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 _plot_ulims( ax, x, y, xerr, color, capsize=5, height_fraction=0.25, elinewidth=2 ): """ Plot upper limits as arrows with cap at value of upper limit. uplim behaviour has been fixed in matplotlib 1.4 """ ax.errorbar( x, y, xerr=xerr, ls="", color=color, elinewidth=elinewidth, capsiz...	[ "def", "_plot_ulims", "(", "ax", ",", "x", ",", "y", ",", "xerr", ",", "color", ",", "capsize", "=", "5", ",", "height_fraction", "=", "0.25", ",", "elinewidth", "=", "2", ")", ":", "ax", ".", "errorbar", "(", "x", ",", "y", ",", "xerr", "=", "...	25.125	0.000958
def write(config): """Commits any pending modifications, ie save a configuration file if it has been marked "dirty" as a result of an normal assignment. The modifications are written to the first writable source in this config object. .. note:: This is a static metho...	[ "def", "write", "(", "config", ")", ":", "root", "=", "config", "while", "root", ".", "_parent", ":", "root", "=", "root", ".", "_parent", "for", "source", "in", "root", ".", "_sources", ":", "if", "source", ".", "writable", "and", "source", ".", "di...	33.333333	0.00243
def batch_indices_iterator(self, batch_size, shuffle=None, **kwargs): """ Create an iterator that generates mini-batch sample indices The generated mini-batches indices take the form of nested lists of either: - 1D NumPy integer arrays - slices The list nesting ...	[ "def", "batch_indices_iterator", "(", "self", ",", "batch_size", ",", "shuffle", "=", "None", ",", "", "", "kwargs", ")", ":", "if", "not", "self", ".", "_random_access", ":", "raise", "TypeError", "(", "'batch_indices_iterator method not supported as '", "'one ...	40.972973	0.001289
def Dependencies(tools): """ Takes in a list of tools that are being updated and returns any tools that depend on linking to them """ dependencies = [] if tools: path_dirs = PathDirs() man = Template(join(path_dirs.meta_dir, 'plugin_manifest.cfg')) for section in man.sect...	[ "def", "Dependencies", "(", "tools", ")", ":", "dependencies", "=", "[", "]", "if", "tools", ":", "path_dirs", "=", "PathDirs", "(", ")", "man", "=", "Template", "(", "join", "(", "path_dirs", ".", "meta_dir", ",", "'plugin_manifest.cfg'", ")", ")", "for...	43.241379	0.00078
def add(self, entity): """ Adds the supplied dict as a new entity """ result = self._http_req('connections', method='POST', payload=entity) status = result['status'] if not status==201: raise ServiceRegistryError(status,"Couldn't add entity") self.debug(0x01,result) return result['decoded']	[ "def", "add", "(", "self", ",", "entity", ")", ":", "result", "=", "self", ".", "_http_req", "(", "'connections'", ",", "method", "=", "'POST'", ",", "payload", "=", "entity", ")", "status", "=", "result", "[", "'status'", "]", "if", "not", "status", ...	27.363636	0.045016
def setup(self): """Collect watchdog information. Collect configuration files, custom executables for test-binary and repair-binary, and stdout/stderr logs. """ conf_file = self.get_option('conf_file') log_dir = '/var/log/watchdog' # Get service configur...	[ "def", "setup", "(", "self", ")", ":", "conf_file", "=", "self", ".", "get_option", "(", "'conf_file'", ")", "log_dir", "=", "'/var/log/watchdog'", "# Get service configuration and sysconfig files", "self", ".", "add_copy_spec", "(", "[", "conf_file", ",", "'/etc/sy...	30.75	0.001576
def update_file(self, file_id, upload_id): """ Send PUT request to /files/{file_id} to update the file contents to upload_id and sets a label. :param file_id: str uuid of file :param upload_id: str uuid of the upload where all the file chunks where uploaded :param label: str shor...	[ "def", "update_file", "(", "self", ",", "file_id", ",", "upload_id", ")", ":", "put_data", "=", "{", "\"upload[id]\"", ":", "upload_id", ",", "}", "return", "self", ".", "_put", "(", "\"/files/\"", "+", "file_id", ",", "put_data", ",", "content_type", "=",...	47.666667	0.008576
def main(): """ NAME lsq_redo.py DESCRIPTION converts a tab delimited LSQ format to PmagPy redo file and edits the magic_measurements table to mark "bad" measurements. SYNTAX lsq_redo.py [-h] [command line options] OPTIONS -h: prints help message and quits ...	[ "def", "main", "(", ")", ":", "letters", "=", "string", ".", "ascii_uppercase", "for", "l", "in", "string", ".", "ascii_lowercase", ":", "letters", "=", "letters", "+", "l", "dir_path", "=", "'.'", "if", "'-WD'", "in", "sys", ".", "argv", ":", "ind", ...	37.522388	0.021701
def scan_module(self, pkgpath, modpath, node): """Scans a module, collecting possible origins for all names, assuming names can only become bound to values in other modules by import.""" def scan_imports(node): if node_type(node) == 'Import': for binding in node.name...	[ "def", "scan_module", "(", "self", ",", "pkgpath", ",", "modpath", ",", "node", ")", ":", "def", "scan_imports", "(", "node", ")", ":", "if", "node_type", "(", "node", ")", "==", "'Import'", ":", "for", "binding", "in", "node", ".", "names", ":", "na...	45.225806	0.002095
def _request(self, method, relative_path_parts, *kwargs): """Sends an HTTP request to the REST API and receives the requested data. Additionally sets up pagination cursors. :param str method: HTTP method name :param relative_path_parts: the relative paths for the request URI :param kwargs: argume...	[ "def", "_request", "(", "self", ",", "method", ",", "", "relative_path_parts", ",", "", "", "kwargs", ")", ":", "uri", "=", "self", ".", "_create_api_uri", "(", "", "relative_path_parts", ")", "response", "=", "get", "(", "uri", ",", "params", "=", ...	42.058824	0.001368
def stop(self): ''' Stop the auth proc. ''' log.info('Stopping auth process') self.__up = False self.socket.close()	[ "def", "stop", "(", "self", ")", ":", "log", ".", "info", "(", "'Stopping auth process'", ")", "self", ".", "__up", "=", "False", "self", ".", "socket", ".", "close", "(", ")" ]	22.428571	0.01227
def respth2ck(argv=None): """Command-line entry point for converting a ReSpecTh XML file to a ChemKED YAML file. """ parser = ArgumentParser( description='Convert a ReSpecTh XML file to a ChemKED YAML file.' ) parser.add_argument('-i', '--input', type=str, ...	[ "def", "respth2ck", "(", "argv", "=", "None", ")", ":", "parser", "=", "ArgumentParser", "(", "description", "=", "'Convert a ReSpecTh XML file to a ChemKED YAML file.'", ")", "parser", ".", "add_argument", "(", "'-i'", ",", "'--input'", ",", "type", "=", "str", ...	38.387755	0.002074
def generate_token(length=30, chars=UNICODE_ASCII_CHARACTER_SET): """Generates a non-guessable OAuth token OAuth (1 and 2) does not specify the format of tokens except that they should be strings of random characters. Tokens should not be guessable and entropy when generating the random characters is i...	[ "def", "generate_token", "(", "length", "=", "30", ",", "chars", "=", "UNICODE_ASCII_CHARACTER_SET", ")", ":", "rand", "=", "SystemRandom", "(", ")", "return", "''", ".", "join", "(", "rand", ".", "choice", "(", "chars", ")", "for", "x", "in", "range", ...	49.9	0.001969
def conforms(element, etype, namespace: Dict[str, Any]) -> bool: """ Determine whether element conforms to etype :param element: Element to test for conformance :param etype: Type to test against :param namespace: Namespace to use to resolve forward references :return: """ etype = proc_forw...	[ "def", "conforms", "(", "element", ",", "etype", ",", "namespace", ":", "Dict", "[", "str", ",", "Any", "]", ")", "->", "bool", ":", "etype", "=", "proc_forward", "(", "etype", ",", "namespace", ")", "if", "is_union", "(", "etype", ")", ":", "return"...	36.769231	0.002041
def slice(objects, position, axis, precision=1e-3, layer=0, datatype=0): """ Slice polygons and polygon sets at given positions along an axis. Parameters ---------- objects : ``PolygonSet``, or list Operand of the slice operation. If this is a list, each element must be a ``Polygon...	[ "def", "slice", "(", "objects", ",", "position", ",", "axis", ",", "precision", "=", "1e-3", ",", "layer", "=", "0", ",", "datatype", "=", "0", ")", ":", "if", "not", "isinstance", "(", "layer", ",", "list", ")", ":", "layer", "=", "[", "layer", ...	35.645161	0.00044
def _process_hdu (self, hdu): "We've hacked the load order a bit to get t0 and mjd0 in _process_main()." if hdu.name == 'EVENTS': pass else: super (Events, self)._process_hdu (hdu)	[ "def", "_process_hdu", "(", "self", ",", "hdu", ")", ":", "if", "hdu", ".", "name", "==", "'EVENTS'", ":", "pass", "else", ":", "super", "(", "Events", ",", "self", ")", ".", "_process_hdu", "(", "hdu", ")" ]	31.857143	0.026201
def schema(name, dct, *, strict=False): """Create a compound tag schema. This function is a short convenience function that makes it easy to subclass the base `CompoundSchema` class. The `name` argument is the name of the class and `dct` should be a dictionnary containing the actual schema....	[ "def", "schema", "(", "name", ",", "dct", ",", "*", ",", "strict", "=", "False", ")", ":", "return", "type", "(", "name", ",", "(", "CompoundSchema", ",", ")", ",", "{", "'__slots__'", ":", "(", ")", ",", "'schema'", ":", "dct", ",", "'strict'", ...	42.3125	0.001445
def route_delete(name, route_table, resource_group, **kwargs): ''' .. versionadded:: 2019.2.0 Delete a route from a route table. :param name: The route to delete. :param route_table: The route table containing the route. :param resource_group: The resource group name assigned to the ...	[ "def", "route_delete", "(", "name", ",", "route_table", ",", "resource_group", ",", "", "", "kwargs", ")", ":", "result", "=", "False", "netconn", "=", "__utils__", "[", "'azurearm.get_client'", "]", "(", "'network'", ",", "", "", "kwargs", ")", "try",...	25.441176	0.001114
def handle_uploaded_files(uploaded_files): """Handles downstream processes using metadata about the uploaded files from React side.""" if uploaded_files: uploaded_files = json.loads(uploaded_files)[0] _id = uploaded_files.get('id') # Strip extension from filename _filename = ...	[ "def", "handle_uploaded_files", "(", "uploaded_files", ")", ":", "if", "uploaded_files", ":", "uploaded_files", "=", "json", ".", "loads", "(", "uploaded_files", ")", "[", "0", "]", "_id", "=", "uploaded_files", ".", "get", "(", "'id'", ")", "# Strip extension...	31.322581	0.000999
def compare_words_lexicographic( word_a, word_b ): """ compare words in Tamil lexicographic order """ # sanity check for words to be all Tamil if ( not all_tamil(word_a) ) or (not all_tamil(word_b)) : #print("## ") #print(word_a) #print(word_b) #print("Both operands need to b...	[ "def", "compare_words_lexicographic", "(", "word_a", ",", "word_b", ")", ":", "# sanity check for words to be all Tamil", "if", "(", "not", "all_tamil", "(", "word_a", ")", ")", "or", "(", "not", "all_tamil", "(", "word_b", ")", ")", ":", "#print(\"## \")", "#pr...	35.909091	0.027127
