kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def _deserialize_property_value(self, to_deserialize: PrimitiveJsonType, deserializer_cls: Type) -> Any: """ Deserializes the given value using the given deserializer. :param to_deserialize: the value to deserialize :param deserializer_cls: the type of deserializer to use :return...	[ "def", "_deserialize_property_value", "(", "self", ",", "to_deserialize", ":", "PrimitiveJsonType", ",", "deserializer_cls", ":", "Type", ")", "->", "Any", ":", "deserializer", "=", "self", ".", "_create_deserializer_of_type_with_cache", "(", "deserializer_cls", ")", ...	52.5	19.5
def write_ctl(name, imap, guidetree, nloci, infer_sptree, infer_delimit, delimit_alg, seed, burnin, nsample, sampfreq, thetaprior, tauprior, traits_df, nu0, kappa0, cleandata, useseqdata, usetraitdata, wdir, finetune, verbose): """ write outfile...	[ "def", "write_ctl", "(", "name", ",", "imap", ",", "guidetree", ",", "nloci", ",", "infer_sptree", ",", "infer_delimit", ",", "delimit_alg", ",", "seed", ",", "burnin", ",", "nsample", ",", "sampfreq", ",", "thetaprior", ",", "tauprior", ",", "traits_df", ...	38.513889	20.152778
def open_relative(self, url, args, kwargs): """Like :func:`open`, but ``url`` can be relative to the currently visited page. """ return self.open(self.absolute_url(url), args, **kwargs)	[ "def", "open_relative", "(", "self", ",", "url", ",", "", "args", ",", "", "", "kwargs", ")", ":", "return", "self", ".", "open", "(", "self", ".", "absolute_url", "(", "url", ")", ",", "", "args", ",", "", "", "kwargs", ")" ]	43.4	10
def checkAndCreate(self, key, payload): """ Function checkAndCreate Check if an object exists and create it if not @param key: The targeted object @param payload: The targeted object description @return RETURN: The id of the object """ if key not in self: ...	[ "def", "checkAndCreate", "(", "self", ",", "key", ",", "payload", ")", ":", "if", "key", "not", "in", "self", ":", "self", "[", "key", "]", "=", "payload", "return", "self", "[", "key", "]", "[", "'id'", "]" ]	33.181818	9.727273
def _map_arg_names(source, mapping): """Map one set of keys to another.""" return {cartopy_name: source[cf_name] for cartopy_name, cf_name in mapping if cf_name in source}	[ "def", "_map_arg_names", "(", "source", ",", "mapping", ")", ":", "return", "{", "cartopy_name", ":", "source", "[", "cf_name", "]", "for", "cartopy_name", ",", "cf_name", "in", "mapping", "if", "cf_name", "in", "source", "}" ]	50	12.25
def per_month(start: datetime, end: datetime, n: int=1): """ Iterates over time range in one month steps. Clamps to number of days in given month. :param start: Start of time range (inclusive) :param end: End of time range (exclusive) :param n: Number of months to step. Default is 1. :retu...	[ "def", "per_month", "(", "start", ":", "datetime", ",", "end", ":", "datetime", ",", "n", ":", "int", "=", "1", ")", ":", "curr", "=", "start", ".", "replace", "(", "day", "=", "1", ",", "hour", "=", "0", ",", "minute", "=", "0", ",", "second",...	36.125	16.625
def get_content_type(self, msg, content_type="HTML"): """ Given an Email.Message object, gets the content-type payload as specified by @content_type. This is the actual body of the email. @Params msg - Email.Message object to get message content for content_type -...	[ "def", "get_content_type", "(", "self", ",", "msg", ",", "content_type", "=", "\"HTML\"", ")", ":", "if", "\"HTML\"", "in", "content_type", ".", "upper", "(", ")", ":", "content_type", "=", "self", ".", "HTML", "elif", "\"PLAIN\"", "in", "content_type", "....	38.842105	15.789474
def is_cupy_array(arr): """Check whether an array is a cupy array""" if cupy is None: return False elif isinstance(arr, cupy.ndarray): return True else: return False	[ "def", "is_cupy_array", "(", "arr", ")", ":", "if", "cupy", "is", "None", ":", "return", "False", "elif", "isinstance", "(", "arr", ",", "cupy", ".", "ndarray", ")", ":", "return", "True", "else", ":", "return", "False" ]	24.75	16.25
def gp_background(): """ plot background methods and S/B vs energy """ inDir, outDir = getWorkDirs() data, REBIN = OrderedDict(), None titles = [ 'SE_{+-}', 'SE@^{corr}_{/Symbol \\261\\261}', 'ME@^{N}_{+-}' ] Apm = OrderedDict([ ('19', 0.026668), ('27', 0.026554), ('39', 0.026816), ('62', 0....	[ "def", "gp_background", "(", ")", ":", "inDir", ",", "outDir", "=", "getWorkDirs", "(", ")", "data", ",", "REBIN", "=", "OrderedDict", "(", ")", ",", "None", "titles", "=", "[", "'SE_{+-}'", ",", "'SE@^{corr}_{/Symbol \\\\261\\\\261}'", ",", "'ME@^{N}_{+-}'", ...	45.5625	19.010417
def interpolate(x, scale=None, output_size=None, mode='linear', align_corners=None): ''' Resize an ND array with interpolation. Scaling factors for spatial dimensions are determined by either ``scale`` or ``output_size``. ``nd = len(scale)`` or ``nd = len(output_size)`` determines the number of ...	[ "def", "interpolate", "(", "x", ",", "scale", "=", "None", ",", "output_size", "=", "None", ",", "mode", "=", "'linear'", ",", "align_corners", "=", "None", ")", ":", "from", ".", "function_bases", "import", "interpolate", "as", "interpolate_base", "import",...	37.816901	23.56338
def save_grid_data(self): """ Save grid data in the data object """ if not self.grid.changes: print('-I- No changes to save') return if self.grid_type == 'age': age_data_type = self.er_magic.age_type self.er_magic.write_ages = True...	[ "def", "save_grid_data", "(", "self", ")", ":", "if", "not", "self", ".", "grid", ".", "changes", ":", "print", "(", "'-I- No changes to save'", ")", "return", "if", "self", ".", "grid_type", "==", "'age'", ":", "age_data_type", "=", "self", ".", "er_magic...	53.171171	28.522523
def list_virtual_machine_scale_set_vm_network_interfaces(scale_set, vm_index, resource_group, **kwargs): ''' .. versionadded:: 2019.2.0 ...	[ "def", "list_virtual_machine_scale_set_vm_network_interfaces", "(", "scale_set", ",", "vm_index", ",", "resource_group", ",", "", "", "kwargs", ")", ":", "result", "=", "{", "}", "netconn", "=", "__utils__", "[", "'azurearm.get_client'", "]", "(", "'network'", "...	33.853659	28.487805
def _submit_metrics(self, metrics, metric_name_and_type_by_property): """ Resolve metric names and types and submit it. """ for metric in metrics: if ( metric.name not in metric_name_and_type_by_property and metric.name.lower() not in metric_na...	[ "def", "_submit_metrics", "(", "self", ",", "metrics", ",", "metric_name_and_type_by_property", ")", ":", "for", "metric", "in", "metrics", ":", "if", "(", "metric", ".", "name", "not", "in", "metric_name_and_type_by_property", "and", "metric", ".", "name", ".",...	44.653846	27.269231
def predict_features(self, df_features, df_target, idx=0, **kwargs): """For one variable, predict its neighbouring nodes. Args: df_features (pandas.DataFrame): df_target (pandas.Series): idx (int): (optional) for printing purposes kwargs (dict): additiona...	[ "def", "predict_features", "(", "self", ",", "df_features", ",", "df_target", ",", "idx", "=", "0", ",", "", "", "kwargs", ")", ":", "X", "=", "df_features", ".", "values", "y", "=", "df_target", ".", "values", "[", ":", ",", "0", "]", "rr", "=",...	31.833333	17.777778
def validate_spec(cls, spec, backends=None): """ Given a specification, validated it against the options tree for the specified backends by raising OptionError for invalid options. If backends is None, validates against all the currently loaded backend. Only useful when ...	[ "def", "validate_spec", "(", "cls", ",", "spec", ",", "backends", "=", "None", ")", ":", "loaded_backends", "=", "Store", ".", "loaded_backends", "(", ")", "if", "backends", "is", "None", "else", "backends", "error_info", "=", "{", "}", "backend_errors", "...	47.833333	21.722222
def explode(): ''' This method assumes that :func:`~exhale.configs.apply_sphinx_configurations` has already been applied. It performs minimal sanity checking, and then performs in order 1. Creates a :class:`~exhale.graph.ExhaleRoot` object. 2. Executes :func:`~exhale.graph.ExhaleRoot.parse...	[ "def", "explode", "(", ")", ":", "# Quick sanity check to make sure the bare minimum have been set in the configs", "err_msg", "=", "\"`configs.{config}` was `None`. Do not call `deploy.explode` directly.\"", "if", "configs", ".", "containmentFolder", "is", "None", ":", "raise", "...	39.15493	26.760563
def _report_container_state_metrics(self, pod_list, instance_tags): """Reports container state & reasons by looking at container statuses""" if pod_list.get('expired_count'): self.gauge(self.NAMESPACE + '.pods.expired', pod_list.get('expired_count'), tags=instance_tags) for pod in p...	[ "def", "_report_container_state_metrics", "(", "self", ",", "pod_list", ",", "instance_tags", ")", ":", "if", "pod_list", ".", "get", "(", "'expired_count'", ")", ":", "self", ".", "gauge", "(", "self", ".", "NAMESPACE", "+", "'.pods.expired'", ",", "pod_list"...	47.28125	28.71875
def get_object_header(self, ref): """ Use this method to quickly examine the type and size of the object behind the given ref. :note: The method will only suffer from the costs of command invocation once and reuses the command in subsequent calls. :return: (hexsha, type_string, size_as_int)""" cm...	[ "def", "get_object_header", "(", "self", ",", "ref", ")", ":", "cmd", "=", "self", ".", "__get_persistent_cmd", "(", "\"cat_file_header\"", ",", "\"cat_file\"", ",", "batch_check", "=", "True", ")", "return", "self", ".", "__get_object_header", "(", "cmd", ","...	43.3	19.7
def crypto_sign_ed25519ph_final_verify(edph, signature, pk): """ Verify a prehashed signature using the public key pk :param edph: the ed25519ph state for the data being verified :type edph: crypto_sign_ed255...	[ "def", "crypto_sign_ed25519ph_final_verify", "(", "edph", ",", "signature", ",", "pk", ")", ":", "ensure", "(", "isinstance", "(", "edph", ",", "crypto_sign_ed25519ph_state", ")", ",", "'edph parameter must be a ed25519ph_state object'", ",", "raising", "=", "exc", "....	39.658537	13.170732
def parse_itms_services(url_data): """Get "url" CGI parameter value as child URL.""" query = url_data.urlparts[3] for k, v, sep in urlutil.parse_qsl(query, keep_blank_values=True): if k == "url": url_data.add_url(v) break	[ "def", "parse_itms_services", "(", "url_data", ")", ":", "query", "=", "url_data", ".", "urlparts", "[", "3", "]", "for", "k", ",", "v", ",", "sep", "in", "urlutil", ".", "parse_qsl", "(", "query", ",", "keep_blank_values", "=", "True", ")", ":", "if",...	37	13.428571
