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 _deserialize(self, stream): """Initialize this instance with index values read from the given stream""" self.version, self.entries, self._extension_data, conten_sha = read_cache(stream) # @UnusedVariable return self	[ "def", "_deserialize", "(", "self", ",", "stream", ")", ":", "self", ".", "version", ",", "self", ".", "entries", ",", "self", ".", "_extension_data", ",", "conten_sha", "=", "read_cache", "(", "stream", ")", "# @UnusedVariable", "return", "self" ]	60.25	0.016393
def file_envs(self, load=None): ''' Return environments for all backends for requests from fileclient ''' if load is None: load = {} load.pop('cmd', None) return self.envs(**load)	[ "def", "file_envs", "(", "self", ",", "load", "=", "None", ")", ":", "if", "load", "is", "None", ":", "load", "=", "{", "}", "load", ".", "pop", "(", "'cmd'", ",", "None", ")", "return", "self", ".", "envs", "(", "", "", "load", ")" ]	29	0.008368
def get_reference(proxy): ''' Return the object that is referenced by the specified proxy. If the proxy has not been bound to a reference for the current thread, the behavior depends on th the ``fallback_to_shared`` flag that has been specified when creating the proxy. If the fl...	[ "def", "get_reference", "(", "proxy", ")", ":", "thread_local", "=", "object", ".", "__getattribute__", "(", "proxy", ",", "'_thread_local'", ")", "try", ":", "return", "thread_local", ".", "reference", "except", "AttributeError", ":", "fallback_to_shared", "=", ...	52.869565	0.001615
def _upstart_enable(name): ''' Enable an Upstart service. ''' if _upstart_is_enabled(name): return _upstart_is_enabled(name) override = '/etc/init/{0}.override'.format(name) files = ['/etc/init/{0}.conf'.format(name), override] for file_name in filter(os.path.isfile, files): ...	[ "def", "_upstart_enable", "(", "name", ")", ":", "if", "_upstart_is_enabled", "(", "name", ")", ":", "return", "_upstart_is_enabled", "(", "name", ")", "override", "=", "'/etc/init/{0}.override'", ".", "format", "(", "name", ")", "files", "=", "[", "'/etc/init...	36.12	0.001079
def has_activity(graph: BELGraph, node: BaseEntity) -> bool: """Return true if over any of the node's edges, it has a molecular activity.""" return _node_has_modifier(graph, node, ACTIVITY)	[ "def", "has_activity", "(", "graph", ":", "BELGraph", ",", "node", ":", "BaseEntity", ")", "->", "bool", ":", "return", "_node_has_modifier", "(", "graph", ",", "node", ",", "ACTIVITY", ")" ]	65	0.010152
def _process_figure(value, fmt): """Processes the figure. Returns a dict containing figure properties.""" # pylint: disable=global-statement global Nreferences # Global references counter global has_unnumbered_figures # Flags unnumbered figures were found global cursec ...	[ "def", "_process_figure", "(", "value", ",", "fmt", ")", ":", "# pylint: disable=global-statement", "global", "Nreferences", "# Global references counter", "global", "has_unnumbered_figures", "# Flags unnumbered figures were found", "global", "cursec", "# Current section", "# Par...	41.049383	0.002056
def read_from_endpoint(self, endpoint, timeout=15): """ Blocking read from an endpoint. Will block until a message is received, or it times out. Also see :meth:`get_endpoint_queue` if you are considering calling this in a loop. .. warning:: Avoid calling this method from an e...	[ "def", "read_from_endpoint", "(", "self", ",", "endpoint", ",", "timeout", "=", "15", ")", ":", "return", "self", ".", "event_handler", ".", "wait_for_event", "(", "(", "_EventType", ".", "Watch", ",", "endpoint", ")", ",", "timeout", "=", "timeout", ")" ]	51.588235	0.010078
def discover_group(group, separator="/", exclude=None): """Produce a list of all services and their addresses in a group A group is an optional form of namespace within the discovery mechanism. If an advertised name has the form <group><sep><name> it is deemed to belong to <group>. Note that the se...	[ "def", "discover_group", "(", "group", ",", "separator", "=", "\"/\"", ",", "exclude", "=", "None", ")", ":", "_start_beacon", "(", ")", "if", "exclude", "is", "None", ":", "names_to_exclude", "=", "set", "(", ")", "else", ":", "names_to_exclude", "=", "...	39.923077	0.009407
def save_json(data, path, fatal=True, logger=None, sort_keys=True, indent=2, **kwargs): """ Args: data (object \| None): Data to serialize and save path (str \| None): Path to file where to save fatal (bool \| None): Abort execution on failure if True logger (callable \| None): Logge...	[ "def", "save_json", "(", "data", ",", "path", ",", "fatal", "=", "True", ",", "logger", "=", "None", ",", "sort_keys", "=", "True", ",", "indent", "=", "2", ",", "", "", "kwargs", ")", ":", "if", "data", "is", "None", "or", "not", "path", ":", ...	31.439024	0.001505
def reverse(self, viewname, args=None, kwargs=None): """ Reverse a blog page, taking different configuration options into account. For example, the blog can be mounted using django-fluent-pages on multiple nodes. """ # TODO: django-fluent-pages needs a public API to get the cur...	[ "def", "reverse", "(", "self", ",", "viewname", ",", "args", "=", "None", ",", "kwargs", "=", "None", ")", ":", "# TODO: django-fluent-pages needs a public API to get the current page.", "current_page", "=", "getattr", "(", "self", ".", "request", ",", "'_current_fl...	61.125	0.010081
def conditional_jit(function=None, **kwargs): # noqa: D202 """Use numba's jit decorator if numba is installed. Notes ----- If called without arguments then return wrapped function. @conditional_jit def my_func(): return else called with arguments @co...	[ "def", "conditional_jit", "(", "function", "=", "None", ",", "", "", "kwargs", ")", ":", "# noqa: D202", "def", "wrapper", "(", "function", ")", ":", "try", ":", "numba", "=", "importlib", ".", "import_module", "(", "\"numba\"", ")", "return", "numba", ...	21.064516	0.001464
def match_https_hostname(cls, hostname): """ :param hostname: a string :returns: an :py:class:`~httpretty.core.URLMatcher` or ``None`` """ items = sorted( cls._entries.items(), key=lambda matcher_entries: matcher_entries[0].priority, reverse=Tr...	[ "def", "match_https_hostname", "(", "cls", ",", "hostname", ")", ":", "items", "=", "sorted", "(", "cls", ".", "_entries", ".", "items", "(", ")", ",", "key", "=", "lambda", "matcher_entries", ":", "matcher_entries", "[", "0", "]", ".", "priority", ",", ...	37.115385	0.00202
async def getaccountbywallet(**params): """Receives account by wallet Accepts: - public key hex or checksum format """ if params.get("message"): params = json.loads(params.get("message")) for coinid in coin_ids: database = client[coinid] wallet_collection = database[settings.WALLET] wallet = await walle...	[ "async", "def", "getaccountbywallet", "(", "", "", "params", ")", ":", "if", "params", ".", "get", "(", "\"message\"", ")", ":", "params", "=", "json", ".", "loads", "(", "params", ".", "get", "(", "\"message\"", ")", ")", "for", "coinid", "in", "c...	31.25	0.037516
def sharedFiles(self): 'iterate over shared files and get their public URI' for f in self.sharing.files.iterchildren(): yield (f.attrib['name'], f.attrib['uuid'], 'https://www.jottacloud.com/p/%s/%s' % (self.jfs.username, f.publicURI.text))	[ "def", "sharedFiles", "(", "self", ")", ":", "for", "f", "in", "self", ".", "sharing", ".", "files", ".", "iterchildren", "(", ")", ":", "yield", "(", "f", ".", "attrib", "[", "'name'", "]", ",", "f", ".", "attrib", "[", "'uuid'", "]", ",", "'htt...	56	0.014085
def save_record(self, instance, update_fields=None, **kwargs): """Saves the record. If `update_fields` is set, this method will use partial_update_object() and will update only the given fields (never `_geoloc` and `_tags`). For more information about partial_update_object: htt...	[ "def", "save_record", "(", "self", ",", "instance", ",", "update_fields", "=", "None", ",", "", "", "kwargs", ")", ":", "if", "not", "self", ".", "_should_index", "(", "instance", ")", ":", "# Should not index, but since we don't now the state of the", "# instan...	43.53125	0.001404
def iter_field_objects(fields): """ Iterate over fields. Supports list of (k, v) tuples and dicts, and lists of :class:`~urllib3.fields.RequestField`. """ if isinstance(fields, dict): i = six.iteritems(fields) else: i = iter(fields) for field in i: if isinstanc...	[ "def", "iter_field_objects", "(", "fields", ")", ":", "if", "isinstance", "(", "fields", ",", "dict", ")", ":", "i", "=", "six", ".", "iteritems", "(", "fields", ")", "else", ":", "i", "=", "iter", "(", "fields", ")", "for", "field", "in", "i", ":"...	23.055556	0.002315
def __leaf(i, j, first, maxfirst, prevleaf, ancestor): """ Determine if j is leaf of i'th row subtree. """ jleaf = 0 if i<=j or first[j] <= maxfirst[i]: return -1, jleaf maxfirst[i] = first[j] jprev = prevleaf[i] prevleaf[i] = j if jprev == -1: jleaf = 1 else: jleaf = 2 if jl...	[ "def", "__leaf", "(", "i", ",", "j", ",", "first", ",", "maxfirst", ",", "prevleaf", ",", "ancestor", ")", ":", "jleaf", "=", "0", "if", "i", "<=", "j", "or", "first", "[", "j", "]", "<=", "maxfirst", "[", "i", "]", ":", "return", "-", "1", "...	25.5	0.013233
def animate(zdata, xdata, ydata, conversionFactorArray, timedata, BoxSize, timeSteps=100, filename="particle"): """ Animates the particle's motion given the z, x and y signal (in Volts) and the conversion factor (to convert between V and nm). Parameters ---------...	[ "def", "animate", "(", "zdata", ",", "xdata", ",", "ydata", ",", "conversionFactorArray", ",", "timedata", ",", "BoxSize", ",", "timeSteps", "=", "100", ",", "filename", "=", "\"particle\"", ")", ":", "timePerFrame", "=", "0.203", "print", "(", "\"This will ...	34.601449	0.000814
def check(projects): """Check the specified projects for Python 3 compatibility.""" log = logging.getLogger('ciu') log.info('{0} top-level projects to check'.format(len(projects))) print('Finding and checking dependencies ...') blockers = dependencies.blockers(projects) print('') for line i...	[ "def", "check", "(", "projects", ")", ":", "log", "=", "logging", ".", "getLogger", "(", "'ciu'", ")", "log", ".", "info", "(", "'{0} top-level projects to check'", ".", "format", "(", "len", "(", "projects", ")", ")", ")", "print", "(", "'Finding and chec...	28.6875	0.00211
def compare2(args): """ %prog compare2 Compare performances of various variant callers on simulated STR datasets. """ p = OptionParser(compare2.__doc__) p.add_option('--maxinsert', default=300, type="int", help="Maximum number of repeats") add_simulate_options(p) opts, ...	[ "def", "compare2", "(", "args", ")", ":", "p", "=", "OptionParser", "(", "compare2", ".", "__doc__", ")", "p", ".", "add_option", "(", "'--maxinsert'", ",", "default", "=", "300", ",", "type", "=", "\"int\"", ",", "help", "=", "\"Maximum number of repeats\...	36.04	0.001621
