kejian/codesearchnet-python-pep8-full · Datasets at Hugging Face

text stringlengths 75 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 0.18
def fit(self, X): """Fit structure-based AD. The training model memorizes the unique set of reaction signature. Parameters ---------- X : after read rdf file Returns ------- self : object """ X = iter2array(X, dtype=ReactionContainer) se...	[ "def", "fit", "(", "self", ",", "X", ")", ":", "X", "=", "iter2array", "(", "X", ",", "dtype", "=", "ReactionContainer", ")", "self", ".", "_train_signatures", "=", "{", "self", ".", "__get_signature", "(", "x", ")", "for", "x", "in", "X", "}", "re...	27.571429	0.007519
def records( self ): """ Returns the record set for the current settings of this browser. :return <orb.RecordSet> """ if ( self.isGroupingActive() ): self._records.setGroupBy(self.currentGrouping()) else: self._records.setGrou...	[ "def", "records", "(", "self", ")", ":", "if", "(", "self", ".", "isGroupingActive", "(", ")", ")", ":", "self", ".", "_records", ".", "setGroupBy", "(", "self", ".", "currentGrouping", "(", ")", ")", "else", ":", "self", ".", "_records", ".", "setGr...	31.727273	0.019499
def _see_remote_link_node(self, node_id, fringe=None, dist=None, check_dsp=lambda x: True): """ See data remote links of the node (set output to remote links). :param node_id: Node id. :type node_id: str :param fringe: Heapq...	[ "def", "_see_remote_link_node", "(", "self", ",", "node_id", ",", "fringe", "=", "None", ",", "dist", "=", "None", ",", "check_dsp", "=", "lambda", "x", ":", "True", ")", ":", "# Namespace shortcut.", "node", ",", "p_id", ",", "c_i", "=", "self", ".", ...	42.564103	0.002356
def _ns_query(self, session): """ Return a SQLAlchemy query that is already namespaced by the app and namespace given to this backend during initialization. Returns: a SQLAlchemy query object """ return session.query(ORMJob).filter(ORMJob.app == self.app, ...	[ "def", "_ns_query", "(", "self", ",", "session", ")", ":", "return", "session", ".", "query", "(", "ORMJob", ")", ".", "filter", "(", "ORMJob", ".", "app", "==", "self", ".", "app", ",", "ORMJob", ".", "namespace", "==", "self", ".", "namespace", ")"...	41.777778	0.007813
def satisifesShapeOr(cntxt: Context, n: Node, se: ShExJ.ShapeOr, _: DebugContext) -> bool: """ Se is a ShapeOr and there is some shape expression se2 in shapeExprs such that satisfies(n, se2, G, m). """ return any(satisfies(cntxt, n, se2) for se2 in se.shapeExprs)	[ "def", "satisifesShapeOr", "(", "cntxt", ":", "Context", ",", "n", ":", "Node", ",", "se", ":", "ShExJ", ".", "ShapeOr", ",", "_", ":", "DebugContext", ")", "->", "bool", ":", "return", "any", "(", "satisfies", "(", "cntxt", ",", "n", ",", "se2", "...	90	0.011029
def tempoAdjust1(self, tempoFactor): """ Adjust tempo based on recent active apical input only :param tempoFactor: scaling signal to MC clock from last sequence item :return: adjusted scaling signal """ if self.apicalIntersect.any(): tempoFactor = tempoFactor * 0.5 else: tempo...	[ "def", "tempoAdjust1", "(", "self", ",", "tempoFactor", ")", ":", "if", "self", ".", "apicalIntersect", ".", "any", "(", ")", ":", "tempoFactor", "=", "tempoFactor", "", "0.5", "else", ":", "tempoFactor", "=", "tempoFactor", "", "2", "return", "tempoFact...	23.6	0.008152
def verify_geospatial_bounds(self, ds): """Checks that the geospatial bounds is well formed OGC WKT""" var = getattr(ds, 'geospatial_bounds', None) check = var is not None if not check: return ratable_result(False, "Global Attributes", # grou...	[ "def", "verify_geospatial_bounds", "(", "self", ",", "ds", ")", ":", "var", "=", "getattr", "(", "ds", ",", "'geospatial_bounds'", ",", "None", ")", "check", "=", "var", "is", "not", "None", "if", "not", "check", ":", "return", "ratable_result", "(", "Fa...	44.55	0.005495
def opacity(self, value): """ Setter for self.__opacity attribute. :param value: Attribute value. :type value: float """ if value is not None: assert type(value) in (int, float), "'{0}' attribute: '{1}' type is not 'int' or 'float'!".format("opacity", ...	[ "def", "opacity", "(", "self", ",", "value", ")", ":", "if", "value", "is", "not", "None", ":", "assert", "type", "(", "value", ")", "in", "(", "int", ",", "float", ")", ",", "\"'{0}' attribute: '{1}' type is not 'int' or 'float'!\"", ".", "format", "(", "...	32.166667	0.006711
def import_csv(file_name, **kwargs): """ Reads control points from a CSV file and generates a 1-dimensional list of control points. It is possible to use a different value separator via ``separator`` keyword argument. The following code segment illustrates the usage of ``separator`` keyword argument. ...	[ "def", "import_csv", "(", "file_name", ",", "", "", "kwargs", ")", ":", "# File delimiters", "sep", "=", "kwargs", ".", "get", "(", "'separator'", ",", "\",\"", ")", "content", "=", "exch", ".", "read_file", "(", "file_name", ",", "skip_lines", "=", "1...	40.275862	0.004181
def initial_closure(self): """Computes the initial closure using the START_foo production.""" first_rule = DottedRule(self.start, 0, END_OF_INPUT) return self.closure([first_rule])	[ "def", "initial_closure", "(", "self", ")", ":", "first_rule", "=", "DottedRule", "(", "self", ".", "start", ",", "0", ",", "END_OF_INPUT", ")", "return", "self", ".", "closure", "(", "[", "first_rule", "]", ")" ]	50.25	0.009804
def visit_Module(self, node): """ Import module define a new variable name. """ duc = SilentDefUseChains() duc.visit(node) for d in duc.locals[node]: self.result[d.name()] = d.node	[ "def", "visit_Module", "(", "self", ",", "node", ")", ":", "duc", "=", "SilentDefUseChains", "(", ")", "duc", ".", "visit", "(", "node", ")", "for", "d", "in", "duc", ".", "locals", "[", "node", "]", ":", "self", ".", "result", "[", "d", ".", "na...	36.5	0.008929
def following(self, user, models, *kwargs): """ Returns a list of actors that the given user is following (eg who im following). Items in the list can be of any model unless a list of restricted models are passed. Eg following(user, User) will only return users following the given user...	[ "def", "following", "(", "self", ",", "user", ",", "", "models", ",", "", "", "kwargs", ")", ":", "return", "[", "follow", ".", "follow_object", "for", "follow", "in", "self", ".", "following_qs", "(", "user", ",", "", "models", ",", "flag", "=",...	51.111111	0.010684
def JGE(cpu, target): """ Jumps short if greater or equal. :param cpu: current CPU. :param target: destination operand. """ cpu.PC = Operators.ITEBV(cpu.address_bit_size, (cpu.SF == cpu.OF), target.read(), cpu.PC)	[ "def", "JGE", "(", "cpu", ",", "target", ")", ":", "cpu", ".", "PC", "=", "Operators", ".", "ITEBV", "(", "cpu", ".", "address_bit_size", ",", "(", "cpu", ".", "SF", "==", "cpu", ".", "OF", ")", ",", "target", ".", "read", "(", ")", ",", "cpu",...	31.875	0.01145
def table(self, rows, col_width=2): '''table will print a table of entries. If the rows is a dictionary, the keys are interpreted as column names. if not, a numbered list is used. ''' labels = [str(x) for x in range(1,len(rows)+1)] if isinstance(rows, dict): ...	[ "def", "table", "(", "self", ",", "rows", ",", "col_width", "=", "2", ")", ":", "labels", "=", "[", "str", "(", "x", ")", "for", "x", "in", "range", "(", "1", ",", "len", "(", "rows", ")", "+", "1", ")", "]", "if", "isinstance", "(", "rows", ...	34.705882	0.008251
def _process_tags(self): """Validate standard tags and initialize attributes. Raise ValueError if tag values are not supported. """ tags = self.tags for code, (name, default, dtype, count, validate) in TIFF_TAGS.items(): if not (name in tags or default is None): ...	[ "def", "_process_tags", "(", "self", ")", ":", "tags", "=", "self", ".", "tags", "for", "code", ",", "(", "name", ",", "default", ",", "dtype", ",", "count", ",", "validate", ")", "in", "TIFF_TAGS", ".", "items", "(", ")", ":", "if", "not", "(", ...	44.758621	0.001131
async def load_saved_device_info(self): """Load device information from the device info file.""" _LOGGER.debug("Loading saved device info.") deviceinfo = [] if self._workdir: _LOGGER.debug("Really Loading saved device info.") try: device_file = '{}...	[ "async", "def", "load_saved_device_info", "(", "self", ")", ":", "_LOGGER", ".", "debug", "(", "\"Loading saved device info.\"", ")", "deviceinfo", "=", "[", "]", "if", "self", ".", "_workdir", ":", "_LOGGER", ".", "debug", "(", "\"Really Loading saved device info...	47.888889	0.002275
def read(self, length=None): """ Reads data from readble BIO. For test purposes. @param length - if specifed, limits amount of data read. If not BIO is read until end of buffer """ if not length is None: if not isinstance(length, inttype) : rai...	[ "def", "read", "(", "self", ",", "length", "=", "None", ")", ":", "if", "not", "length", "is", "None", ":", "if", "not", "isinstance", "(", "length", ",", "inttype", ")", ":", "raise", "TypeError", "(", "\"length to read should be number\"", ")", "buf", ...	40.121212	0.00295
def restore(self, fade=False): """Restore the state of a device to that which was previously saved. For coordinator devices restore everything. For slave devices only restore volume etc., not transport info (transport info comes from the slave's coordinator). Args: ...	[ "def", "restore", "(", "self", ",", "fade", "=", "False", ")", ":", "try", ":", "if", "self", ".", "is_coordinator", ":", "self", ".", "_restore_coordinator", "(", ")", "finally", ":", "self", ".", "_restore_volume", "(", "fade", ")", "# Now everything is ...	34.916667	0.002323
def attr(self, kw=None, _attributes=None, **attrs): """Add a general or graph/node/edge attribute statement. Args: kw: Attributes target (``None`` or ``'graph'``, ``'node'``, ``'edge'``). attrs: Attributes to be set (must be strings, may be empty). See the :ref:`usage e...	[ "def", "attr", "(", "self", ",", "kw", "=", "None", ",", "_attributes", "=", "None", ",", "", "", "attrs", ")", ":", "if", "kw", "is", "not", "None", "and", "kw", ".", "lower", "(", ")", "not", "in", "(", "'graph'", ",", "'node'", ",", "'edge...	44.2	0.005537
def _function(self): """ This is the actual function that will be executed. It uses only information that is provided in the settings property will be overwritten in the __init__ """ plant = self.instruments['plant']['instance'] controler = self.instruments['controler']['...	[ "def", "_function", "(", "self", ")", ":", "plant", "=", "self", ".", "instruments", "[", "'plant'", "]", "[", "'instance'", "]", "controler", "=", "self", ".", "instruments", "[", "'controler'", "]", "[", "'instance'", "]", "plant", ".", "update", "(", ...	41.622222	0.003652