def cross(vec1, vec2): """Returns the cross product of two Vectors""" if isinstance(vec1, Vector3) and isinstance(vec2, Vector3): vec3 = Vector3() vec3.x = (vec1.y * vec2.z) - (vec1.z * vec2.y) vec3.y = (vec1.z * vec2.x) - (vec1.x * vec2.z) vec3.z = (vec1....	[ "def", "cross", "(", "vec1", ",", "vec2", ")", ":", "if", "isinstance", "(", "vec1", ",", "Vector3", ")", "and", "isinstance", "(", "vec2", ",", "Vector3", ")", ":", "vec3", "=", "Vector3", "(", ")", "vec3", ".", "x", "=", "(", "vec1", ".", "y", ...	44.3	17.7
def set_count_auto(self, count=None): """Sets workers count. By default sets it to detected number of available cores :param int count: """ count = count or self._section.vars.CPU_CORES self._set('workers', count) return self._section	[ "def", "set_count_auto", "(", "self", ",", "count", "=", "None", ")", ":", "count", "=", "count", "or", "self", ".", "_section", ".", "vars", ".", "CPU_CORES", "self", ".", "_set", "(", "'workers'", ",", "count", ")", "return", "self", ".", "_section" ...	23.583333	19.333333
def inline(self) -> str: """ Return an inline string of the Identity :return: """ return "{pubkey}:{signature}:{timestamp}:{uid}".format( pubkey=self.pubkey, signature=self.signatures[0], timestamp=self.timestamp, uid=self.uid)	[ "def", "inline", "(", "self", ")", "->", "str", ":", "return", "\"{pubkey}:{signature}:{timestamp}:{uid}\"", ".", "format", "(", "pubkey", "=", "self", ".", "pubkey", ",", "signature", "=", "self", ".", "signatures", "[", "0", "]", ",", "timestamp", "=", "...	30.6	9.8
def get_field_info(self, field): """ This method is basically a mirror from rest_framework==3.3.3 We are currently pinned to rest_framework==3.1.1. If we upgrade, this can be refactored and simplified to rely more heavily on rest_framework's built in logic. """ ...	[ "def", "get_field_info", "(", "self", ",", "field", ")", ":", "field_info", "=", "self", ".", "get_attributes", "(", "field", ")", "field_info", "[", "\"required\"", "]", "=", "getattr", "(", "field", ",", "\"required\"", ",", "False", ")", "field_info", "...	38.931034	21.551724
def separation_in_list(separation_indices, separation_indices_list): """ Checks if the separation indices of a plane are already in the list :param separation_indices: list of separation indices (three arrays of integers) :param separation_indices_list: list of the list of separation indices to be compa...	[ "def", "separation_in_list", "(", "separation_indices", ",", "separation_indices_list", ")", ":", "sorted_separation", "=", "sort_separation", "(", "separation_indices", ")", "for", "sep", "in", "separation_indices_list", ":", "if", "len", "(", "sep", "[", "1", "]",...	54	26.5
def tvdb_login(api_key): """ Logs into TVDb using the provided api key Note: You can register for a free TVDb key at thetvdb.com/?tab=apiregister Online docs: api.thetvdb.com/swagger#!/Authentication/post_login= """ url = "https://api.thetvdb.com/login" body = {"apikey": api_key} status, co...	[ "def", "tvdb_login", "(", "api_key", ")", ":", "url", "=", "\"https://api.thetvdb.com/login\"", "body", "=", "{", "\"apikey\"", ":", "api_key", "}", "status", ",", "content", "=", "_request_json", "(", "url", ",", "body", "=", "body", ",", "cache", "=", "F...	41.285714	17
def add(self, item, group_by=None): """General purpose class to group items by certain criteria.""" key = None if not group_by: group_by = self.group_by if group_by: # if group_by is a function, use it with item as argument if hasattr(group_by, '__ca...	[ "def", "add", "(", "self", ",", "item", ",", "group_by", "=", "None", ")", ":", "key", "=", "None", "if", "not", "group_by", ":", "group_by", "=", "self", ".", "group_by", "if", "group_by", ":", "# if group_by is a function, use it with item as argument", "if"...	36.357143	18.821429
def gc_content_plot (self): """ Create the HTML for the FastQC GC content plot """ data = dict() data_norm = dict() for s_name in self.fastqc_data: try: data[s_name] = {d['gc_content']: d['count'] for d in self.fastqc_data[s_name]['per_sequence_gc_content']} ...	[ "def", "gc_content_plot", "(", "self", ")", ":", "data", "=", "dict", "(", ")", "data_norm", "=", "dict", "(", ")", "for", "s_name", "in", "self", ".", "fastqc_data", ":", "try", ":", "data", "[", "s_name", "]", "=", "{", "d", "[", "'gc_content'", ...	48.298246	24.245614
async def getArtifact(self, args, kwargs): """ Get Artifact from Run Get artifact by `<name>` from a specific run. Public Artifacts*, in-order to get an artifact you need the scope `queue:get-artifact:<name>`, where `<name>` is the name of the artifact. But if the...	[ "async", "def", "getArtifact", "(", "self", ",", "", "args", ",", "", "", "kwargs", ")", ":", "return", "await", "self", ".", "_makeApiCall", "(", "self", ".", "funcinfo", "[", "\"getArtifact\"", "]", ",", "", "args", ",", "", "", "kwargs", ")"...	58.321839	34.896552
def _list_resource_descriptors(args, _): """Lists the resource descriptors in the project.""" project_id = args['project'] pattern = args['type'] or '*' descriptors = gcm.ResourceDescriptors(project_id=project_id) dataframe = descriptors.as_dataframe(pattern=pattern) return _render_dataframe(dataframe)	[ "def", "_list_resource_descriptors", "(", "args", ",", "_", ")", ":", "project_id", "=", "args", "[", "'project'", "]", "pattern", "=", "args", "[", "'type'", "]", "or", "'*'", "descriptors", "=", "gcm", ".", "ResourceDescriptors", "(", "project_id", "=", ...	44.142857	8.428571
def _reindex_multi(self, axes, copy, fill_value): """ We are guaranteed non-Nones in the axes. """ new_index, row_indexer = self.index.reindex(axes['index']) new_columns, col_indexer = self.columns.reindex(axes['columns']) if row_indexer is not None and col_indexer is n...	[ "def", "_reindex_multi", "(", "self", ",", "axes", ",", "copy", ",", "fill_value", ")", ":", "new_index", ",", "row_indexer", "=", "self", ".", "index", ".", "reindex", "(", "axes", "[", "'index'", "]", ")", "new_columns", ",", "col_indexer", "=", "self"...	48.684211	23
def cmd_kill(opts): """Kill some or all containers """ kill_signal = opts.signal if hasattr(opts, 'signal') else "SIGKILL" __with_containers(opts, Blockade.kill, signal=kill_signal)	[ "def", "cmd_kill", "(", "opts", ")", ":", "kill_signal", "=", "opts", ".", "signal", "if", "hasattr", "(", "opts", ",", "'signal'", ")", "else", "\"SIGKILL\"", "__with_containers", "(", "opts", ",", "Blockade", ".", "kill", ",", "signal", "=", "kill_signal...	38.6	14.8
def install(self): # pragma: no cover """Install/download ssh keys from LDAP for consumption by SSH.""" keys = self.get_keys_from_ldap() for user, ssh_keys in keys.items(): user_dir = API.__authorized_keys_path(user) if not os.path.isdir(user_dir): os.mak...	[ "def", "install", "(", "self", ")", ":", "# pragma: no cover", "keys", "=", "self", ".", "get_keys_from_ldap", "(", ")", "for", "user", ",", "ssh_keys", "in", "keys", ".", "items", "(", ")", ":", "user_dir", "=", "API", ".", "__authorized_keys_path", "(", ...	53.7	11.4
def srcmdl_xml(self, kwargs): """ return the file name for source model xml files """ kwargs_copy = self.base_dict.copy() kwargs_copy.update(kwargs) localpath = NameFactory.srcmdl_xml_format.format(**kwargs_copy) if kwargs.get('fullpath', False): return se...	[ "def", "srcmdl_xml", "(", "self", ",", "", "", "kwargs", ")", ":", "kwargs_copy", "=", "self", ".", "base_dict", ".", "copy", "(", ")", "kwargs_copy", ".", "update", "(", "", "", "kwargs", ")", "localpath", "=", "NameFactory", ".", "srcmdl_xml_format...	41	8.555556
def list_lbaas_members(self, lbaas_pool, retrieve_all=True, _params): """Fetches a list of all lbaas_members for a project.""" return self.list('members', self.lbaas_members_path % lbaas_pool, retrieve_all, _params)	[ "def", "list_lbaas_members", "(", "self", ",", "lbaas_pool", ",", "retrieve_all", "=", "True", ",", "", "", "_params", ")", ":", "return", "self", ".", "list", "(", "'members'", ",", "self", ".", "lbaas_members_path", "%", "lbaas_pool", ",", "retrieve_all"...	64.25	18.25
def _move_stream_token(coordinator, token): """Move to the Stream position described by the token. The following rules are applied when interpolation is required: - If a shard does not exist (past the trim_horizon) it is ignored. If that shard had children, its children are also checked against the ...	[ "def", "_move_stream_token", "(", "coordinator", ",", "token", ")", ":", "stream_arn", "=", "coordinator", ".", "stream_arn", "=", "token", "[", "\"stream_arn\"", "]", "# 0) Everything will be rebuilt from the DescribeStream masked by the token.", "coordinator", ".", "roots...	55.618182	28.872727
def dt_dt(sdat, tstart=None, tend=None): """Derivative of temperature. Compute dT/dt as a function of time using an explicit Euler scheme. Args: sdat (:class:`~stagpy.stagyydata.StagyyData`): a StagyyData instance. tstart (float): time at which the computation should start. Use the ...	[ "def", "dt_dt", "(", "sdat", ",", "tstart", "=", "None", ",", "tend", "=", "None", ")", ":", "tseries", "=", "sdat", ".", "tseries_between", "(", "tstart", ",", "tend", ")", "time", "=", "tseries", "[", "'t'", "]", ".", "values", "temp", "=", "tser...	39.75	21.15
def vertex_to_face_color(vertex_colors, faces): """ Convert a list of vertex colors to face colors. Parameters ---------- vertex_colors: (n,(3,4)), colors faces: (m,3) int, face indexes Returns ----------- face_colors: (m,4) colors """ vertex_colors = to_rgba(verte...	[ "def", "vertex_to_face_color", "(", "vertex_colors", ",", "faces", ")", ":", "vertex_colors", "=", "to_rgba", "(", "vertex_colors", ")", "face_colors", "=", "vertex_colors", "[", "faces", "]", ".", "mean", "(", "axis", "=", "1", ")", "return", "face_colors", ...	25.375	14.625
def _create_dict_with_nested_keys_and_val(cls, keys, value): """Recursively constructs a nested dictionary with the keys pointing to the value. For example: Given the list of keys ['a', 'b', 'c', 'd'] and a primitive value 'hello world', the method will produce the nested dictionary {'a': {'b': {'c...	[ "def", "_create_dict_with_nested_keys_and_val", "(", "cls", ",", "keys", ",", "value", ")", ":", "if", "len", "(", "keys", ")", ">", "1", ":", "new_keys", "=", "keys", "[", ":", "-", "1", "]", "new_val", "=", "{", "keys", "[", "-", "1", "]", ":", ...	43.782609	24.26087
def gif(self, gif_id, strict=False): """ Retrieves a specifc gif from giphy based on unique id :param gif_id: Unique giphy gif ID :type gif_id: string :param strict: Whether an exception should be raised when no results :type strict: boolean """ resp = se...	[ "def", "gif", "(", "self", ",", "gif_id", ",", "strict", "=", "False", ")", ":", "resp", "=", "self", ".", "_fetch", "(", "gif_id", ")", "if", "resp", "[", "'data'", "]", ":", "return", "GiphyImage", "(", "resp", "[", "'data'", "]", ")", "elif", ...	33.0625	13.9375
