kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def cancel(self): """Cancel a running :meth:`iterconsume` session.""" for consumer_tag in self._open_consumers.values(): try: self.backend.cancel(consumer_tag) except KeyError: pass self._open_consumers.clear()	[ "def", "cancel", "(", "self", ")", ":", "for", "consumer_tag", "in", "self", ".", "_open_consumers", ".", "values", "(", ")", ":", "try", ":", "self", ".", "backend", ".", "cancel", "(", "consumer_tag", ")", "except", "KeyError", ":", "pass", "self", "...	35.375	13.75
def run_tfba(self, reaction): """Run FBA and tFBA on model.""" solver = self._get_solver(integer=True) p = fluxanalysis.FluxBalanceProblem(self._mm, solver) start_time = time.time() p.add_thermodynamic() try: p.maximize(reaction) except fluxanalysi...	[ "def", "run_tfba", "(", "self", ",", "reaction", ")", ":", "solver", "=", "self", ".", "_get_solver", "(", "integer", "=", "True", ")", "p", "=", "fluxanalysis", ".", "FluxBalanceProblem", "(", "self", ".", "_mm", ",", "solver", ")", "start_time", "=", ...	28.6	19.4
def _wrap_ele(self, block, view, frag, extra_data=None): """ Does the guts of the wrapping the same way for both xblocks and asides. Their wrappers provide other info in extra_data which gets put into the dom data- attrs. """ wrapped = Fragment() data = { 'usa...	[ "def", "_wrap_ele", "(", "self", ",", "block", ",", "view", ",", "frag", ",", "extra_data", "=", "None", ")", ":", "wrapped", "=", "Fragment", "(", ")", "data", "=", "{", "'usage'", ":", "block", ".", "scope_ids", ".", "usage_id", ",", "'block-type'", ...	40.119048	22.404762
def twenty_five_neurons_mix_stimulated(): "Object allocation" "If M = 0 then only object will be allocated" params = pcnn_parameters(); params.AF = 0.1; params.AL = 0.0; params.AT = 0.7; params.VF = 1.0; params.VL = 1.0; params.VT = 10.0; params.M = 0.0; ...	[ "def", "twenty_five_neurons_mix_stimulated", "(", ")", ":", "\"If M = 0 then only object will be allocated\"", "params", "=", "pcnn_parameters", "(", ")", "params", ".", "AF", "=", "0.1", "params", ".", "AL", "=", "0.0", "params", ".", "AT", "=", "0.7", "params", ...	33.222222	18.444444
def dtrajs(self): """ get discrete trajectories """ if not self._estimated: self.logger.info("not yet parametrized, running now.") self.parametrize() return self._chain[-1].dtrajs	[ "def", "dtrajs", "(", "self", ")", ":", "if", "not", "self", ".", "_estimated", ":", "self", ".", "logger", ".", "info", "(", "\"not yet parametrized, running now.\"", ")", "self", ".", "parametrize", "(", ")", "return", "self", ".", "_chain", "[", "-", ...	37	11.833333
def tlv_parse(data): """ Parses a bytestring of TLV values into a dict with the tags as keys.""" parsed = {} while data: t, l, data = ord_byte(data[0]), ord_byte(data[1]), data[2:] parsed[t], data = data[:l], data[l:] return parsed	[ "def", "tlv_parse", "(", "data", ")", ":", "parsed", "=", "{", "}", "while", "data", ":", "t", ",", "l", ",", "data", "=", "ord_byte", "(", "data", "[", "0", "]", ")", ",", "ord_byte", "(", "data", "[", "1", "]", ")", ",", "data", "[", "2", ...	36.714286	17.714286
def reset_spyder(self): """ Quit and reset Spyder and then Restart application. """ answer = QMessageBox.warning(self, _("Warning"), _("Spyder will restart and reset to default settings: <br><br>" "Do you want to continue?"), QMessageBox.Ye...	[ "def", "reset_spyder", "(", "self", ")", ":", "answer", "=", "QMessageBox", ".", "warning", "(", "self", ",", "_", "(", "\"Warning\"", ")", ",", "_", "(", "\"Spyder will restart and reset to default settings: <br><br>\"", "\"Do you want to continue?\"", ")", ",", "Q...	40.7	10.7
def find_first_wt_parent(self, with_ip=False): """ Recursively looks at the part_of parent ancestry line (ignoring pooled_from parents) and returns a parent Biosample ID if its wild_type attribute is True. Args: with_ip: `bool`. True means to restrict the search to the firs...	[ "def", "find_first_wt_parent", "(", "self", ",", "with_ip", "=", "False", ")", ":", "parent_id", "=", "self", ".", "part_of_id", "if", "not", "parent_id", ":", "return", "False", "parent", "=", "Biosample", "(", "parent_id", ")", "if", "parent", ".", "wild...	46.074074	24.074074
async def result(self) -> T: """\ Wait for the task's termination; either the result is returned or a raised exception is reraised. If an event is sent before the task terminates, an `EventException` is raised with the event as argument. """ try: event = await self.re...	[ "async", "def", "result", "(", "self", ")", "->", "T", ":", "try", ":", "event", "=", "await", "self", ".", "recv_event", "(", ")", "except", "Component", ".", "Success", "as", "succ", ":", "# success was thrown; return the result", "result", ",", "=", "su...	43.666667	18.944444