def get_vnetwork_hosts_output_vnetwork_hosts_vswitch(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") get_vnetwork_hosts = ET.Element("get_vnetwork_hosts") config = get_vnetwork_hosts output = ET.SubElement(get_vnetwork_hosts, "output") vn...	[ "def", "get_vnetwork_hosts_output_vnetwork_hosts_vswitch", "(", "self", ",", "", "", "kwargs", ")", ":", "config", "=", "ET", ".", "Element", "(", "\"config\"", ")", "get_vnetwork_hosts", "=", "ET", ".", "Element", "(", "\"get_vnetwork_hosts\"", ")", "config", ...	42.846154	0.003515
def getlevel(self, threshold): """ Returns all clusters with a maximum distance of threshold in between each other :param threshold: the maximum distance between clusters. See :py:meth:`~cluster.cluster.Cluster.getlevel` """ # if it's not worth clustering, ju...	[ "def", "getlevel", "(", "self", ",", "threshold", ")", ":", "# if it's not worth clustering, just return the data", "if", "len", "(", "self", ".", "_input", ")", "<=", "1", ":", "return", "self", ".", "_input", "# initialize the cluster if not yet done", "if", "not"...	29	0.003515
def leehom_general_stats_table(self): """ Take the parsed stats from the leeHom report and add it to the basic stats table at the top of the report """ headers = {} headers['merged_trimming'] = { 'title': '{} Merged (Trimming)'.format(config.read_count_prefix), '...	[ "def", "leehom_general_stats_table", "(", "self", ")", ":", "headers", "=", "{", "}", "headers", "[", "'merged_trimming'", "]", "=", "{", "'title'", ":", "'{} Merged (Trimming)'", ".", "format", "(", "config", ".", "read_count_prefix", ")", ",", "'description'",...	45.227273	0.003937
def _mirror_groups(self): """ Mirrors the user's LDAP groups in the Django database and updates the user's membership. """ target_group_names = frozenset(self._get_groups().get_group_names()) current_group_names = frozenset(self._user.groups.values_list('name', flat=True)...	[ "def", "_mirror_groups", "(", "self", ")", ":", "target_group_names", "=", "frozenset", "(", "self", ".", "_get_groups", "(", ")", ".", "get_group_names", "(", ")", ")", "current_group_names", "=", "frozenset", "(", "self", ".", "_user", ".", "groups", ".", ...	48.75	0.007547
def parse_star_report (self, raw_data): """ Parse the final STAR log file. """ regexes = { 'total_reads': r"Number of input reads \\|\s+(\d+)", 'avg_input_read_length': r"Average input read length \\|\s+([\d\.]+)", 'uniquely_mapped': ...	[ "def", "parse_star_report", "(", "self", ",", "raw_data", ")", ":", "regexes", "=", "{", "'total_reads'", ":", "r\"Number of input reads \\\|\\s+(\\d+)\"", ",", "'avg_input_read_length'", ":", "r\"Average input read length \\\|\\s+([\\d\\.]+)\"", ",", "'uniquely_mapped'", ":", ...	70.45098	0.009058
def __get_file(self, file): """ Get request file and do a security check """ file_object = None if file['name'] in request.files: file_object = request.files[file['name']] clean_filename = secure_filename(file_object.filename) if clean_filename == '': ...	[ "def", "__get_file", "(", "self", ",", "file", ")", ":", "file_object", "=", "None", "if", "file", "[", "'name'", "]", "in", "request", ".", "files", ":", "file_object", "=", "request", ".", "files", "[", "file", "[", "'name'", "]", "]", "clean_filenam...	44.428571	0.00315
def alphanum_order(triples): """ Sort a list of triples by relation name. Embedded integers are sorted numerically, but otherwise the sorting is alphabetic. """ return sorted( triples, key=lambda t: [ int(t) if t.isdigit() else t for t in re.split(r'([0-9...	[ "def", "alphanum_order", "(", "triples", ")", ":", "return", "sorted", "(", "triples", ",", "key", "=", "lambda", "t", ":", "[", "int", "(", "t", ")", "if", "t", ".", "isdigit", "(", ")", "else", "t", "for", "t", "in", "re", ".", "split", "(", ...	24.714286	0.002786
def field_uuid(self, attr, options): """Creates a form element for the UUID type.""" options['validators'].append(validators.UUIDValidator(attr.entity)) return wtf_fields.StringField, options	[ "def", "field_uuid", "(", "self", ",", "attr", ",", "options", ")", ":", "options", "[", "'validators'", "]", ".", "append", "(", "validators", ".", "UUIDValidator", "(", "attr", ".", "entity", ")", ")", "return", "wtf_fields", ".", "StringField", ",", "...	53	0.009302
def vocab_to_json(vocab: Vocab, path: str): """ Saves vocabulary in human-readable json. :param vocab: Vocabulary mapping. :param path: Output file path. """ with open(path, "w", encoding=C.VOCAB_ENCODING) as out: json.dump(vocab, out, indent=4, ensure_ascii=False) logger.info('...	[ "def", "vocab_to_json", "(", "vocab", ":", "Vocab", ",", "path", ":", "str", ")", ":", "with", "open", "(", "path", ",", "\"w\"", ",", "encoding", "=", "C", ".", "VOCAB_ENCODING", ")", "as", "out", ":", "json", ".", "dump", "(", "vocab", ",", "out"...	34.3	0.002841
def _get_interpolator(method, vectorizeable_only=False, **kwargs): '''helper function to select the appropriate interpolator class returns interpolator class and keyword arguments for the class ''' interp1d_methods = ['linear', 'nearest', 'zero', 'slinear', 'quadratic', 'cubic',...	[ "def", "_get_interpolator", "(", "method", ",", "vectorizeable_only", "=", "False", ",", "", "", "kwargs", ")", ":", "interp1d_methods", "=", "[", "'linear'", ",", "'nearest'", ",", "'zero'", ",", "'slinear'", ",", "'quadratic'", ",", "'cubic'", ",", "'pol...	38.384615	0.000489
def _plotxw(self,args,*kwargs): #pragma: no cover """ NAME: plotxw PURPOSE: plot the spectrum of x INPUT: bovy_plot.bovy_plot args and kwargs OUTPUT: x(t) HISTORY: 2010-09-21 - Written - Bovy (NYU) """ ...	[ "def", "_plotxw", "(", "self", ",", "", "args", ",", "", "", "kwargs", ")", ":", "#pragma: no cover", "xw", "=", "self", ".", "xw", "(", ")", "#BOVY: CHECK THAT THIS IS CORRECT", "plot", ".", "bovy_plot", "(", "2.", "", "m", ".", "pi", "*", "nu", ...	30.157895	0.021997
def holdout(self, train_perc=0.7, num_rep=50, stratified=True, return_ids_only=False, format='MLDataset'): """ Builds a generator for train and test sets for cross-validation. """ ids_in_class = {cid: self....	[ "def", "holdout", "(", "self", ",", "train_perc", "=", "0.7", ",", "num_rep", "=", "50", ",", "stratified", "=", "True", ",", "return_ids_only", "=", "False", ",", "format", "=", "'MLDataset'", ")", ":", "ids_in_class", "=", "{", "cid", ":", "self", "....	41.413043	0.006154
def _map_segmentation_mask_to_stft_domain(mask, times, frequencies, stft_times, stft_frequencies): """ Maps the given `mask`, which is in domain (`frequencies`, `times`) to the new domain (`stft_frequencies`, `stft_times`) and returns the result. """ assert mask.shape == (frequencies.shape[0], times...	[ "def", "_map_segmentation_mask_to_stft_domain", "(", "mask", ",", "times", ",", "frequencies", ",", "stft_times", ",", "stft_frequencies", ")", ":", "assert", "mask", ".", "shape", "==", "(", "frequencies", ".", "shape", "[", "0", "]", ",", "times", ".", "sh...	45.956522	0.007414
def main(): """Quick test for QSUsb class.""" import argparse parser = argparse.ArgumentParser() parser.add_argument('--url', help='QSUSB URL [http://127.0.0.1:2020]', default='http://127.0.0.1:2020') parser.add_argument('--file', help='a test file from /&devices') parser...	[ "def", "main", "(", ")", ":", "import", "argparse", "parser", "=", "argparse", ".", "ArgumentParser", "(", ")", "parser", ".", "add_argument", "(", "'--url'", ",", "help", "=", "'QSUSB URL [http://127.0.0.1:2020]'", ",", "default", "=", "'http://127.0.0.1:2020'", ...	33.604651	0.000672
def error(msg: str, resource: Optional['Resource'] = None, stream_id: Optional[int] = None): """ Logs a message to the Pulumi CLI's error channel, associating it with a resource and stream_id if provided. :param str msg: The message to send to the Pulumi CLI. :param Optional[Resource] resource: If ...	[ "def", "error", "(", "msg", ":", "str", ",", "resource", ":", "Optional", "[", "'Resource'", "]", "=", "None", ",", "stream_id", ":", "Optional", "[", "int", "]", "=", "None", ")", ":", "engine", "=", "get_engine", "(", ")", "if", "engine", "is", "...	47.928571	0.00731
def _fits_inside_predicate(self): """ Return a function taking an integer point size argument that returns \|True\| if the text in this fitter can be wrapped to fit entirely within its extents when rendered at that point size. """ def predicate(point_size): """ ...	[ "def", "_fits_inside_predicate", "(", "self", ")", ":", "def", "predicate", "(", "point_size", ")", ":", "\"\"\"\n Return \|True\| if the text in line_source can be wrapped to fit\n entirely within extents when rendered at point_size using the\n font defi...	43.647059	0.002639
def report(self, fraction=None): """report the total progress for the current stack, optionally given the local fraction completed. fraction=None: if given, used as the fraction of the local method so far completed. runtimes=None: if given, used as the expected runtimes for the current stack. """ r = Dict() ...	[ "def", "report", "(", "self", ",", "fraction", "=", "None", ")", ":", "r", "=", "Dict", "(", ")", "local_key", "=", "self", ".", "stack_key", "if", "local_key", "is", "None", ":", "return", "{", "}", "runtimes", "=", "self", ".", "runtimes", "(", "...	39.555556	0.03155
def percolate(self, index, doc_types, query): """ Match a query with a document """ if doc_types is None: raise RuntimeError('percolate() must be supplied with at least one doc_type') path = self._make_path(index, doc_types, '_percolate') body = self._encode_...	[ "def", "percolate", "(", "self", ",", "index", ",", "doc_types", ",", "query", ")", ":", "if", "doc_types", "is", "None", ":", "raise", "RuntimeError", "(", "'percolate() must be supplied with at least one doc_type'", ")", "path", "=", "self", ".", "_make_path", ...	37.6	0.007792
def complex_state_generator_bravo(last_state=''): """Pick a state.""" from random import choice states = ['ALPHA', 'BRAVO', 'BRAVO', 'DONE'] if last_state: states.remove(last_state) # Slightly lower chances of previous state. state = choice(states) logging.info('Generating a state......	[ "def", "complex_state_generator_bravo", "(", "last_state", "=", "''", ")", ":", "from", "random", "import", "choice", "states", "=", "[", "'ALPHA'", ",", "'BRAVO'", ",", "'BRAVO'", ",", "'DONE'", "]", "if", "last_state", ":", "states", ".", "remove", "(", ...	26	0.002857
async def download_media(self, args, kwargs): """ Downloads the media contained in the message, if any. Shorthand for `telethon.client.downloads.DownloadMethods.download_media` with the ``message`` already set. """ return await self._client.download_media(self, args, ...	[ "async", "def", "download_media", "(", "self", ",", "", "args", ",", "", "", "kwargs", ")", ":", "return", "await", "self", ".", "_client", ".", "download_media", "(", "self", ",", "", "args", ",", "", "", "kwargs", ")" ]	46.142857	0.006079