async def get_files_to_delete(self) -> List[str]: """ Determine the files to delete when rolling over. """ dir_name, base_name = os.path.split(self.absolute_file_path) file_names = await self.loop.run_in_executor( None, lambda: os.listdir(dir_name) ) r...	[ "async", "def", "get_files_to_delete", "(", "self", ")", "->", "List", "[", "str", "]", ":", "dir_name", ",", "base_name", "=", "os", ".", "path", ".", "split", "(", "self", ".", "absolute_file_path", ")", "file_names", "=", "await", "self", ".", "loop",...	37.6	12.9
def is_read_only(cls, db: DATABASE_SUPPORTER_FWD_REF, logger: logging.Logger = None) -> bool: """Do we have read-only access?""" def convert_enums(row_): # All these columns are of type enum('N', 'Y'); # https://dev.mysql.com/doc/refman/...	[ "def", "is_read_only", "(", "cls", ",", "db", ":", "DATABASE_SUPPORTER_FWD_REF", ",", "logger", ":", "logging", ".", "Logger", "=", "None", ")", "->", "bool", ":", "def", "convert_enums", "(", "row_", ")", ":", "# All these columns are of type enum('N', 'Y');", ...	41.060241	15.084337
def read_text(self, file_handle): """Parse the TEXT segment of the FCS file. The TEXT segment contains meta data associated with the FCS file. Converting all meta keywords to lower case. """ header = self.annotation['__header__'] # For convenience ##### # Read ...	[ "def", "read_text", "(", "self", ",", "file_handle", ")", ":", "header", "=", "self", ".", "annotation", "[", "'__header__'", "]", "# For convenience", "#####", "# Read in the TEXT segment of the FCS file", "# There are some differences in how the", "file_handle", ".", "s...	39.529412	24.985294
def getStore(self, name, domain): """Convenience method for the REPL. I got tired of typing this string every time I logged in.""" return IRealm(self.original.store.parent).accountByAddress(name, domain).avatars.open()	[ "def", "getStore", "(", "self", ",", "name", ",", "domain", ")", ":", "return", "IRealm", "(", "self", ".", "original", ".", "store", ".", "parent", ")", ".", "accountByAddress", "(", "name", ",", "domain", ")", ".", "avatars", ".", "open", "(", ")" ...	77.333333	20.666667
def local_targets(self): """Iterator over the targets defined in this build file.""" for node in self.node: if (node.repo, node.path) == (self.target.repo, self.target.path): yield node	[ "def", "local_targets", "(", "self", ")", ":", "for", "node", "in", "self", ".", "node", ":", "if", "(", "node", ".", "repo", ",", "node", ".", "path", ")", "==", "(", "self", ".", "target", ".", "repo", ",", "self", ".", "target", ".", "path", ...	45	15.6
def referenced(word, article=INDEFINITE, gender=MALE, role=SUBJECT): """ Returns a string with the article + the word. """ return "%s %s" % (_article(word, article, gender, role), word)	[ "def", "referenced", "(", "word", ",", "article", "=", "INDEFINITE", ",", "gender", "=", "MALE", ",", "role", "=", "SUBJECT", ")", ":", "return", "\"%s %s\"", "%", "(", "_article", "(", "word", ",", "article", ",", "gender", ",", "role", ")", ",", "w...	48.5	13.5
def extend_from_instances(self, params: Params, instances: Iterable['adi.Instance'] = ()) -> None: """ Extends an already generated vocabulary using a collection of instances. """ min_count = params.pop("min_count", None) ...	[ "def", "extend_from_instances", "(", "self", ",", "params", ":", "Params", ",", "instances", ":", "Iterable", "[", "'adi.Instance'", "]", "=", "(", ")", ")", "->", "None", ":", "min_count", "=", "params", ".", "pop", "(", "\"min_count\"", ",", "None", ")...	56.962963	22.740741
def parse_data(self, sline): """This function builds the addRawResults dictionary using the header values of the labels section as sample Ids. """ if sline[0] == '': return 0 for idx, label in enumerate(self._labels_values[sline[0]]): if label != '': ...	[ "def", "parse_data", "(", "self", ",", "sline", ")", ":", "if", "sline", "[", "0", "]", "==", "''", ":", "return", "0", "for", "idx", ",", "label", "in", "enumerate", "(", "self", ".", "_labels_values", "[", "sline", "[", "0", "]", "]", ")", ":",...	42.1	18.6
def add_schema(self, database, schema): """Add a schema to the set of known schemas (case-insensitive) :param str database: The database name to add. :param str schema: The schema name to add. """ self.schemas.add((_lower(database), _lower(schema)))	[ "def", "add_schema", "(", "self", ",", "database", ",", "schema", ")", ":", "self", ".", "schemas", ".", "add", "(", "(", "_lower", "(", "database", ")", ",", "_lower", "(", "schema", ")", ")", ")" ]	40.571429	12.142857
def get_contact(self, contact_id): """ Get single contact """ url = self.CONTACTS_ID_URL % contact_id connection = Connection(self.token) connection.set_url(self.production, url) return connection.get_request()	[ "def", "get_contact", "(", "self", ",", "contact_id", ")", ":", "url", "=", "self", ".", "CONTACTS_ID_URL", "%", "contact_id", "connection", "=", "Connection", "(", "self", ".", "token", ")", "connection", ".", "set_url", "(", "self", ".", "production", ",...	25.9	11.9
def plot_ARD(kernel, filtering=None, legend=False, canvas=None, **kwargs): """ If an ARD kernel is present, plot a bar representation using matplotlib :param fignum: figure number of the plot :param filtering: list of names, which to use for plotting ARD parameters. Only kernels w...	[ "def", "plot_ARD", "(", "kernel", ",", "filtering", "=", "None", ",", "legend", "=", "False", ",", "canvas", "=", "None", ",", "", "", "kwargs", ")", ":", "Tango", ".", "reset", "(", ")", "ard_params", "=", "np", ".", "atleast_2d", "(", "kernel", ...	35.346939	24.571429
def to_unicode(string): """ Ensure a passed string is unicode """ if isinstance(string, six.binary_type): return string.decode('utf8') if isinstance(string, six.text_type): return string if six.PY2: return unicode(string) return str(string)	[ "def", "to_unicode", "(", "string", ")", ":", "if", "isinstance", "(", "string", ",", "six", ".", "binary_type", ")", ":", "return", "string", ".", "decode", "(", "'utf8'", ")", "if", "isinstance", "(", "string", ",", "six", ".", "text_type", ")", ":",...	25.636364	9.090909
def value_to_string(self, obj): """This descriptor acts as a Field, as far as the serializer is concerned.""" try: return force_unicode(self.__get__(obj)) except TypeError: return str(self.__get__(obj))	[ "def", "value_to_string", "(", "self", ",", "obj", ")", ":", "try", ":", "return", "force_unicode", "(", "self", ".", "__get__", "(", "obj", ")", ")", "except", "TypeError", ":", "return", "str", "(", "self", ".", "__get__", "(", "obj", ")", ")" ]	40.833333	10.666667
def suspend(self): """ Suspends this router. """ status = yield from self.get_status() if status == "running": yield from self._hypervisor.send('vm suspend "{name}"'.format(name=self._name)) self.status = "suspended" log.info('Router "{name}" ...	[ "def", "suspend", "(", "self", ")", ":", "status", "=", "yield", "from", "self", ".", "get_status", "(", ")", "if", "status", "==", "\"running\"", ":", "yield", "from", "self", ".", "_hypervisor", ".", "send", "(", "'vm suspend \"{name}\"'", ".", "format",...	37.5	20.3
def parse_bookmark_json (data): """Parse complete JSON data for Chromium Bookmarks.""" for entry in data["roots"].values(): for url, name in parse_bookmark_node(entry): yield url, name	[ "def", "parse_bookmark_json", "(", "data", ")", ":", "for", "entry", "in", "data", "[", "\"roots\"", "]", ".", "values", "(", ")", ":", "for", "url", ",", "name", "in", "parse_bookmark_node", "(", "entry", ")", ":", "yield", "url", ",", "name" ]	41.6	6.8
def init_config(self, app): """Initialize configuration. :param app: An instance of :class:`~flask.Flask`. """ _vars = ['BASE_TEMPLATE', 'COVER_TEMPLATE', 'SETTINGS_TEMPLATE'] # Sets RequireJS config and SASS binary as well if not already set. for k in dir(config): ...	[ "def", "init_config", "(", "self", ",", "app", ")", ":", "_vars", "=", "[", "'BASE_TEMPLATE'", ",", "'COVER_TEMPLATE'", ",", "'SETTINGS_TEMPLATE'", "]", "# Sets RequireJS config and SASS binary as well if not already set.", "for", "k", "in", "dir", "(", "config", ")",...	38.909091	20.681818
def pivot(self, speed, durationS=-1.0): """ pivot() controls the pivot speed of the RedBot. The values of the pivot function inputs range from -255:255, with -255 indicating a full speed counter-clockwise rotation. 255 indicates a full speed clockwise rotation """ ...	[ "def", "pivot", "(", "self", ",", "speed", ",", "durationS", "=", "-", "1.0", ")", ":", "if", "speed", "<", "0", ":", "self", ".", "left_fwd", "(", "min", "(", "abs", "(", "speed", ")", ",", "255", ")", ")", "self", ".", "right_rev", "(", "min"...	41	15.375
def apply_handler_to_root_log(handler: logging.Handler, remove_existing: bool = False) -> None: """ Applies a handler to all logs, optionally removing existing handlers. Should ONLY be called from the ``if __name__ == 'main'`` script; see https://docs.python.org/3.4/howto/...	[ "def", "apply_handler_to_root_log", "(", "handler", ":", "logging", ".", "Handler", ",", "remove_existing", ":", "bool", "=", "False", ")", "->", "None", ":", "rootlog", "=", "logging", ".", "getLogger", "(", ")", "if", "remove_existing", ":", "rootlog", "."...	36.111111	21.777778
def trace_buffer_capacity(self): """Retrieves the trace buffer's current capacity. Args: self (JLink): the ``JLink`` instance. Returns: The current capacity of the trace buffer. This is not necessarily the maximum possible size the buffer could be configured with...	[ "def", "trace_buffer_capacity", "(", "self", ")", ":", "cmd", "=", "enums", ".", "JLinkTraceCommand", ".", "GET_CONF_CAPACITY", "data", "=", "ctypes", ".", "c_uint32", "(", "0", ")", "res", "=", "self", ".", "_dll", ".", "JLINKARM_TRACE_Control", "(", "cmd",...	37.8125	20.9375
def _conf(cls, opts): """Setup logging via ini-file from logging_conf_file option.""" if not opts.logging_conf_file: return False if not os.path.exists(opts.logging_conf_file): # FileNotFoundError added only in Python 3.3 # https://docs.python.org/3/whatsnew/...	[ "def", "_conf", "(", "cls", ",", "opts", ")", ":", "if", "not", "opts", ".", "logging_conf_file", ":", "return", "False", "if", "not", "os", ".", "path", ".", "exists", "(", "opts", ".", "logging_conf_file", ")", ":", "# FileNotFoundError added only in Pytho...	47.666667	28.083333
