] start_dates_doc = state_mgmt.get(start_dates_doc_key) if start_dates_doc and start_dates_doc.get("start_dates"): date = [ dt["start_dt"] ...

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def _z(self, x): """Standardize input `x` to a unit normal.""" with tf.name_scope("standardize"): return (x - self.loc) / self.scale

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def hide(self, fromQtmacs: bool=False): """ Overloaded ``hide()`` function to avoid calling it accidentally. This method is a (weak) security mechanism to prevent programmers from using the ``hide`` method as originally intended by Qt, ie. to hide a window. However, in Q...

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def run_script(self, filename, wdir, args, debug, post_mortem, current_client, clear_variables): """Run script in current or dedicated client""" norm = lambda text: remove_backslashes(to_text_string(text)) # Run Cython files in a dedicated console is_cython = os...

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def start(self): """Start performing the action.""" self.status = 'pending' self.thing.action_notify(self) self.perform_action() self.finish()

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def populate_items(self, request): '''populate and returns filtered items''' self._items = self.get_items(request) return self.items

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def send(self, url, data, headers): """ Spawn an async request to a remote webserver. """ eventlet.spawn(self._send_payload, (url, data, headers))

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def _availableResultsFraction( self ): """Private method to return the fraction of results available, as a real number between 0 and 1. This does not update the results fetched from the cluster. :returns: the fraction of available results""" tr = self.notebook().numberOfResults() + self...

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def get(self, *args, **kw): """Load the configuration if necessary and forward the call to the parent.""" if not self._loaded: self.load_config() return super(FedmsgConfig, self).get(*args, **kw)

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def set_identifier(self, uid): """ Sets unique id for this epub :Args: - uid: Value of unique identifier for this book """ self.uid = uid self.set_unique_metadata('DC', 'identifier', self.uid, {'id': self.IDENTIFIER_ID})

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def settings_and_attributes(self): """Return a combined dictionary of setting values and attribute values.""" attrs = self.setting_values() attrs.update(self.__dict__) skip = ["_instance_settings", "aliases"] for a in skip: del attrs[a] return attrs

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def mendelian_errors2(args): """ %prog mendelian_errors2 Trios.summary.csv Plot Mendelian errors as calculated by mendelian(). File `Trios.summary.csv` looks like: Name,Motif,Inheritance,N_Correct,N_Error,N_missing,ErrorRate [N_Error / (N_Correct + N_Error))] DM1,CTG,AD,790,12,0,1.5% DM2,C...

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def parseFile(filename): """parse an XML file and build a tree. Automatic support for ZLIB/Compress compressed document is provided by default if found at compile-time. """ ret = libxml2mod.xmlParseFile(filename) if ret is None:raise parserError('xmlParseFile() failed') return xmlDoc(_obj=r...

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def print_param_values(self_): """Print the values of all this object's Parameters.""" self = self_.self for name,val in self.param.get_param_values(): print('%s.%s = %s' % (self.name,name,val))

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def _exit_gracefully(self, signum, frame): """ Helper method to clean up DAG file processors to avoid leaving orphan processes. """ self.log.info("Exiting gracefully upon receiving signal %s", signum) self.terminate() self.end() self.log.debug("Finished terminatin...

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def matchItem(self, item): ''' [OPTIONAL] Attempts to find the specified item and returns an item that describes the same object although it's specific properties may be different. For example, a contact whose name is an identical match, but whose telephone number has changed would return the ma...

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def inspect_phone(self, gps_lat_long = [137.0000,100.0000], moving = False, move_dist_2_mn = 4, on_charge = True, screen_saver = False): """ FUNCTION STUB - TODO The intention is to get data from the mobile in the format: gps_lat = 137.000 gps_lng = 100.00...

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def receive_trial_result(self, parameter_id, parameters, value): """ Record an observation of the objective function Parameters ---------- parameter_id : int parameters : dict value : dict/float if value is dict, it should have "default" key. ...

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def build_extra_headers(request, proxyMode, orgaMode, currentOrga): """Build the list of extra headers""" things_to_add = {} # If in proxymode, add needed infos to headers if proxyMode: # User for prop in settings.PIAPI_USERDATA: if hasattr(request.user, prop): ...

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def to_subject_id(s): ''' to_subject_id(s) coerces the given string or number into an integer subject id. If s is not a valid subejct id, raises an exception. ''' if not pimms.is_number(s) and not pimms.is_str(s): raise ValueError('invalid type for subject id: %s' % str(type(s))) if pi...