def _StructMessageToJsonObject(message, unused_including_default=False): """Converts Struct message according to Proto3 JSON Specification.""" fields = message.fields ret = {} for key in fields: ret[key] = _ValueMessageToJsonObject(fields[key]) return ret	[ "def", "_StructMessageToJsonObject", "(", "message", ",", "unused_including_default", "=", "False", ")", ":", "fields", "=", "message", ".", "fields", "ret", "=", "{", "}", "for", "key", "in", "fields", ":", "ret", "[", "key", "]", "=", "_ValueMessageToJsonO...	37.571429	0.022305
def WalkControl(control: Control, includeTop: bool = False, maxDepth: int = 0xFFFFFFFF): """ control: `Control` or its subclass. includeTop: bool, if True, yield (control, 0) first. maxDepth: int, enum depth. Yield 2 items tuple(control: Control, depth: int). """ if includeTop: yield...	[ "def", "WalkControl", "(", "control", ":", "Control", ",", "includeTop", ":", "bool", "=", "False", ",", "maxDepth", ":", "int", "=", "0xFFFFFFFF", ")", ":", "if", "includeTop", ":", "yield", "control", ",", "0", "if", "maxDepth", "<=", "0", ":", "retu...	32.678571	0.002123
def publish(self, synchronous=True, **kwargs): """Helper for publishing an existing content view. :param synchronous: What should happen if the server returns an HTTP 202 (accepted) status code? Wait for the task to complete if ``True``. Immediately return the server's response ...	[ "def", "publish", "(", "self", ",", "synchronous", "=", "True", ",", "", "", "kwargs", ")", ":", "kwargs", "=", "kwargs", ".", "copy", "(", ")", "# shadow the passed-in kwargs", "if", "'data'", "in", "kwargs", "and", "'id'", "not", "in", "kwargs", "[",...	53.222222	0.002051
def step(self, data): """ Run convolution over a single position. The data must be exactly as wide as the convolution filters. :param data: Shape: (batch_size, kernel_width, num_hidden). :return: Single result of a convolution. Shape: (batch_size, 1, num_hidden). """ # ...	[ "def", "step", "(", "self", ",", "data", ")", ":", "# As we only run convolution over a single window that is exactly the size of the convolutional filter", "# we can use FullyConnected instead of Convolution for efficiency reasons. Additionally we do not need to", "# perform any masking.", "n...	48.296296	0.004511
def compare_agents(EnvFactory, AgentFactories, n=10, steps=1000): """See how well each of several agents do in n instances of an environment. Pass in a factory (constructor) for environments, and several for agents. Create n instances of the environment, and run each agent in copies of each one for step...	[ "def", "compare_agents", "(", "EnvFactory", ",", "AgentFactories", ",", "n", "=", "10", ",", "steps", "=", "1000", ")", ":", "envs", "=", "[", "EnvFactory", "(", ")", "for", "i", "in", "range", "(", "n", ")", "]", "return", "[", "(", "A", ",", "t...	63.25	0.001949
def get_concept_item_mapping(self, concepts=None, lang=None): """ Get mapping of concepts to items belonging to concept. Args: concepts (list of Concept): Defaults to None meaning all concepts lang (str): language of concepts, if None use language of concepts Re...	[ "def", "get_concept_item_mapping", "(", "self", ",", "concepts", "=", "None", ",", "lang", "=", "None", ")", ":", "if", "concepts", "is", "None", ":", "concepts", "=", "self", ".", "filter", "(", "active", "=", "True", ")", "if", "lang", "is", "not", ...	44.695652	0.00381
def timestr_mod24(timestr: str) -> int: """ Given a GTFS HH:MM:SS time string, return a timestring in the same format but with the hours taken modulo 24. """ try: hours, mins, secs = [int(x) for x in timestr.split(":")] hours %= 24 result = f"{hours:02d}:{mins:02d}:{secs:02d}...	[ "def", "timestr_mod24", "(", "timestr", ":", "str", ")", "->", "int", ":", "try", ":", "hours", ",", "mins", ",", "secs", "=", "[", "int", "(", "x", ")", "for", "x", "in", "timestr", ".", "split", "(", "\":\"", ")", "]", "hours", "%=", "24", "r...	30.166667	0.005362
def transmission_rate(self): """ Returns the upstream, downstream values as a tuple in bytes per second. Use this for periodical calling. """ sent = self.bytes_sent received = self.bytes_received traffic_call = time.time() time_delta = traffic_call - self....	[ "def", "transmission_rate", "(", "self", ")", ":", "sent", "=", "self", ".", "bytes_sent", "received", "=", "self", ".", "bytes_received", "traffic_call", "=", "time", ".", "time", "(", ")", "time_delta", "=", "traffic_call", "-", "self", ".", "last_traffic_...	42.466667	0.004608
def completions(self): """ Return :class:`classes.Completion` objects. Those objects contain information about the completions, more than just names. :return: Completion objects, sorted by name. :rtype: list of :class:`classes.Completion` """ debug.speed('complet...	[ "def", "completions", "(", "self", ")", ":", "debug", ".", "speed", "(", "'completions start'", ")", "comps", "=", "self", ".", "_evaluator", ".", "complete", "(", ")", "debug", ".", "speed", "(", "'completions end'", ")", "return", "sorted", "(", "comps",...	35.692308	0.004202
def is_file(value, **kwargs): """Indicate whether ``value`` is a file that exists on the local filesystem. :param value: The value to evaluate. :returns: ``True`` if ``value`` is valid, ``False`` if it is not. :rtype: :class:`bool <python:bool>` :raises SyntaxError: if ``kwargs`` contains duplica...	[ "def", "is_file", "(", "value", ",", "", "", "kwargs", ")", ":", "try", ":", "value", "=", "validators", ".", "file_exists", "(", "value", ",", "", "", "kwargs", ")", "except", "SyntaxError", "as", "error", ":", "raise", "error", "except", "Excepti...	29.15	0.004983
def profile_df(df): """ Generate a profile of data in a dataframe. Args: df: the Pandas dataframe. """ # The bootstrap CSS messes up the Datalab display so we tweak it to not have an effect. # TODO(gram): strip it out rather than this kludge. return IPython.core.display.HTML( pandas_profiling.Pro...	[ "def", "profile_df", "(", "df", ")", ":", "# The bootstrap CSS messes up the Datalab display so we tweak it to not have an effect.", "# TODO(gram): strip it out rather than this kludge.", "return", "IPython", ".", "core", ".", "display", ".", "HTML", "(", "pandas_profiling", ".",...	36.7	0.018617
def restore_definition(self, project, definition_id, deleted): """RestoreDefinition. Restores a deleted definition :param str project: Project ID or project name :param int definition_id: The identifier of the definition to restore. :param bool deleted: When false, restores a del...	[ "def", "restore_definition", "(", "self", ",", "project", ",", "definition_id", ",", "deleted", ")", ":", "route_values", "=", "{", "}", "if", "project", "is", "not", "None", ":", "route_values", "[", "'project'", "]", "=", "self", ".", "_serialize", ".", ...	55.363636	0.00565
def started(name): ''' Check if volume has been started name name of the volume .. code-block:: yaml mycluster: glusterfs.started: [] ''' ret = {'name': name, 'changes': {}, 'comment': '', 'result': False} volinfo = __salt__['glu...	[ "def", "started", "(", "name", ")", ":", "ret", "=", "{", "'name'", ":", "name", ",", "'changes'", ":", "{", "}", ",", "'comment'", ":", "''", ",", "'result'", ":", "False", "}", "volinfo", "=", "__salt__", "[", "'glusterfs.info'", "]", "(", ")", "...	26.071429	0.00088
def _create_warm_start_tuner(self, additional_parents, warm_start_type, estimator=None): """Creates a new ``HyperparameterTuner`` with ``WarmStartConfig``, where type will be equal to ``warm_start_type`` and``parents`` would be equal to union of ``additional_parents`` and self. Args: ...	[ "def", "_create_warm_start_tuner", "(", "self", ",", "additional_parents", ",", "warm_start_type", ",", "estimator", "=", "None", ")", ":", "all_parents", "=", "{", "self", ".", "latest_tuning_job", ".", "name", "}", "if", "additional_parents", ":", "all_parents",...	61.25	0.008707
def operate_on_bulb(self, method, params=None): """ Build socket and send command to the bulb through it :param method: method you want to use :param params: parameters needed for this method (can be a string if ony one parameter is needed) :type method: str ...	[ "def", "operate_on_bulb", "(", "self", ",", "method", ",", "params", "=", "None", ")", ":", "# Get the message", "self", ".", "command", "=", "YeelightCommand", "(", "self", ".", "next_cmd_id", "(", ")", ",", "method", ",", "params", ")", "# Send with socket...	41.3	0.00355
def __create_table_if_not_exists(self): # type: () -> None """Creates table in Dynamodb resource if it doesn't exist and create_table is set as True. :rtype: None :raises: PersistenceException: When `create_table` fails on dynamodb resource. """ if se...	[ "def", "__create_table_if_not_exists", "(", "self", ")", ":", "# type: () -> None", "if", "self", ".", "create_table", ":", "try", ":", "self", ".", "dynamodb", ".", "create_table", "(", "TableName", "=", "self", ".", "table_name", ",", "KeySchema", "=", "[", ...	37.368421	0.002059
def create_working_dir(config, prefix): ''' Create a fresh temporary directory, based on the fiven prefix. Returns the new path. ''' # Fetch base directory from executor configuration basepath = config.get("Execution", "directory") if not prefix: prefix = 'opensubmit' f...	[ "def", "create_working_dir", "(", "config", ",", "prefix", ")", ":", "# Fetch base directory from executor configuration", "basepath", "=", "config", ".", "get", "(", "\"Execution\"", ",", "\"directory\"", ")", "if", "not", "prefix", ":", "prefix", "=", "'opensubmit...	31.352941	0.001821
def max_variance_genes(data, nbins=5, frac=0.2): """ This function identifies the genes that have the max variance across a number of bins sorted by mean. Args: data (array): genes x cells nbins (int): number of bins to sort genes by mean expression level. Default: 10. frac (flo...	[ "def", "max_variance_genes", "(", "data", ",", "nbins", "=", "5", ",", "frac", "=", "0.2", ")", ":", "# TODO: profile, make more efficient for large matrices", "# 8000 cells: 0.325 seconds", "# top time: sparse.csc_tocsr, csc_matvec, astype, copy, mul_scalar", "# 73233 cells: 5.347...	35.930233	0.004411
def _load_calib(self): """Load and compute intrinsic and extrinsic calibration parameters.""" # We'll build the calibration parameters as a dictionary, then # convert it to a namedtuple to prevent it from being modified later data = {} # Load the calibration file calib_f...	[ "def", "_load_calib", "(", "self", ")", ":", "# We'll build the calibration parameters as a dictionary, then", "# convert it to a namedtuple to prevent it from being modified later", "data", "=", "{", "}", "# Load the calibration file", "calib_filepath", "=", "os", ".", "path", "...	43.581818	0.000816
def list_domains(**kwargs): ''' Return a list of available domains. :param connection: libvirt connection URI, overriding defaults .. versionadded:: 2019.2.0 :param username: username to connect with, overriding defaults .. versionadded:: 2019.2.0 :param password: password to conn...	[ "def", "list_domains", "(", "", "", "kwargs", ")", ":", "vms", "=", "[", "]", "conn", "=", "__get_conn", "(", "", "", "kwargs", ")", "for", "dom", "in", "_get_domain", "(", "conn", ",", "iterable", "=", "True", ")", ":", "vms", ".", "append", ...	23.269231	0.001587