def label_context(label_info, multi_line=True, sep=': '): """ Create an unabiguous label string If facetting over a single variable, `label_value` is used, if two or more variables then `label_both` is used. Parameters ---------- label_info : series Series whose values will be retu...	[ "def", "label_context", "(", "label_info", ",", "multi_line", "=", "True", ",", "sep", "=", "': '", ")", ":", "if", "len", "(", "label_info", ")", "==", "1", ":", "return", "label_value", "(", "label_info", ",", "multi_line", ")", "else", ":", "return", ...	28.518519	19.777778
def from_input(cls, input_file=sys.stdin, modify=None, backend=None): """ Creates a Task object, directly from the stdin, by reading one line. If modify=True, two lines are used, first line interpreted as the original state of the Task object, and second line as its new, modified...	[ "def", "from_input", "(", "cls", ",", "input_file", "=", "sys", ".", "stdin", ",", "modify", "=", "None", ",", "backend", "=", "None", ")", ":", "# Detect the hook type if not given directly", "name", "=", "os", ".", "path", ".", "basename", "(", "sys", "....	41.128205	24.25641
def load_dictionary(filename): """Load dictionary from .spydata file""" filename = osp.abspath(filename) old_cwd = getcwd() tmp_folder = tempfile.mkdtemp() os.chdir(tmp_folder) data = None error_message = None try: with tarfile.open(filename, "r") as tar: tar.extracta...	[ "def", "load_dictionary", "(", "filename", ")", ":", "filename", "=", "osp", ".", "abspath", "(", "filename", ")", "old_cwd", "=", "getcwd", "(", ")", "tmp_folder", "=", "tempfile", ".", "mkdtemp", "(", ")", "os", ".", "chdir", "(", "tmp_folder", ")", ...	39.195122	14.95122
def watch(self, filepath, func=None, delay=None, ignore=None): """Add the given filepath for watcher list. Once you have intialized a server, watch file changes before serve the server:: server.watch('static/*.stylus', 'make static') def alert(): print('...	[ "def", "watch", "(", "self", ",", "filepath", ",", "func", "=", "None", ",", "delay", "=", "None", ",", "ignore", "=", "None", ")", ":", "if", "isinstance", "(", "func", ",", "string_types", ")", ":", "cmd", "=", "func", "func", "=", "shell", "(", ...	41.793103	20.413793
def to_dataframe(self, bqstorage_client=None, dtypes=None, progress_bar_type=None): """Create an empty dataframe. Args: bqstorage_client (Any): Ignored. Added for compatibility with RowIterator. dtypes (Any): Ignored. Added for compatibility with ...	[ "def", "to_dataframe", "(", "self", ",", "bqstorage_client", "=", "None", ",", "dtypes", "=", "None", ",", "progress_bar_type", "=", "None", ")", ":", "if", "pandas", "is", "None", ":", "raise", "ValueError", "(", "_NO_PANDAS_ERROR", ")", "return", "pandas",...	35.555556	18.111111
def convert(input_file_name, **kwargs): """Convert CSV file to HTML table""" delimiter = kwargs["delimiter"] or "," quotechar = kwargs["quotechar"] or "\|" if six.PY2: delimiter = delimiter.encode("utf-8") quotechar = quotechar.encode("utf-8") # Read CSV and form a header and rows l...	[ "def", "convert", "(", "input_file_name", ",", "", "", "kwargs", ")", ":", "delimiter", "=", "kwargs", "[", "\"delimiter\"", "]", "or", "\",\"", "quotechar", "=", "kwargs", "[", "\"quotechar\"", "]", "or", "\"\|\"", "if", "six", ".", "PY2", ":", "delimi...	33.30303	15.181818
def process_info(pid=None): '''Returns a dictionary of system information for the process ``pid``. It uses the psutil_ module for the purpose. If psutil_ is not available it returns an empty dictionary. .. _psutil: http://code.google.com/p/psutil/ ''' if psutil is None: # pragma nocover ...	[ "def", "process_info", "(", "pid", "=", "None", ")", ":", "if", "psutil", "is", "None", ":", "# pragma nocover", "return", "{", "}", "pid", "=", "pid", "or", "os", ".", "getpid", "(", ")", "try", ":", "p", "=", "psutil", ".", "Process", "(", "pi...	34.652174	18.913043
def load_from_string(self, content, container, **kwargs): """ Load config from given string 'cnf_content'. :param content: Config content string :param container: callble to make a container object later :param kwargs: optional keyword parameters to be sanitized :: dict ...	[ "def", "load_from_string", "(", "self", ",", "content", ",", "container", ",", "", "", "kwargs", ")", ":", "return", "self", ".", "load_from_stream", "(", "anyconfig", ".", "compat", ".", "StringIO", "(", "content", ")", ",", "container", ",", "", ""...	42	20.166667
def n50(args): """ %prog n50 filename Given a file with a list of numbers denoting contig lengths, calculate N50. Input file can be both FASTA or a list of sizes. """ from jcvi.graphics.histogram import loghistogram p = OptionParser(n50.__doc__) p.add_option("--print0", default=False, ...	[ "def", "n50", "(", "args", ")", ":", "from", "jcvi", ".", "graphics", ".", "histogram", "import", "loghistogram", "p", "=", "OptionParser", "(", "n50", ".", "__doc__", ")", "p", ".", "add_option", "(", "\"--print0\"", ",", "default", "=", "False", ",", ...	27.826923	20.211538
def __remove_trailing_empty_lines(lines): """ Removes leading empty lines from a list of lines. :param list[str] lines: The lines. """ lines.reverse() tmp = DocBlockReflection.__remove_leading_empty_lines(lines) lines.reverse() tmp.reverse() retu...	[ "def", "__remove_trailing_empty_lines", "(", "lines", ")", ":", "lines", ".", "reverse", "(", ")", "tmp", "=", "DocBlockReflection", ".", "__remove_leading_empty_lines", "(", "lines", ")", "lines", ".", "reverse", "(", ")", "tmp", ".", "reverse", "(", ")", "...	26.25	16.916667
def median(data): """Calculate the median of a list.""" data.sort() num_values = len(data) half = num_values // 2 if num_values % 2: return data[half] return 0.5 * (data[half-1] + data[half])	[ "def", "median", "(", "data", ")", ":", "data", ".", "sort", "(", ")", "num_values", "=", "len", "(", "data", ")", "half", "=", "num_values", "//", "2", "if", "num_values", "%", "2", ":", "return", "data", "[", "half", "]", "return", "0.5", "*", ...	27	14.125
def get_content(self, start=None, end=None): """ Retrieve the content of the requested resource which is located at the given absolute path. This method should either return a byte string or an iterator of byte strings. The latter is preferred for large files as it helps...	[ "def", "get_content", "(", "self", ",", "start", "=", "None", ",", "end", "=", "None", ")", ":", "with", "open", "(", "self", ".", "filepath", ",", "\"rb\"", ")", "as", "file", ":", "if", "start", "is", "not", "None", ":", "file", ".", "seek", "(...	39.035714	10.821429
def get_tag_cloud(context, steps=6, min_count=None, template='zinnia/tags/tag_cloud.html'): """ Return a cloud of published tags. """ tags = Tag.objects.usage_for_queryset( Entry.published.all(), counts=True, min_count=min_count) return {'template': template, ...	[ "def", "get_tag_cloud", "(", "context", ",", "steps", "=", "6", ",", "min_count", "=", "None", ",", "template", "=", "'zinnia/tags/tag_cloud.html'", ")", ":", "tags", "=", "Tag", ".", "objects", ".", "usage_for_queryset", "(", "Entry", ".", "published", ".",...	36.363636	6.363636
def get_fee(speed=FEE_SPEED_MEDIUM): """Gets the recommended satoshi per byte fee. :param speed: One of: 'fast', 'medium', 'slow'. :type speed: ``string`` :rtype: ``int`` """ if speed == FEE_SPEED_FAST: return DEFAULT_FEE_FAST elif speed == FEE_SPEED_MEDIUM: return DEFAULT_F...	[ "def", "get_fee", "(", "speed", "=", "FEE_SPEED_MEDIUM", ")", ":", "if", "speed", "==", "FEE_SPEED_FAST", ":", "return", "DEFAULT_FEE_FAST", "elif", "speed", "==", "FEE_SPEED_MEDIUM", ":", "return", "DEFAULT_FEE_MEDIUM", "elif", "speed", "==", "FEE_SPEED_SLOW", ":...	29.533333	11.8
def hypo_list(nodes): """ :param nodes: a hypoList node with N hypocenter nodes :returns: a numpy array of shape (N, 3) with strike, dip and weight """ check_weights(nodes) data = [] for node in nodes: data.append([node['alongStrike'], node['downDip'], node['weight']]) return num...	[ "def", "hypo_list", "(", "nodes", ")", ":", "check_weights", "(", "nodes", ")", "data", "=", "[", "]", "for", "node", "in", "nodes", ":", "data", ".", "append", "(", "[", "node", "[", "'alongStrike'", "]", ",", "node", "[", "'downDip'", "]", ",", "...	33.2	16.8
def is_standard(action): """ actions which are general "store" instructions. e.g. anything which has an argument style like: $ script.py -f myfilename.txt """ boolean_actions = ( _StoreConstAction, _StoreFalseAction, _StoreTrueAction ) return (not action.choices ...	[ "def", "is_standard", "(", "action", ")", ":", "boolean_actions", "=", "(", "_StoreConstAction", ",", "_StoreFalseAction", ",", "_StoreTrueAction", ")", "return", "(", "not", "action", ".", "choices", "and", "not", "isinstance", "(", "action", ",", "_CountAction...	35.923077	11.307692
def sort_values(expr, by, ascending=True): """ Sort the collection by values. `sort` is an alias name for `sort_values` :param expr: collection :param by: the sequence or sequences to sort :param ascending: Sort ascending vs. descending. Sepecify list for multiple sort orders. ...	[ "def", "sort_values", "(", "expr", ",", "by", ",", "ascending", "=", "True", ")", ":", "if", "not", "isinstance", "(", "by", ",", "list", ")", ":", "by", "=", "[", "by", ",", "]", "by", "=", "[", "it", "(", "expr", ")", "if", "inspect", ".", ...	40	21.090909
def transformer_image_decoder(targets, encoder_output, ed_attention_bias, hparams, name=None): """Transformer image decoder over targets with local attention. Args: targets: Tensor of shape [...	[ "def", "transformer_image_decoder", "(", "targets", ",", "encoder_output", ",", "ed_attention_bias", ",", "hparams", ",", "name", "=", "None", ")", ":", "with", "tf", ".", "variable_scope", "(", "name", ",", "default_name", "=", "\"transformer_dec\"", ")", ":", ...	43.853659	17.707317
def add_site_states(self, site, states): """Create new states on an agent site if the state doesn't exist.""" for state in states: if state not in self.site_states[site]: self.site_states[site].append(state)	[ "def", "add_site_states", "(", "self", ",", "site", ",", "states", ")", ":", "for", "state", "in", "states", ":", "if", "state", "not", "in", "self", ".", "site_states", "[", "site", "]", ":", "self", ".", "site_states", "[", "site", "]", ".", "appen...	49.4	7
def register(self, model, values=None, instance_values=None): """ Registers a model with this group. :param values: A list of values that should be incremented \ whenever invalidate_cache is called for a instance or class \ of this type. :param instance_values: A list o...	[ "def", "register", "(", "self", ",", "model", ",", "values", "=", "None", ",", "instance_values", "=", "None", ")", ":", "if", "model", "in", "self", ".", "_models", ":", "raise", "Exception", "(", "\"%s is already registered\"", "%", "model", ")", "self",...	37.833333	22.5