def point_in_tetrahedron(tetra, pt): ''' point_in_tetrahedron(tetrahedron, point) yields True if the given point is in the given tetrahedron. If either tetrahedron or point (or both) are lists of shapes/points, then this calculation is automatically threaded over all the given arguments. ''' ...	[ "def", "point_in_tetrahedron", "(", "tetra", ",", "pt", ")", ":", "bcs", "=", "tetrahedral_barycentric_coordinates", "(", "tetra", ",", "pt", ")", "return", "np", ".", "logical_not", "(", "np", ".", "all", "(", "np", ".", "isclose", "(", "bcs", ",", "0",...	53.625	0.009174
def run( self, cluster_config, rg_parser, partition_measurer, cluster_balancer, args, ): """Initialize cluster_config, args, and zk then call run_command.""" self.cluster_config = cluster_config self.args = args ...	[ "def", "run", "(", "self", ",", "cluster_config", ",", "rg_parser", ",", "partition_measurer", ",", "cluster_balancer", ",", "args", ",", ")", ":", "self", ".", "cluster_config", "=", "cluster_config", "self", ".", "args", "=", "args", "with", "ZK", "(", "...	33.119048	0.002095
def encode_osgi_props(ed): # type: (EndpointDescription) -> Dict[str, str] """ Prepares a dictionary of OSGi properties for the given EndpointDescription """ result_props = {} intfs = ed.get_interfaces() result_props[OBJECTCLASS] = " ".join(intfs) for intf in intfs: pkg_name = pa...	[ "def", "encode_osgi_props", "(", "ed", ")", ":", "# type: (EndpointDescription) -> Dict[str, str]", "result_props", "=", "{", "}", "intfs", "=", "ed", ".", "get_interfaces", "(", ")", "result_props", "[", "OBJECTCLASS", "]", "=", "\" \"", ".", "join", "(", "intf...	38.117647	0.000752
def dump_conf(self, config_pathname=None): """write a config file to the pathname specified in the parameter. The file extention determines the type of file written and must match a registered type. parameters: config_pathname - the full path and filename of the target conf...	[ "def", "dump_conf", "(", "self", ",", "config_pathname", "=", "None", ")", ":", "if", "not", "config_pathname", ":", "config_pathname", "=", "self", ".", "_get_option", "(", "'admin.dump_conf'", ")", ".", "value", "opener", "=", "functools", ".", "partial", ...	37.636364	0.002356
def post_attachment(self, bugid, attachment): '''http://bugzilla.readthedocs.org/en/latest/api/core/v1/attachment.html#create-attachment''' assert type(attachment) is DotDict assert 'data' in attachment assert 'file_name' in attachment assert 'summary' in attachment if (n...	[ "def", "post_attachment", "(", "self", ",", "bugid", ",", "attachment", ")", ":", "assert", "type", "(", "attachment", ")", "is", "DotDict", "assert", "'data'", "in", "attachment", "assert", "'file_name'", "in", "attachment", "assert", "'summary'", "in", "atta...	55.909091	0.0128
def tasks_file_to_task_descriptors(tasks, retries, input_file_param_util, output_file_param_util): """Parses task parameters from a TSV. Args: tasks: Dict containing the path to a TSV file and task numbers to run variables, input, and output parameters as column headings....	[ "def", "tasks_file_to_task_descriptors", "(", "tasks", ",", "retries", ",", "input_file_param_util", ",", "output_file_param_util", ")", ":", "task_descriptors", "=", "[", "]", "path", "=", "tasks", "[", "'path'", "]", "task_min", "=", "tasks", ".", "get", "(", ...	34.284091	0.008376
def get_user_enclaves(self): """ Gets the list of enclaves that the user has access to. :return: A list of \|EnclavePermissions\| objects, each representing an enclave and whether the requesting user has read, create, and update access to it. """ resp = self._client.g...	[ "def", "get_user_enclaves", "(", "self", ")", ":", "resp", "=", "self", ".", "_client", ".", "get", "(", "\"enclaves\"", ")", "return", "[", "EnclavePermissions", ".", "from_dict", "(", "enclave", ")", "for", "enclave", "in", "resp", ".", "json", "(", ")...	40.7	0.009615
def get_success_url(self): """Get the url depending on what type of configuration I deleted.""" if self.stage_id: url = reverse('projects_stage_view', args=(self.project_id, self.stage_id)) else: url = reverse('projects_project_view', args=(self.project_id,)) re...	[ "def", "get_success_url", "(", "self", ")", ":", "if", "self", ".", "stage_id", ":", "url", "=", "reverse", "(", "'projects_stage_view'", ",", "args", "=", "(", "self", ".", "project_id", ",", "self", ".", "stage_id", ")", ")", "else", ":", "url", "=",...	35.555556	0.009146
def _create_label(self, array): """Create sample PDS3 label for NumPy Array. It is called by 'image.py' to create PDS3Image object from Numpy Array. Returns ------- PVLModule label for the given NumPy array. Usage: self.label = _create_label(array) """ ...	[ "def", "_create_label", "(", "self", ",", "array", ")", ":", "if", "len", "(", "array", ".", "shape", ")", "==", "3", ":", "bands", "=", "array", ".", "shape", "[", "0", "]", "lines", "=", "array", ".", "shape", "[", "1", "]", "line_samples", "="...	32.2	0.001507
def clistream(reporter, args, *kwargs): """ Handle stream data on command line interface, and returns statistics of success, error, and total amount. More detailed information is available on underlying feature, :mod:`clitool.processor`. :param Handler: [DEPRECATED] Handler for file-like streams...	[ "def", "clistream", "(", "reporter", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "# Follow the rule of `parse_arguments()`", "files", "=", "kwargs", ".", "get", "(", "'files'", ")", "encoding", "=", "kwargs", ".", "get", "(", "'input_encoding'", ","...	38.914286	0.001433
def optimize_logger_level(logger, log_level): """ At runtime, when logging is not active, replace the .debug() call with a no-op. """ function_name = _log_functions[log_level] if getattr(logger, function_name) is _dummy_log: return False is_level_logged = logger.isEnabledFor(log_lev...	[ "def", "optimize_logger_level", "(", "logger", ",", "log_level", ")", ":", "function_name", "=", "_log_functions", "[", "log_level", "]", "if", "getattr", "(", "logger", ",", "function_name", ")", "is", "_dummy_log", ":", "return", "False", "is_level_logged", "=...	29.785714	0.002326
def validate_config_parameters(config_json, allowed_keys, allowed_types): """Validate parameters in config file.""" custom_fields = config_json.get(defs.PARAMETERS, []) for field in custom_fields: validate_field(field, allowed_keys, allowed_types) default = field.get(defs.DEFAULT) fi...	[ "def", "validate_config_parameters", "(", "config_json", ",", "allowed_keys", ",", "allowed_types", ")", ":", "custom_fields", "=", "config_json", ".", "get", "(", "defs", ".", "PARAMETERS", ",", "[", "]", ")", "for", "field", "in", "custom_fields", ":", "vali...	49.222222	0.002217
def positive_volume_index(close_data, volume): """ Positive Volume Index (PVI). Formula: PVI0 = 1 IF Vt > Vt-1 PVIt = PVIt-1 + (CLOSEt - CLOSEt-1 / CLOSEt-1 * PVIt-1) ELSE: PVIt = PVIt-1 """ catch_errors.check_for_input_len_diff(close_data, volume) pvi = np.zeros(len...	[ "def", "positive_volume_index", "(", "close_data", ",", "volume", ")", ":", "catch_errors", ".", "check_for_input_len_diff", "(", "close_data", ",", "volume", ")", "pvi", "=", "np", ".", "zeros", "(", "len", "(", "volume", ")", ")", "pvi", "[", "0", "]", ...	26.55	0.001818
def round_to_n(x, n): """ Round to sig figs """ return round(x, -int(np.floor(np.log10(x))) + (n - 1))	[ "def", "round_to_n", "(", "x", ",", "n", ")", ":", "return", "round", "(", "x", ",", "-", "int", "(", "np", ".", "floor", "(", "np", ".", "log10", "(", "x", ")", ")", ")", "+", "(", "n", "-", "1", ")", ")" ]	22.8	0.008475
def scheduled(self, offset=0, count=25): '''Return all the currently-scheduled jobs''' return self.client('jobs', 'scheduled', self.name, offset, count)	[ "def", "scheduled", "(", "self", ",", "offset", "=", "0", ",", "count", "=", "25", ")", ":", "return", "self", ".", "client", "(", "'jobs'", ",", "'scheduled'", ",", "self", ".", "name", ",", "offset", ",", "count", ")" ]	55.333333	0.011905
def greylisting(data): """ Run ChIP-seq greylisting """ input_bam = data.get("work_bam_input", None) if not input_bam: logger.info("No input BAM file detected, skipping greylisting.") return None try: greylister = config_utils.get_program("chipseq-greylist", data) exc...	[ "def", "greylisting", "(", "data", ")", ":", "input_bam", "=", "data", ".", "get", "(", "\"work_bam_input\"", ",", "None", ")", "if", "not", "input_bam", ":", "logger", ".", "info", "(", "\"No input BAM file detected, skipping greylisting.\"", ")", "return", "No...	42.071429	0.00249
def checkout(self, ref, cb=None): """Checkout a bundle from the remote. Returns a file-like object""" if self.is_api: return self._checkout_api(ref, cb=cb) else: return self._checkout_fs(ref, cb=cb)	[ "def", "checkout", "(", "self", ",", "ref", ",", "cb", "=", "None", ")", ":", "if", "self", ".", "is_api", ":", "return", "self", ".", "_checkout_api", "(", "ref", ",", "cb", "=", "cb", ")", "else", ":", "return", "self", ".", "_checkout_fs", "(", ...	40.166667	0.00813
def designPrimers(p3_args, input_log=None, output_log=None, err_log=None): ''' Return the raw primer3_core output for the provided primer3 args. Returns an ordered dict of the boulderIO-format primer3 output file ''' sp = subprocess.Popen([pjoin(PRIMER3_HOME, 'primer3_core')], ...	[ "def", "designPrimers", "(", "p3_args", ",", "input_log", "=", "None", ",", "output_log", "=", "None", ",", "err_log", "=", "None", ")", ":", "sp", "=", "subprocess", ".", "Popen", "(", "[", "pjoin", "(", "PRIMER3_HOME", ",", "'primer3_core'", ")", "]", ...	41	0.001083
def follow_path(self, path, weight=None): """Go to several :class:`Place`s in succession, deciding how long to spend in each by consulting the ``weight`` stat of the :class:`Portal` connecting the one :class:`Place` to the next. Return the total number of turns the travel will take. Rai...	[ "def", "follow_path", "(", "self", ",", "path", ",", "weight", "=", "None", ")", ":", "if", "len", "(", "path", ")", "<", "2", ":", "raise", "ValueError", "(", "\"Paths need at least 2 nodes\"", ")", "eng", "=", "self", ".", "character", ".", "engine", ...	41.020408	0.000972
def binarize_percent(netin, level, sign='pos', axis='time'): """ Binarizes a network proprtionally. When axis='time' (only one available at the moment) then the top values for each edge time series are considered. Parameters ---------- netin : array or dict network (graphlet or contact rep...	[ "def", "binarize_percent", "(", "netin", ",", "level", ",", "sign", "=", "'pos'", ",", "axis", "=", "'time'", ")", ":", "netin", ",", "netinfo", "=", "process_input", "(", "netin", ",", "[", "'C'", ",", "'G'", ",", "'TO'", "]", ")", "# Set diagonal to ...	38.469697	0.002304