def _identifier_filtered_iterator(graph): """Iterate over names in the given namespace.""" for data in graph: for pair in _get_node_names(data): yield pair for member in data.get(MEMBERS, []): for pair in _get_node_names(member): yield pair for ((_, ...	[ "def", "_identifier_filtered_iterator", "(", "graph", ")", ":", "for", "data", "in", "graph", ":", "for", "pair", "in", "_get_node_names", "(", "data", ")", ":", "yield", "pair", "for", "member", "in", "data", ".", "get", "(", "MEMBERS", ",", "[", "]", ...	37.393939	0.00237
def register_device(ctx, device, model, nickname, client_type): """Registers a device instance under an existing device model. Device instance fields must start with a letter or number. The device ID can only contain letters, numbers, and the following symbols: period (.), hyphen (-), underscore (_), a...	[ "def", "register_device", "(", "ctx", ",", "device", ",", "model", ",", "nickname", ",", "client_type", ")", ":", "session", ",", "api_url", ",", "project_id", "=", "build_client_from_context", "(", "ctx", ")", "device_base_url", "=", "'/'", ".", "join", "("...	41.828571	0.000668
def stop(self): """ Stop all functions running in the thread handler.""" for run_event in self.run_events: run_event.clear() for thread in self.thread_pool: thread.join()	[ "def", "stop", "(", "self", ")", ":", "for", "run_event", "in", "self", ".", "run_events", ":", "run_event", ".", "clear", "(", ")", "for", "thread", "in", "self", ".", "thread_pool", ":", "thread", ".", "join", "(", ")" ]	30.428571	0.009132
def print_evaluation(period=1, show_stdv=True): """Create a callback that prints the evaluation results. Parameters ---------- period : int, optional (default=1) The period to print the evaluation results. show_stdv : bool, optional (default=True) Whether to show stdv (if provided)....	[ "def", "print_evaluation", "(", "period", "=", "1", ",", "show_stdv", "=", "True", ")", ":", "def", "_callback", "(", "env", ")", ":", "if", "period", ">", "0", "and", "env", ".", "evaluation_result_list", "and", "(", "env", ".", "iteration", "+", "1",...	36.666667	0.005063
def smart_search_prefix(self): """ Perform a smart search. The smart search function tries extract a query from a text string. This query is then passed to the search_prefix function, which performs the search. """ search_options = {} extra_query = N...	[ "def", "smart_search_prefix", "(", "self", ")", ":", "search_options", "=", "{", "}", "extra_query", "=", "None", "vrf_filter", "=", "None", "if", "'query_id'", "in", "request", ".", "json", ":", "search_options", "[", "'query_id'", "]", "=", "request", ".",...	38.447619	0.000966
def _get_stitch_report_path(self): """Checks if stitch report label / path is set. Returns absolute path.""" if self.Parameters['-r'].isOn(): stitch_path = self._absolute(str(self.Parameters['-r'].Value)) return stitch_path elif self.Parameters['-r'].isOff(): ...	[ "def", "_get_stitch_report_path", "(", "self", ")", ":", "if", "self", ".", "Parameters", "[", "'-r'", "]", ".", "isOn", "(", ")", ":", "stitch_path", "=", "self", ".", "_absolute", "(", "str", "(", "self", ".", "Parameters", "[", "'-r'", "]", ".", "...	46.428571	0.009063
def set_nightlight(self, state): """Sets the night light state of the smart plug""" packet = bytearray(16) packet[0] = 2 if self.check_power(): packet[4] = 3 if state else 1 else: packet[4] = 2 if state else 0 self.send_packet(0x6a, packet)	[ "def", "set_nightlight", "(", "self", ",", "state", ")", ":", "packet", "=", "bytearray", "(", "16", ")", "packet", "[", "0", "]", "=", "2", "if", "self", ".", "check_power", "(", ")", ":", "packet", "[", "4", "]", "=", "3", "if", "state", "else"...	29.777778	0.01087
def on_site(self, site_id=None): """Return a :class:`QuerySet` of pages that are published on the site defined by the ``SITE_ID`` setting. :param site_id: specify the id of the site object to filter with. """ if settings.PAGE_USE_SITE_ID: if not site_id: ...	[ "def", "on_site", "(", "self", ",", "site_id", "=", "None", ")", ":", "if", "settings", ".", "PAGE_USE_SITE_ID", ":", "if", "not", "site_id", ":", "site_id", "=", "settings", ".", "SITE_ID", "return", "self", ".", "filter", "(", "sites", "=", "site_id", ...	37.454545	0.004739
def set_mode(self, mode): """Configure how this console will react to the cursor writing past the end if the console. This is for methods that use the virtual cursor, such as :any:`print_str`. Args: mode (Text): The mode to set. Possible settings are: ...	[ "def", "set_mode", "(", "self", ",", "mode", ")", ":", "MODES", "=", "[", "'error'", ",", "'scroll'", "]", "if", "mode", ".", "lower", "(", ")", "not", "in", "MODES", ":", "raise", "TDLError", "(", "'mode must be one of %s, got %s'", "%", "(", "MODES", ...	35.592593	0.00304
def refresh_manifest(self, synchronous=True, **kwargs): """Refresh previously imported manifest for Red Hat provider. :param synchronous: What should happen if the server returns an HTTP 202 (accepted) status code? Wait for the task to complete if ``True``. Immediately return th...	[ "def", "refresh_manifest", "(", "self", ",", "synchronous", "=", "True", ",", "", "", "kwargs", ")", ":", "kwargs", "=", "kwargs", ".", "copy", "(", ")", "# shadow the passed-in kwargs", "kwargs", ".", "update", "(", "self", ".", "_server_config", ".", "...	40.708333	0.002
def extend_name(suffix): """A factory for class decorators that modify the class name by appending some text to it. Example: @extend_name('_Foo') class Class: pass assert Class.__name__ == 'Class_Foo' """ def dec(cls): name = '{}{}'.format(cls.__name__, su...	[ "def", "extend_name", "(", "suffix", ")", ":", "def", "dec", "(", "cls", ")", ":", "name", "=", "'{}{}'", ".", "format", "(", "cls", ".", "__name__", ",", "suffix", ")", "setattr", "(", "cls", ",", "'__name__'", ",", "name", ")", "return", "cls", "...	21.222222	0.005013
def _build_key_wrapping_specification(self, value): """ Build a KeyWrappingSpecification struct from a dictionary. Args: value (dict): A dictionary containing the key/value pairs for a KeyWrappingSpecification struct. Returns: KeyWrappingSpecific...	[ "def", "_build_key_wrapping_specification", "(", "self", ",", "value", ")", ":", "if", "value", "is", "None", ":", "return", "None", "if", "not", "isinstance", "(", "value", ",", "dict", ")", ":", "raise", "TypeError", "(", "\"Key wrapping specification must be ...	37.647059	0.001523
def clustal_align_protein(recs, work_dir, outfmt="fasta"): """ Align given proteins with clustalw. recs are iterable of Biopython SeqIO objects """ fasta_file = op.join(work_dir, "prot-start.fasta") align_file = op.join(work_dir, "prot.aln") SeqIO.write(recs, file(fasta_file, "w"), "fasta") ...	[ "def", "clustal_align_protein", "(", "recs", ",", "work_dir", ",", "outfmt", "=", "\"fasta\"", ")", ":", "fasta_file", "=", "op", ".", "join", "(", "work_dir", ",", "\"prot-start.fasta\"", ")", "align_file", "=", "op", ".", "join", "(", "work_dir", ",", "\...	37.333333	0.003731
def _refresh(self, http): """Refreshes the access token. Since the underlying App Engine app_identity implementation does its own caching we can skip all the storage hoops and just to a refresh using the API. Args: http: unused HTTP object Raises: ...	[ "def", "_refresh", "(", "self", ",", "http", ")", ":", "try", ":", "scopes", "=", "self", ".", "scope", ".", "split", "(", ")", "(", "token", ",", "_", ")", "=", "app_identity", ".", "get_access_token", "(", "scopes", ",", "service_account_id", "=", ...	33.6	0.002894
def generateInstaller(self, outpath='.', signed=False): """ Generates the installer for this builder. :param outpath \| <str> """ log.info('Generating Installer....') # generate the options for the installer opts = { 'name': self.name(), ...	[ "def", "generateInstaller", "(", "self", ",", "outpath", "=", "'.'", ",", "signed", "=", "False", ")", ":", "log", ".", "info", "(", "'Generating Installer....'", ")", "# generate the options for the installer", "opts", "=", "{", "'name'", ":", "self", ".", "n...	36.543307	0.001259
def _or16(ins): ''' Compares & pops top 2 operands out of the stack, and checks if the 1st operand OR (logical) 2nd operand (top of the stack), pushes 0 if False, 1 if True. 16 bit un/signed version Optimizations: If any of the operators are constants: Returns either 0 or ...	[ "def", "_or16", "(", "ins", ")", ":", "op1", ",", "op2", "=", "tuple", "(", "ins", ".", "quad", "[", "2", ":", "]", ")", "if", "_int_ops", "(", "op1", ",", "op2", ")", "is", "not", "None", ":", "op1", ",", "op2", "=", "_int_ops", "(", "op1", ...	28.305556	0.000949
def remove_component(self, name): """Removes an existing component with a given name, invalidating all the values computed by the previous component.""" if name not in self.components: raise Exception("No component named %s" % name) del self.components[name] del self....	[ "def", "remove_component", "(", "self", ",", "name", ")", ":", "if", "name", "not", "in", "self", ".", "components", ":", "raise", "Exception", "(", "\"No component named %s\"", "%", "name", ")", "del", "self", ".", "components", "[", "name", "]", "del", ...	41.818182	0.006383
def translate_paths (properties, path): """ Interpret all path properties in 'properties' as relative to 'path' The property values are assumed to be in system-specific form, and will be translated into normalized form. """ assert is_iterable_typed(properties, Property) result = [] ...	[ "def", "translate_paths", "(", "properties", ",", "path", ")", ":", "assert", "is_iterable_typed", "(", "properties", ",", "Property", ")", "result", "=", "[", "]", "for", "p", "in", "properties", ":", "if", "p", ".", "feature", ".", "path", ":", "values...	30.208333	0.005348
def predict(self, h=5): """ Makes forecast with the estimated model Parameters ---------- h : int (default : 5) How many steps ahead would you like to forecast? Returns ---------- - pd.DataFrame with predicted values """ ...	[ "def", "predict", "(", "self", ",", "h", "=", "5", ")", ":", "if", "self", ".", "latent_variables", ".", "estimated", "is", "False", ":", "raise", "Exception", "(", "\"No latent variables estimated!\"", ")", "else", ":", "predictions", ",", "_", ",", "_", ...	34.666667	0.011696
def _process_key_val(self, instance, key, val): ''' Logic to let the plugin instance process the redis key/val Split out for unit testing @param instance: the plugin instance @param key: the redis key @param val: the key value from redis ''' if instance.c...	[ "def", "_process_key_val", "(", "self", ",", "instance", ",", "key", ",", "val", ")", ":", "if", "instance", ".", "check_precondition", "(", "key", ",", "val", ")", ":", "combined", "=", "'{k}:{v}'", ".", "format", "(", "k", "=", "key", ",", "v", "="...	38.2	0.002554