def _request(self, method, path, server=None, **kwargs): """Execute a request to the cluster A server is selected from the server pool. """ while True: next_server = server or self._get_server() try: response = self.server_pool[next_server].reques...	[ "def", "_request", "(", "self", ",", "method", ",", "path", ",", "server", "=", "None", ",", "", "", "kwargs", ")", ":", "while", "True", ":", "next_server", "=", "server", "or", "self", ".", "_get_server", "(", ")", "try", ":", "response", "=", ...	48.840909	17.431818
def run(classes, args=None, msg_stream=sys.stdout, verbose=False, util=None, event_loop=None, post_init_callback=None, green_mode=None, raises=False): """ Provides a simple way to run a tango server. It handles exceptions by writting a message to the msg_stream. The `classes` pa...	[ "def", "run", "(", "classes", ",", "args", "=", "None", ",", "msg_stream", "=", "sys", ".", "stdout", ",", "verbose", "=", "False", ",", "util", "=", "None", ",", "event_loop", "=", "None", ",", "post_init_callback", "=", "None", ",", "green_mode", "="...	31.779221	19.974026
def clear_tc(self, owner, data, clear_type): """Delete threat intel from ThreatConnect platform. Args: owner (str): The ThreatConnect owner. data (dict): The data for the threat intel to clear. clear_type (str): The type of clear action. """ batch = s...	[ "def", "clear_tc", "(", "self", ",", "owner", ",", "data", ",", "clear_type", ")", ":", "batch", "=", "self", ".", "tcex", ".", "batch", "(", "owner", ",", "action", "=", "'Delete'", ")", "tc_type", "=", "data", ".", "get", "(", "'type'", ")", "pat...	42.387755	16.632653
def get_current_item(self): """Returns (first) selected item or None""" l = self.selectedIndexes() if len(l) > 0: return self.model().get_item(l[0])	[ "def", "get_current_item", "(", "self", ")", ":", "l", "=", "self", ".", "selectedIndexes", "(", ")", "if", "len", "(", "l", ")", ">", "0", ":", "return", "self", ".", "model", "(", ")", ".", "get_item", "(", "l", "[", "0", "]", ")" ]	36	8.6
def add_leverage(self): """ Adds leverage term to the model Returns ---------- None (changes instance attributes) """ if self.leverage is True: pass else: self.leverage = True self.z_no += 1 ...	[ "def", "add_leverage", "(", "self", ")", ":", "if", "self", ".", "leverage", "is", "True", ":", "pass", "else", ":", "self", ".", "leverage", "=", "True", "self", ".", "z_no", "+=", "1", "for", "i", "in", "range", "(", "len", "(", "self", ".", "X...	43.392857	30.428571
def _maybe_expand_trailing_dim(observed_time_series_tensor): """Ensures `observed_time_series_tensor` has a trailing dimension of size 1. The `tfd.LinearGaussianStateSpaceModel` Distribution has event shape of `[num_timesteps, observation_size]`, but canonical BSTS models are univariate, so their observation_s...	[ "def", "_maybe_expand_trailing_dim", "(", "observed_time_series_tensor", ")", ":", "with", "tf", ".", "compat", ".", "v1", ".", "name_scope", "(", "'maybe_expand_trailing_dim'", ",", "values", "=", "[", "observed_time_series_tensor", "]", ")", ":", "if", "(", "obs...	46.641026	24.102564
def _disbatch_runner_async(self, chunk): ''' Disbatch runner client_async commands ''' pub_data = self.saltclients['runner'](chunk) raise tornado.gen.Return(pub_data)	[ "def", "_disbatch_runner_async", "(", "self", ",", "chunk", ")", ":", "pub_data", "=", "self", ".", "saltclients", "[", "'runner'", "]", "(", "chunk", ")", "raise", "tornado", ".", "gen", ".", "Return", "(", "pub_data", ")" ]	33.5	12.833333
def deserialize(to_deserialize, args, kwargs): """ Deserializes a string into a PyMongo BSON """ if isinstance(to_deserialize, string_types): if re.match('^[0-9a-f]{24}$', to_deserialize): return ObjectId(to_deserialize) try: return bson_loads(to_deserialize, ...	[ "def", "deserialize", "(", "to_deserialize", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "if", "isinstance", "(", "to_deserialize", ",", "string_types", ")", ":", "if", "re", ".", "match", "(", "'^[0-9a-f]{24}$'", ",", "to_deserialize", ")", ":", ...	38.076923	16.076923
def inspect_io_obj(obj): """ :param obj: a path string, a pathlib.Path or a file / file-like object :return: A tuple of (objtype, objpath, objopener) :raises: UnknownFileTypeError """ itype = guess_io_type(obj) if itype == IOI_PATH_STR: ipath = anyconfig.utils.normpath(obj) ...	[ "def", "inspect_io_obj", "(", "obj", ")", ":", "itype", "=", "guess_io_type", "(", "obj", ")", "if", "itype", "==", "IOI_PATH_STR", ":", "ipath", "=", "anyconfig", ".", "utils", ".", "normpath", "(", "obj", ")", "ext", "=", "anyconfig", ".", "utils", "...	33.035714	15.678571
def message(message_type, payload, payload_length): """ Build a message. """ return packet.build( Container( type=message_type, id=1, refer=0, sent=Container( secs=0, usecs=0 ), recv=Container( ...	[ "def", "message", "(", "message_type", ",", "payload", ",", "payload_length", ")", ":", "return", "packet", ".", "build", "(", "Container", "(", "type", "=", "message_type", ",", "id", "=", "1", ",", "refer", "=", "0", ",", "sent", "=", "Container", "(...	23.421053	17.315789
async def get_data(self): """Get details of OpenSenseMap station.""" try: async with async_timeout.timeout(5, loop=self._loop): response = await self._session.get(self.base_url) _LOGGER.info( "Response from OpenSenseMap API: %s", response.status) ...	[ "async", "def", "get_data", "(", "self", ")", ":", "try", ":", "async", "with", "async_timeout", ".", "timeout", "(", "5", ",", "loop", "=", "self", ".", "_loop", ")", ":", "response", "=", "await", "self", ".", "_session", ".", "get", "(", "self", ...	42.357143	21.928571
def get_instance(self, instance_id, project_id=None): """ Gets information about a particular instance. :param project_id: Optional, The ID of the GCP project that owns the Cloud Spanner database. If set to None or missing, the default project_id from the GCP connection is used. ...	[ "def", "get_instance", "(", "self", ",", "instance_id", ",", "project_id", "=", "None", ")", ":", "instance", "=", "self", ".", "_get_client", "(", "project_id", "=", "project_id", ")", ".", "instance", "(", "instance_id", "=", "instance_id", ")", "if", "n...	43.6875	22.3125
def failure(self): """Update the timer to reflect a failed call""" self.short_interval += self.short_unit self.long_interval += self.long_unit self.short_interval = min(self.short_interval, self.max_short_timer) self.long_interval = min(self.long_interval, self.max_long_timer) ...	[ "def", "failure", "(", "self", ")", ":", "self", ".", "short_interval", "+=", "self", ".", "short_unit", "self", ".", "long_interval", "+=", "self", ".", "long_unit", "self", ".", "short_interval", "=", "min", "(", "self", ".", "short_interval", ",", "self...	48.857143	15.857143
def Connect(host='localhost', port=443, user='root', pwd='', service="hostd", adapter="SOAP", namespace=None, path="/sdk", connectionPoolTimeout=CONNECTION_POOL_IDLE_TIMEOUT_SEC, version=None, keyFile=None, certFile=None, thumbprint=None, sslContext=None, b64token=None, m...	[ "def", "Connect", "(", "host", "=", "'localhost'", ",", "port", "=", "443", ",", "user", "=", "'root'", ",", "pwd", "=", "''", ",", "service", "=", "\"hostd\"", ",", "adapter", "=", "\"SOAP\"", ",", "namespace", "=", "None", ",", "path", "=", "\"/sdk...	35.52381	20.714286
def diff(self): """The Difference between a PDA and a DFA""" self.mmb.complement(self.alphabet) self.mmb.minimize() print 'start intersection' self.mmc = self._intesect() print 'end intersection' return self.mmc	[ "def", "diff", "(", "self", ")", ":", "self", ".", "mmb", ".", "complement", "(", "self", ".", "alphabet", ")", "self", ".", "mmb", ".", "minimize", "(", ")", "print", "'start intersection'", "self", ".", "mmc", "=", "self", ".", "_intesect", "(", ")...	32.5	9.5
def centralManager_didDisconnectPeripheral_error_(self, manager, peripheral, error): """Called when a device is disconnected.""" logger.debug('centralManager_didDisconnectPeripheral called') # Get the device and remove it from the device list, then fire its # disconnected event. ...	[ "def", "centralManager_didDisconnectPeripheral_error_", "(", "self", ",", "manager", ",", "peripheral", ",", "error", ")", ":", "logger", ".", "debug", "(", "'centralManager_didDisconnectPeripheral called'", ")", "# Get the device and remove it from the device list, then fire its...	53.8	17.3
def check_credentials(client): """ Checks credentials for given socket. """ pid, uid, gid = get_peercred(client) euid = os.geteuid() client_name = "PID:%s UID:%s GID:%s" % (pid, uid, gid) if uid not in (0, euid): raise SuspiciousClient("Can't accept client with %s. It doesn't match ...	[ "def", "check_credentials", "(", "client", ")", ":", "pid", ",", "uid", ",", "gid", "=", "get_peercred", "(", "client", ")", "euid", "=", "os", ".", "geteuid", "(", ")", "client_name", "=", "\"PID:%s UID:%s GID:%s\"", "%", "(", "pid", ",", "uid", ",", ...	32.533333	20.4
def mayContainTextNodes(node): """ Returns True if the passed-in node is probably a text element, or at least one of its descendants is probably a text element. If False is returned, it is guaranteed that the passed-in node has no business having text-based attributes. If True is returned, the...	[ "def", "mayContainTextNodes", "(", "node", ")", ":", "# Cached result of a prior call?", "try", ":", "return", "node", ".", "mayContainTextNodes", "except", "AttributeError", ":", "pass", "result", "=", "True", "# Default value", "# Comment, text and CDATA nodes don't have ...	39.414634	19.804878
def is_valid(self, csdl): """ Checks if the given CSDL is valid. Uses API documented at http://dev.datasift.com/docs/api/rest-api/endpoints/validate :param csdl: CSDL to validate :type csdl: str :returns: Boolean indicating the validity of the CSDL :...	[ "def", "is_valid", "(", "self", ",", "csdl", ")", ":", "try", ":", "self", ".", "validate", "(", "csdl", ")", "except", "DataSiftApiException", "as", "e", ":", "if", "e", ".", "response", ".", "status_code", "==", "400", ":", "return", "False", "else",...	34.789474	20.631579
def context_chunks(self, context): """ Retrieves all tokens, divided into the chunks in context ``context``. If ``context`` is not found in a feature, then the feature will be treated as a single chunk. Parameters ---------- context : str Context nam...	[ "def", "context_chunks", "(", "self", ",", "context", ")", ":", "chunks", "=", "[", "]", "papers", "=", "[", "]", "for", "paper", ",", "feature", "in", "self", ".", "features", ".", "iteritems", "(", ")", ":", "if", "context", "in", "feature", ".", ...	30.064516	19.16129