def compute_one_decoding_video_metrics(iterator, feed_dict, num_videos): """Computes the average of all the metric for one decoding. Args: iterator: dataset iterator. feed_dict: feed dict to initialize iterator. num_videos: number of videos. Returns: all_psnr: 2-D Numpy array, shape=(num_samples...	[ "def", "compute_one_decoding_video_metrics", "(", "iterator", ",", "feed_dict", ",", "num_videos", ")", ":", "output", ",", "target", "=", "iterator", ".", "get_next", "(", ")", "metrics", "=", "psnr_and_ssim", "(", "output", ",", "target", ")", "with", "tf", ...	33.066667	0.009794
def is_not_none(entity, prop, name): "bool: True if the value of a property is not None." return is_not_empty(entity, prop, name) and name in entity._data and getattr(entity, name) is not None	[ "def", "is_not_none", "(", "entity", ",", "prop", ",", "name", ")", ":", "return", "is_not_empty", "(", "entity", ",", "prop", ",", "name", ")", "and", "name", "in", "entity", ".", "_data", "and", "getattr", "(", "entity", ",", "name", ")", "is", "no...	66	0.01
def extract(self, progress = True, recurse = True, tex_only = False, extract_manifest = False, path = None, **kwargs): if path is None: path = self.folder_out if tex_only: kwargs['use_cache'] = False utils.mkdir_silent(path) utime(path, (self.time, sel...	[ "def", "extract", "(", "self", ",", "progress", "=", "True", ",", "recurse", "=", "True", ",", "tex_only", "=", "False", ",", "extract_manifest", "=", "False", ",", "path", "=", "None", ",", "", "", "kwargs", ")", ":", "if", "path", "is", "None", ...	42.6	0.009178
def _send_broker_aware_request(self, payloads, encoder_fn, decoder_fn): """ Group a list of request payloads by topic+partition and send them to the leader broker for that partition using the supplied encode/decode functions Arguments: payloads: list of object-like enti...	[ "def", "_send_broker_aware_request", "(", "self", ",", "payloads", ",", "encoder_fn", ",", "decoder_fn", ")", ":", "# encoders / decoders do not maintain ordering currently", "# so we need to keep this so we can rebuild order before returning", "original_ordering", "=", "[", "(", ...	44.666667	0.000712
def to_avro(file_path_or_buffer, df, schema=None, codec='null', append=False): """ Avro file writer. Args: file_path_or_buffer: Output file path or file-like object. df: pd.DataFrame. schema: Dict of Avro schema. If it's set None, inferring schema. ap...	[ "def", "to_avro", "(", "file_path_or_buffer", ",", "df", ",", "schema", "=", "None", ",", "codec", "=", "'null'", ",", "append", "=", "False", ")", ":", "if", "schema", "is", "None", ":", "schema", "=", "__schema_infer", "(", "df", ")", "open_mode", "=...	37.448276	0.001795
def compress(condition, data, axis=0, out=None, blen=None, storage=None, create='array', **kwargs): """Return selected slices of an array along given axis.""" # setup if out is not None: # argument is only there for numpy API compatibility raise NotImplementedError('out argumen...	[ "def", "compress", "(", "condition", ",", "data", ",", "axis", "=", "0", ",", "out", "=", "None", ",", "blen", "=", "None", ",", "storage", "=", "None", ",", "create", "=", "'array'", ",", "", "", "kwargs", ")", ":", "# setup", "if", "out", "is...	32.86	0.001773
def parse_json(pairs): """ modified from: https://stackoverflow.com/questions/956867/how-to-get-string-objects-instead-of-unicode-from-json#34796078 pass this to the object_pairs_hook kwarg of json.load/loads """ new_pairs = [] for key, value in pairs: if isinstance(value, unicode):...	[ "def", "parse_json", "(", "pairs", ")", ":", "new_pairs", "=", "[", "]", "for", "key", ",", "value", "in", "pairs", ":", "if", "isinstance", "(", "value", ",", "unicode", ")", ":", "value", "=", "value", ".", "encode", "(", "'utf-8'", ")", "if", "i...	32.6	0.001988
def import_(zpool=None, new_name=None, **kwargs): ''' .. versionadded:: 2015.5.0 Import storage pools or list pools available for import zpool : string Optional name of storage pool new_name : string Optional new name for the storage pool mntopts : string Comma-separa...	[ "def", "import_", "(", "zpool", "=", "None", ",", "new_name", "=", "None", ",", "", "", "kwargs", ")", ":", "## Configure pool", "# NOTE: initialize the defaults", "flags", "=", "[", "]", "opts", "=", "{", "}", "target", "=", "[", "]", "# NOTE: push pool...	31.173554	0.001799
def remove_headerReference(self, type_): """Return rId of w:headerReference child of type_ after removing it.""" headerReference = self.get_headerReference(type_) rId = headerReference.rId self.remove(headerReference) return rId	[ "def", "remove_headerReference", "(", "self", ",", "type_", ")", ":", "headerReference", "=", "self", ".", "get_headerReference", "(", "type_", ")", "rId", "=", "headerReference", ".", "rId", "self", ".", "remove", "(", "headerReference", ")", "return", "rId" ...	44.166667	0.011111
def _add_gene_associations(self, r_id, r_genes, gene_ids, r_tag): """Adds all the different kinds of genes into a list.""" genes = ET.SubElement( r_tag, _tag('geneProductAssociation', FBC_V2)) if isinstance(r_genes, list): e = Expression(And(*(Variable(i) for i in r_genes...	[ "def", "_add_gene_associations", "(", "self", ",", "r_id", ",", "r_genes", ",", "gene_ids", ",", "r_tag", ")", ":", "genes", "=", "ET", ".", "SubElement", "(", "r_tag", ",", "_tag", "(", "'geneProductAssociation'", ",", "FBC_V2", ")", ")", "if", "isinstanc...	48.961538	0.001541
def make_pkh_output_script(pubkey, witness=False): ''' bytearray -> bytearray ''' if witness and not riemann.network.SEGWIT: raise ValueError( 'Network {} does not support witness scripts.' .format(riemann.get_current_network_name())) output_script = bytearray() ...	[ "def", "make_pkh_output_script", "(", "pubkey", ",", "witness", "=", "False", ")", ":", "if", "witness", "and", "not", "riemann", ".", "network", ".", "SEGWIT", ":", "raise", "ValueError", "(", "'Network {} does not support witness scripts.'", ".", "format", "(", ...	34.68	0.001122
def post_url(self): """ Determine which page this post lives on within the topic and return link to anchor within that page """ topic = self.topic topic_page = topic.post_set.filter(id__lt=self.id).count() / get_paginate_by() + 1 return "{0}page{1}/#post-{2...	[ "def", "post_url", "(", "self", ")", ":", "topic", "=", "self", ".", "topic", "topic_page", "=", "topic", ".", "post_set", ".", "filter", "(", "id__lt", "=", "self", ".", "id", ")", ".", "count", "(", ")", "/", "get_paginate_by", "(", ")", "+", "1"...	45.75	0.010724
def find_vasp_calculations(): """ Returns a list of all subdirectories that contain either a vasprun.xml file or a compressed vasprun.xml.gz file. Args: None Returns: (List): list of all VASP calculation subdirectories. """ dir_list = [ './' + re.sub( r'vasprun\.xml', '', p...	[ "def", "find_vasp_calculations", "(", ")", ":", "dir_list", "=", "[", "'./'", "+", "re", ".", "sub", "(", "r'vasprun\\.xml'", ",", "''", ",", "path", ")", "for", "path", "in", "glob", ".", "iglob", "(", "'**/vasprun.xml'", ",", "recursive", "=", "True", ...	38.428571	0.027223
def edge(s, path, edge, alpha=1.0): """ Visualization of a single edge between two nodes. """ path.moveto(edge.node1.x, edge.node1.y) if edge.node2.style == BACK: path.curveto( edge.node1.x, edge.node2.y, edge.node2.x, edge.node2.y, ...	[ "def", "edge", "(", "s", ",", "path", ",", "edge", ",", "alpha", "=", "1.0", ")", ":", "path", ".", "moveto", "(", "edge", ".", "node1", ".", "x", ",", "edge", ".", "node1", ".", "y", ")", "if", "edge", ".", "node2", ".", "style", "==", "BACK...	22.9	0.010482
def _compute_zones_sizes(self): """Compute panel zone sizes.""" # Left panels left = 0 for panel in self.panels_for_zone(Panel.Position.LEFT): if not panel.isVisible(): continue size_hint = panel.sizeHint() left += size_hint.width() ...	[ "def", "_compute_zones_sizes", "(", "self", ")", ":", "# Left panels", "left", "=", "0", "for", "panel", "in", "self", ".", "panels_for_zone", "(", "Panel", ".", "Position", ".", "LEFT", ")", ":", "if", "not", "panel", ".", "isVisible", "(", ")", ":", ...	35.393939	0.001667
def _build_command(self): """ Command to start the IOU process. (to be passed to subprocess.Popen()) IOU command line: Usage: <image> [options] <application id> <image>: unix-js-m \| unix-is-m \| unix-i-m \| ... <application id>: instance identifier (0 < id <= 1024)...	[ "def", "_build_command", "(", "self", ")", ":", "command", "=", "[", "self", ".", "_path", "]", "if", "len", "(", "self", ".", "_ethernet_adapters", ")", "!=", "2", ":", "command", ".", "extend", "(", "[", "\"-e\"", ",", "str", "(", "len", "(", "se...	42.583333	0.001435
def _filter_kwargs(names, dict_): """Filter out kwargs from a dictionary. Parameters ---------- names : set[str] The names to select from ``dict_``. dict_ : dict[str, any] The dictionary to select from. Returns ------- kwargs : dict[str, any] ``dict_`` where the...	[ "def", "_filter_kwargs", "(", "names", ",", "dict_", ")", ":", "return", "{", "k", ":", "v", "for", "k", ",", "v", "in", "dict_", ".", "items", "(", ")", "if", "k", "in", "names", "and", "v", "is", "not", "None", "}" ]	26.764706	0.002123
def from_df(cls, path:PathOrStr, train_df:DataFrame, valid_df:DataFrame, test_df:Optional[DataFrame]=None, tokenizer:Tokenizer=None, vocab:Vocab=None, classes:Collection[str]=None, text_cols:IntsOrStrs=1, label_cols:IntsOrStrs=0, label_delim:str=None, chunksize:int=10000, max_vocab:int=6...	[ "def", "from_df", "(", "cls", ",", "path", ":", "PathOrStr", ",", "train_df", ":", "DataFrame", ",", "valid_df", ":", "DataFrame", ",", "test_df", ":", "Optional", "[", "DataFrame", "]", "=", "None", ",", "tokenizer", ":", "Tokenizer", "=", "None", ",", ...	88.882353	0.043877
def connect(self, callback, weak=False): """ Connects a new callback to this signal. :param callback: The callback to connect. :param weak: If `True`, only holds a weak reference to the specified callback. `callback` will be called whenever `emit` gets called on the...	[ "def", "connect", "(", "self", ",", "callback", ",", "weak", "=", "False", ")", ":", "if", "weak", ":", "callback", "=", "ref", "(", "callback", ",", "self", ".", "_callbacks", ".", "remove", ")", "self", ".", "_callbacks", ".", "append", "(", "callb...	36.5	0.001779
def any_datetime_field(field, **kwargs): """ Return random value for DateTimeField, skips auto_now and auto_now_add fields >>> result = any_field(models.DateTimeField()) >>> type(result) <type 'datetime.datetime'> """ from_date = kwargs.get('from_date', datetime(1990, 1, 1)) ...	[ "def", "any_datetime_field", "(", "field", ",", "", "", "kwargs", ")", ":", "from_date", "=", "kwargs", ".", "get", "(", "'from_date'", ",", "datetime", "(", "1990", ",", "1", ",", "1", ")", ")", "to_date", "=", "kwargs", ".", "get", "(", "'to_date...	35.833333	0.002268