def get_policy_for_vhost(self, vhost, name): """ Get a specific policy for a vhost. :param vhost: The virtual host the policy is for :type vhost: str :param name: The name of the policy :type name: str """ return self._api_get('/api/policies/{0}/{1}'.form...	[ "def", "get_policy_for_vhost", "(", "self", ",", "vhost", ",", "name", ")", ":", "return", "self", ".", "_api_get", "(", "'/api/policies/{0}/{1}'", ".", "format", "(", "urllib", ".", "parse", ".", "quote_plus", "(", "vhost", ")", ",", "urllib", ".", "parse...	31.461538	0.004751
def _ParseEntryArrayObject(self, file_object, file_offset): """Parses an entry array object. Args: file_object (dfvfs.FileIO): a file-like object. file_offset (int): offset of the entry array object relative to the start of the file-like object. Returns: systemd_journal_entry_a...	[ "def", "_ParseEntryArrayObject", "(", "self", ",", "file_object", ",", "file_offset", ")", ":", "entry_array_object_map", "=", "self", ".", "_GetDataTypeMap", "(", "'systemd_journal_entry_array_object'", ")", "try", ":", "entry_array_object", ",", "_", "=", "self", ...	36.5	0.00471
def in6_mactoifaceid(mac, ulbit=None): """ Compute the interface ID in modified EUI-64 format associated to the Ethernet address provided as input. value taken by U/L bit in the interface identifier is basically the reversed value of that in given MAC address it can be forced to a specific value...	[ "def", "in6_mactoifaceid", "(", "mac", ",", "ulbit", "=", "None", ")", ":", "if", "len", "(", "mac", ")", "!=", "17", ":", "return", "None", "m", "=", "\"\"", ".", "join", "(", "mac", ".", "split", "(", "':'", ")", ")", "if", "len", "(", "m", ...	37.6	0.001297
def set_cors_config(app): """ Flask-Cors (3.x.x) extension set the config as CORS_, But we'll hold the config in CORS key. This function will convert them to CORS_ values :param app: :return: """ if "CORS" in app.config: for k, v in app.config["CORS"].items(): _ =...	[ "def", "set_cors_config", "(", "app", ")", ":", "if", "\"CORS\"", "in", "app", ".", "config", ":", "for", "k", ",", "v", "in", "app", ".", "config", "[", "\"CORS\"", "]", ".", "items", "(", ")", ":", "_", "=", "\"CORS_\"", "+", "k", ".", "upper",...	30.615385	0.002439
def get_splits_up_to(self, date_to: datetime) -> List[Split]: """ returns splits only up to the given date """ query = ( self.book.session.query(Split) .join(Transaction) .filter(Split.account == self.account, Transaction.post_date <= date_to.date(...	[ "def", "get_splits_up_to", "(", "self", ",", "date_to", ":", "datetime", ")", "->", "List", "[", "Split", "]", ":", "query", "=", "(", "self", ".", "book", ".", "session", ".", "query", "(", "Split", ")", ".", "join", "(", "Transaction", ")", ".", ...	39	0.005571
def set_properties(self, subset=None, **kwargs): """ Convenience method for setting one or more non-data dependent properties or each cell. Parameters ---------- subset : IndexSlice a valid slice for ``data`` to limit the style application to kwargs :...	[ "def", "set_properties", "(", "self", ",", "subset", "=", "None", ",", "", "", "kwargs", ")", ":", "values", "=", "';'", ".", "join", "(", "'{p}: {v}'", ".", "format", "(", "p", "=", "p", ",", "v", "=", "v", ")", "for", "p", ",", "v", "in", ...	32.076923	0.003492
def add_module_file(plpy, td): """Database trigger for adding a module file. When a legacy ``index.cnxml`` is added, this trigger transforms it into html and stores it as ``index.cnxml.html``. When a cnx-publishing ``index.cnxml.html`` is added, this trigger checks if ``index.html.cnxml`` exists be...	[ "def", "add_module_file", "(", "plpy", ",", "td", ")", ":", "module_ident", "=", "td", "[", "'new'", "]", "[", "'module_ident'", "]", "filename", "=", "td", "[", "'new'", "]", "[", "'filename'", "]", "msg", "=", "\"produce {}->{} for module_ident = {}\"", "d...	37.384615	0.000401
def add_service(self, name, long_name, preregistered=False, notify=True): """Add a service to the list of tracked services. Args: name (string): A unique short service name for the service long_name (string): A longer, user friendly name for the service preregistered...	[ "def", "add_service", "(", "self", ",", "name", ",", "long_name", ",", "preregistered", "=", "False", ",", "notify", "=", "True", ")", ":", "if", "name", "in", "self", ".", "services", ":", "raise", "ArgumentError", "(", "\"Could not add service because the lo...	33.59375	0.004521
def get_environ(self, sock): """Create WSGI environ entries to be merged into each request.""" cipher = sock.cipher() ssl_environ = { "wsgi.url_scheme": "https", "HTTPS": "on", 'SSL_PROTOCOL': cipher[1], 'SSL_CIPHER': cipher[0] ## SSL_VE...	[ "def", "get_environ", "(", "self", ",", "sock", ")", ":", "cipher", "=", "sock", ".", "cipher", "(", ")", "ssl_environ", "=", "{", "\"wsgi.url_scheme\"", ":", "\"https\"", ",", "\"HTTPS\"", ":", "\"on\"", ",", "'SSL_PROTOCOL'", ":", "cipher", "[", "1", "...	39.416667	0.012397
def evalfunc(cls, func, args, kwargs): """Evaluate a function with error propagation. Inputs: ------- ``func``: callable this is the function to be evaluated. Should return either a number or a np.ndarray. ``args``: other positional ar...	[ "def", "evalfunc", "(", "cls", ",", "func", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "def", "do_random", "(", "x", ")", ":", "if", "isinstance", "(", "x", ",", "cls", ")", ":", "return", "x", ".", "random", "(", ")", "else", ":", ...	41.590164	0.001925
def resources(self, start=1, num=10): """ Resources lists all file resources for the organization. The start and num paging parameters are supported. Inputs: start - the number of the first entry in the result set response ...	[ "def", "resources", "(", "self", ",", "start", "=", "1", ",", "num", "=", "10", ")", ":", "url", "=", "self", ".", "_url", "+", "\"/resources\"", "params", "=", "{", "\"f\"", ":", "\"json\"", ",", "\"start\"", ":", "start", ",", "\"num\"", ":", "nu...	36.608696	0.012731
def _Backward3_v_Ph(P, h): """Backward equation for region 3, v=f(P,h) Parameters ---------- P : float Pressure, [MPa] h : float Specific enthalpy, [kJ/kg] Returns ------- v : float Specific volume, [m³/kg] """ hf = _h_3ab(P) if h <= hf: retu...	[ "def", "_Backward3_v_Ph", "(", "P", ",", "h", ")", ":", "hf", "=", "_h_3ab", "(", "P", ")", "if", "h", "<=", "hf", ":", "return", "_Backward3a_v_Ph", "(", "P", ",", "h", ")", "else", ":", "return", "_Backward3b_v_Ph", "(", "P", ",", "h", ")" ]	18.7	0.002545
def nvmlDeviceSetComputeMode(handle, mode): r""" /** * Set the compute mode for the device. * * For all products. * Requires root/admin permissions. * * The compute mode determines whether a GPU can be used for compute operations and whether it can * be shared across contexts....	[ "def", "nvmlDeviceSetComputeMode", "(", "handle", ",", "mode", ")", ":", "fn", "=", "_nvmlGetFunctionPointer", "(", "\"nvmlDeviceSetComputeMode\"", ")", "ret", "=", "fn", "(", "handle", ",", "_nvmlComputeMode_t", "(", "mode", ")", ")", "_nvmlCheckReturn", "(", "...	46.421053	0.005552
def resp2flask(resp): """Convert an oic.utils.http_util instance to Flask.""" if isinstance(resp, Redirect) or isinstance(resp, SeeOther): code = int(resp.status.split()[0]) raise cherrypy.HTTPRedirect(resp.message, code) return resp.message, resp.status, resp.headers	[ "def", "resp2flask", "(", "resp", ")", ":", "if", "isinstance", "(", "resp", ",", "Redirect", ")", "or", "isinstance", "(", "resp", ",", "SeeOther", ")", ":", "code", "=", "int", "(", "resp", ".", "status", ".", "split", "(", ")", "[", "0", "]", ...	48.5	0.003378
def value(self, n: Node) -> str: """Return the text value of the node""" id_n = id(n) idcache = self.id_cache if id_n not in idcache: return "" name = idcache[id_n] tag_cache = self.tag_cache if name not in tag_cache: raise Exception("Incoh...	[ "def", "value", "(", "self", ",", "n", ":", "Node", ")", "->", "str", ":", "id_n", "=", "id", "(", "n", ")", "idcache", "=", "self", ".", "id_cache", "if", "id_n", "not", "in", "idcache", ":", "return", "\"\"", "name", "=", "idcache", "[", "id_n"...	33.625	0.003617
def institutes(): """Display a list of all user institutes.""" institute_objs = user_institutes(store, current_user) institutes = [] for ins_obj in institute_objs: sanger_recipients = [] for user_mail in ins_obj.get('sanger_recipients',[]): user_obj = store.user(user_mail) ...	[ "def", "institutes", "(", ")", ":", "institute_objs", "=", "user_institutes", "(", "store", ",", "current_user", ")", "institutes", "=", "[", "]", "for", "ins_obj", "in", "institute_objs", ":", "sanger_recipients", "=", "[", "]", "for", "user_mail", "in", "i...	39.08	0.002997
def reload(self): """ Reload configuration """ self.read_config() for section in self._override_config: self.set_section_config(section, self._override_config[section])	[ "def", "reload", "(", "self", ")", ":", "self", ".", "read_config", "(", ")", "for", "section", "in", "self", ".", "_override_config", ":", "self", ".", "set_section_config", "(", "section", ",", "self", ".", "_override_config", "[", "section", "]", ")" ]	26.75	0.00905
def put(self, request, args, *kwargs): """ custom put method to support django-reversion """ with reversion.create_revision(): reversion.set_user(request.user) reversion.set_comment('changed through the RESTful API from ip %s' % request.META['REMOTE_ADDR']) return s...	[ "def", "put", "(", "self", ",", "request", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "with", "reversion", ".", "create_revision", "(", ")", ":", "reversion", ".", "set_user", "(", "request", ".", "user", ")", "reversion", ".", "set_comment",...	58.5	0.008427
def multizone_member_added(self, member_uuid): """Handle added audio group member.""" casts = self._casts if member_uuid not in casts: casts[member_uuid] = {'listeners': [], 'groups': set()} casts[member_uuid]['groups'].add(self._group_uuid) ...	[ "def", "multizone_member_added", "(", "self", ",", "member_uuid", ")", ":", "casts", "=", "self", ".", "_casts", "if", "member_uuid", "not", "in", "casts", ":", "casts", "[", "member_uuid", "]", "=", "{", "'listeners'", ":", "[", "]", ",", "'groups'", ":...	48	0.004545
def element_id_by_label(browser, label): """Return the id of a label's for attribute""" label = XPathSelector(browser, unicode('//label[contains(., "%s")]' % label)) if not label: return False return label.get_attribute('for')	[ "def", "element_id_by_label", "(", "browser", ",", "label", ")", ":", "label", "=", "XPathSelector", "(", "browser", ",", "unicode", "(", "'//label[contains(., \"%s\")]'", "%", "label", ")", ")", "if", "not", "label", ":", "return", "False", "return", "label",...	38.571429	0.003623