def _deserialize_property_value(self, to_deserialize: PrimitiveJsonType, deserializer_cls: Type) -> Any: """ Deserializes the given value using the given deserializer. :param to_deserialize: the value to deserialize :param deserializer_cls: the type of deserializer to use :return...

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52.5

19.5

def write_ctl(name, imap, guidetree, nloci, infer_sptree, infer_delimit, delimit_alg, seed, burnin, nsample, sampfreq, thetaprior, tauprior, traits_df, nu0, kappa0, cleandata, useseqdata, usetraitdata, wdir, finetune, verbose): """ write outfile...

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38.513889

20.152778

def open_relative(self, url, *args, **kwargs): """Like :func:`open`, but ``url`` can be relative to the currently visited page. """ return self.open(self.absolute_url(url), *args, **kwargs)

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43.4

10

def checkAndCreate(self, key, payload): """ Function checkAndCreate Check if an object exists and create it if not @param key: The targeted object @param payload: The targeted object description @return RETURN: The id of the object """ if key not in self: ...

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33.181818

9.727273

def _map_arg_names(source, mapping): """Map one set of keys to another.""" return {cartopy_name: source[cf_name] for cartopy_name, cf_name in mapping if cf_name in source}

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50

12.25

def per_month(start: datetime, end: datetime, n: int=1): """ Iterates over time range in one month steps. Clamps to number of days in given month. :param start: Start of time range (inclusive) :param end: End of time range (exclusive) :param n: Number of months to step. Default is 1. :retu...

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36.125

16.625

def get_content_type(self, msg, content_type="HTML"): """ Given an Email.Message object, gets the content-type payload as specified by @content_type. This is the actual body of the email. @Params msg - Email.Message object to get message content for content_type -...

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38.842105

15.789474

def is_cupy_array(arr): """Check whether an array is a cupy array""" if cupy is None: return False elif isinstance(arr, cupy.ndarray): return True else: return False

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24.75

16.25

def gp_background(): """ plot background methods and S/B vs energy """ inDir, outDir = getWorkDirs() data, REBIN = OrderedDict(), None titles = [ 'SE_{+-}', 'SE@^{corr}_{/Symbol \\261\\261}', 'ME@^{N}_{+-}' ] Apm = OrderedDict([ ('19', 0.026668), ('27', 0.026554), ('39', 0.026816), ('62', 0....

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45.5625

19.010417

def interpolate(x, scale=None, output_size=None, mode='linear', align_corners=None): ''' Resize an ND array with interpolation. Scaling factors for spatial dimensions are determined by either ``scale`` or ``output_size``. ``nd = len(scale)`` or ``nd = len(output_size)`` determines the number of ...

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37.816901

23.56338

def save_grid_data(self): """ Save grid data in the data object """ if not self.grid.changes: print('-I- No changes to save') return if self.grid_type == 'age': age_data_type = self.er_magic.age_type self.er_magic.write_ages = True...

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53.171171

28.522523

def list_virtual_machine_scale_set_vm_network_interfaces(scale_set, vm_index, resource_group, **kwargs): ''' .. versionadded:: 2019.2.0 ...

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33.853659

28.487805

def _submit_metrics(self, metrics, metric_name_and_type_by_property): """ Resolve metric names and types and submit it. """ for metric in metrics: if ( metric.name not in metric_name_and_type_by_property and metric.name.lower() not in metric_na...

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44.653846

27.269231

def predict_features(self, df_features, df_target, idx=0, **kwargs): """For one variable, predict its neighbouring nodes. Args: df_features (pandas.DataFrame): df_target (pandas.Series): idx (int): (optional) for printing purposes kwargs (dict): additiona...

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31.833333

17.777778

def validate_spec(cls, spec, backends=None): """ Given a specification, validated it against the options tree for the specified backends by raising OptionError for invalid options. If backends is None, validates against all the currently loaded backend. Only useful when ...

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47.833333

21.722222

def explode(): ''' This method **assumes** that :func:`~exhale.configs.apply_sphinx_configurations` has already been applied. It performs minimal sanity checking, and then performs in order 1. Creates a :class:`~exhale.graph.ExhaleRoot` object. 2. Executes :func:`~exhale.graph.ExhaleRoot.parse...

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39.15493

26.760563

def _report_container_state_metrics(self, pod_list, instance_tags): """Reports container state & reasons by looking at container statuses""" if pod_list.get('expired_count'): self.gauge(self.NAMESPACE + '.pods.expired', pod_list.get('expired_count'), tags=instance_tags) for pod in p...

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47.28125

28.71875

def get_object_header(self, ref): """ Use this method to quickly examine the type and size of the object behind the given ref. :note: The method will only suffer from the costs of command invocation once and reuses the command in subsequent calls. :return: (hexsha, type_string, size_as_int)""" cm...

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43.3

19.7

def crypto_sign_ed25519ph_final_verify(edph, signature, pk): """ Verify a prehashed signature using the public key pk :param edph: the ed25519ph state for the data being verified :type edph: crypto_sign_ed255...

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39.658537

13.170732

def parse_itms_services(url_data): """Get "url" CGI parameter value as child URL.""" query = url_data.urlparts[3] for k, v, sep in urlutil.parse_qsl(query, keep_blank_values=True): if k == "url": url_data.add_url(v) break

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37

13.428571

def cross(vec1, vec2): """Returns the cross product of two Vectors""" if isinstance(vec1, Vector3) and isinstance(vec2, Vector3): vec3 = Vector3() vec3.x = (vec1.y * vec2.z) - (vec1.z * vec2.y) vec3.y = (vec1.z * vec2.x) - (vec1.x * vec2.z) vec3.z = (vec1....