def make_clust(net, dist_type='cosine', run_clustering=True, dendro=True, requested_views=['pct_row_sum', 'N_row_sum'], linkage_type='average', sim_mat=False, filter_sim=0.1, calc_cat_pval=False, sim_mat_views=['N_row_sum'], ...	[ "def", "make_clust", "(", "net", ",", "dist_type", "=", "'cosine'", ",", "run_clustering", "=", "True", ",", "dendro", "=", "True", ",", "requested_views", "=", "[", "'pct_row_sum'", ",", "'N_row_sum'", "]", ",", "linkage_type", "=", "'average'", ",", "sim_m...	32.131313	0.015554
def dual_obj_grad(alpha, beta, a, b, C, regul): """ Compute objective value and gradients of dual objective. Parameters ---------- alpha: array, shape = len(a) beta: array, shape = len(b) Current iterate of dual potentials. a: array, shape = len(a) b: array, shape = len(b) ...	[ "def", "dual_obj_grad", "(", "alpha", ",", "beta", ",", "a", ",", "b", ",", "C", ",", "regul", ")", ":", "obj", "=", "np", ".", "dot", "(", "alpha", ",", "a", ")", "+", "np", ".", "dot", "(", "beta", ",", "b", ")", "grad_alpha", "=", "a", "...	26.452381	0.000868
def admin_tools_render_dashboard(context, location='index', dashboard=None): """ Template tag that renders the dashboard, it takes two optional arguments: ``location`` The location of the dashboard, it can be 'index' (for the admin index dashboard) or 'app_index' (for the app index dashboar...	[ "def", "admin_tools_render_dashboard", "(", "context", ",", "location", "=", "'index'", ",", "dashboard", "=", "None", ")", ":", "if", "dashboard", "is", "None", ":", "dashboard", "=", "get_dashboard", "(", "context", ",", "location", ")", "dashboard", ".", ...	34.42	0.000565
def parse_gene_set(gene_set_fp): """Parses gene set file and returns a (group)-(gene set) dictionary. Attribute: gene_set_fp (str): File path to a gene set file. """ group_gene_set_dict = OrderedDict() with open(gene_set_fp) as inFile: for line in inFile.readlines(): ...	[ "def", "parse_gene_set", "(", "gene_set_fp", ")", ":", "group_gene_set_dict", "=", "OrderedDict", "(", ")", "with", "open", "(", "gene_set_fp", ")", "as", "inFile", ":", "for", "line", "in", "inFile", ".", "readlines", "(", ")", ":", "tokens", "=", "line",...	31.375	0.001934
def prompt_file(prompt, default=None): """Prompt a file name with autocompletion""" def complete(text: str, state): text = text.replace('~', HOME) sugg = (glob.glob(text + '*') + [None])[state] if sugg is None: return sugg = sugg.replace(HOME, '~') sugg = ...	[ "def", "prompt_file", "(", "prompt", ",", "default", "=", "None", ")", ":", "def", "complete", "(", "text", ":", "str", ",", "state", ")", ":", "text", "=", "text", ".", "replace", "(", "'~'", ",", "HOME", ")", "sugg", "=", "(", "glob", ".", "glo...	24.088235	0.001174
def replace_certificate_signing_request_status(self, name, body, **kwargs): # noqa: E501 """replace_certificate_signing_request_status # noqa: E501 replace status of the specified CertificateSigningRequest # noqa: E501 This method makes a synchronous HTTP request by default. To make an ...	[ "def", "replace_certificate_signing_request_status", "(", "self", ",", "name", ",", "body", ",", "", "", "kwargs", ")", ":", "# noqa: E501", "kwargs", "[", "'_return_http_data_only'", "]", "=", "True", "if", "kwargs", ".", "get", "(", "'async_req'", ")", ":"...	63.625	0.00129
def getSimpleFileData(self, fileInfo, data): """Function to initialize the simple data for file info""" result = fileInfo[fileInfo.find(data + "</td>"):] result = result[:result.find("</A></td>")] result = result[result.rfind(">") + 1:] return result	[ "def", "getSimpleFileData", "(", "self", ",", "fileInfo", ",", "data", ")", ":", "result", "=", "fileInfo", "[", "fileInfo", ".", "find", "(", "data", "+", "\"</td>\"", ")", ":", "]", "result", "=", "result", "[", ":", "result", ".", "find", "(", "\"...	42.5	0.026923
def shell_exec(command): """Executes the given shell command and returns its output.""" out = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT).communicate()[0] return out.decode('utf-8')	[ "def", "shell_exec", "(", "command", ")", ":", "out", "=", "subprocess", ".", "Popen", "(", "command", ",", "shell", "=", "True", ",", "stdout", "=", "subprocess", ".", "PIPE", ",", "stderr", "=", "subprocess", ".", "STDOUT", ")", ".", "communicate", "...	58.5	0.008439
def timezone(haystack_tz, version=LATEST_VER): """ Retrieve the Haystack timezone """ tz_map = get_tz_map(version=version) try: tz_name = tz_map[haystack_tz] except KeyError: raise ValueError('%s is not a recognised timezone on this host' \ % haystack_tz) retu...	[ "def", "timezone", "(", "haystack_tz", ",", "version", "=", "LATEST_VER", ")", ":", "tz_map", "=", "get_tz_map", "(", "version", "=", "version", ")", "try", ":", "tz_name", "=", "tz_map", "[", "haystack_tz", "]", "except", "KeyError", ":", "raise", "ValueE...	30.454545	0.008696
def parse_args(self, args): """ Parse arguments and return an arguments object >>> from margaritashotgun.cli import Cli >>> cli = CLi() >>> cli.parse_args(sys.argv[1:]) :type args: list :param args: list of arguments """ parser = argp...	[ "def", "parse_args", "(", "self", ",", "args", ")", ":", "parser", "=", "argparse", ".", "ArgumentParser", "(", "description", "=", "'Remote memory aquisition wrapper for LiME'", ")", "root", "=", "parser", ".", "add_mutually_exclusive_group", "(", "required", "=", ...	47.794521	0.000842
def prepare_check(data): """Prepare check for catalog endpoint Parameters: data (Object or ObjectID): Check ID or check definition Returns: Tuple[str, dict]: where first is ID and second is check definition """ if not data: return None, {} if isinstance(data, str): ...	[ "def", "prepare_check", "(", "data", ")", ":", "if", "not", "data", ":", "return", "None", ",", "{", "}", "if", "isinstance", "(", "data", ",", "str", ")", ":", "return", "data", ",", "{", "}", "result", "=", "{", "}", "if", "\"ID\"", "in", "data...	27.652174	0.00152
def parse_hgnc_genes(lines): """Parse lines with hgnc formated genes This is designed to take a dump with genes from HGNC. This is downloaded from: ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt Args: lines(iterable(str)): An iterable with HGN...	[ "def", "parse_hgnc_genes", "(", "lines", ")", ":", "header", "=", "[", "]", "logger", ".", "info", "(", "\"Parsing hgnc genes...\"", ")", "for", "index", ",", "line", "in", "enumerate", "(", "lines", ")", ":", "if", "index", "==", "0", ":", "header", "...	34.428571	0.001346
def check_last_err(func, self, args, *kwargs): """Check and raise deferred errors before running the function This method checks :python:`_last_err` before running the wrapped function. If present and not None, the exception will be raised with its original traceback. """ if self._last_err ...	[ "def", "check_last_err", "(", "func", ",", "self", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "if", "self", ".", "_last_err", "is", "not", "None", ":", "try", ":", "if", "six", ".", "PY2", ":", "six", ".", "reraise", "(", "type", "(", ...	34.771429	0.000799
def _send_ffd(self, pid, aplx_data, address): """Send flood-fill data packets.""" block = 0 pos = 0 aplx_size = len(aplx_data) while pos < aplx_size: # Get the next block of data, send and progress the block # counter and the address data = ap...	[ "def", "_send_ffd", "(", "self", ",", "pid", ",", "aplx_data", ",", "address", ")", ":", "block", "=", "0", "pos", "=", "0", "aplx_size", "=", "len", "(", "aplx_data", ")", "while", "pos", "<", "aplx_size", ":", "# Get the next block of data, send and progre...	36.545455	0.002424
def zernike(zernike_indexes,labels,indexes): """Compute the Zernike features for the labels with the label #s in indexes returns the score per labels and an array of one image per zernike feature """ # # "Reverse_indexes" is -1 if a label # is not to be processed. Otherwise # reverse_index[...	[ "def", "zernike", "(", "zernike_indexes", ",", "labels", ",", "indexes", ")", ":", "#", "# \"Reverse_indexes\" is -1 if a label # is not to be processed. Otherwise", "# reverse_index[label] gives you the index into indexes of the label", "# and other similarly shaped vectors (like the resu...	36.78	0.010064
def set_index(data,col_index): """ Sets the index if the index is not present :param data: pandas table :param col_index: column name which will be assigned as a index """ if col_index in data: data=data.reset_index().set_index(col_index) if 'index' in data: del dat...	[ "def", "set_index", "(", "data", ",", "col_index", ")", ":", "if", "col_index", "in", "data", ":", "data", "=", "data", ".", "reset_index", "(", ")", ".", "set_index", "(", "col_index", ")", "if", "'index'", "in", "data", ":", "del", "data", "[", "'i...	28.117647	0.010121
def _apply_uncertainty_to_geometry(self, source, value): """ Modify ``source`` geometry with the uncertainty value ``value`` """ if self.uncertainty_type == 'simpleFaultDipRelative': source.modify('adjust_dip', dict(increment=value)) elif self.uncertainty_type == 'sim...	[ "def", "_apply_uncertainty_to_geometry", "(", "self", ",", "source", ",", "value", ")", ":", "if", "self", ".", "uncertainty_type", "==", "'simpleFaultDipRelative'", ":", "source", ".", "modify", "(", "'adjust_dip'", ",", "dict", "(", "increment", "=", "value", ...	53.894737	0.001919
def get_layers(self, class_: Type[L], became: bool=True) -> List[L]: """ Proxy to stack """ return self.stack.get_layers(class_, became)	[ "def", "get_layers", "(", "self", ",", "class_", ":", "Type", "[", "L", "]", ",", "became", ":", "bool", "=", "True", ")", "->", "List", "[", "L", "]", ":", "return", "self", ".", "stack", ".", "get_layers", "(", "class_", ",", "became", ")" ]	32.8	0.02381
def session(self): """ Returns the current db session """ if not self.__session: self.__session = dal.get_default_session() return self.__session	[ "def", "session", "(", "self", ")", ":", "if", "not", "self", ".", "__session", ":", "self", ".", "__session", "=", "dal", ".", "get_default_session", "(", ")", "return", "self", ".", "__session" ]	35.4	0.01105
def address_to_ip(address): """Convert a hostname to a numerical IP addresses in an address. This should be a no-op if address already contains an actual numerical IP address. Args: address: This can be either a string containing a hostname (or an IP address) and a port or it can b...	[ "def", "address_to_ip", "(", "address", ")", ":", "address_parts", "=", "address", ".", "split", "(", "\":\"", ")", "ip_address", "=", "socket", ".", "gethostbyname", "(", "address_parts", "[", "0", "]", ")", "# Make sure localhost isn't resolved to the loopback ip"...	36.25	0.001344
def generate_header_signature(secret, payload, request_type): '''Authorize a client based on encrypting the payload with the client secret, timestamp, and other metadata ''' # Use the payload to generate a digest push\|collection\|name\|tag\|user timestamp = generate_timestamp() credential = ...	[ "def", "generate_header_signature", "(", "secret", ",", "payload", ",", "request_type", ")", ":", "# Use the payload to generate a digest push\|collection\|name\|tag\|user", "timestamp", "=", "generate_timestamp", "(", ")", "credential", "=", "\"%s/%s\"", "%", "(", "request_t...	43.727273	0.014257