def fit(self, X): """Fit structure-based AD. The training model memorizes the unique set of reaction signature. Parameters ---------- X : after read rdf file Returns ------- self : object """ X = iter2array(X, dtype=ReactionContainer) se...

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def records( self ): """ Returns the record set for the current settings of this browser. :return <orb.RecordSet> """ if ( self.isGroupingActive() ): self._records.setGroupBy(self.currentGrouping()) else: self._records.setGrou...

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def _see_remote_link_node(self, node_id, fringe=None, dist=None, check_dsp=lambda x: True): """ See data remote links of the node (set output to remote links). :param node_id: Node id. :type node_id: str :param fringe: Heapq...

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def _ns_query(self, session): """ Return a SQLAlchemy query that is already namespaced by the app and namespace given to this backend during initialization. Returns: a SQLAlchemy query object """ return session.query(ORMJob).filter(ORMJob.app == self.app, ...

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def satisifesShapeOr(cntxt: Context, n: Node, se: ShExJ.ShapeOr, _: DebugContext) -> bool: """ Se is a ShapeOr and there is some shape expression se2 in shapeExprs such that satisfies(n, se2, G, m). """ return any(satisfies(cntxt, n, se2) for se2 in se.shapeExprs)

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def tempoAdjust1(self, tempoFactor): """ Adjust tempo based on recent active apical input only :param tempoFactor: scaling signal to MC clock from last sequence item :return: adjusted scaling signal """ if self.apicalIntersect.any(): tempoFactor = tempoFactor * 0.5 else: tempo...

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def verify_geospatial_bounds(self, ds): """Checks that the geospatial bounds is well formed OGC WKT""" var = getattr(ds, 'geospatial_bounds', None) check = var is not None if not check: return ratable_result(False, "Global Attributes", # grou...

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def opacity(self, value): """ Setter for **self.__opacity** attribute. :param value: Attribute value. :type value: float """ if value is not None: assert type(value) in (int, float), "'{0}' attribute: '{1}' type is not 'int' or 'float'!".format("opacity", ...

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def import_csv(file_name, **kwargs): """ Reads control points from a CSV file and generates a 1-dimensional list of control points. It is possible to use a different value separator via ``separator`` keyword argument. The following code segment illustrates the usage of ``separator`` keyword argument. ...

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def initial_closure(self): """Computes the initial closure using the START_foo production.""" first_rule = DottedRule(self.start, 0, END_OF_INPUT) return self.closure([first_rule])

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def visit_Module(self, node): """ Import module define a new variable name. """ duc = SilentDefUseChains() duc.visit(node) for d in duc.locals[node]: self.result[d.name()] = d.node

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def following(self, user, *models, **kwargs): """ Returns a list of actors that the given user is following (eg who im following). Items in the list can be of any model unless a list of restricted models are passed. Eg following(user, User) will only return users following the given user...

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def JGE(cpu, target): """ Jumps short if greater or equal. :param cpu: current CPU. :param target: destination operand. """ cpu.PC = Operators.ITEBV(cpu.address_bit_size, (cpu.SF == cpu.OF), target.read(), cpu.PC)

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def table(self, rows, col_width=2): '''table will print a table of entries. If the rows is a dictionary, the keys are interpreted as column names. if not, a numbered list is used. ''' labels = [str(x) for x in range(1,len(rows)+1)] if isinstance(rows, dict): ...

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def _process_tags(self): """Validate standard tags and initialize attributes. Raise ValueError if tag values are not supported. """ tags = self.tags for code, (name, default, dtype, count, validate) in TIFF_TAGS.items(): if not (name in tags or default is None): ...

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async def load_saved_device_info(self): """Load device information from the device info file.""" _LOGGER.debug("Loading saved device info.") deviceinfo = [] if self._workdir: _LOGGER.debug("Really Loading saved device info.") try: device_file = '{}...

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def read(self, length=None): """ Reads data from readble BIO. For test purposes. @param length - if specifed, limits amount of data read. If not BIO is read until end of buffer """ if not length is None: if not isinstance(length, inttype) : rai...