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44.3

17.7

def set_count_auto(self, count=None): """Sets workers count. By default sets it to detected number of available cores :param int count: """ count = count or self._section.vars.CPU_CORES self._set('workers', count) return self._section

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23.583333

19.333333

def inline(self) -> str: """ Return an inline string of the Identity :return: """ return "{pubkey}:{signature}:{timestamp}:{uid}".format( pubkey=self.pubkey, signature=self.signatures[0], timestamp=self.timestamp, uid=self.uid)

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30.6

9.8

def get_field_info(self, field): """ This method is basically a mirror from rest_framework==3.3.3 We are currently pinned to rest_framework==3.1.1. If we upgrade, this can be refactored and simplified to rely more heavily on rest_framework's built in logic. """ ...

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38.931034

21.551724

def separation_in_list(separation_indices, separation_indices_list): """ Checks if the separation indices of a plane are already in the list :param separation_indices: list of separation indices (three arrays of integers) :param separation_indices_list: list of the list of separation indices to be compa...

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54

26.5

def tvdb_login(api_key): """ Logs into TVDb using the provided api key Note: You can register for a free TVDb key at thetvdb.com/?tab=apiregister Online docs: api.thetvdb.com/swagger#!/Authentication/post_login= """ url = "https://api.thetvdb.com/login" body = {"apikey": api_key} status, co...

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41.285714

17

def add(self, item, group_by=None): """General purpose class to group items by certain criteria.""" key = None if not group_by: group_by = self.group_by if group_by: # if group_by is a function, use it with item as argument if hasattr(group_by, '__ca...

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36.357143

18.821429

def gc_content_plot (self): """ Create the HTML for the FastQC GC content plot """ data = dict() data_norm = dict() for s_name in self.fastqc_data: try: data[s_name] = {d['gc_content']: d['count'] for d in self.fastqc_data[s_name]['per_sequence_gc_content']} ...

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48.298246

24.245614

async def getArtifact(self, *args, **kwargs): """ Get Artifact from Run Get artifact by `<name>` from a specific run. **Public Artifacts**, in-order to get an artifact you need the scope `queue:get-artifact:<name>`, where `<name>` is the name of the artifact. But if the...

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58.321839

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def _list_resource_descriptors(args, _): """Lists the resource descriptors in the project.""" project_id = args['project'] pattern = args['type'] or '*' descriptors = gcm.ResourceDescriptors(project_id=project_id) dataframe = descriptors.as_dataframe(pattern=pattern) return _render_dataframe(dataframe)

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44.142857

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def _reindex_multi(self, axes, copy, fill_value): """ We are guaranteed non-Nones in the axes. """ new_index, row_indexer = self.index.reindex(axes['index']) new_columns, col_indexer = self.columns.reindex(axes['columns']) if row_indexer is not None and col_indexer is n...

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48.684211

23

def cmd_kill(opts): """Kill some or all containers """ kill_signal = opts.signal if hasattr(opts, 'signal') else "SIGKILL" __with_containers(opts, Blockade.kill, signal=kill_signal)

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38.6

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def install(self): # pragma: no cover """Install/download ssh keys from LDAP for consumption by SSH.""" keys = self.get_keys_from_ldap() for user, ssh_keys in keys.items(): user_dir = API.__authorized_keys_path(user) if not os.path.isdir(user_dir): os.mak...

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53.7

11.4

def srcmdl_xml(self, **kwargs): """ return the file name for source model xml files """ kwargs_copy = self.base_dict.copy() kwargs_copy.update(**kwargs) localpath = NameFactory.srcmdl_xml_format.format(**kwargs_copy) if kwargs.get('fullpath', False): return se...

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41

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def list_lbaas_members(self, lbaas_pool, retrieve_all=True, **_params): """Fetches a list of all lbaas_members for a project.""" return self.list('members', self.lbaas_members_path % lbaas_pool, retrieve_all, **_params)

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64.25

18.25

def _move_stream_token(coordinator, token): """Move to the Stream position described by the token. The following rules are applied when interpolation is required: - If a shard does not exist (past the trim_horizon) it is ignored. If that shard had children, its children are also checked against the ...

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55.618182

28.872727

def dt_dt(sdat, tstart=None, tend=None): """Derivative of temperature. Compute dT/dt as a function of time using an explicit Euler scheme. Args: sdat (:class:`~stagpy.stagyydata.StagyyData`): a StagyyData instance. tstart (float): time at which the computation should start. Use the ...

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39.75

21.15

def vertex_to_face_color(vertex_colors, faces): """ Convert a list of vertex colors to face colors. Parameters ---------- vertex_colors: (n,(3,4)), colors faces: (m,3) int, face indexes Returns ----------- face_colors: (m,4) colors """ vertex_colors = to_rgba(verte...

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25.375

14.625

def _create_dict_with_nested_keys_and_val(cls, keys, value): """Recursively constructs a nested dictionary with the keys pointing to the value. For example: Given the list of keys ['a', 'b', 'c', 'd'] and a primitive value 'hello world', the method will produce the nested dictionary {'a': {'b': {'c...

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43.782609

24.26087

def gif(self, gif_id, strict=False): """ Retrieves a specifc gif from giphy based on unique id :param gif_id: Unique giphy gif ID :type gif_id: string :param strict: Whether an exception should be raised when no results :type strict: boolean """ resp = se...

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33.0625

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async def get_files_to_delete(self) -> List[str]: """ Determine the files to delete when rolling over. """ dir_name, base_name = os.path.split(self.absolute_file_path) file_names = await self.loop.run_in_executor( None, lambda: os.listdir(dir_name) ) r...

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37.6

12.9

def is_read_only(cls, db: DATABASE_SUPPORTER_FWD_REF, logger: logging.Logger = None) -> bool: """Do we have read-only access?""" def convert_enums(row_): # All these columns are of type enum('N', 'Y'); # https://dev.mysql.com/doc/refman/...

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41.060241

15.084337

def read_text(self, file_handle): """Parse the TEXT segment of the FCS file. The TEXT segment contains meta data associated with the FCS file. Converting all meta keywords to lower case. """ header = self.annotation['__header__'] # For convenience ##### # Read ...

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39.529412

24.985294

def getStore(self, name, domain): """Convenience method for the REPL. I got tired of typing this string every time I logged in.""" return IRealm(self.original.store.parent).accountByAddress(name, domain).avatars.open()

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77.333333

20.666667

def local_targets(self): """Iterator over the targets defined in this build file.""" for node in self.node: if (node.repo, node.path) == (self.target.repo, self.target.path): yield node

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45

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def referenced(word, article=INDEFINITE, gender=MALE, role=SUBJECT): """ Returns a string with the article + the word. """ return "%s %s" % (_article(word, article, gender, role), word)

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48.5

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def extend_from_instances(self, params: Params, instances: Iterable['adi.Instance'] = ()) -> None: """ Extends an already generated vocabulary using a collection of instances. """ min_count = params.pop("min_count", None) ...

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56.962963

22.740741

def parse_data(self, sline): """This function builds the addRawResults dictionary using the header values of the labels section as sample Ids. """ if sline[0] == '': return 0 for idx, label in enumerate(self._labels_values[sline[0]]): if label != '': ...

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42.1

18.6

def add_schema(self, database, schema): """Add a schema to the set of known schemas (case-insensitive) :param str database: The database name to add. :param str schema: The schema name to add. """ self.schemas.add((_lower(database), _lower(schema)))

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40.571429

12.142857

def get_contact(self, contact_id): """ Get single contact """ url = self.CONTACTS_ID_URL % contact_id connection = Connection(self.token) connection.set_url(self.production, url) return connection.get_request()

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25.9

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def plot_ARD(kernel, filtering=None, legend=False, canvas=None, **kwargs): """ If an ARD kernel is present, plot a bar representation using matplotlib :param fignum: figure number of the plot :param filtering: list of names, which to use for plotting ARD parameters. Only kernels w...

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35.346939

24.571429

def to_unicode(string): """ Ensure a passed string is unicode """ if isinstance(string, six.binary_type): return string.decode('utf8') if isinstance(string, six.text_type): return string if six.PY2: return unicode(string) return str(string)

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25.636364

9.090909

def value_to_string(self, obj): """This descriptor acts as a Field, as far as the serializer is concerned.""" try: return force_unicode(self.__get__(obj)) except TypeError: return str(self.__get__(obj))

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40.833333

10.666667

def suspend(self): """ Suspends this router. """ status = yield from self.get_status() if status == "running": yield from self._hypervisor.send('vm suspend "{name}"'.format(name=self._name)) self.status = "suspended" log.info('Router "{name}" ...

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37.5

20.3

def parse_bookmark_json (data): """Parse complete JSON data for Chromium Bookmarks.""" for entry in data["roots"].values(): for url, name in parse_bookmark_node(entry): yield url, name

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41.6

6.8

def init_config(self, app): """Initialize configuration. :param app: An instance of :class:`~flask.Flask`. """ _vars = ['BASE_TEMPLATE', 'COVER_TEMPLATE', 'SETTINGS_TEMPLATE'] # Sets RequireJS config and SASS binary as well if not already set. for k in dir(config): ...

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38.909091

20.681818

def pivot(self, speed, durationS=-1.0): """ pivot() controls the pivot speed of the RedBot. The values of the pivot function inputs range from -255:255, with -255 indicating a full speed counter-clockwise rotation. 255 indicates a full speed clockwise rotation """ ...

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41

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def apply_handler_to_root_log(handler: logging.Handler, remove_existing: bool = False) -> None: """ Applies a handler to all logs, optionally removing existing handlers. Should ONLY be called from the ``if __name__ == 'main'`` script; see https://docs.python.org/3.4/howto/...

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36.111111

21.777778

def trace_buffer_capacity(self): """Retrieves the trace buffer's current capacity. Args: self (JLink): the ``JLink`` instance. Returns: The current capacity of the trace buffer. This is not necessarily the maximum possible size the buffer could be configured with...

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37.8125

20.9375

def _conf(cls, opts): """Setup logging via ini-file from logging_conf_file option.""" if not opts.logging_conf_file: return False if not os.path.exists(opts.logging_conf_file): # FileNotFoundError added only in Python 3.3 # https://docs.python.org/3/whatsnew/...

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47.666667

28.083333

def label_context(label_info, multi_line=True, sep=': '): """ Create an unabiguous label string If facetting over a single variable, `label_value` is used, if two or more variables then `label_both` is used. Parameters ---------- label_info : series Series whose values will be retu...