def split_Text( text, file_name, verbose = True ): ''' Tokenizes the text (from file_name) into sentences, and if the number of sentences exceeds max_sentences, splits the text into smaller texts. Returns a list containing the original text (if no splitting was required), or a list c...	[ "def", "split_Text", "(", "text", ",", "file_name", ",", "verbose", "=", "True", ")", ":", "if", "verbose", ":", "print", "(", "' processing '", "+", "file_name", "+", "' ... '", ",", "end", "=", "\"\"", ")", "# Tokenize text into sentences", "start", "=", ...	44.777778	0.027115
def file_upload(context, id, name, path, jobstate_id, test_id, mime): """file_upload(context, id, path) Upload a file in a job >>> dcictl job-upload-file [OPTIONS] :param string id: ID of the job to attach file to [required] :param string name: Name of the file [required] :param string path: ...	[ "def", "file_upload", "(", "context", ",", "id", ",", "name", ",", "path", ",", "jobstate_id", ",", "test_id", ",", "mime", ")", ":", "result", "=", "dci_file", ".", "create_with_stream", "(", "context", ",", "name", "=", "name", ",", "job_id", "=", "i...	44.045455	0.00101
def parseExtensionArgs(self, args, is_openid1, strict=False): """Parse the provider authentication policy arguments into the internal state of this object @param args: unqualified provider authentication policy arguments @param strict: Whether to raise an exception when bad...	[ "def", "parseExtensionArgs", "(", "self", ",", "args", ",", "is_openid1", ",", "strict", "=", "False", ")", ":", "policies_str", "=", "args", ".", "get", "(", "'auth_policies'", ")", "if", "policies_str", ":", "auth_policies", "=", "policies_str", ".", "spli...	35.090909	0.00084
def validate(self, instance, value): """Determine if array is valid based on shape and dtype""" if not isinstance(value, (tuple, list, np.ndarray)): self.error(instance, value) if self.coerce: value = self.wrapper(value) valid_class = ( self.wrapper if...	[ "def", "validate", "(", "self", ",", "instance", ",", "value", ")", ":", "if", "not", "isinstance", "(", "value", ",", "(", "tuple", ",", "list", ",", "np", ".", "ndarray", ")", ")", ":", "self", ".", "error", "(", "instance", ",", "value", ")", ...	40.52	0.001929
def merge_bams(self, input_bams, merged_bam, in_sorted="TRUE", tmp_dir=None): """ Combine multiple files into one. The tmp_dir parameter is important because on poorly configured systems, the default can sometimes fill up. :param Iterable[str] input_bams: Paths to files to comb...	[ "def", "merge_bams", "(", "self", ",", "input_bams", ",", "merged_bam", ",", "in_sorted", "=", "\"TRUE\"", ",", "tmp_dir", "=", "None", ")", ":", "if", "not", "len", "(", "input_bams", ")", ">", "1", ":", "print", "(", "\"No merge required\"", ")", "retu...	39.166667	0.001384
def hardware_info(self, mask=0xFFFFFFFF): """Returns a list of 32 integer values corresponding to the bitfields specifying the power consumption of the target. The values returned by this function only have significance if the J-Link is powering the target. The words, indexed, ...	[ "def", "hardware_info", "(", "self", ",", "mask", "=", "0xFFFFFFFF", ")", ":", "buf", "=", "(", "ctypes", ".", "c_uint32", "*", "32", ")", "(", ")", "res", "=", "self", ".", "_dll", ".", "JLINKARM_GetHWInfo", "(", "mask", ",", "ctypes", ".", "byref",...	39.142857	0.001425
def _as_medium(exchanges, tolerance=1e-6, exports=False): """Convert a solution to medium. Arguments --------- exchanges : list of cobra.reaction The exchange reactions to consider. tolerance : positive double The absolute tolerance for fluxes. Fluxes with an absolute value ...	[ "def", "_as_medium", "(", "exchanges", ",", "tolerance", "=", "1e-6", ",", "exports", "=", "False", ")", ":", "LOGGER", ".", "debug", "(", "\"Formatting medium.\"", ")", "medium", "=", "pd", ".", "Series", "(", ")", "for", "rxn", "in", "exchanges", ":", ...	27.818182	0.001053
def _polytree_node_to_shapely(node): """ Recurses down a Clipper PolyTree, extracting the results as Shapely objects. Returns a tuple of (list of polygons, list of children) """ polygons = [] children = [] for ch in node.Childs: p, c = _polytree_node_to_shapely(ch) poly...	[ "def", "_polytree_node_to_shapely", "(", "node", ")", ":", "polygons", "=", "[", "]", "children", "=", "[", "]", "for", "ch", "in", "node", ".", "Childs", ":", "p", ",", "c", "=", "_polytree_node_to_shapely", "(", "ch", ")", "polygons", ".", "extend", ...	35.096386	0.000668
def deploy_templates(): """ Deploy any templates from your shortest TEMPLATE_DIRS setting """ deployed = None if not hasattr(env, 'project_template_dir'): #the normal pattern would mean the shortest path is the main one. #its probably the last listed length = 1000 ...	[ "def", "deploy_templates", "(", ")", ":", "deployed", "=", "None", "if", "not", "hasattr", "(", "env", ",", "'project_template_dir'", ")", ":", "#the normal pattern would mean the shortest path is the main one.", "#its probably the last listed", "length", "=", "1000", "fo...	35.956522	0.015312
def ping( self, destination, source=c.PING_SOURCE, ttl=c.PING_TTL, timeout=c.PING_TIMEOUT, size=c.PING_SIZE, count=c.PING_COUNT, vrf=c.PING_VRF, ): """ Execute ping on the device and returns a dictionary with the result. Output ...	[ "def", "ping", "(", "self", ",", "destination", ",", "source", "=", "c", ".", "PING_SOURCE", ",", "ttl", "=", "c", ".", "PING_TTL", ",", "timeout", "=", "c", ".", "PING_TIMEOUT", ",", "size", "=", "c", ".", "PING_SIZE", ",", "count", "=", "c", ".",...	36.960317	0.001255
def fetch(context, data): """Do an HTTP GET on the ``url`` specified in the inbound data.""" url = data.get('url') attempt = data.pop('retry_attempt', 1) try: result = context.http.get(url, lazy=True) rules = context.get('rules', {'match_all': {}}) if not Rule.get_rule(rules).app...	[ "def", "fetch", "(", "context", ",", "data", ")", ":", "url", "=", "data", ".", "get", "(", "'url'", ")", "attempt", "=", "data", ".", "pop", "(", "'retry_attempt'", ",", "1", ")", "try", ":", "result", "=", "context", ".", "http", ".", "get", "(...	38.617647	0.000743
def batch_length(batch): '''Determine the number of samples in a batch. Parameters ---------- batch : dict A batch dictionary. Each value must implement `len`. All values must have the same `len`. Returns ------- n : int >= 0 or None The number of samples in this b...	[ "def", "batch_length", "(", "batch", ")", ":", "n", "=", "None", "for", "value", "in", "six", ".", "itervalues", "(", "batch", ")", ":", "if", "n", "is", "None", ":", "n", "=", "len", "(", "value", ")", "elif", "len", "(", "value", ")", "!=", "...	21.466667	0.001486
def _run_prospector(filename, stamp_file_name, disabled_linters, show_lint_files): """Run prospector.""" linter_tools = [ "pep257", "pep8", "pyflakes" ] if can_run_pylint(): linter_tools.append("pylint") # ...	[ "def", "_run_prospector", "(", "filename", ",", "stamp_file_name", ",", "disabled_linters", ",", "show_lint_files", ")", ":", "linter_tools", "=", "[", "\"pep257\"", ",", "\"pep8\"", ",", "\"pyflakes\"", "]", "if", "can_run_pylint", "(", ")", ":", "linter_tools", ...	32.348837	0.000698
def save(self, collection): """ Save an asset collection to the service. """ assert isinstance(collection, predix.data.asset.AssetCollection), "Expected AssetCollection" collection.validate() self.put_collection(collection.uri, collection.__dict__)	[ "def", "save", "(", "self", ",", "collection", ")", ":", "assert", "isinstance", "(", "collection", ",", "predix", ".", "data", ".", "asset", ".", "AssetCollection", ")", ",", "\"Expected AssetCollection\"", "collection", ".", "validate", "(", ")", "self", "...	41.428571	0.010135
def get_rec_features(self, features=None): """ Returns a df of features for recalled items """ if features is None: features = self.dist_funcs.keys() elif not isinstance(features, list): features = [features] return self.rec.applymap(lambda x: {k:v...	[ "def", "get_rec_features", "(", "self", ",", "features", "=", "None", ")", ":", "if", "features", "is", "None", ":", "features", "=", "self", ".", "dist_funcs", ".", "keys", "(", ")", "elif", "not", "isinstance", "(", "features", ",", "list", ")", ":",...	41.888889	0.012987
def is_zhuyin_compatible(s): """Checks if s is consists of Zhuyin-compatible characters. This does not check if s contains valid Zhuyin syllables; for that see :func:`is_zhuyin`. Besides Zhuyin characters and tone marks, spaces are also accepted. This function checks that all characters in s...	[ "def", "is_zhuyin_compatible", "(", "s", ")", ":", "printable_zhuyin", "=", "zhon", ".", "zhuyin", ".", "characters", "+", "zhon", ".", "zhuyin", ".", "marks", "+", "' '", "return", "_is_pattern_match", "(", "'[%s]+'", "%", "printable_zhuyin", ",", "s", ")" ...	41	0.001835
def write(self, oprot): ''' Write this object to the given output protocol and return self. :type oprot: thryft.protocol._output_protocol._OutputProtocol :rtype: pastpy.gen.database.impl.online.online_database_object_detail_image.OnlineDatabaseObjectDetailImage ''' opro...	[ "def", "write", "(", "self", ",", "oprot", ")", ":", "oprot", ".", "write_struct_begin", "(", "'OnlineDatabaseObjectDetailImage'", ")", "oprot", ".", "write_field_begin", "(", "name", "=", "'full_size_url'", ",", "type", "=", "11", ",", "id", "=", "None", ")...	32.906977	0.002059
def generic_in(self, **kwargs): '''Bypass buggy GenericReferenceField querying issue''' query = {} for key, value in kwargs.items(): if not value: continue # Optimize query for when there is only one value if isinstance(value, (list, tuple)) an...	[ "def", "generic_in", "(", "self", ",", "", "", "kwargs", ")", ":", "query", "=", "{", "}", "for", "key", ",", "value", "in", "kwargs", ".", "items", "(", ")", ":", "if", "not", "value", ":", "continue", "# Optimize query for when there is only one value"...	50	0.001635
def expires_at(self): """ A :py:obj:`~datetime.datetime` of when this signature expires, if a signature expiration date is specified. Otherwise, ``None`` """ if 'SignatureExpirationTime' in self._signature.subpackets: expd = next(iter(self._signature.subpackets['Signa...	[ "def", "expires_at", "(", "self", ")", ":", "if", "'SignatureExpirationTime'", "in", "self", ".", "_signature", ".", "subpackets", ":", "expd", "=", "next", "(", "iter", "(", "self", ".", "_signature", ".", "subpackets", "[", "'SignatureExpirationTime'", "]", ...	44.555556	0.00978