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def create_more_container_files(sourceDir, suffix, maxElements, containers, containers2): """Creates additional files for the individual MPL-containers.""" # Create files for each MPL-container with 20 to 'maxElements' elements # which will be used during generation. for container in containers: ...

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def logging_level(level): """ Temporarily modify param's logging level. """ level = level.upper() levels = [DEBUG, INFO, WARNING, ERROR, CRITICAL, VERBOSE] level_names = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL', 'VERBOSE'] if level not in level_names: raise Exception("Level ...

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def byte_str(s="", encoding="utf-8", input_encoding="utf-8", errors="strict"): """ Returns a byte string version of 's', encoded as specified in 'encoding'. Accepts str & unicode objects, interpreting non-unicode strings as byte strings encoded using the given input encoding. """ assert isinst...

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def add_logging_level(name, value, method_name=None): ''' Comprehensively adds a new logging level to the ``logging`` module and the currently configured logging class. Derived from: https://stackoverflow.com/a/35804945/450917 ''' if not method_name: method_name = name.lower() ...

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def get_plan_from_dual(alpha, beta, C, regul): """ Retrieve optimal transportation plan from optimal dual potentials. Parameters ---------- alpha: array, shape = len(a) beta: array, shape = len(b) Optimal dual potentials. C: array, shape = len(a) x len(b) Ground cost matrix....

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def decode_lazy(rlp, sedes=None, **sedes_kwargs): """Decode an RLP encoded object in a lazy fashion. If the encoded object is a bytestring, this function acts similar to :func:`rlp.decode`. If it is a list however, a :class:`LazyList` is returned instead. This object will decode the string lazily, avoi...

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def set_sampling_strategies(self, filter, strategy_and_params): """Set sampling strategy for the sensors of all the group's clients. Only sensors that match the specified filter are considered. See the `KATCPResource.set_sampling_strategies` docstring for parameter definitions and more ...

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def close(self): """Close the pool by closing and removing all of the connections""" for cid in list(self.connections.keys()): self.remove(self.connections[cid].handle) LOGGER.debug('Pool %s closed', self.id)

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def calculate_solidity(labels,indexes=None): """Calculate the area of each label divided by the area of its convex hull labels - a label matrix indexes - the indexes of the labels to measure """ if indexes is not None: """ Convert to compat 32bit integer """ indexes = np.array(i...

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def declare_dict(self): """Return declared sections, terms and synonyms as a dict""" # Run the parser, if it has not been run yet. if not self.root: for _ in self: pass return { 'sections': self._declared_sections, 'terms': self._declared_terms, ...

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def Poll(generator=None, condition=None, interval=None, timeout=None): """Periodically calls generator function until a condition is satisfied.""" if not generator: raise ValueError("generator has to be a lambda") if not condition: raise ValueError("condition has to be a lambda") if interval is None:...

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def _get_bokeh_chart(self, x_field, y_field, chart_type, label, opts, style, options={}, **kwargs): """ Get a Bokeh chart object """ if isinstance(x_field, list): kdims = x_field else: kdims = [x_field] if isinstance(y_fiel...

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def _perform_version(self, version): """Inner method for version upgrade. Not intended for standalone use. This method performs the actual version upgrade with all the pre, post operations and addons upgrades. :param version: The migration version to upgrade to :type version: I...

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def request(self, method: str, url: StrOrURL, **kwargs: Any) -> '_RequestContextManager': """Perform HTTP request.""" return _RequestContextManager(self._request(method, url, **kwargs))

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def WriteToFD(self, fd): """Write out the updated configuration to the fd.""" if self.writeback: self.writeback.SaveDataToFD(self.writeback_data, fd) else: raise RuntimeError("Attempting to write a configuration without a " "writeback location.")

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def update(self, language=values.unset, tagged_text=values.unset, source_channel=values.unset): """ Update the SampleInstance :param unicode language: The ISO language-country string that specifies the language used for the sample :param unicode tagged_text: The text exam...

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def hdf5_cache(filepath=None, parent=None, group=None, names=None, typed=False, hashed_key=False, **h5dcreate_kwargs): """HDF5 cache decorator. Parameters ---------- filepath : string, optional Path to HDF5 file. If None a temporary file name will be used. parent : string, op...

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def call_functions_parallel(*worker_defs): """Call specified functions in parallel. :param *worker_defs: Each positional argument can be either of a function to be called or a tuple which consists of a function, a list of positional arguments) and keyword arguments (optional). If you ne...

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