def map(kvs: Mapping[K, V], meta=None) -> Map[K, V]: # pylint:disable=redefined-builtin """Creates a new map.""" return Map(pmap(initial=kvs), meta=meta)	[ "def", "map", "(", "kvs", ":", "Mapping", "[", "K", ",", "V", "]", ",", "meta", "=", "None", ")", "->", "Map", "[", "K", ",", "V", "]", ":", "# pylint:disable=redefined-builtin", "return", "Map", "(", "pmap", "(", "initial", "=", "kvs", ")", ",", ...	53.333333	0.012346
def invert(self,nz,A,C): """ Inversion and resolution of a tridiagonal matrix A X = C Input: nz number of layers a(,1) lower diagonal (Ai,i-1) a(,2) principal diagonal (Ai,i) a(*,3) upper diagonal (Ai,i+1) c Output ...	[ "def", "invert", "(", "self", ",", "nz", ",", "A", ",", "C", ")", ":", "X", "=", "[", "0", "for", "i", "in", "range", "(", "nz", ")", "]", "for", "i", "in", "reversed", "(", "range", "(", "nz", "-", "1", ")", ")", ":", "C", "[", "i", "]...	25.074074	0.01138
def haarpsi_weight_map(img1, img2, axis): r"""Weighting map for directional features along an axis. Parameters ---------- img1, img2 : array-like The images to compare. They must have equal shape. axis : {0, 1} Direction in which to look for edge similarities. Returns -----...	[ "def", "haarpsi_weight_map", "(", "img1", ",", "img2", ",", "axis", ")", ":", "# TODO: generalize for nD", "impl", "=", "'pyfftw'", "if", "PYFFTW_AVAILABLE", "else", "'numpy'", "# Haar wavelet filters for level 3", "dec_lo_lvl3", "=", "np", ".", "repeat", "(", "[", ...	32.056338	0.000426
def _run_command(self, ssh, cmd, pty=True): """Run a command remotely via SSH. :param object ssh: The SSHClient :param str cmd: The command to execute :param list cmd: The `shlex.split` command to execute :param bool pty: Whether to allocate a pty :return: tuple: The st...	[ "def", "_run_command", "(", "self", ",", "ssh", ",", "cmd", ",", "pty", "=", "True", ")", ":", "if", "isinstance", "(", "cmd", ",", "str", ")", ":", "cmd", "=", "shlex", ".", "split", "(", "cmd", ")", "if", "type", "(", "cmd", ")", "is", "not",...	33.366667	0.001942
def get_provisioned_gsi_write_units(table_name, gsi_name): """ Returns the number of provisioned write units for the table :type table_name: str :param table_name: Name of the DynamoDB table :type gsi_name: str :param gsi_name: Name of the GSI :returns: int -- Number of write units """ ...	[ "def", "get_provisioned_gsi_write_units", "(", "table_name", ",", "gsi_name", ")", ":", "try", ":", "desc", "=", "DYNAMODB_CONNECTION", ".", "describe_table", "(", "table_name", ")", "except", "JSONResponseError", ":", "raise", "for", "gsi", "in", "desc", "[", "...	33.041667	0.001225
def copyError(self, to): """Save the original error to the new place. """ if to is None: to__o = None else: to__o = to._o ret = libxml2mod.xmlCopyError(self._o, to__o) return ret	[ "def", "copyError", "(", "self", ",", "to", ")", ":", "if", "to", "is", "None", ":", "to__o", "=", "None", "else", ":", "to__o", "=", "to", ".", "_o", "ret", "=", "libxml2mod", ".", "xmlCopyError", "(", "self", ".", "_o", ",", "to__o", ")", "retu...	35.5	0.018349
def maybe_a(generator): """ Generates either an arbitrary value of the specified generator or None. This is a class factory, it makes a class which is a closure around the specified generator. """ class MaybeAGenerator(ArbitraryInterface): """ A closure class around the generato...	[ "def", "maybe_a", "(", "generator", ")", ":", "class", "MaybeAGenerator", "(", "ArbitraryInterface", ")", ":", "\"\"\"\n A closure class around the generator specified above, which generates\n either that generator or None.\n \"\"\"", "@", "classmethod", "def", "...	31.181818	0.001414
def _parseTlsDirectory(self, rva, size, magic = consts.PE32): """ Parses the TLS directory. @type rva: int @param rva: The RVA where the TLS directory starts. @type size: int @param size: The size of the TLS directory. @type magic: int ...	[ "def", "_parseTlsDirectory", "(", "self", ",", "rva", ",", "size", ",", "magic", "=", "consts", ".", "PE32", ")", ":", "data", "=", "self", ".", "getDataAtRva", "(", "rva", ",", "size", ")", "rd", "=", "utils", ".", "ReadData", "(", "data", ")", "i...	35.730769	0.013627
def analisar_retorno(retorno, classe_resposta=RespostaSAT, campos=RespostaSAT.CAMPOS, campos_alternativos=[], funcao=None, manter_verbatim=True): """Analisa o retorno (supostamente um retorno de uma função do SAT) conforme o padrão e campos esperados. O retorno deverá possuir dados separados ent...	[ "def", "analisar_retorno", "(", "retorno", ",", "classe_resposta", "=", "RespostaSAT", ",", "campos", "=", "RespostaSAT", ".", "CAMPOS", ",", "campos_alternativos", "=", "[", "]", ",", "funcao", "=", "None", ",", "manter_verbatim", "=", "True", ")", ":", "if...	38.617021	0.002417
def wrap_text(paragraph, line_count, min_char_per_line=0): """Wraps the given text to the specified number of lines.""" one_string = strip_all_white_space(paragraph) if min_char_per_line: lines = wrap(one_string, width=min_char_per_line) try: return lines[:line_count] except IndexError: return lines els...	[ "def", "wrap_text", "(", "paragraph", ",", "line_count", ",", "min_char_per_line", "=", "0", ")", ":", "one_string", "=", "strip_all_white_space", "(", "paragraph", ")", "if", "min_char_per_line", ":", "lines", "=", "wrap", "(", "one_string", ",", "width", "="...	33.272727	0.029255
def alpha_from_cov(plotman, alpha_cov): '''Calculate alpha values from the coverage/2.5. ''' abscov = np.abs(load_cov('inv/coverage.mag')) if alpha_cov: normcov = np.divide(abscov, 2.5) normcov[np.where(normcov > 1)] = 1 mask = np.subtract(1, normcov) alpha = plotman.parm...	[ "def", "alpha_from_cov", "(", "plotman", ",", "alpha_cov", ")", ":", "abscov", "=", "np", ".", "abs", "(", "load_cov", "(", "'inv/coverage.mag'", ")", ")", "if", "alpha_cov", ":", "normcov", "=", "np", ".", "divide", "(", "abscov", ",", "2.5", ")", "no...	35.333333	0.002299
def ethnicities_clean(): """ Get dictionary of unformatted ethnicity types mapped to clean corresponding ethnicity strings """ eths_clean = {} fname = pkg_resources.resource_filename(__name__, 'resources/Ethnicity_Groups.csv') with open(fname, 'rU') as csvfile: reader = csv.reader(csvfile, delimiter = ',')...	[ "def", "ethnicities_clean", "(", ")", ":", "eths_clean", "=", "{", "}", "fname", "=", "pkg_resources", ".", "resource_filename", "(", "__name__", ",", "'resources/Ethnicity_Groups.csv'", ")", "with", "open", "(", "fname", ",", "'rU'", ")", "as", "csvfile", ":"...	32.411765	0.022928
def _Liquid(T, P=0.1): """Supplementary release on properties of liquid water at 0.1 MPa Parameters ---------- T : float Temperature, [K] P : float Pressure, [MPa] Although this relation is for P=0.1MPa, can be extrapoled at pressure 0.3 MPa Returns ------- ...	[ "def", "_Liquid", "(", "T", ",", "P", "=", "0.1", ")", ":", "# Check input in range of validity", "if", "T", "<=", "253.15", "or", "T", ">=", "383.15", "or", "P", "<", "0.1", "or", "P", ">", "0.3", ":", "raise", "NotImplementedError", "(", "\"Incoming ou...	33.829545	0.000163
def load_models_using_filepattern( self, filename_pattern, model, glob_args, is_main_model=False, encoding='utf-8', add_to_local_models=True): """ add a new model to all relevant objects Args: filename_pattern: models to be loaded model: model hol...	[ "def", "load_models_using_filepattern", "(", "self", ",", "filename_pattern", ",", "model", ",", "glob_args", ",", "is_main_model", "=", "False", ",", "encoding", "=", "'utf-8'", ",", "add_to_local_models", "=", "True", ")", ":", "if", "(", "model", ")", ":", ...	41.172414	0.001637
def run(self): """ Listen to the stream and send events to the client. """ channel = self._ssh_client.get_transport().open_session() self._channel = channel channel.exec_command("gerrit stream-events") stdout = channel.makefile() stderr = channel.makefile_stderr() ...	[ "def", "run", "(", "self", ")", ":", "channel", "=", "self", ".", "_ssh_client", ".", "get_transport", "(", ")", ".", "open_session", "(", ")", "self", ".", "_channel", "=", "channel", "channel", ".", "exec_command", "(", "\"gerrit stream-events\"", ")", "...	42.318182	0.002101
def _commandline(self, args, kwargs): """Returns the command line (without pipes) as a list.""" # transform_args() is a hook (used in GromacsCommand very differently!) return [self.command_name] + self.transform_args(args, **kwargs)	[ "def", "_commandline", "(", "self", ",", "", "args", ",", "", "", "kwargs", ")", ":", "# transform_args() is a hook (used in GromacsCommand very differently!)", "return", "[", "self", ".", "command_name", "]", "+", "self", ".", "transform_args", "(", "", "args...	64.5	0.019157
def solve_coupled_ecc_solution(F0, e0, gamma0, phase0, mc, q, t): """ Compute the solution to the coupled system of equations from from Peters (1964) and Barack & Cutler (2004) at a given time. :param F0: Initial orbital frequency [Hz] :param e0: Initial orbital eccentricity :param gam...	[ "def", "solve_coupled_ecc_solution", "(", "F0", ",", "e0", ",", "gamma0", ",", "phase0", ",", "mc", ",", "q", ",", "t", ")", ":", "y0", "=", "np", ".", "array", "(", "[", "F0", ",", "e0", ",", "gamma0", ",", "phase0", "]", ")", "y", ",", "infod...	29.888889	0.012005
def get_range_by_effective_partition_key(self, effective_partition_key_value): """Gets the range containing the given partition key :param str effective_partition_key_value: The partition key value. :return: The partition key range. :rtype: dict """ ...	[ "def", "get_range_by_effective_partition_key", "(", "self", ",", "effective_partition_key_value", ")", ":", "if", "_CollectionRoutingMap", ".", "MinimumInclusiveEffectivePartitionKey", "==", "effective_partition_key_value", ":", "return", "self", ".", "_orderedPartitionKeyRanges"...	41.666667	0.010056
def clinical_kernel(x, y=None): """Computes clinical kernel The clinical kernel distinguishes between continuous ordinal,and nominal variables. Parameters ---------- x : pandas.DataFrame, shape = (n_samples_x, n_features) Training data y : pandas.DataFrame, shape = (n_samples_y, n...	[ "def", "clinical_kernel", "(", "x", ",", "y", "=", "None", ")", ":", "if", "y", "is", "not", "None", ":", "if", "x", ".", "shape", "[", "1", "]", "!=", "y", ".", "shape", "[", "1", "]", ":", "raise", "ValueError", "(", "'x and y have different numb...	30.702128	0.001343
def _next(self): """Get the next summary and present it.""" self.summaries.rotate(-1) current_summary = self.summaries[0] self._update_summary(current_summary)	[ "def", "_next", "(", "self", ")", ":", "self", ".", "summaries", ".", "rotate", "(", "-", "1", ")", "current_summary", "=", "self", ".", "summaries", "[", "0", "]", "self", ".", "_update_summary", "(", "current_summary", ")" ]	37.4	0.010471