def main(): """ This example demonstrates how to generate pretty equations from the analytic expressions found in ``chempy.kinetics.integrated``. """ t, kf, t0, major, minor, prod, beta = sympy.symbols( 't k_f t0 Y Z X beta', negative=False) for f in funcs: args = [t, kf, prod, m...	[ "def", "main", "(", ")", ":", "t", ",", "kf", ",", "t0", ",", "major", ",", "minor", ",", "prod", ",", "beta", "=", "sympy", ".", "symbols", "(", "'t k_f t0 Y Z X beta'", ",", "negative", "=", "False", ")", "for", "f", "in", "funcs", ":", "args", ...	47.578947	0.002169
def makeService(opt): """Make a service :params opt: dictionary-like object with 'freq', 'config' and 'messages' :returns: twisted.application.internet.TimerService that at opt['freq'] checks for stale processes in opt['config'], and sends restart messages through opt['messages'...	[ "def", "makeService", "(", "opt", ")", ":", "restarter", ",", "path", "=", "parseConfig", "(", "opt", ")", "now", "=", "time", ".", "time", "(", ")", "checker", "=", "functools", ".", "partial", "(", "check", ",", "path", ",", "now", ")", "beatcheck"...	41.866667	0.001558
def _get_host_libc_from_host_compiler(self): """Locate the host's libc-dev installation using a specified host compiler's search dirs.""" compiler_exe = self.get_options().host_compiler # Implicitly, we are passing in the environment of the executing pants process to # `get_compiler_library_dirs()`. ...	[ "def", "_get_host_libc_from_host_compiler", "(", "self", ")", ":", "compiler_exe", "=", "self", ".", "get_options", "(", ")", ".", "host_compiler", "# Implicitly, we are passing in the environment of the executing pants process to", "# `get_compiler_library_dirs()`.", "# These dire...	50.08	0.008621
def _add_person_to_group(person, group): """ Call datastores after adding a person to a group. """ from karaage.datastores import add_accounts_to_group from karaage.datastores import add_accounts_to_project from karaage.datastores import add_accounts_to_institute a_list = person.account_set add...	[ "def", "_add_person_to_group", "(", "person", ",", "group", ")", ":", "from", "karaage", ".", "datastores", "import", "add_accounts_to_group", "from", "karaage", ".", "datastores", "import", "add_accounts_to_project", "from", "karaage", ".", "datastores", "import", ...	44.666667	0.001828
def doc_type(self, doc_type, *kwargs): """ Set the type to search through. You can supply a single value or multiple. Values can be strings or subclasses of ``Document``. You can also pass in any keyword arguments, mapping a doc_type to a callback that should be used instead o...	[ "def", "doc_type", "(", "self", ",", "", "doc_type", ",", "", "*", "kwargs", ")", ":", "# .doc_type() resets", "s", "=", "self", ".", "_clone", "(", ")", "if", "not", "doc_type", "and", "not", "kwargs", ":", "s", ".", "_doc_type", "=", "[", "]", ...	33.6	0.002315
def parse_instancepath(parser, event, node): #pylint: disable=unused-argument """Parse the CIM/XML INSTANCEPATH element and return an instancname <!ELEMENT INSTANCEPATH (NAMESPACEPATH, INSTANCENAME)> """ (next_event, next_node) = six.next(parser) if not _is_start(next_event, next_no...	[ "def", "parse_instancepath", "(", "parser", ",", "event", ",", "node", ")", ":", "#pylint: disable=unused-argument", "(", "next_event", ",", "next_node", ")", "=", "six", ".", "next", "(", "parser", ")", "if", "not", "_is_start", "(", "next_event", ",", "nex...	30.037037	0.002389
def getByteStatistic(self, wanInterfaceId=1, timeout=1): """Execute GetTotalBytesSent&GetTotalBytesReceived actions to get WAN statistics. :param int wanInterfaceId: the id of the WAN device :param float timeout: the timeout to wait for the action to be executed :return: a tuple of two ...	[ "def", "getByteStatistic", "(", "self", ",", "wanInterfaceId", "=", "1", ",", "timeout", "=", "1", ")", ":", "namespace", "=", "Wan", ".", "getServiceType", "(", "\"getByteStatistic\"", ")", "+", "str", "(", "wanInterfaceId", ")", "uri", "=", "self", ".", ...	50.0625	0.008578
def f_df_nc(self,x): ''' Wrapper of the derivative of f: takes an input x with size of the not fixed dimensions expands it and evaluates the gradient of the entire function. ''' x = np.atleast_2d(x) xx = self.context_manager._expand_vector(x) f_nocontext_xx , df...	[ "def", "f_df_nc", "(", "self", ",", "x", ")", ":", "x", "=", "np", ".", "atleast_2d", "(", "x", ")", "xx", "=", "self", ".", "context_manager", ".", "_expand_vector", "(", "x", ")", "f_nocontext_xx", ",", "df_nocontext_xx", "=", "self", ".", "f_df", ...	48	0.014315
def confirms(self, txid): """Returns number of confirms or None if unpublished.""" txid = deserialize.txid(txid) return self.service.confirms(txid)	[ "def", "confirms", "(", "self", ",", "txid", ")", ":", "txid", "=", "deserialize", ".", "txid", "(", "txid", ")", "return", "self", ".", "service", ".", "confirms", "(", "txid", ")" ]	42	0.011696
def wait_for_tasks(self, tasks): """Given the service instance si and tasks, it returns after all the tasks are complete """ property_collector = self.service_instance.RetrieveContent().propertyCollector task_list = [str(task) for task in tasks] # Create filter obj_...	[ "def", "wait_for_tasks", "(", "self", ",", "tasks", ")", ":", "property_collector", "=", "self", ".", "service_instance", ".", "RetrieveContent", "(", ")", ".", "propertyCollector", "task_list", "=", "[", "str", "(", "task", ")", "for", "task", "in", "tasks"...	47.777778	0.002279
def triads(reference_labels, estimated_labels): """Compare chords along triad (root & quality to #5) relationships. Examples -------- >>> (ref_intervals, ... ref_labels) = mir_eval.io.load_labeled_intervals('ref.lab') >>> (est_intervals, ... est_labels) = mir_eval.io.load_labeled_interval...	[ "def", "triads", "(", "reference_labels", ",", "estimated_labels", ")", ":", "validate", "(", "reference_labels", ",", "estimated_labels", ")", "ref_roots", ",", "ref_semitones", "=", "encode_many", "(", "reference_labels", ",", "False", ")", "[", ":", "2", "]",...	37.76087	0.000561
def astra_algorithm(direction, ndim, vol_id, sino_id, proj_id, impl): """Create an ASTRA algorithm object to run the projector. Parameters ---------- direction : {'forward', 'backward'} For ``'forward'``, apply the forward projection, for ``'backward'`` the backprojection. ndim : {2...	[ "def", "astra_algorithm", "(", "direction", ",", "ndim", ",", "vol_id", ",", "sino_id", ",", "proj_id", ",", "impl", ")", ":", "if", "direction", "not", "in", "(", "'forward'", ",", "'backward'", ")", ":", "raise", "ValueError", "(", "\"`direction` '{}' not ...	37.150943	0.000495
def ser_iuwt_recomposition(in1, scale_adjust, smoothed_array): """ This function calls the a trous algorithm code to recompose the input into a single array. This is the implementation of the isotropic undecimated wavelet transform recomposition for a single CPU core. INPUTS: in1 (no de...	[ "def", "ser_iuwt_recomposition", "(", "in1", ",", "scale_adjust", ",", "smoothed_array", ")", ":", "wavelet_filter", "=", "(", "1.", "/", "16", ")", "*", "np", ".", "array", "(", "[", "1", ",", "4", ",", "6", ",", "4", ",", "1", "]", ")", "# Filter...	44.378378	0.010131
def get_devices(filename, bundled): """Get a Devices object from a file. :param filename: full path of the file to parse or name of the resource. :param is_resource: boolean indicating if it is a resource. :rtype: Devices """ loader = Loader(filename, bundled) data = loader.data devi...	[ "def", "get_devices", "(", "filename", ",", "bundled", ")", ":", "loader", "=", "Loader", "(", "filename", ",", "bundled", ")", "data", "=", "loader", ".", "data", "devices", "=", "Devices", "(", ")", "# Iterate through the resources and generate each individual d...	31.586207	0.001059
def dragEnterEvent( self, event ): """ Processes the drag drop event using the filter set by the \ setDragDropFilter :param event \| <QDragEvent> """ filt = self.dragDropFilter() if ( not filt ): super(XCalendarWidget, self).dragE...	[ "def", "dragEnterEvent", "(", "self", ",", "event", ")", ":", "filt", "=", "self", ".", "dragDropFilter", "(", ")", "if", "(", "not", "filt", ")", ":", "super", "(", "XCalendarWidget", ",", "self", ")", ".", "dragEnterEvent", "(", "event", ")", "return...	29.307692	0.022901
def common_mean_watson(Data1, Data2, NumSims=5000, print_result=True, plot='no', save=False, save_folder='.', fmt='svg'): """ Conduct a Watson V test for a common mean on two directional data sets. This function calculates Watson's V statistic from input files through Monte Carlo simulation in order to...	[ "def", "common_mean_watson", "(", "Data1", ",", "Data2", ",", "NumSims", "=", "5000", ",", "print_result", "=", "True", ",", "plot", "=", "'no'", ",", "save", "=", "False", ",", "save_folder", "=", "'.'", ",", "fmt", "=", "'svg'", ")", ":", "pars_1", ...	41.552147	0.001154
def bitmap_pattern_to_list(self, bmp_pat): """ takes a list of bitmap points (drawn via Life screen) and converts to a list of full coordinates """ res = [] x = 1 y = 1 lines = bmp_pat.split('\n') for line in lines: y += 1 ...	[ "def", "bitmap_pattern_to_list", "(", "self", ",", "bmp_pat", ")", ":", "res", "=", "[", "]", "x", "=", "1", "y", "=", "1", "lines", "=", "bmp_pat", ".", "split", "(", "'\\n'", ")", "for", "line", "in", "lines", ":", "y", "+=", "1", "for", "char"...	27.1875	0.011111
def subj_has_perm(self, subj_str, perm_str): """Returns: bool: ``True`` if ``subj_str`` has perm equal to or higher than ``perm_str``. """ self._assert_valid_permission(perm_str) return perm_str in self.get_effective_perm_list(subj_str)	[ "def", "subj_has_perm", "(", "self", ",", "subj_str", ",", "perm_str", ")", ":", "self", ".", "_assert_valid_permission", "(", "perm_str", ")", "return", "perm_str", "in", "self", ".", "get_effective_perm_list", "(", "subj_str", ")" ]	33.875	0.010791
def connected_emulators(self, host=enums.JLinkHost.USB): """Returns a list of all the connected emulators. Args: self (JLink): the ``JLink`` instance host (int): host type to search (default: ``JLinkHost.USB``) Returns: List of ``JLinkConnectInfo`` specifying the ...	[ "def", "connected_emulators", "(", "self", ",", "host", "=", "enums", ".", "JLinkHost", ".", "USB", ")", ":", "res", "=", "self", ".", "_dll", ".", "JLINKARM_EMU_GetList", "(", "host", ",", "0", ",", "0", ")", "if", "res", "<", "0", ":", "raise", "...	33.416667	0.002424
def most_frequent_terms(self, depth): """ Get the X most frequent terms in the text, and then probe down to get any other terms that have the same count as the last term. Args: depth (int): The number of terms. Returns: set: The set of frequent terms. ...	[ "def", "most_frequent_terms", "(", "self", ",", "depth", ")", ":", "counts", "=", "self", ".", "term_counts", "(", ")", "# Get the top X terms and the instance count of the last word.", "top_terms", "=", "set", "(", "list", "(", "counts", ".", "keys", "(", ")", ...	33.08	0.00235