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28.518519

19.777778

def from_input(cls, input_file=sys.stdin, modify=None, backend=None): """ Creates a Task object, directly from the stdin, by reading one line. If modify=True, two lines are used, first line interpreted as the original state of the Task object, and second line as its new, modified...

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41.128205

24.25641

def load_dictionary(filename): """Load dictionary from .spydata file""" filename = osp.abspath(filename) old_cwd = getcwd() tmp_folder = tempfile.mkdtemp() os.chdir(tmp_folder) data = None error_message = None try: with tarfile.open(filename, "r") as tar: tar.extracta...

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39.195122

14.95122

def watch(self, filepath, func=None, delay=None, ignore=None): """Add the given filepath for watcher list. Once you have intialized a server, watch file changes before serve the server:: server.watch('static/*.stylus', 'make static') def alert(): print('...

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41.793103

20.413793

def to_dataframe(self, bqstorage_client=None, dtypes=None, progress_bar_type=None): """Create an empty dataframe. Args: bqstorage_client (Any): Ignored. Added for compatibility with RowIterator. dtypes (Any): Ignored. Added for compatibility with ...

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35.555556

18.111111

def convert(input_file_name, **kwargs): """Convert CSV file to HTML table""" delimiter = kwargs["delimiter"] or "," quotechar = kwargs["quotechar"] or "|" if six.PY2: delimiter = delimiter.encode("utf-8") quotechar = quotechar.encode("utf-8") # Read CSV and form a header and rows l...

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33.30303

15.181818

def process_info(pid=None): '''Returns a dictionary of system information for the process ``pid``. It uses the psutil_ module for the purpose. If psutil_ is not available it returns an empty dictionary. .. _psutil: http://code.google.com/p/psutil/ ''' if psutil is None: # pragma nocover ...

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34.652174

18.913043

def load_from_string(self, content, container, **kwargs): """ Load config from given string 'cnf_content'. :param content: Config content string :param container: callble to make a container object later :param kwargs: optional keyword parameters to be sanitized :: dict ...

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42

20.166667

def n50(args): """ %prog n50 filename Given a file with a list of numbers denoting contig lengths, calculate N50. Input file can be both FASTA or a list of sizes. """ from jcvi.graphics.histogram import loghistogram p = OptionParser(n50.__doc__) p.add_option("--print0", default=False, ...

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27.826923

20.211538

def __remove_trailing_empty_lines(lines): """ Removes leading empty lines from a list of lines. :param list[str] lines: The lines. """ lines.reverse() tmp = DocBlockReflection.__remove_leading_empty_lines(lines) lines.reverse() tmp.reverse() retu...

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26.25

16.916667

def median(data): """Calculate the median of a list.""" data.sort() num_values = len(data) half = num_values // 2 if num_values % 2: return data[half] return 0.5 * (data[half-1] + data[half])

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27

14.125

def get_content(self, start=None, end=None): """ Retrieve the content of the requested resource which is located at the given absolute path. This method should either return a byte string or an iterator of byte strings. The latter is preferred for large files as it helps...

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39.035714

10.821429

def get_tag_cloud(context, steps=6, min_count=None, template='zinnia/tags/tag_cloud.html'): """ Return a cloud of published tags. """ tags = Tag.objects.usage_for_queryset( Entry.published.all(), counts=True, min_count=min_count) return {'template': template, ...

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36.363636

6.363636

def get_fee(speed=FEE_SPEED_MEDIUM): """Gets the recommended satoshi per byte fee. :param speed: One of: 'fast', 'medium', 'slow'. :type speed: ``string`` :rtype: ``int`` """ if speed == FEE_SPEED_FAST: return DEFAULT_FEE_FAST elif speed == FEE_SPEED_MEDIUM: return DEFAULT_F...

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29.533333

11.8

def hypo_list(nodes): """ :param nodes: a hypoList node with N hypocenter nodes :returns: a numpy array of shape (N, 3) with strike, dip and weight """ check_weights(nodes) data = [] for node in nodes: data.append([node['alongStrike'], node['downDip'], node['weight']]) return num...

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33.2

16.8

def is_standard(action): """ actions which are general "store" instructions. e.g. anything which has an argument style like: $ script.py -f myfilename.txt """ boolean_actions = ( _StoreConstAction, _StoreFalseAction, _StoreTrueAction ) return (not action.choices ...

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35.923077

11.307692

def sort_values(expr, by, ascending=True): """ Sort the collection by values. `sort` is an alias name for `sort_values` :param expr: collection :param by: the sequence or sequences to sort :param ascending: Sort ascending vs. descending. Sepecify list for multiple sort orders. ...

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40

21.090909

def transformer_image_decoder(targets, encoder_output, ed_attention_bias, hparams, name=None): """Transformer image decoder over targets with local attention. Args: targets: Tensor of shape [...

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43.853659

17.707317

def add_site_states(self, site, states): """Create new states on an agent site if the state doesn't exist.""" for state in states: if state not in self.site_states[site]: self.site_states[site].append(state)

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49.4

7

def register(self, model, values=None, instance_values=None): """ Registers a model with this group. :param values: A list of values that should be incremented \ whenever invalidate_cache is called for a instance or class \ of this type. :param instance_values: A list o...

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37.833333

22.5

def _request(self, method, path, server=None, **kwargs): """Execute a request to the cluster A server is selected from the server pool. """ while True: next_server = server or self._get_server() try: response = self.server_pool[next_server].reques...

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48.840909

17.431818

def run(classes, args=None, msg_stream=sys.stdout, verbose=False, util=None, event_loop=None, post_init_callback=None, green_mode=None, raises=False): """ Provides a simple way to run a tango server. It handles exceptions by writting a message to the msg_stream. The `classes` pa...

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31.779221

19.974026

def clear_tc(self, owner, data, clear_type): """Delete threat intel from ThreatConnect platform. Args: owner (str): The ThreatConnect owner. data (dict): The data for the threat intel to clear. clear_type (str): The type of clear action. """ batch = s...

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42.387755

16.632653

def get_current_item(self): """Returns (first) selected item or None""" l = self.selectedIndexes() if len(l) > 0: return self.model().get_item(l[0])

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36

8.6

def add_leverage(self): """ Adds leverage term to the model Returns ---------- None (changes instance attributes) """ if self.leverage is True: pass else: self.leverage = True self.z_no += 1 ...

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43.392857

30.428571

def _maybe_expand_trailing_dim(observed_time_series_tensor): """Ensures `observed_time_series_tensor` has a trailing dimension of size 1. The `tfd.LinearGaussianStateSpaceModel` Distribution has event shape of `[num_timesteps, observation_size]`, but canonical BSTS models are univariate, so their observation_s...

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46.641026

24.102564

def _disbatch_runner_async(self, chunk): ''' Disbatch runner client_async commands ''' pub_data = self.saltclients['runner'](chunk) raise tornado.gen.Return(pub_data)

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33.5

12.833333

def deserialize(to_deserialize, *args, **kwargs): """ Deserializes a string into a PyMongo BSON """ if isinstance(to_deserialize, string_types): if re.match('^[0-9a-f]{24}$', to_deserialize): return ObjectId(to_deserialize) try: return bson_loads(to_deserialize, *...

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38.076923

16.076923

def inspect_io_obj(obj): """ :param obj: a path string, a pathlib.Path or a file / file-like object :return: A tuple of (objtype, objpath, objopener) :raises: UnknownFileTypeError """ itype = guess_io_type(obj) if itype == IOI_PATH_STR: ipath = anyconfig.utils.normpath(obj) ...

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33.035714

15.678571

def message(message_type, payload, payload_length): """ Build a message. """ return packet.build( Container( type=message_type, id=1, refer=0, sent=Container( secs=0, usecs=0 ), recv=Container( ...

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23.421053

17.315789

async def get_data(self): """Get details of OpenSenseMap station.""" try: async with async_timeout.timeout(5, loop=self._loop): response = await self._session.get(self.base_url) _LOGGER.info( "Response from OpenSenseMap API: %s", response.status) ...

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42.357143

21.928571

def get_instance(self, instance_id, project_id=None): """ Gets information about a particular instance. :param project_id: Optional, The ID of the GCP project that owns the Cloud Spanner database. If set to None or missing, the default project_id from the GCP connection is used. ...

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43.6875

22.3125

def failure(self): """Update the timer to reflect a failed call""" self.short_interval += self.short_unit self.long_interval += self.long_unit self.short_interval = min(self.short_interval, self.max_short_timer) self.long_interval = min(self.long_interval, self.max_long_timer) ...

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48.857143

15.857143

def Connect(host='localhost', port=443, user='root', pwd='', service="hostd", adapter="SOAP", namespace=None, path="/sdk", connectionPoolTimeout=CONNECTION_POOL_IDLE_TIMEOUT_SEC, version=None, keyFile=None, certFile=None, thumbprint=None, sslContext=None, b64token=None, m...

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35.52381

20.714286

def diff(self): """The Difference between a PDA and a DFA""" self.mmb.complement(self.alphabet) self.mmb.minimize() print 'start intersection' self.mmc = self._intesect() print 'end intersection' return self.mmc

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32.5

9.5

def centralManager_didDisconnectPeripheral_error_(self, manager, peripheral, error): """Called when a device is disconnected.""" logger.debug('centralManager_didDisconnectPeripheral called') # Get the device and remove it from the device list, then fire its # disconnected event. ...

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53.8

17.3

def check_credentials(client): """ Checks credentials for given socket. """ pid, uid, gid = get_peercred(client) euid = os.geteuid() client_name = "PID:%s UID:%s GID:%s" % (pid, uid, gid) if uid not in (0, euid): raise SuspiciousClient("Can't accept client with %s. It doesn't match ...

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32.533333

20.4

def mayContainTextNodes(node): """ Returns True if the passed-in node is probably a text element, or at least one of its descendants is probably a text element. If False is returned, it is guaranteed that the passed-in node has no business having text-based attributes. If True is returned, the...

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39.414634

19.804878

def is_valid(self, csdl): """ Checks if the given CSDL is valid. Uses API documented at http://dev.datasift.com/docs/api/rest-api/endpoints/validate :param csdl: CSDL to validate :type csdl: str :returns: Boolean indicating the validity of the CSDL :...

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34.789474

20.631579

def context_chunks(self, context): """ Retrieves all tokens, divided into the chunks in context ``context``. If ``context`` is not found in a feature, then the feature will be treated as a single chunk. Parameters ---------- context : str Context nam...

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30.064516

19.16129