def chunk(self, chunks=None, name_prefix='xarray-', token=None, lock=False): """Coerce all arrays in this dataset into dask arrays with the given chunks. Non-dask arrays in this dataset will be converted to dask arrays. Dask arrays will be rechunked to the given chunk size...	[ "def", "chunk", "(", "self", ",", "chunks", "=", "None", ",", "name_prefix", "=", "'xarray-'", ",", "token", "=", "None", ",", "lock", "=", "False", ")", ":", "try", ":", "from", "dask", ".", "base", "import", "tokenize", "except", "ImportError", ":", ...	37.53125	0.001217
def notify(title, message, prio='ALERT', facility='LOCAL5', fmt='[{title}] {message}', retcode=None): """ Uses the ``syslog`` core Python module, which is not available on Windows platforms. Optional parameters: * ``prio`` - Syslog prority ...	[ "def", "notify", "(", "title", ",", "message", ",", "prio", "=", "'ALERT'", ",", "facility", "=", "'LOCAL5'", ",", "fmt", "=", "'[{title}] {message}'", ",", "retcode", "=", "None", ")", ":", "prio_map", "=", "{", "'EMERG'", ":", "syslog", ".", "LOG_EMERG...	25.574468	0.0004
def flatten(l, types=(list, float)): """ Flat nested list of lists into a single list. """ l = [item if isinstance(item, types) else [item] for item in l] return [item for sublist in l for item in sublist]	[ "def", "flatten", "(", "l", ",", "types", "=", "(", "list", ",", "float", ")", ")", ":", "l", "=", "[", "item", "if", "isinstance", "(", "item", ",", "types", ")", "else", "[", "item", "]", "for", "item", "in", "l", "]", "return", "[", "item", ...	36.666667	0.013333
def nodeListGetString(self, list, inLine): """Build the string equivalent to the text contained in the Node list made of TEXTs and ENTITY_REFs """ if list is None: list__o = None else: list__o = list._o ret = libxml2mod.xmlNodeListGetString(self._o, list__o, inLine) re...	[ "def", "nodeListGetString", "(", "self", ",", "list", ",", "inLine", ")", ":", "if", "list", "is", "None", ":", "list__o", "=", "None", "else", ":", "list__o", "=", "list", ".", "_o", "ret", "=", "libxml2mod", ".", "xmlNodeListGetString", "(", "self", ...	46	0.012195
def compile(self): ''' This function aims at giving every operator enough information so that all operator conversions can happen independently. We also want to check, fix, and simplify the network structure here. ''' self._prune() self._resolve_duplicates() self....	[ "def", "compile", "(", "self", ")", ":", "self", ".", "_prune", "(", ")", "self", ".", "_resolve_duplicates", "(", ")", "self", ".", "_fix_shapes", "(", ")", "self", ".", "_infer_all_types", "(", ")", "self", ".", "_check_structure", "(", ")" ]	38.8	0.010076
def simple_interaction(snps,pheno,Inter,Inter0=None,covs = None,K=None,test='lrt'): """ I-variate fixed effects interaction test for phenotype specific SNP effects Args: snps: [N x S] SP.array of S SNPs for N individuals (test SNPs) pheno: [N x 1] SP.array of 1 phenotype for N individual...	[ "def", "simple_interaction", "(", "snps", ",", "pheno", ",", "Inter", ",", "Inter0", "=", "None", ",", "covs", "=", "None", ",", "K", "=", "None", ",", "test", "=", "'lrt'", ")", ":", "N", "=", "snps", ".", "shape", "[", "0", "]", "if", "covs", ...	39.409091	0.015757
def parse_value(self, value): """Cast value to `bool`.""" parsed = super(BoolField, self).parse_value(value) return bool(parsed) if parsed is not None else None	[ "def", "parse_value", "(", "self", ",", "value", ")", ":", "parsed", "=", "super", "(", "BoolField", ",", "self", ")", ".", "parse_value", "(", "value", ")", "return", "bool", "(", "parsed", ")", "if", "parsed", "is", "not", "None", "else", "None" ]	45.25	0.01087
def _calc_jaccard( markers1: dict, markers2: dict, ): """Calculate jaccard index between the values of two dictionaries Note: dict values must be sets """ jacc_results=np.zeros((len(markers1), len(markers2))) j=0 for marker_group in markers1: tmp = [len(markers2[i].intersection...	[ "def", "_calc_jaccard", "(", "markers1", ":", "dict", ",", "markers2", ":", "dict", ",", ")", ":", "jacc_results", "=", "np", ".", "zeros", "(", "(", "len", "(", "markers1", ")", ",", "len", "(", "markers2", ")", ")", ")", "j", "=", "0", "for", "...	27.166667	0.011858
def RegisterLateBindingCallback(target_name, callback, **kwargs): """Registers a callback to be invoked when the RDFValue named is declared.""" _LATE_BINDING_STORE.setdefault(target_name, []).append((callback, kwargs))	[ "def", "RegisterLateBindingCallback", "(", "target_name", ",", "callback", ",", "", "", "kwargs", ")", ":", "_LATE_BINDING_STORE", ".", "setdefault", "(", "target_name", ",", "[", "]", ")", ".", "append", "(", "(", "callback", ",", "kwargs", ")", ")" ]	73.333333	0.013514
def sweep(self): """ Runs through entire dataset. Returns TSS error, total correct, total count, pcorrect (a dict of layer data) """ self.preSweep() if self.loadOrder == []: raise NetworkError('No loadOrder for the inputs. Make sure inputs are properly set.',...	[ "def", "sweep", "(", "self", ")", ":", "self", ".", "preSweep", "(", ")", "if", "self", ".", "loadOrder", "==", "[", "]", ":", "raise", "NetworkError", "(", "'No loadOrder for the inputs. Make sure inputs are properly set.'", ",", "self", ".", "loadOrder", ")", ...	52.545455	0.009342
def update(request, ident, stateless=False, **kwargs): 'Generate update json response' dash_app, app = DashApp.locate_item(ident, stateless) request_body = json.loads(request.body.decode('utf-8')) if app.use_dash_dispatch(): # Force call through dash view_func = app.locate_endpoint_fun...	[ "def", "update", "(", "request", ",", "ident", ",", "stateless", "=", "False", ",", "", "", "kwargs", ")", ":", "dash_app", ",", "app", "=", "DashApp", ".", "locate_item", "(", "ident", ",", "stateless", ")", "request_body", "=", "json", ".", "loads"...	34.219512	0.002079
def __neighbor_indexes_points(self, optic_object): """! @brief Return neighbors of the specified object in case of sequence of points. @param[in] optic_object (optics_descriptor): Object for which neighbors should be returned in line with connectivity radius. @return (list) List ...	[ "def", "__neighbor_indexes_points", "(", "self", ",", "optic_object", ")", ":", "kdnodes", "=", "self", ".", "__kdtree", ".", "find_nearest_dist_nodes", "(", "self", ".", "__sample_pointer", "[", "optic_object", ".", "index_object", "]", ",", "self", ".", "__eps...	55.333333	0.01037
def elem_add(self, idx=None, name=None, **kwargs): """ Add an element of this model :param idx: element idx :param name: element name :param kwargs: keyword arguments of the parameters :return: allocated idx """ idx = self.system.devman.register_element(...	[ "def", "elem_add", "(", "self", ",", "idx", "=", "None", ",", "name", "=", "None", ",", "", "", "kwargs", ")", ":", "idx", "=", "self", ".", "system", ".", "devman", ".", "register_element", "(", "dev_name", "=", "self", ".", "_name", ",", "idx",...	31.704918	0.001003
def collapse_addresses(addresses): """Collapse a list of IP objects. Example: collapse_addresses([IPv4Network('192.0.2.0/25'), IPv4Network('192.0.2.128/25')]) -> [IPv4Network('192.0.2.0/24')] Args: addresses: An iterator of IPv4Network...	[ "def", "collapse_addresses", "(", "addresses", ")", ":", "i", "=", "0", "addrs", "=", "[", "]", "ips", "=", "[", "]", "nets", "=", "[", "]", "# split IP addresses and networks", "for", "ip", "in", "addresses", ":", "if", "isinstance", "(", "ip", ",", "...	32	0.000551
def add_permission_view_menu(self, permission_name, view_menu_name): """ Adds a permission on a view or menu to the backend :param permission_name: name of the permission to add: 'can_add','can_edit' etc... :param view_menu_name: name of the v...	[ "def", "add_permission_view_menu", "(", "self", ",", "permission_name", ",", "view_menu_name", ")", ":", "if", "not", "(", "permission_name", "and", "view_menu_name", ")", ":", "return", "None", "pv", "=", "self", ".", "find_permission_view_menu", "(", "permission...	36.586207	0.001837
def _custom_validate(self, verify, trust_bundle): """ Called when we have set custom validation. We do this in two cases: first, when cert validation is entirely disabled; and second, when using a custom trust DB. """ # If we disabled cert validation, just say: cool. ...	[ "def", "_custom_validate", "(", "self", ",", "verify", ",", "trust_bundle", ")", ":", "# If we disabled cert validation, just say: cool.", "if", "not", "verify", ":", "return", "# We want data in memory, so load it up.", "if", "os", ".", "path", ".", "isfile", "(", "t...	36.163934	0.000883
def fstab(jail): ''' Display contents of a fstab(5) file defined in specified jail's configuration. If no file is defined, return False. CLI Example: .. code-block:: bash salt '*' jail.fstab <jail name> ''' ret = [] config = show_config(jail) if 'fstab' in config: ...	[ "def", "fstab", "(", "jail", ")", ":", "ret", "=", "[", "]", "config", "=", "show_config", "(", "jail", ")", "if", "'fstab'", "in", "config", ":", "c_fstab", "=", "config", "[", "'fstab'", "]", "elif", "'mount.fstab'", "in", "config", ":", "c_fstab", ...	32.860465	0.000687
def get_var_name(nc): """Guesses the variable_name of an open NetCDF file """ non_variable_names = [ 'lat', 'lat_bnds', 'lon', 'lon_bnds', 'time', 'latitude', 'longitude', 'bnds' ] _vars = set(nc.variables.keys()) _vars.difference...	[ "def", "get_var_name", "(", "nc", ")", ":", "non_variable_names", "=", "[", "'lat'", ",", "'lat_bnds'", ",", "'lon'", ",", "'lon_bnds'", ",", "'time'", ",", "'latitude'", ",", "'longitude'", ",", "'bnds'", "]", "_vars", "=", "set", "(", "nc", ".", "varia...	20	0.002387
def LabelValueTable(self, keys=None): """Return LabelValue with FSM derived keys.""" keys = keys or self.superkey # pylint: disable=E1002 return super(CliTable, self).LabelValueTable(keys)	[ "def", "LabelValueTable", "(", "self", ",", "keys", "=", "None", ")", ":", "keys", "=", "keys", "or", "self", ".", "superkey", "# pylint: disable=E1002", "return", "super", "(", "CliTable", ",", "self", ")", ".", "LabelValueTable", "(", "keys", ")" ]	43.2	0.009091
def set_scene_config(self, scene_id, config): """reconfigure a scene by scene ID""" if not scene_id in self.state.scenes: # does that scene_id exist? err_msg = "Requested to reconfigure scene {sceneNum}, which does not exist".format(sceneNum=scene_id) logging.info(err_msg) ...	[ "def", "set_scene_config", "(", "self", ",", "scene_id", ",", "config", ")", ":", "if", "not", "scene_id", "in", "self", ".", "state", ".", "scenes", ":", "# does that scene_id exist?", "err_msg", "=", "\"Requested to reconfigure scene {sceneNum}, which does not exist\"...	63.666667	0.010323