def _deserialize(self, stream): """Initialize this instance with index values read from the given stream""" self.version, self.entries, self._extension_data, conten_sha = read_cache(stream) # @UnusedVariable return self

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def file_envs(self, load=None): ''' Return environments for all backends for requests from fileclient ''' if load is None: load = {} load.pop('cmd', None) return self.envs(**load)

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def get_reference(proxy): ''' Return the object that is referenced by the specified proxy. If the proxy has not been bound to a reference for the current thread, the behavior depends on th the ``fallback_to_shared`` flag that has been specified when creating the proxy. If the fl...

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def _upstart_enable(name): ''' Enable an Upstart service. ''' if _upstart_is_enabled(name): return _upstart_is_enabled(name) override = '/etc/init/{0}.override'.format(name) files = ['/etc/init/{0}.conf'.format(name), override] for file_name in filter(os.path.isfile, files): ...

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def has_activity(graph: BELGraph, node: BaseEntity) -> bool: """Return true if over any of the node's edges, it has a molecular activity.""" return _node_has_modifier(graph, node, ACTIVITY)

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def _process_figure(value, fmt): """Processes the figure. Returns a dict containing figure properties.""" # pylint: disable=global-statement global Nreferences # Global references counter global has_unnumbered_figures # Flags unnumbered figures were found global cursec ...

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def read_from_endpoint(self, endpoint, timeout=15): """ Blocking read from an endpoint. Will block until a message is received, or it times out. Also see :meth:`get_endpoint_queue` if you are considering calling this in a loop. .. warning:: Avoid calling this method from an e...

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def discover_group(group, separator="/", exclude=None): """Produce a list of all services and their addresses in a group A group is an optional form of namespace within the discovery mechanism. If an advertised name has the form <group><sep><name> it is deemed to belong to <group>. Note that the se...

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def save_json(data, path, fatal=True, logger=None, sort_keys=True, indent=2, **kwargs): """ Args: data (object | None): Data to serialize and save path (str | None): Path to file where to save fatal (bool | None): Abort execution on failure if True logger (callable | None): Logge...

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def reverse(self, viewname, args=None, kwargs=None): """ Reverse a blog page, taking different configuration options into account. For example, the blog can be mounted using *django-fluent-pages* on multiple nodes. """ # TODO: django-fluent-pages needs a public API to get the cur...

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def conditional_jit(function=None, **kwargs): # noqa: D202 """Use numba's jit decorator if numba is installed. Notes ----- If called without arguments then return wrapped function. @conditional_jit def my_func(): return else called with arguments @co...

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def match_https_hostname(cls, hostname): """ :param hostname: a string :returns: an :py:class:`~httpretty.core.URLMatcher` or ``None`` """ items = sorted( cls._entries.items(), key=lambda matcher_entries: matcher_entries[0].priority, reverse=Tr...

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async def getaccountbywallet(**params): """Receives account by wallet Accepts: - public key hex or checksum format """ if params.get("message"): params = json.loads(params.get("message")) for coinid in coin_ids: database = client[coinid] wallet_collection = database[settings.WALLET] wallet = await walle...

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def sharedFiles(self): 'iterate over shared files and get their public URI' for f in self.sharing.files.iterchildren(): yield (f.attrib['name'], f.attrib['uuid'], 'https://www.jottacloud.com/p/%s/%s' % (self.jfs.username, f.publicURI.text))

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def save_record(self, instance, update_fields=None, **kwargs): """Saves the record. If `update_fields` is set, this method will use partial_update_object() and will update only the given fields (never `_geoloc` and `_tags`). For more information about partial_update_object: htt...

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def iter_field_objects(fields): """ Iterate over fields. Supports list of (k, v) tuples and dicts, and lists of :class:`~urllib3.fields.RequestField`. """ if isinstance(fields, dict): i = six.iteritems(fields) else: i = iter(fields) for field in i: if isinstanc...

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def __leaf(i, j, first, maxfirst, prevleaf, ancestor): """ Determine if j is leaf of i'th row subtree. """ jleaf = 0 if i<=j or first[j] <= maxfirst[i]: return -1, jleaf maxfirst[i] = first[j] jprev = prevleaf[i] prevleaf[i] = j if jprev == -1: jleaf = 1 else: jleaf = 2 if jl...