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def restore(self, fade=False): """Restore the state of a device to that which was previously saved. For coordinator devices restore everything. For slave devices only restore volume etc., not transport info (transport info comes from the slave's coordinator). Args: ...

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def attr(self, kw=None, _attributes=None, **attrs): """Add a general or graph/node/edge attribute statement. Args: kw: Attributes target (``None`` or ``'graph'``, ``'node'``, ``'edge'``). attrs: Attributes to be set (must be strings, may be empty). See the :ref:`usage e...

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def _function(self): """ This is the actual function that will be executed. It uses only information that is provided in the settings property will be overwritten in the __init__ """ plant = self.instruments['plant']['instance'] controler = self.instruments['controler']['...

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def get_vnetwork_hosts_output_vnetwork_hosts_vswitch(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") get_vnetwork_hosts = ET.Element("get_vnetwork_hosts") config = get_vnetwork_hosts output = ET.SubElement(get_vnetwork_hosts, "output") vn...

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def getlevel(self, threshold): """ Returns all clusters with a maximum distance of *threshold* in between each other :param threshold: the maximum distance between clusters. See :py:meth:`~cluster.cluster.Cluster.getlevel` """ # if it's not worth clustering, ju...

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def leehom_general_stats_table(self): """ Take the parsed stats from the leeHom report and add it to the basic stats table at the top of the report """ headers = {} headers['merged_trimming'] = { 'title': '{} Merged (Trimming)'.format(config.read_count_prefix), '...

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def _mirror_groups(self): """ Mirrors the user's LDAP groups in the Django database and updates the user's membership. """ target_group_names = frozenset(self._get_groups().get_group_names()) current_group_names = frozenset(self._user.groups.values_list('name', flat=True)...

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def parse_star_report (self, raw_data): """ Parse the final STAR log file. """ regexes = { 'total_reads': r"Number of input reads \|\s+(\d+)", 'avg_input_read_length': r"Average input read length \|\s+([\d\.]+)", 'uniquely_mapped': ...

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def __get_file(self, file): """ Get request file and do a security check """ file_object = None if file['name'] in request.files: file_object = request.files[file['name']] clean_filename = secure_filename(file_object.filename) if clean_filename == '': ...

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def alphanum_order(triples): """ Sort a list of triples by relation name. Embedded integers are sorted numerically, but otherwise the sorting is alphabetic. """ return sorted( triples, key=lambda t: [ int(t) if t.isdigit() else t for t in re.split(r'([0-9...

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def field_uuid(self, attr, options): """Creates a form element for the UUID type.""" options['validators'].append(validators.UUIDValidator(attr.entity)) return wtf_fields.StringField, options

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def vocab_to_json(vocab: Vocab, path: str): """ Saves vocabulary in human-readable json. :param vocab: Vocabulary mapping. :param path: Output file path. """ with open(path, "w", encoding=C.VOCAB_ENCODING) as out: json.dump(vocab, out, indent=4, ensure_ascii=False) logger.info('...

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def _get_interpolator(method, vectorizeable_only=False, **kwargs): '''helper function to select the appropriate interpolator class returns interpolator class and keyword arguments for the class ''' interp1d_methods = ['linear', 'nearest', 'zero', 'slinear', 'quadratic', 'cubic',...

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def _plotxw(self,*args,**kwargs): #pragma: no cover """ NAME: plotxw PURPOSE: plot the spectrum of x INPUT: bovy_plot.bovy_plot args and kwargs OUTPUT: x(t) HISTORY: 2010-09-21 - Written - Bovy (NYU) """ ...

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def holdout(self, train_perc=0.7, num_rep=50, stratified=True, return_ids_only=False, format='MLDataset'): """ Builds a generator for train and test sets for cross-validation. """ ids_in_class = {cid: self....

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def _map_segmentation_mask_to_stft_domain(mask, times, frequencies, stft_times, stft_frequencies): """ Maps the given `mask`, which is in domain (`frequencies`, `times`) to the new domain (`stft_frequencies`, `stft_times`) and returns the result. """ assert mask.shape == (frequencies.shape[0], times...

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def main(): """Quick test for QSUsb class.""" import argparse parser = argparse.ArgumentParser() parser.add_argument('--url', help='QSUSB URL [http://127.0.0.1:2020]', default='http://127.0.0.1:2020') parser.add_argument('--file', help='a test file from /&devices') parser...

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def error(msg: str, resource: Optional['Resource'] = None, stream_id: Optional[int] = None): """ Logs a message to the Pulumi CLI's error channel, associating it with a resource and stream_id if provided. :param str msg: The message to send to the Pulumi CLI. :param Optional[Resource] resource: If ...

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def _fits_inside_predicate(self): """ Return a function taking an integer point size argument that returns |True| if the text in this fitter can be wrapped to fit entirely within its extents when rendered at that point size. """ def predicate(point_size): """ ...

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def report(self, fraction=None): """report the total progress for the current stack, optionally given the local fraction completed. fraction=None: if given, used as the fraction of the local method so far completed. runtimes=None: if given, used as the expected runtimes for the current stack. """ r = Dict() ...

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def percolate(self, index, doc_types, query): """ Match a query with a document """ if doc_types is None: raise RuntimeError('percolate() must be supplied with at least one doc_type') path = self._make_path(index, doc_types, '_percolate') body = self._encode_...

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def complex_state_generator_bravo(last_state=''): """Pick a state.""" from random import choice states = ['ALPHA', 'BRAVO', 'BRAVO', 'DONE'] if last_state: states.remove(last_state) # Slightly lower chances of previous state. state = choice(states) logging.info('Generating a state......

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async def download_media(self, *args, **kwargs): """ Downloads the media contained in the message, if any. Shorthand for `telethon.client.downloads.DownloadMethods.download_media` with the ``message`` already set. """ return await self._client.download_media(self, *args, ...

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def _StructMessageToJsonObject(message, unused_including_default=False): """Converts Struct message according to Proto3 JSON Specification.""" fields = message.fields ret = {} for key in fields: ret[key] = _ValueMessageToJsonObject(fields[key]) return ret

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def WalkControl(control: Control, includeTop: bool = False, maxDepth: int = 0xFFFFFFFF): """ control: `Control` or its subclass. includeTop: bool, if True, yield (control, 0) first. maxDepth: int, enum depth. Yield 2 items tuple(control: Control, depth: int). """ if includeTop: yield...

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def publish(self, synchronous=True, **kwargs): """Helper for publishing an existing content view. :param synchronous: What should happen if the server returns an HTTP 202 (accepted) status code? Wait for the task to complete if ``True``. Immediately return the server's response ...

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def step(self, data): """ Run convolution over a single position. The data must be exactly as wide as the convolution filters. :param data: Shape: (batch_size, kernel_width, num_hidden). :return: Single result of a convolution. Shape: (batch_size, 1, num_hidden). """ # ...

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def compare_agents(EnvFactory, AgentFactories, n=10, steps=1000): """See how well each of several agents do in n instances of an environment. Pass in a factory (constructor) for environments, and several for agents. Create n instances of the environment, and run each agent in copies of each one for step...

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def get_concept_item_mapping(self, concepts=None, lang=None): """ Get mapping of concepts to items belonging to concept. Args: concepts (list of Concept): Defaults to None meaning all concepts lang (str): language of concepts, if None use language of concepts Re...

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def timestr_mod24(timestr: str) -> int: """ Given a GTFS HH:MM:SS time string, return a timestring in the same format but with the hours taken modulo 24. """ try: hours, mins, secs = [int(x) for x in timestr.split(":")] hours %= 24 result = f"{hours:02d}:{mins:02d}:{secs:02d}...

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def transmission_rate(self): """ Returns the upstream, downstream values as a tuple in bytes per second. Use this for periodical calling. """ sent = self.bytes_sent received = self.bytes_received traffic_call = time.time() time_delta = traffic_call - self....

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def completions(self): """ Return :class:`classes.Completion` objects. Those objects contain information about the completions, more than just names. :return: Completion objects, sorted by name. :rtype: list of :class:`classes.Completion` """ debug.speed('complet...

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def is_file(value, **kwargs): """Indicate whether ``value`` is a file that exists on the local filesystem. :param value: The value to evaluate. :returns: ``True`` if ``value`` is valid, ``False`` if it is not. :rtype: :class:`bool <python:bool>` :raises SyntaxError: if ``kwargs`` contains duplica...

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def profile_df(df): """ Generate a profile of data in a dataframe. Args: df: the Pandas dataframe. """ # The bootstrap CSS messes up the Datalab display so we tweak it to not have an effect. # TODO(gram): strip it out rather than this kludge. return IPython.core.display.HTML( pandas_profiling.Pro...

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def restore_definition(self, project, definition_id, deleted): """RestoreDefinition. Restores a deleted definition :param str project: Project ID or project name :param int definition_id: The identifier of the definition to restore. :param bool deleted: When false, restores a del...

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def started(name): ''' Check if volume has been started name name of the volume .. code-block:: yaml mycluster: glusterfs.started: [] ''' ret = {'name': name, 'changes': {}, 'comment': '', 'result': False} volinfo = __salt__['glu...

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def _create_warm_start_tuner(self, additional_parents, warm_start_type, estimator=None): """Creates a new ``HyperparameterTuner`` with ``WarmStartConfig``, where type will be equal to ``warm_start_type`` and``parents`` would be equal to union of ``additional_parents`` and self. Args: ...

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def operate_on_bulb(self, method, params=None): """ Build socket and send command to the bulb through it :param method: method you want to use :param params: parameters needed for this method (can be a string if ony one parameter is needed) :type method: str ...

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def __create_table_if_not_exists(self): # type: () -> None """Creates table in Dynamodb resource if it doesn't exist and create_table is set as True. :rtype: None :raises: PersistenceException: When `create_table` fails on dynamodb resource. """ if se...

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def create_working_dir(config, prefix): ''' Create a fresh temporary directory, based on the fiven prefix. Returns the new path. ''' # Fetch base directory from executor configuration basepath = config.get("Execution", "directory") if not prefix: prefix = 'opensubmit' f...

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def max_variance_genes(data, nbins=5, frac=0.2): """ This function identifies the genes that have the max variance across a number of bins sorted by mean. Args: data (array): genes x cells nbins (int): number of bins to sort genes by mean expression level. Default: 10. frac (flo...