async def set_slave_neighbors(self): '''Set neighbor environments for all the slave environments. Assumes that :attr:`neighbors` are set for this multi-environment. ''' for i, elem in enumerate(self._slave_origins): o, addr = elem r_slave = await self.env.connect(...	[ "async", "def", "set_slave_neighbors", "(", "self", ")", ":", "for", "i", ",", "elem", "in", "enumerate", "(", "self", ".", "_slave_origins", ")", ":", "o", ",", "addr", "=", "elem", "r_slave", "=", "await", "self", ".", "env", ".", "connect", "(", "...	50.5	0.001022
def morphDataLists(fromList, toList, stepList): ''' Iteratively morph fromList into toList using the values 0 to 1 in stepList stepList: a value of 0 means no change and a value of 1 means a complete change to the other value ''' # If there are more than 1 pitch value, then we align the da...	[ "def", "morphDataLists", "(", "fromList", ",", "toList", ",", "stepList", ")", ":", "# If there are more than 1 pitch value, then we align the data in", "# relative time.", "# Each data point comes with a timestamp. The earliest timestamp is 0", "# and the latest timestamp is 1. Using th...	42.363636	0.001049
def failure_line_summary(formatter, failure_line): """ Create a mozlog formatted error summary string from the given failure_line. Create a string which can be compared to a TextLogError.line string to see if they match. """ if failure_line.action == "test_result": action = "test_status...	[ "def", "failure_line_summary", "(", "formatter", ",", "failure_line", ")", ":", "if", "failure_line", ".", "action", "==", "\"test_result\"", ":", "action", "=", "\"test_status\"", "if", "failure_line", ".", "subtest", "is", "not", "None", "else", "\"test_end\"", ...	30.785714	0.00225
def place(vertices_resources, nets, machine, constraints, random=default_random): """A random placer. This algorithm performs uniform-random placement of vertices (completely ignoring connectivty) and thus in the general case is likely to produce very poor quality placements. It exists primar...	[ "def", "place", "(", "vertices_resources", ",", "nets", ",", "machine", ",", "constraints", ",", "random", "=", "default_random", ")", ":", "# Within the algorithm we modify the resource availability values in the", "# machine to account for the effects of the current placement. As...	42.965909	0.000259
def genemania_force_directed(self,curveSteepness=None,defaultEdgeWeight=None,\ defaultSpringCoefficient=None,defaultSpringLength=None,EdgeAttribute=None,\ ignoreHiddenElements=None,isDeterministic=None,maxNodeMass=None,\ maxWeightCutoff=None,midpointEdges=None,minNodeMass=None,minWeightCutoff=None,\ network=Non...	[ "def", "genemania_force_directed", "(", "self", ",", "curveSteepness", "=", "None", ",", "defaultEdgeWeight", "=", "None", ",", "defaultSpringCoefficient", "=", "None", ",", "defaultSpringLength", "=", "None", ",", "EdgeAttribute", "=", "None", ",", "ignoreHiddenEle...	58.137931	0.038787
def _build_xpath_expr(attrs): """Build an xpath expression to simulate bs4's ability to pass in kwargs to search for attributes when using the lxml parser. Parameters ---------- attrs : dict A dict of HTML attributes. These are NOT checked for validity. Returns ------- expr : u...	[ "def", "_build_xpath_expr", "(", "attrs", ")", ":", "# give class attribute as class_ because class is a python keyword", "if", "'class_'", "in", "attrs", ":", "attrs", "[", "'class'", "]", "=", "attrs", ".", "pop", "(", "'class_'", ")", "s", "=", "[", "\"@{key}={...	32.7	0.001486
def get_cycle_mrkr(self, end=False): """Mark cycle start or end. Parameters ---------- end : bool If True, marks a cycle end; otherwise, it's a cycle start """ if self.annot is None: # remove if buttons are disabled self.parent.statusBar().showMe...	[ "def", "get_cycle_mrkr", "(", "self", ",", "end", "=", "False", ")", ":", "if", "self", ".", "annot", "is", "None", ":", "# remove if buttons are disabled", "self", ".", "parent", ".", "statusBar", "(", ")", ".", "showMessage", "(", "'No score file loaded'", ...	32.636364	0.001803
def convert_namespaces_ast( ast, api_url: str = None, namespace_targets: Mapping[str, List[str]] = None, canonicalize: bool = False, decanonicalize: bool = False, ): """Recursively convert namespaces of BEL Entities in BEL AST using API endpoint Canonicalization and decanonicalization is de...	[ "def", "convert_namespaces_ast", "(", "ast", ",", "api_url", ":", "str", "=", "None", ",", "namespace_targets", ":", "Mapping", "[", "str", ",", "List", "[", "str", "]", "]", "=", "None", ",", "canonicalize", ":", "bool", "=", "False", ",", "decanonicali...	33.694915	0.002444
def set_key(key: str, value: typing.List[str], persists: bool = True): """ Removes the specified key from the cauldron configs if the key exists :param key: The key in the cauldron configs object to remove :param value: :param persists: """ if key.endswith('_path') or key.endswith(...	[ "def", "set_key", "(", "key", ":", "str", ",", "value", ":", "typing", ".", "List", "[", "str", "]", ",", "persists", ":", "bool", "=", "True", ")", ":", "if", "key", ".", "endswith", "(", "'_path'", ")", "or", "key", ".", "endswith", "(", "'_pat...	30.35	0.001597
def _check_load_paths(load_path): ''' Checks the validity of the load_path, returns a sanitized version with invalid paths removed. ''' if load_path is None or not isinstance(load_path, six.string_types): return None _paths = [] for _path in load_path.split(':'): if os.path...	[ "def", "_check_load_paths", "(", "load_path", ")", ":", "if", "load_path", "is", "None", "or", "not", "isinstance", "(", "load_path", ",", "six", ".", "string_types", ")", ":", "return", "None", "_paths", "=", "[", "]", "for", "_path", "in", "load_path", ...	26.7	0.001808
def notification(self): """Provide access to the currently displayed notification. Returns: :py:class:`BaseNotification`: FoxPuppet BaseNotification object. """ with self.selenium.context(self.selenium.CONTEXT_CHROME): try: root = self.selenium.f...	[ "def", "notification", "(", "self", ")", ":", "with", "self", ".", "selenium", ".", "context", "(", "self", ".", "selenium", ".", "CONTEXT_CHROME", ")", ":", "try", ":", "root", "=", "self", ".", "selenium", ".", "find_element", "(", "*", "self", ".", ...	37.409091	0.00237
def run(src, grammar=NODEBOX, format=None, outputfile=None, iterations=1, buff=None, window=True, title=None, fullscreen=None, close_window=False, server=False, port=7777, show_vars=False, vars=None, namespac...	[ "def", "run", "(", "src", ",", "grammar", "=", "NODEBOX", ",", "format", "=", "None", ",", "outputfile", "=", "None", ",", "iterations", "=", "1", ",", "buff", "=", "None", ",", "window", "=", "True", ",", "title", "=", "None", ",", "fullscreen", "...	30.05042	0.001354
def start(self): """ Start daemonization process. """ # If pidfile already exists, we should read pid from there; to overwrite it, if locking # will fail, because locking attempt somehow purges the file contents. if os.path.isfile(self.pid): with open(self.pid...	[ "def", "start", "(", "self", ")", ":", "# If pidfile already exists, we should read pid from there; to overwrite it, if locking", "# will fail, because locking attempt somehow purges the file contents.", "if", "os", ".", "path", ".", "isfile", "(", "self", ".", "pid", ")", ":",...	37.494382	0.002043
def get_config_section(self, name): """ Get a section of a configuration """ if self.config.has_section(name): return self.config.items(name) return []	[ "def", "get_config_section", "(", "self", ",", "name", ")", ":", "if", "self", ".", "config", ".", "has_section", "(", "name", ")", ":", "return", "self", ".", "config", ".", "items", "(", "name", ")", "return", "[", "]" ]	28.142857	0.009852
def equation_of_time_pvcdrom(dayofyear): """ Equation of time from PVCDROM. `PVCDROM`_ is a website by Solar Power Lab at Arizona State University (ASU) .. _PVCDROM: http://www.pveducation.org/pvcdrom/2-properties-sunlight/solar-time Parameters ---------- dayofyear : numeric Retu...	[ "def", "equation_of_time_pvcdrom", "(", "dayofyear", ")", ":", "# day angle relative to Vernal Equinox, typically March 22 (day number 81)", "bday", "=", "_calculate_simple_day_angle", "(", "dayofyear", ")", "-", "(", "2.0", "", "np", ".", "pi", "/", "365.0", ")", "",...	29.5625	0.002047
def _ParseShVariables(self, lines): """Extract env_var and path values from sh derivative shells. Iterates over each line, word by word searching for statements that set the path. These are either variables, or conditions that would allow a variable to be set later in the line (e.g. export). Args:...	[ "def", "_ParseShVariables", "(", "self", ",", "lines", ")", ":", "paths", "=", "{", "}", "for", "line", "in", "lines", ":", "for", "entry", "in", "line", ":", "if", "\"=\"", "in", "entry", ":", "# Pad out the list so that it's always 2 elements, even if the spli...	35.21875	0.01209
def iter_lines(f): """ :param f: :type f: file :return: """ linenum = 1 try: for text in f.readlines(): # ignore lines that consist entirely of whitespace if text.isspace(): continue indent,value = parse_line(text) yield...	[ "def", "iter_lines", "(", "f", ")", ":", "linenum", "=", "1", "try", ":", "for", "text", "in", "f", ".", "readlines", "(", ")", ":", "# ignore lines that consist entirely of whitespace", "if", "text", ".", "isspace", "(", ")", ":", "continue", "indent", ",...	25.176471	0.011261
def round_to_sigfigs(num, sigfigs): """ Rounds a number rounded to a specific number of significant figures instead of to a specific precision. """ if type(sigfigs) != int: raise TypeError("Number of significant figures must be integer.") elif sigfigs < 1: raise ValueError("Numbe...	[ "def", "round_to_sigfigs", "(", "num", ",", "sigfigs", ")", ":", "if", "type", "(", "sigfigs", ")", "!=", "int", ":", "raise", "TypeError", "(", "\"Number of significant figures must be integer.\"", ")", "elif", "sigfigs", "<", "1", ":", "raise", "ValueError", ...	35.466667	0.001832
def DIV(self, a, b): """Integer division operation""" try: result = Operators.UDIV(a, b) except ZeroDivisionError: result = 0 return Operators.ITEBV(256, b == 0, 0, result)	[ "def", "DIV", "(", "self", ",", "a", ",", "b", ")", ":", "try", ":", "result", "=", "Operators", ".", "UDIV", "(", "a", ",", "b", ")", "except", "ZeroDivisionError", ":", "result", "=", "0", "return", "Operators", ".", "ITEBV", "(", "256", ",", "...	31.714286	0.008772
def next(self): """Returns the next batch of data.""" if self.curr_idx == len(self.idx): raise StopIteration i, j = self.idx[self.curr_idx] self.curr_idx += 1 if self.major_axis == 1: data = self.nddata[i][j:j+self.batch_size].T label = self.n...	[ "def", "next", "(", "self", ")", ":", "if", "self", ".", "curr_idx", "==", "len", "(", "self", ".", "idx", ")", ":", "raise", "StopIteration", "i", ",", "j", "=", "self", ".", "idx", "[", "self", ".", "curr_idx", "]", "self", ".", "curr_idx", "+=...	40.863636	0.002174