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def animate(zdata, xdata, ydata, conversionFactorArray, timedata, BoxSize, timeSteps=100, filename="particle"): """ Animates the particle's motion given the z, x and y signal (in Volts) and the conversion factor (to convert between V and nm). Parameters ---------...

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def check(projects): """Check the specified projects for Python 3 compatibility.""" log = logging.getLogger('ciu') log.info('{0} top-level projects to check'.format(len(projects))) print('Finding and checking dependencies ...') blockers = dependencies.blockers(projects) print('') for line i...

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def compare2(args): """ %prog compare2 Compare performances of various variant callers on simulated STR datasets. """ p = OptionParser(compare2.__doc__) p.add_option('--maxinsert', default=300, type="int", help="Maximum number of repeats") add_simulate_options(p) opts, ...

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def point_in_tetrahedron(tetra, pt): ''' point_in_tetrahedron(tetrahedron, point) yields True if the given point is in the given tetrahedron. If either tetrahedron or point (or both) are lists of shapes/points, then this calculation is automatically threaded over all the given arguments. ''' ...

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def run( self, cluster_config, rg_parser, partition_measurer, cluster_balancer, args, ): """Initialize cluster_config, args, and zk then call run_command.""" self.cluster_config = cluster_config self.args = args ...

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def encode_osgi_props(ed): # type: (EndpointDescription) -> Dict[str, str] """ Prepares a dictionary of OSGi properties for the given EndpointDescription """ result_props = {} intfs = ed.get_interfaces() result_props[OBJECTCLASS] = " ".join(intfs) for intf in intfs: pkg_name = pa...

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def dump_conf(self, config_pathname=None): """write a config file to the pathname specified in the parameter. The file extention determines the type of file written and must match a registered type. parameters: config_pathname - the full path and filename of the target conf...

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def post_attachment(self, bugid, attachment): '''http://bugzilla.readthedocs.org/en/latest/api/core/v1/attachment.html#create-attachment''' assert type(attachment) is DotDict assert 'data' in attachment assert 'file_name' in attachment assert 'summary' in attachment if (n...

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def tasks_file_to_task_descriptors(tasks, retries, input_file_param_util, output_file_param_util): """Parses task parameters from a TSV. Args: tasks: Dict containing the path to a TSV file and task numbers to run variables, input, and output parameters as column headings....

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def get_user_enclaves(self): """ Gets the list of enclaves that the user has access to. :return: A list of |EnclavePermissions| objects, each representing an enclave and whether the requesting user has read, create, and update access to it. """ resp = self._client.g...

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def get_success_url(self): """Get the url depending on what type of configuration I deleted.""" if self.stage_id: url = reverse('projects_stage_view', args=(self.project_id, self.stage_id)) else: url = reverse('projects_project_view', args=(self.project_id,)) re...

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def _create_label(self, array): """Create sample PDS3 label for NumPy Array. It is called by 'image.py' to create PDS3Image object from Numpy Array. Returns ------- PVLModule label for the given NumPy array. Usage: self.label = _create_label(array) """ ...

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def clistream(reporter, *args, **kwargs): """ Handle stream data on command line interface, and returns statistics of success, error, and total amount. More detailed information is available on underlying feature, :mod:`clitool.processor`. :param Handler: [DEPRECATED] Handler for file-like streams...

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def optimize_logger_level(logger, log_level): """ At runtime, when logging is not active, replace the .debug() call with a no-op. """ function_name = _log_functions[log_level] if getattr(logger, function_name) is _dummy_log: return False is_level_logged = logger.isEnabledFor(log_lev...

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def validate_config_parameters(config_json, allowed_keys, allowed_types): """Validate parameters in config file.""" custom_fields = config_json.get(defs.PARAMETERS, []) for field in custom_fields: validate_field(field, allowed_keys, allowed_types) default = field.get(defs.DEFAULT) fi...

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def positive_volume_index(close_data, volume): """ Positive Volume Index (PVI). Formula: PVI0 = 1 IF Vt > Vt-1 PVIt = PVIt-1 + (CLOSEt - CLOSEt-1 / CLOSEt-1 * PVIt-1) ELSE: PVIt = PVIt-1 """ catch_errors.check_for_input_len_diff(close_data, volume) pvi = np.zeros(len...

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def round_to_n(x, n): """ Round to sig figs """ return round(x, -int(np.floor(np.log10(x))) + (n - 1))

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def scheduled(self, offset=0, count=25): '''Return all the currently-scheduled jobs''' return self.client('jobs', 'scheduled', self.name, offset, count)

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def greylisting(data): """ Run ChIP-seq greylisting """ input_bam = data.get("work_bam_input", None) if not input_bam: logger.info("No input BAM file detected, skipping greylisting.") return None try: greylister = config_utils.get_program("chipseq-greylist", data) exc...

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def checkout(self, ref, cb=None): """Checkout a bundle from the remote. Returns a file-like object""" if self.is_api: return self._checkout_api(ref, cb=cb) else: return self._checkout_fs(ref, cb=cb)

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def designPrimers(p3_args, input_log=None, output_log=None, err_log=None): ''' Return the raw primer3_core output for the provided primer3 args. Returns an ordered dict of the boulderIO-format primer3 output file ''' sp = subprocess.Popen([pjoin(PRIMER3_HOME, 'primer3_core')], ...

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def follow_path(self, path, weight=None): """Go to several :class:`Place`s in succession, deciding how long to spend in each by consulting the ``weight`` stat of the :class:`Portal` connecting the one :class:`Place` to the next. Return the total number of turns the travel will take. Rai...

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def binarize_percent(netin, level, sign='pos', axis='time'): """ Binarizes a network proprtionally. When axis='time' (only one available at the moment) then the top values for each edge time series are considered. Parameters ---------- netin : array or dict network (graphlet or contact rep...

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def make_clust(net, dist_type='cosine', run_clustering=True, dendro=True, requested_views=['pct_row_sum', 'N_row_sum'], linkage_type='average', sim_mat=False, filter_sim=0.1, calc_cat_pval=False, sim_mat_views=['N_row_sum'], ...

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def dual_obj_grad(alpha, beta, a, b, C, regul): """ Compute objective value and gradients of dual objective. Parameters ---------- alpha: array, shape = len(a) beta: array, shape = len(b) Current iterate of dual potentials. a: array, shape = len(a) b: array, shape = len(b) ...

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def admin_tools_render_dashboard(context, location='index', dashboard=None): """ Template tag that renders the dashboard, it takes two optional arguments: ``location`` The location of the dashboard, it can be 'index' (for the admin index dashboard) or 'app_index' (for the app index dashboar...

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def parse_gene_set(gene_set_fp): """Parses gene set file and returns a (group)-(gene set) dictionary. Attribute: gene_set_fp (str): File path to a gene set file. """ group_gene_set_dict = OrderedDict() with open(gene_set_fp) as inFile: for line in inFile.readlines(): ...

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def prompt_file(prompt, default=None): """Prompt a file name with autocompletion""" def complete(text: str, state): text = text.replace('~', HOME) sugg = (glob.glob(text + '*') + [None])[state] if sugg is None: return sugg = sugg.replace(HOME, '~') sugg = ...

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def replace_certificate_signing_request_status(self, name, body, **kwargs): # noqa: E501 """replace_certificate_signing_request_status # noqa: E501 replace status of the specified CertificateSigningRequest # noqa: E501 This method makes a synchronous HTTP request by default. To make an ...

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def getSimpleFileData(self, fileInfo, data): """Function to initialize the simple data for file info""" result = fileInfo[fileInfo.find(data + "</td>"):] result = result[:result.find("</A></td>")] result = result[result.rfind(">") + 1:] return result

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def shell_exec(command): """Executes the given shell command and returns its output.""" out = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT).communicate()[0] return out.decode('utf-8')

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def timezone(haystack_tz, version=LATEST_VER): """ Retrieve the Haystack timezone """ tz_map = get_tz_map(version=version) try: tz_name = tz_map[haystack_tz] except KeyError: raise ValueError('%s is not a recognised timezone on this host' \ % haystack_tz) retu...

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def parse_args(self, args): """ Parse arguments and return an arguments object >>> from margaritashotgun.cli import Cli >>> cli = CLi() >>> cli.parse_args(sys.argv[1:]) :type args: list :param args: list of arguments """ parser = argp...

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def prepare_check(data): """Prepare check for catalog endpoint Parameters: data (Object or ObjectID): Check ID or check definition Returns: Tuple[str, dict]: where first is ID and second is check definition """ if not data: return None, {} if isinstance(data, str): ...

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def parse_hgnc_genes(lines): """Parse lines with hgnc formated genes This is designed to take a dump with genes from HGNC. This is downloaded from: ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt Args: lines(iterable(str)): An iterable with HGN...

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def check_last_err(func, self, *args, **kwargs): """Check and raise deferred errors before running the function This method checks :python:`_last_err` before running the wrapped function. If present and not None, the exception will be raised with its original traceback. """ if self._last_err ...

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def _send_ffd(self, pid, aplx_data, address): """Send flood-fill data packets.""" block = 0 pos = 0 aplx_size = len(aplx_data) while pos < aplx_size: # Get the next block of data, send and progress the block # counter and the address data = ap...

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def zernike(zernike_indexes,labels,indexes): """Compute the Zernike features for the labels with the label #s in indexes returns the score per labels and an array of one image per zernike feature """ # # "Reverse_indexes" is -1 if a label # is not to be processed. Otherwise # reverse_index[...

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def set_index(data,col_index): """ Sets the index if the index is not present :param data: pandas table :param col_index: column name which will be assigned as a index """ if col_index in data: data=data.reset_index().set_index(col_index) if 'index' in data: del dat...

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def _apply_uncertainty_to_geometry(self, source, value): """ Modify ``source`` geometry with the uncertainty value ``value`` """ if self.uncertainty_type == 'simpleFaultDipRelative': source.modify('adjust_dip', dict(increment=value)) elif self.uncertainty_type == 'sim...

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def get_layers(self, class_: Type[L], became: bool=True) -> List[L]: """ Proxy to stack """ return self.stack.get_layers(class_, became)

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def session(self): """ Returns the current db session """ if not self.__session: self.__session = dal.get_default_session() return self.__session

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def address_to_ip(address): """Convert a hostname to a numerical IP addresses in an address. This should be a no-op if address already contains an actual numerical IP address. Args: address: This can be either a string containing a hostname (or an IP address) and a port or it can b...