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def _load_calib(self): """Load and compute intrinsic and extrinsic calibration parameters.""" # We'll build the calibration parameters as a dictionary, then # convert it to a namedtuple to prevent it from being modified later data = {} # Load the calibration file calib_f...

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def list_domains(**kwargs): ''' Return a list of available domains. :param connection: libvirt connection URI, overriding defaults .. versionadded:: 2019.2.0 :param username: username to connect with, overriding defaults .. versionadded:: 2019.2.0 :param password: password to conn...

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def _identifier_filtered_iterator(graph): """Iterate over names in the given namespace.""" for data in graph: for pair in _get_node_names(data): yield pair for member in data.get(MEMBERS, []): for pair in _get_node_names(member): yield pair for ((_, ...

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def register_device(ctx, device, model, nickname, client_type): """Registers a device instance under an existing device model. Device instance fields must start with a letter or number. The device ID can only contain letters, numbers, and the following symbols: period (.), hyphen (-), underscore (_), a...

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def stop(self): """ Stop all functions running in the thread handler.""" for run_event in self.run_events: run_event.clear() for thread in self.thread_pool: thread.join()

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def print_evaluation(period=1, show_stdv=True): """Create a callback that prints the evaluation results. Parameters ---------- period : int, optional (default=1) The period to print the evaluation results. show_stdv : bool, optional (default=True) Whether to show stdv (if provided)....

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def smart_search_prefix(self): """ Perform a smart search. The smart search function tries extract a query from a text string. This query is then passed to the search_prefix function, which performs the search. """ search_options = {} extra_query = N...

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def _get_stitch_report_path(self): """Checks if stitch report label / path is set. Returns absolute path.""" if self.Parameters['-r'].isOn(): stitch_path = self._absolute(str(self.Parameters['-r'].Value)) return stitch_path elif self.Parameters['-r'].isOff(): ...

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def set_nightlight(self, state): """Sets the night light state of the smart plug""" packet = bytearray(16) packet[0] = 2 if self.check_power(): packet[4] = 3 if state else 1 else: packet[4] = 2 if state else 0 self.send_packet(0x6a, packet)

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def on_site(self, site_id=None): """Return a :class:`QuerySet` of pages that are published on the site defined by the ``SITE_ID`` setting. :param site_id: specify the id of the site object to filter with. """ if settings.PAGE_USE_SITE_ID: if not site_id: ...

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def set_mode(self, mode): """Configure how this console will react to the cursor writing past the end if the console. This is for methods that use the virtual cursor, such as :any:`print_str`. Args: mode (Text): The mode to set. Possible settings are: ...

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def refresh_manifest(self, synchronous=True, **kwargs): """Refresh previously imported manifest for Red Hat provider. :param synchronous: What should happen if the server returns an HTTP 202 (accepted) status code? Wait for the task to complete if ``True``. Immediately return th...

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def extend_name(suffix): """A factory for class decorators that modify the class name by appending some text to it. Example: @extend_name('_Foo') class Class: pass assert Class.__name__ == 'Class_Foo' """ def dec(cls): name = '{}{}'.format(cls.__name__, su...

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def _build_key_wrapping_specification(self, value): """ Build a KeyWrappingSpecification struct from a dictionary. Args: value (dict): A dictionary containing the key/value pairs for a KeyWrappingSpecification struct. Returns: KeyWrappingSpecific...

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def clustal_align_protein(recs, work_dir, outfmt="fasta"): """ Align given proteins with clustalw. recs are iterable of Biopython SeqIO objects """ fasta_file = op.join(work_dir, "prot-start.fasta") align_file = op.join(work_dir, "prot.aln") SeqIO.write(recs, file(fasta_file, "w"), "fasta") ...

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def _refresh(self, http): """Refreshes the access token. Since the underlying App Engine app_identity implementation does its own caching we can skip all the storage hoops and just to a refresh using the API. Args: http: unused HTTP object Raises: ...

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def generateInstaller(self, outpath='.', signed=False): """ Generates the installer for this builder. :param outpath | <str> """ log.info('Generating Installer....') # generate the options for the installer opts = { 'name': self.name(), ...

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def _or16(ins): ''' Compares & pops top 2 operands out of the stack, and checks if the 1st operand OR (logical) 2nd operand (top of the stack), pushes 0 if False, 1 if True. 16 bit un/signed version Optimizations: If any of the operators are constants: Returns either 0 or ...

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def remove_component(self, name): """Removes an existing component with a given name, invalidating all the values computed by the previous component.""" if name not in self.components: raise Exception("No component named %s" % name) del self.components[name] del self....

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def translate_paths (properties, path): """ Interpret all path properties in 'properties' as relative to 'path' The property values are assumed to be in system-specific form, and will be translated into normalized form. """ assert is_iterable_typed(properties, Property) result = [] ...

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def predict(self, h=5): """ Makes forecast with the estimated model Parameters ---------- h : int (default : 5) How many steps ahead would you like to forecast? Returns ---------- - pd.DataFrame with predicted values """ ...

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def _process_key_val(self, instance, key, val): ''' Logic to let the plugin instance process the redis key/val Split out for unit testing @param instance: the plugin instance @param key: the redis key @param val: the key value from redis ''' if instance.c...

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def get_policy_for_vhost(self, vhost, name): """ Get a specific policy for a vhost. :param vhost: The virtual host the policy is for :type vhost: str :param name: The name of the policy :type name: str """ return self._api_get('/api/policies/{0}/{1}'.form...

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def _ParseEntryArrayObject(self, file_object, file_offset): """Parses an entry array object. Args: file_object (dfvfs.FileIO): a file-like object. file_offset (int): offset of the entry array object relative to the start of the file-like object. Returns: systemd_journal_entry_a...

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36.5

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def in6_mactoifaceid(mac, ulbit=None): """ Compute the interface ID in modified EUI-64 format associated to the Ethernet address provided as input. value taken by U/L bit in the interface identifier is basically the reversed value of that in given MAC address it can be forced to a specific value...

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def set_cors_config(app): """ Flask-Cors (3.x.x) extension set the config as CORS_*, But we'll hold the config in CORS key. This function will convert them to CORS_* values :param app: :return: """ if "CORS" in app.config: for k, v in app.config["CORS"].items(): _ =...

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def get_splits_up_to(self, date_to: datetime) -> List[Split]: """ returns splits only up to the given date """ query = ( self.book.session.query(Split) .join(Transaction) .filter(Split.account == self.account, Transaction.post_date <= date_to.date(...

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def set_properties(self, subset=None, **kwargs): """ Convenience method for setting one or more non-data dependent properties or each cell. Parameters ---------- subset : IndexSlice a valid slice for ``data`` to limit the style application to kwargs :...

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32.076923

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def add_module_file(plpy, td): """Database trigger for adding a module file. When a legacy ``index.cnxml`` is added, this trigger transforms it into html and stores it as ``index.cnxml.html``. When a cnx-publishing ``index.cnxml.html`` is added, this trigger checks if ``index.html.cnxml`` exists be...

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37.384615

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def add_service(self, name, long_name, preregistered=False, notify=True): """Add a service to the list of tracked services. Args: name (string): A unique short service name for the service long_name (string): A longer, user friendly name for the service preregistered...

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33.59375

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def get_environ(self, sock): """Create WSGI environ entries to be merged into each request.""" cipher = sock.cipher() ssl_environ = { "wsgi.url_scheme": "https", "HTTPS": "on", 'SSL_PROTOCOL': cipher[1], 'SSL_CIPHER': cipher[0] ## SSL_VE...

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39.416667

0.012397

def evalfunc(cls, func, *args, **kwargs): """Evaluate a function with error propagation. Inputs: ------- ``func``: callable this is the function to be evaluated. Should return either a number or a np.ndarray. ``*args``: other positional ar...

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41.590164

0.001925

def resources(self, start=1, num=10): """ Resources lists all file resources for the organization. The start and num paging parameters are supported. Inputs: start - the number of the first entry in the result set response ...

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36.608696

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def _Backward3_v_Ph(P, h): """Backward equation for region 3, v=f(P,h) Parameters ---------- P : float Pressure, [MPa] h : float Specific enthalpy, [kJ/kg] Returns ------- v : float Specific volume, [m³/kg] """ hf = _h_3ab(P) if h <= hf: retu...

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18.7

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def nvmlDeviceSetComputeMode(handle, mode): r""" /** * Set the compute mode for the device. * * For all products. * Requires root/admin permissions. * * The compute mode determines whether a GPU can be used for compute operations and whether it can * be shared across contexts....

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def resp2flask(resp): """Convert an oic.utils.http_util instance to Flask.""" if isinstance(resp, Redirect) or isinstance(resp, SeeOther): code = int(resp.status.split()[0]) raise cherrypy.HTTPRedirect(resp.message, code) return resp.message, resp.status, resp.headers

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48.5

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def value(self, n: Node) -> str: """Return the text value of the node""" id_n = id(n) idcache = self.id_cache if id_n not in idcache: return "" name = idcache[id_n] tag_cache = self.tag_cache if name not in tag_cache: raise Exception("Incoh...

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33.625

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def institutes(): """Display a list of all user institutes.""" institute_objs = user_institutes(store, current_user) institutes = [] for ins_obj in institute_objs: sanger_recipients = [] for user_mail in ins_obj.get('sanger_recipients',[]): user_obj = store.user(user_mail) ...

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39.08

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def reload(self): """ Reload configuration """ self.read_config() for section in self._override_config: self.set_section_config(section, self._override_config[section])

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26.75

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def put(self, request, *args, **kwargs): """ custom put method to support django-reversion """ with reversion.create_revision(): reversion.set_user(request.user) reversion.set_comment('changed through the RESTful API from ip %s' % request.META['REMOTE_ADDR']) return s...

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58.5

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def multizone_member_added(self, member_uuid): """Handle added audio group member.""" casts = self._casts if member_uuid not in casts: casts[member_uuid] = {'listeners': [], 'groups': set()} casts[member_uuid]['groups'].add(self._group_uuid) ...

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48

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def element_id_by_label(browser, label): """Return the id of a label's for attribute""" label = XPathSelector(browser, unicode('//label[contains(., "%s")]' % label)) if not label: return False return label.get_attribute('for')

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38.571429

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