def _plot_ulims( ax, x, y, xerr, color, capsize=5, height_fraction=0.25, elinewidth=2 ): """ Plot upper limits as arrows with cap at value of upper limit. uplim behaviour has been fixed in matplotlib 1.4 """ ax.errorbar( x, y, xerr=xerr, ls="", color=color, elinewidth=elinewidth, capsiz...

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def write(config): """Commits any pending modifications, ie save a configuration file if it has been marked "dirty" as a result of an normal assignment. The modifications are written to the first writable source in this config object. .. note:: This is a static metho...

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def batch_indices_iterator(self, batch_size, shuffle=None, **kwargs): """ Create an iterator that generates mini-batch sample indices The generated mini-batches indices take the form of nested lists of either: - 1D NumPy integer arrays - slices The list nesting ...

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def Dependencies(tools): """ Takes in a list of tools that are being updated and returns any tools that depend on linking to them """ dependencies = [] if tools: path_dirs = PathDirs() man = Template(join(path_dirs.meta_dir, 'plugin_manifest.cfg')) for section in man.sect...

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def add(self, entity): """ Adds the supplied dict as a new entity """ result = self._http_req('connections', method='POST', payload=entity) status = result['status'] if not status==201: raise ServiceRegistryError(status,"Couldn't add entity") self.debug(0x01,result) return result['decoded']

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def setup(self): """Collect watchdog information. Collect configuration files, custom executables for test-binary and repair-binary, and stdout/stderr logs. """ conf_file = self.get_option('conf_file') log_dir = '/var/log/watchdog' # Get service configur...

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def update_file(self, file_id, upload_id): """ Send PUT request to /files/{file_id} to update the file contents to upload_id and sets a label. :param file_id: str uuid of file :param upload_id: str uuid of the upload where all the file chunks where uploaded :param label: str shor...

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def main(): """ NAME lsq_redo.py DESCRIPTION converts a tab delimited LSQ format to PmagPy redo file and edits the magic_measurements table to mark "bad" measurements. SYNTAX lsq_redo.py [-h] [command line options] OPTIONS -h: prints help message and quits ...

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def scan_module(self, pkgpath, modpath, node): """Scans a module, collecting possible origins for all names, assuming names can only become bound to values in other modules by import.""" def scan_imports(node): if node_type(node) == 'Import': for binding in node.name...

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def _request(self, method, *relative_path_parts, **kwargs): """Sends an HTTP request to the REST API and receives the requested data. Additionally sets up pagination cursors. :param str method: HTTP method name :param relative_path_parts: the relative paths for the request URI :param kwargs: argume...

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def stop(self): ''' Stop the auth proc. ''' log.info('Stopping auth process') self.__up = False self.socket.close()

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def respth2ck(argv=None): """Command-line entry point for converting a ReSpecTh XML file to a ChemKED YAML file. """ parser = ArgumentParser( description='Convert a ReSpecTh XML file to a ChemKED YAML file.' ) parser.add_argument('-i', '--input', type=str, ...

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def generate_token(length=30, chars=UNICODE_ASCII_CHARACTER_SET): """Generates a non-guessable OAuth token OAuth (1 and 2) does not specify the format of tokens except that they should be strings of random characters. Tokens should not be guessable and entropy when generating the random characters is i...

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def conforms(element, etype, namespace: Dict[str, Any]) -> bool: """ Determine whether element conforms to etype :param element: Element to test for conformance :param etype: Type to test against :param namespace: Namespace to use to resolve forward references :return: """ etype = proc_forw...

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def slice(objects, position, axis, precision=1e-3, layer=0, datatype=0): """ Slice polygons and polygon sets at given positions along an axis. Parameters ---------- objects : ``PolygonSet``, or list Operand of the slice operation. If this is a list, each element must be a ``Polygon...

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def _process_hdu (self, hdu): "We've hacked the load order a bit to get t0 and mjd0 in _process_main()." if hdu.name == 'EVENTS': pass else: super (Events, self)._process_hdu (hdu)

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def schema(name, dct, *, strict=False): """Create a compound tag schema. This function is a short convenience function that makes it easy to subclass the base `CompoundSchema` class. The `name` argument is the name of the class and `dct` should be a dictionnary containing the actual schema....