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def generate_header_signature(secret, payload, request_type): '''Authorize a client based on encrypting the payload with the client secret, timestamp, and other metadata ''' # Use the payload to generate a digest push|collection|name|tag|user timestamp = generate_timestamp() credential = ...

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def split_Text( text, file_name, verbose = True ): ''' Tokenizes the *text* (from *file_name*) into sentences, and if the number of sentences exceeds *max_sentences*, splits the text into smaller texts. Returns a list containing the original text (if no splitting was required), or a list c...

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def file_upload(context, id, name, path, jobstate_id, test_id, mime): """file_upload(context, id, path) Upload a file in a job >>> dcictl job-upload-file [OPTIONS] :param string id: ID of the job to attach file to [required] :param string name: Name of the file [required] :param string path: ...

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def parseExtensionArgs(self, args, is_openid1, strict=False): """Parse the provider authentication policy arguments into the internal state of this object @param args: unqualified provider authentication policy arguments @param strict: Whether to raise an exception when bad...

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def validate(self, instance, value): """Determine if array is valid based on shape and dtype""" if not isinstance(value, (tuple, list, np.ndarray)): self.error(instance, value) if self.coerce: value = self.wrapper(value) valid_class = ( self.wrapper if...

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def merge_bams(self, input_bams, merged_bam, in_sorted="TRUE", tmp_dir=None): """ Combine multiple files into one. The tmp_dir parameter is important because on poorly configured systems, the default can sometimes fill up. :param Iterable[str] input_bams: Paths to files to comb...

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def hardware_info(self, mask=0xFFFFFFFF): """Returns a list of 32 integer values corresponding to the bitfields specifying the power consumption of the target. The values returned by this function only have significance if the J-Link is powering the target. The words, indexed, ...

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def _as_medium(exchanges, tolerance=1e-6, exports=False): """Convert a solution to medium. Arguments --------- exchanges : list of cobra.reaction The exchange reactions to consider. tolerance : positive double The absolute tolerance for fluxes. Fluxes with an absolute value ...

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def _polytree_node_to_shapely(node): """ Recurses down a Clipper PolyTree, extracting the results as Shapely objects. Returns a tuple of (list of polygons, list of children) """ polygons = [] children = [] for ch in node.Childs: p, c = _polytree_node_to_shapely(ch) poly...

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def deploy_templates(): """ Deploy any templates from your shortest TEMPLATE_DIRS setting """ deployed = None if not hasattr(env, 'project_template_dir'): #the normal pattern would mean the shortest path is the main one. #its probably the last listed length = 1000 ...

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def ping( self, destination, source=c.PING_SOURCE, ttl=c.PING_TTL, timeout=c.PING_TIMEOUT, size=c.PING_SIZE, count=c.PING_COUNT, vrf=c.PING_VRF, ): """ Execute ping on the device and returns a dictionary with the result. Output ...

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def fetch(context, data): """Do an HTTP GET on the ``url`` specified in the inbound data.""" url = data.get('url') attempt = data.pop('retry_attempt', 1) try: result = context.http.get(url, lazy=True) rules = context.get('rules', {'match_all': {}}) if not Rule.get_rule(rules).app...

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def batch_length(batch): '''Determine the number of samples in a batch. Parameters ---------- batch : dict A batch dictionary. Each value must implement `len`. All values must have the same `len`. Returns ------- n : int >= 0 or None The number of samples in this b...

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def _run_prospector(filename, stamp_file_name, disabled_linters, show_lint_files): """Run prospector.""" linter_tools = [ "pep257", "pep8", "pyflakes" ] if can_run_pylint(): linter_tools.append("pylint") # ...

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def save(self, collection): """ Save an asset collection to the service. """ assert isinstance(collection, predix.data.asset.AssetCollection), "Expected AssetCollection" collection.validate() self.put_collection(collection.uri, collection.__dict__)

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def get_rec_features(self, features=None): """ Returns a df of features for recalled items """ if features is None: features = self.dist_funcs.keys() elif not isinstance(features, list): features = [features] return self.rec.applymap(lambda x: {k:v...

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def is_zhuyin_compatible(s): """Checks if *s* is consists of Zhuyin-compatible characters. This does not check if *s* contains valid Zhuyin syllables; for that see :func:`is_zhuyin`. Besides Zhuyin characters and tone marks, spaces are also accepted. This function checks that all characters in *s*...

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def write(self, oprot): ''' Write this object to the given output protocol and return self. :type oprot: thryft.protocol._output_protocol._OutputProtocol :rtype: pastpy.gen.database.impl.online.online_database_object_detail_image.OnlineDatabaseObjectDetailImage ''' opro...

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def generic_in(self, **kwargs): '''Bypass buggy GenericReferenceField querying issue''' query = {} for key, value in kwargs.items(): if not value: continue # Optimize query for when there is only one value if isinstance(value, (list, tuple)) an...

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def expires_at(self): """ A :py:obj:`~datetime.datetime` of when this signature expires, if a signature expiration date is specified. Otherwise, ``None`` """ if 'SignatureExpirationTime' in self._signature.subpackets: expd = next(iter(self._signature.subpackets['Signa...

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def main(): """ This example demonstrates how to generate pretty equations from the analytic expressions found in ``chempy.kinetics.integrated``. """ t, kf, t0, major, minor, prod, beta = sympy.symbols( 't k_f t0 Y Z X beta', negative=False) for f in funcs: args = [t, kf, prod, m...

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def makeService(opt): """Make a service :params opt: dictionary-like object with 'freq', 'config' and 'messages' :returns: twisted.application.internet.TimerService that at opt['freq'] checks for stale processes in opt['config'], and sends restart messages through opt['messages'...

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def _get_host_libc_from_host_compiler(self): """Locate the host's libc-dev installation using a specified host compiler's search dirs.""" compiler_exe = self.get_options().host_compiler # Implicitly, we are passing in the environment of the executing pants process to # `get_compiler_library_dirs()`. ...

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def _add_person_to_group(person, group): """ Call datastores after adding a person to a group. """ from karaage.datastores import add_accounts_to_group from karaage.datastores import add_accounts_to_project from karaage.datastores import add_accounts_to_institute a_list = person.account_set add...

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def doc_type(self, *doc_type, **kwargs): """ Set the type to search through. You can supply a single value or multiple. Values can be strings or subclasses of ``Document``. You can also pass in any keyword arguments, mapping a doc_type to a callback that should be used instead o...

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def parse_instancepath(parser, event, node): #pylint: disable=unused-argument """Parse the CIM/XML INSTANCEPATH element and return an instancname <!ELEMENT INSTANCEPATH (NAMESPACEPATH, INSTANCENAME)> """ (next_event, next_node) = six.next(parser) if not _is_start(next_event, next_no...

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def getByteStatistic(self, wanInterfaceId=1, timeout=1): """Execute GetTotalBytesSent&GetTotalBytesReceived actions to get WAN statistics. :param int wanInterfaceId: the id of the WAN device :param float timeout: the timeout to wait for the action to be executed :return: a tuple of two ...

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def f_df_nc(self,x): ''' Wrapper of the derivative of *f*: takes an input x with size of the not fixed dimensions expands it and evaluates the gradient of the entire function. ''' x = np.atleast_2d(x) xx = self.context_manager._expand_vector(x) f_nocontext_xx , df...

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def confirms(self, txid): """Returns number of confirms or None if unpublished.""" txid = deserialize.txid(txid) return self.service.confirms(txid)

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def wait_for_tasks(self, tasks): """Given the service instance si and tasks, it returns after all the tasks are complete """ property_collector = self.service_instance.RetrieveContent().propertyCollector task_list = [str(task) for task in tasks] # Create filter obj_...

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def triads(reference_labels, estimated_labels): """Compare chords along triad (root & quality to #5) relationships. Examples -------- >>> (ref_intervals, ... ref_labels) = mir_eval.io.load_labeled_intervals('ref.lab') >>> (est_intervals, ... est_labels) = mir_eval.io.load_labeled_interval...

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def astra_algorithm(direction, ndim, vol_id, sino_id, proj_id, impl): """Create an ASTRA algorithm object to run the projector. Parameters ---------- direction : {'forward', 'backward'} For ``'forward'``, apply the forward projection, for ``'backward'`` the backprojection. ndim : {2...

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def ser_iuwt_recomposition(in1, scale_adjust, smoothed_array): """ This function calls the a trous algorithm code to recompose the input into a single array. This is the implementation of the isotropic undecimated wavelet transform recomposition for a single CPU core. INPUTS: in1 (no de...

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def get_devices(filename, bundled): """Get a Devices object from a file. :param filename: full path of the file to parse or name of the resource. :param is_resource: boolean indicating if it is a resource. :rtype: Devices """ loader = Loader(filename, bundled) data = loader.data devi...

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def dragEnterEvent( self, event ): """ Processes the drag drop event using the filter set by the \ setDragDropFilter :param event | <QDragEvent> """ filt = self.dragDropFilter() if ( not filt ): super(XCalendarWidget, self).dragE...

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def common_mean_watson(Data1, Data2, NumSims=5000, print_result=True, plot='no', save=False, save_folder='.', fmt='svg'): """ Conduct a Watson V test for a common mean on two directional data sets. This function calculates Watson's V statistic from input files through Monte Carlo simulation in order to...

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def bitmap_pattern_to_list(self, bmp_pat): """ takes a list of bitmap points (drawn via Life screen) and converts to a list of full coordinates """ res = [] x = 1 y = 1 lines = bmp_pat.split('\n') for line in lines: y += 1 ...

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def subj_has_perm(self, subj_str, perm_str): """Returns: bool: ``True`` if ``subj_str`` has perm equal to or higher than ``perm_str``. """ self._assert_valid_permission(perm_str) return perm_str in self.get_effective_perm_list(subj_str)

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def connected_emulators(self, host=enums.JLinkHost.USB): """Returns a list of all the connected emulators. Args: self (JLink): the ``JLink`` instance host (int): host type to search (default: ``JLinkHost.USB``) Returns: List of ``JLinkConnectInfo`` specifying the ...

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def most_frequent_terms(self, depth): """ Get the X most frequent terms in the text, and then probe down to get any other terms that have the same count as the last term. Args: depth (int): The number of terms. Returns: set: The set of frequent terms. ...

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