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def route_delete(name, route_table, resource_group, **kwargs): ''' .. versionadded:: 2019.2.0 Delete a route from a route table. :param name: The route to delete. :param route_table: The route table containing the route. :param resource_group: The resource group name assigned to the ...

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def handle_uploaded_files(uploaded_files): """Handles downstream processes using metadata about the uploaded files from React side.""" if uploaded_files: uploaded_files = json.loads(uploaded_files)[0] _id = uploaded_files.get('id') # Strip extension from filename _filename = ...

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def compare_words_lexicographic( word_a, word_b ): """ compare words in Tamil lexicographic order """ # sanity check for words to be all Tamil if ( not all_tamil(word_a) ) or (not all_tamil(word_b)) : #print("## ") #print(word_a) #print(word_b) #print("Both operands need to b...

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def compute_one_decoding_video_metrics(iterator, feed_dict, num_videos): """Computes the average of all the metric for one decoding. Args: iterator: dataset iterator. feed_dict: feed dict to initialize iterator. num_videos: number of videos. Returns: all_psnr: 2-D Numpy array, shape=(num_samples...

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def is_not_none(entity, prop, name): "bool: True if the value of a property is not None." return is_not_empty(entity, prop, name) and name in entity._data and getattr(entity, name) is not None

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def extract(self, progress = True, recurse = True, tex_only = False, extract_manifest = False, path = None, **kwargs): if path is None: path = self.folder_out if tex_only: kwargs['use_cache'] = False utils.mkdir_silent(path) utime(path, (self.time, sel...

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def _send_broker_aware_request(self, payloads, encoder_fn, decoder_fn): """ Group a list of request payloads by topic+partition and send them to the leader broker for that partition using the supplied encode/decode functions Arguments: payloads: list of object-like enti...

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def to_avro(file_path_or_buffer, df, schema=None, codec='null', append=False): """ Avro file writer. Args: file_path_or_buffer: Output file path or file-like object. df: pd.DataFrame. schema: Dict of Avro schema. If it's set None, inferring schema. ap...

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def compress(condition, data, axis=0, out=None, blen=None, storage=None, create='array', **kwargs): """Return selected slices of an array along given axis.""" # setup if out is not None: # argument is only there for numpy API compatibility raise NotImplementedError('out argumen...

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def parse_json(pairs): """ modified from: https://stackoverflow.com/questions/956867/how-to-get-string-objects-instead-of-unicode-from-json#34796078 pass this to the object_pairs_hook kwarg of json.load/loads """ new_pairs = [] for key, value in pairs: if isinstance(value, unicode):...

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def import_(zpool=None, new_name=None, **kwargs): ''' .. versionadded:: 2015.5.0 Import storage pools or list pools available for import zpool : string Optional name of storage pool new_name : string Optional new name for the storage pool mntopts : string Comma-separa...

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def remove_headerReference(self, type_): """Return rId of w:headerReference child of *type_* after removing it.""" headerReference = self.get_headerReference(type_) rId = headerReference.rId self.remove(headerReference) return rId

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def _add_gene_associations(self, r_id, r_genes, gene_ids, r_tag): """Adds all the different kinds of genes into a list.""" genes = ET.SubElement( r_tag, _tag('geneProductAssociation', FBC_V2)) if isinstance(r_genes, list): e = Expression(And(*(Variable(i) for i in r_genes...

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def make_pkh_output_script(pubkey, witness=False): ''' bytearray -> bytearray ''' if witness and not riemann.network.SEGWIT: raise ValueError( 'Network {} does not support witness scripts.' .format(riemann.get_current_network_name())) output_script = bytearray() ...

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def post_url(self): """ Determine which page this post lives on within the topic and return link to anchor within that page """ topic = self.topic topic_page = topic.post_set.filter(id__lt=self.id).count() / get_paginate_by() + 1 return "{0}page{1}/#post-{2...

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def find_vasp_calculations(): """ Returns a list of all subdirectories that contain either a vasprun.xml file or a compressed vasprun.xml.gz file. Args: None Returns: (List): list of all VASP calculation subdirectories. """ dir_list = [ './' + re.sub( r'vasprun\.xml', '', p...

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def edge(s, path, edge, alpha=1.0): """ Visualization of a single edge between two nodes. """ path.moveto(edge.node1.x, edge.node1.y) if edge.node2.style == BACK: path.curveto( edge.node1.x, edge.node2.y, edge.node2.x, edge.node2.y, ...

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def _compute_zones_sizes(self): """Compute panel zone sizes.""" # Left panels left = 0 for panel in self.panels_for_zone(Panel.Position.LEFT): if not panel.isVisible(): continue size_hint = panel.sizeHint() left += size_hint.width() ...

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def _build_command(self): """ Command to start the IOU process. (to be passed to subprocess.Popen()) IOU command line: Usage: <image> [options] <application id> <image>: unix-js-m | unix-is-m | unix-i-m | ... <application id>: instance identifier (0 < id <= 1024)...

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def _filter_kwargs(names, dict_): """Filter out kwargs from a dictionary. Parameters ---------- names : set[str] The names to select from ``dict_``. dict_ : dict[str, any] The dictionary to select from. Returns ------- kwargs : dict[str, any] ``dict_`` where the...

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def from_df(cls, path:PathOrStr, train_df:DataFrame, valid_df:DataFrame, test_df:Optional[DataFrame]=None, tokenizer:Tokenizer=None, vocab:Vocab=None, classes:Collection[str]=None, text_cols:IntsOrStrs=1, label_cols:IntsOrStrs=0, label_delim:str=None, chunksize:int=10000, max_vocab:int=6...

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def connect(self, callback, weak=False): """ Connects a new callback to this signal. :param callback: The callback to connect. :param weak: If `True`, only holds a weak reference to the specified callback. `callback` will be called whenever `emit` gets called on the...

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def any_datetime_field(field, **kwargs): """ Return random value for DateTimeField, skips auto_now and auto_now_add fields >>> result = any_field(models.DateTimeField()) >>> type(result) <type 'datetime.datetime'> """ from_date = kwargs.get('from_date', datetime(1990, 1, 1)) ...

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def map(kvs: Mapping[K, V], meta=None) -> Map[K, V]: # pylint:disable=redefined-builtin """Creates a new map.""" return Map(pmap(initial=kvs), meta=meta)

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def invert(self,nz,A,C): """ Inversion and resolution of a tridiagonal matrix A X = C Input: nz number of layers a(*,1) lower diagonal (Ai,i-1) a(*,2) principal diagonal (Ai,i) a(*,3) upper diagonal (Ai,i+1) c Output ...

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def haarpsi_weight_map(img1, img2, axis): r"""Weighting map for directional features along an axis. Parameters ---------- img1, img2 : array-like The images to compare. They must have equal shape. axis : {0, 1} Direction in which to look for edge similarities. Returns -----...

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def _run_command(self, ssh, cmd, pty=True): """Run a command remotely via SSH. :param object ssh: The SSHClient :param str cmd: The command to execute :param list cmd: The `shlex.split` command to execute :param bool pty: Whether to allocate a pty :return: tuple: The st...

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def get_provisioned_gsi_write_units(table_name, gsi_name): """ Returns the number of provisioned write units for the table :type table_name: str :param table_name: Name of the DynamoDB table :type gsi_name: str :param gsi_name: Name of the GSI :returns: int -- Number of write units """ ...

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def copyError(self, to): """Save the original error to the new place. """ if to is None: to__o = None else: to__o = to._o ret = libxml2mod.xmlCopyError(self._o, to__o) return ret

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def maybe_a(generator): """ Generates either an arbitrary value of the specified generator or None. This is a class factory, it makes a class which is a closure around the specified generator. """ class MaybeAGenerator(ArbitraryInterface): """ A closure class around the generato...

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def _parseTlsDirectory(self, rva, size, magic = consts.PE32): """ Parses the TLS directory. @type rva: int @param rva: The RVA where the TLS directory starts. @type size: int @param size: The size of the TLS directory. @type magic: int ...

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def analisar_retorno(retorno, classe_resposta=RespostaSAT, campos=RespostaSAT.CAMPOS, campos_alternativos=[], funcao=None, manter_verbatim=True): """Analisa o retorno (supostamente um retorno de uma função do SAT) conforme o padrão e campos esperados. O retorno deverá possuir dados separados ent...

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def wrap_text(paragraph, line_count, min_char_per_line=0): """Wraps the given text to the specified number of lines.""" one_string = strip_all_white_space(paragraph) if min_char_per_line: lines = wrap(one_string, width=min_char_per_line) try: return lines[:line_count] except IndexError: return lines els...

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def alpha_from_cov(plotman, alpha_cov): '''Calculate alpha values from the coverage/2.5. ''' abscov = np.abs(load_cov('inv/coverage.mag')) if alpha_cov: normcov = np.divide(abscov, 2.5) normcov[np.where(normcov > 1)] = 1 mask = np.subtract(1, normcov) alpha = plotman.parm...

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def ethnicities_clean(): """ Get dictionary of unformatted ethnicity types mapped to clean corresponding ethnicity strings """ eths_clean = {} fname = pkg_resources.resource_filename(__name__, 'resources/Ethnicity_Groups.csv') with open(fname, 'rU') as csvfile: reader = csv.reader(csvfile, delimiter = ',')...

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def _Liquid(T, P=0.1): """Supplementary release on properties of liquid water at 0.1 MPa Parameters ---------- T : float Temperature, [K] P : float Pressure, [MPa] Although this relation is for P=0.1MPa, can be extrapoled at pressure 0.3 MPa Returns ------- ...

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def load_models_using_filepattern( self, filename_pattern, model, glob_args, is_main_model=False, encoding='utf-8', add_to_local_models=True): """ add a new model to all relevant objects Args: filename_pattern: models to be loaded model: model hol...

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def run(self): """ Listen to the stream and send events to the client. """ channel = self._ssh_client.get_transport().open_session() self._channel = channel channel.exec_command("gerrit stream-events") stdout = channel.makefile() stderr = channel.makefile_stderr() ...

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def _commandline(self, *args, **kwargs): """Returns the command line (without pipes) as a list.""" # transform_args() is a hook (used in GromacsCommand very differently!) return [self.command_name] + self.transform_args(*args, **kwargs)

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def solve_coupled_ecc_solution(F0, e0, gamma0, phase0, mc, q, t): """ Compute the solution to the coupled system of equations from from Peters (1964) and Barack & Cutler (2004) at a given time. :param F0: Initial orbital frequency [Hz] :param e0: Initial orbital eccentricity :param gam...

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def get_range_by_effective_partition_key(self, effective_partition_key_value): """Gets the range containing the given partition key :param str effective_partition_key_value: The partition key value. :return: The partition key range. :rtype: dict """ ...

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def clinical_kernel(x, y=None): """Computes clinical kernel The clinical kernel distinguishes between continuous ordinal,and nominal variables. Parameters ---------- x : pandas.DataFrame, shape = (n_samples_x, n_features) Training data y : pandas.DataFrame, shape = (n_samples_y, n...

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def _next(self): """Get the next summary and present it.""" self.summaries.rotate(-1) current_summary = self.summaries[0] self._update_summary(current_summary)

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def chunk(self, chunks=None, name_prefix='xarray-', token=None, lock=False): """Coerce all arrays in this dataset into dask arrays with the given chunks. Non-dask arrays in this dataset will be converted to dask arrays. Dask arrays will be rechunked to the given chunk size...

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def notify(title, message, prio='ALERT', facility='LOCAL5', fmt='[{title}] {message}', retcode=None): """ Uses the ``syslog`` core Python module, which is not available on Windows platforms. Optional parameters: * ``prio`` - Syslog prority ...

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def flatten(l, types=(list, float)): """ Flat nested list of lists into a single list. """ l = [item if isinstance(item, types) else [item] for item in l] return [item for sublist in l for item in sublist]

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def nodeListGetString(self, list, inLine): """Build the string equivalent to the text contained in the Node list made of TEXTs and ENTITY_REFs """ if list is None: list__o = None else: list__o = list._o ret = libxml2mod.xmlNodeListGetString(self._o, list__o, inLine) re...

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46

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def compile(self): ''' This function aims at giving every operator enough information so that all operator conversions can happen independently. We also want to check, fix, and simplify the network structure here. ''' self._prune() self._resolve_duplicates() self....

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def simple_interaction(snps,pheno,Inter,Inter0=None,covs = None,K=None,test='lrt'): """ I-variate fixed effects interaction test for phenotype specific SNP effects Args: snps: [N x S] SP.array of S SNPs for N individuals (test SNPs) pheno: [N x 1] SP.array of 1 phenotype for N individual...

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def parse_value(self, value): """Cast value to `bool`.""" parsed = super(BoolField, self).parse_value(value) return bool(parsed) if parsed is not None else None

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def _calc_jaccard( markers1: dict, markers2: dict, ): """Calculate jaccard index between the values of two dictionaries Note: dict values must be sets """ jacc_results=np.zeros((len(markers1), len(markers2))) j=0 for marker_group in markers1: tmp = [len(markers2[i].intersection...

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27.166667

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def RegisterLateBindingCallback(target_name, callback, **kwargs): """Registers a callback to be invoked when the RDFValue named is declared.""" _LATE_BINDING_STORE.setdefault(target_name, []).append((callback, kwargs))

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73.333333

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def sweep(self): """ Runs through entire dataset. Returns TSS error, total correct, total count, pcorrect (a dict of layer data) """ self.preSweep() if self.loadOrder == []: raise NetworkError('No loadOrder for the inputs. Make sure inputs are properly set.',...

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def update(request, ident, stateless=False, **kwargs): 'Generate update json response' dash_app, app = DashApp.locate_item(ident, stateless) request_body = json.loads(request.body.decode('utf-8')) if app.use_dash_dispatch(): # Force call through dash view_func = app.locate_endpoint_fun...

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def __neighbor_indexes_points(self, optic_object): """! @brief Return neighbors of the specified object in case of sequence of points. @param[in] optic_object (optics_descriptor): Object for which neighbors should be returned in line with connectivity radius. @return (list) List ...

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def elem_add(self, idx=None, name=None, **kwargs): """ Add an element of this model :param idx: element idx :param name: element name :param kwargs: keyword arguments of the parameters :return: allocated idx """ idx = self.system.devman.register_element(...

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def collapse_addresses(addresses): """Collapse a list of IP objects. Example: collapse_addresses([IPv4Network('192.0.2.0/25'), IPv4Network('192.0.2.128/25')]) -> [IPv4Network('192.0.2.0/24')] Args: addresses: An iterator of IPv4Network...

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def add_permission_view_menu(self, permission_name, view_menu_name): """ Adds a permission on a view or menu to the backend :param permission_name: name of the permission to add: 'can_add','can_edit' etc... :param view_menu_name: name of the v...

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def _custom_validate(self, verify, trust_bundle): """ Called when we have set custom validation. We do this in two cases: first, when cert validation is entirely disabled; and second, when using a custom trust DB. """ # If we disabled cert validation, just say: cool. ...

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def fstab(jail): ''' Display contents of a fstab(5) file defined in specified jail's configuration. If no file is defined, return False. CLI Example: .. code-block:: bash salt '*' jail.fstab <jail name> ''' ret = [] config = show_config(jail) if 'fstab' in config: ...

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def get_var_name(nc): """Guesses the variable_name of an open NetCDF file """ non_variable_names = [ 'lat', 'lat_bnds', 'lon', 'lon_bnds', 'time', 'latitude', 'longitude', 'bnds' ] _vars = set(nc.variables.keys()) _vars.difference...

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def LabelValueTable(self, keys=None): """Return LabelValue with FSM derived keys.""" keys = keys or self.superkey # pylint: disable=E1002 return super(CliTable, self).LabelValueTable(keys)

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def set_scene_config(self, scene_id, config): """reconfigure a scene by scene ID""" if not scene_id in self.state.scenes: # does that scene_id exist? err_msg = "Requested to reconfigure scene {sceneNum}, which does not exist".format(sceneNum=scene_id) logging.info(err_msg) ...

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async def set_slave_neighbors(self): '''Set neighbor environments for all the slave environments. Assumes that :attr:`neighbors` are set for this multi-environment. ''' for i, elem in enumerate(self._slave_origins): o, addr = elem r_slave = await self.env.connect(...

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def morphDataLists(fromList, toList, stepList): ''' Iteratively morph fromList into toList using the values 0 to 1 in stepList stepList: a value of 0 means no change and a value of 1 means a complete change to the other value ''' # If there are more than 1 pitch value, then we align the da...

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def failure_line_summary(formatter, failure_line): """ Create a mozlog formatted error summary string from the given failure_line. Create a string which can be compared to a TextLogError.line string to see if they match. """ if failure_line.action == "test_result": action = "test_status...

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def place(vertices_resources, nets, machine, constraints, random=default_random): """A random placer. This algorithm performs uniform-random placement of vertices (completely ignoring connectivty) and thus in the general case is likely to produce very poor quality placements. It exists primar...

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def genemania_force_directed(self,curveSteepness=None,defaultEdgeWeight=None,\ defaultSpringCoefficient=None,defaultSpringLength=None,EdgeAttribute=None,\ ignoreHiddenElements=None,isDeterministic=None,maxNodeMass=None,\ maxWeightCutoff=None,midpointEdges=None,minNodeMass=None,minWeightCutoff=None,\ network=Non...

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def _build_xpath_expr(attrs): """Build an xpath expression to simulate bs4's ability to pass in kwargs to search for attributes when using the lxml parser. Parameters ---------- attrs : dict A dict of HTML attributes. These are NOT checked for validity. Returns ------- expr : u...

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def get_cycle_mrkr(self, end=False): """Mark cycle start or end. Parameters ---------- end : bool If True, marks a cycle end; otherwise, it's a cycle start """ if self.annot is None: # remove if buttons are disabled self.parent.statusBar().showMe...

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def convert_namespaces_ast( ast, api_url: str = None, namespace_targets: Mapping[str, List[str]] = None, canonicalize: bool = False, decanonicalize: bool = False, ): """Recursively convert namespaces of BEL Entities in BEL AST using API endpoint Canonicalization and decanonicalization is de...

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def set_key(key: str, value: typing.List[str], persists: bool = True): """ Removes the specified key from the cauldron configs if the key exists :param key: The key in the cauldron configs object to remove :param value: :param persists: """ if key.endswith('_path') or key.endswith(...

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def _check_load_paths(load_path): ''' Checks the validity of the load_path, returns a sanitized version with invalid paths removed. ''' if load_path is None or not isinstance(load_path, six.string_types): return None _paths = [] for _path in load_path.split(':'): if os.path...

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def notification(self): """Provide access to the currently displayed notification. Returns: :py:class:`BaseNotification`: FoxPuppet BaseNotification object. """ with self.selenium.context(self.selenium.CONTEXT_CHROME): try: root = self.selenium.f...

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def run(src, grammar=NODEBOX, format=None, outputfile=None, iterations=1, buff=None, window=True, title=None, fullscreen=None, close_window=False, server=False, port=7777, show_vars=False, vars=None, namespac...

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def start(self): """ Start daemonization process. """ # If pidfile already exists, we should read pid from there; to overwrite it, if locking # will fail, because locking attempt somehow purges the file contents. if os.path.isfile(self.pid): with open(self.pid...

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def get_config_section(self, name): """ Get a section of a configuration """ if self.config.has_section(name): return self.config.items(name) return []

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def equation_of_time_pvcdrom(dayofyear): """ Equation of time from PVCDROM. `PVCDROM`_ is a website by Solar Power Lab at Arizona State University (ASU) .. _PVCDROM: http://www.pveducation.org/pvcdrom/2-properties-sunlight/solar-time Parameters ---------- dayofyear : numeric Retu...

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def _ParseShVariables(self, lines): """Extract env_var and path values from sh derivative shells. Iterates over each line, word by word searching for statements that set the path. These are either variables, or conditions that would allow a variable to be set later in the line (e.g. export). Args:...

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def iter_lines(f): """ :param f: :type f: file :return: """ linenum = 1 try: for text in f.readlines(): # ignore lines that consist entirely of whitespace if text.isspace(): continue indent,value = parse_line(text) yield...

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def round_to_sigfigs(num, sigfigs): """ Rounds a number rounded to a specific number of significant figures instead of to a specific precision. """ if type(sigfigs) != int: raise TypeError("Number of significant figures must be integer.") elif sigfigs < 1: raise ValueError("Numbe...

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def DIV(self, a, b): """Integer division operation""" try: result = Operators.UDIV(a, b) except ZeroDivisionError: result = 0 return Operators.ITEBV(256, b == 0, 0, result)

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def next(self): """Returns the next batch of data.""" if self.curr_idx == len(self.idx): raise StopIteration i, j = self.idx[self.curr_idx] self.curr_idx += 1 if self.major_axis == 1: data = self.nddata[i][j:j+self.batch_size].T label = self.n...

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