def _from_record(data): """ Infer a BigQuery table schema from a list of fields or a dictionary. The typeof the elements is used. For a list, the field names are simply 'Column1', 'Column2', etc. Args: data: The list of fields or dictionary. Returns: A list of dictionaries containing fi...	[ "def", "_from_record", "(", "data", ")", ":", "if", "isinstance", "(", "data", ",", "dict", ")", ":", "return", "Schema", ".", "_from_dict_record", "(", "data", ")", "elif", "isinstance", "(", "data", ",", "list", ")", ":", "return", "Schema", ".", "_f...	37.882353	21.176471
def copy_path(self): """Return a copy of the current path. :returns: A list of ``(path_operation, coordinates)`` tuples of a :ref:`PATH_OPERATION` string and a tuple of floats coordinates whose content depends on the operation type: * :obj:`M...	[ "def", "copy_path", "(", "self", ")", ":", "path", "=", "cairo", ".", "cairo_copy_path", "(", "self", ".", "_pointer", ")", "result", "=", "list", "(", "_iter_path", "(", "path", ")", ")", "cairo", ".", "cairo_path_destroy", "(", "path", ")", "return", ...	37.6	17.3
def get_photos_info(photoset_id): """Request the photos information with the photoset id :param photoset_id: The photoset id of flickr :type photoset_id: str :return: photos information :rtype: list """ args = _get_request_args( 'flickr.photosets.getPhotos', photoset_id=phot...	[ "def", "get_photos_info", "(", "photoset_id", ")", ":", "args", "=", "_get_request_args", "(", "'flickr.photosets.getPhotos'", ",", "photoset_id", "=", "photoset_id", ")", "resp", "=", "requests", ".", "post", "(", "API_URL", ",", "data", "=", "args", ")", "re...	29.764706	12.764706
def _spawn_thread(self, target): """ Create a thread """ t = Thread(target=target) t.daemon = True t.start() return t	[ "def", "_spawn_thread", "(", "self", ",", "target", ")", ":", "t", "=", "Thread", "(", "target", "=", "target", ")", "t", ".", "daemon", "=", "True", "t", ".", "start", "(", ")", "return", "t" ]	25.333333	13.166667
def _is_url_like_archive(url): # type: (str) -> bool """Return whether the URL looks like an archive. """ filename = Link(url).filename for bad_ext in ARCHIVE_EXTENSIONS: if filename.endswith(bad_ext): return True return False	[ "def", "_is_url_like_archive", "(", "url", ")", ":", "# type: (str) -> bool", "filename", "=", "Link", "(", "url", ")", ".", "filename", "for", "bad_ext", "in", "ARCHIVE_EXTENSIONS", ":", "if", "filename", ".", "endswith", "(", "bad_ext", ")", ":", "return", ...	29.111111	8.555556
def geo_haystack(self, name, bucket_size): """ Create a Haystack index. See: http://www.mongodb.org/display/DOCS/Geospatial+Haystack+Indexing :param name: Name of the indexed column :param bucket_size: Size of the haystack buckets (see mongo docs) """ self.c...	[ "def", "geo_haystack", "(", "self", ",", "name", ",", "bucket_size", ")", ":", "self", ".", "components", ".", "append", "(", "(", "name", ",", "'geoHaystack'", ")", ")", "self", ".", "__bucket_size", "=", "bucket_size", "return", "self" ]	41.1	16
def GetDateRange(self): """Return the range over which this ServicePeriod is valid. The range includes exception dates that add service outside of (start_date, end_date), but doesn't shrink the range if exception dates take away service at the edges of the range. Returns: A tuple of "YYYYMMD...	[ "def", "GetDateRange", "(", "self", ")", ":", "start", "=", "self", ".", "start_date", "end", "=", "self", ".", "end_date", "for", "date", ",", "(", "exception_type", ",", "_", ")", "in", "self", ".", "date_exceptions", ".", "items", "(", ")", ":", "...	31.962963	20.555556
def getVersionString(): """ Function return string with version information. It is performed by use one of three procedures: git describe, file in .git dir and file __VERSION__. """ version_string = None try: version_string = subprocess.check_output(['git', 'describe']) except: ...	[ "def", "getVersionString", "(", ")", ":", "version_string", "=", "None", "try", ":", "version_string", "=", "subprocess", ".", "check_output", "(", "[", "'git'", ",", "'describe'", "]", ")", "except", ":", "logger", ".", "warning", "(", "'Command \"git describ...	35.393939	20.30303
def unified_load(namespace, subclasses=None, recurse=False): """Provides a unified interface to both the module and class loaders, finding modules by default or classes if given a ``subclasses`` parameter. """ if subclasses is not None: return ClassLoader(recurse=recurse).load(namespace, subcla...	[ "def", "unified_load", "(", "namespace", ",", "subclasses", "=", "None", ",", "recurse", "=", "False", ")", ":", "if", "subclasses", "is", "not", "None", ":", "return", "ClassLoader", "(", "recurse", "=", "recurse", ")", ".", "load", "(", "namespace", ",...	44.333333	22.333333
def _lmder1_linear_full_rank(n, m, factor, target_fnorm1, target_fnorm2): """A full-rank linear function (lmder test #1)""" def func(params, vec): s = params.sum() temp = 2. * s / m + 1 vec[:] = -temp vec[:params.size] += params def jac(params, jac): # jac.shape = (...	[ "def", "_lmder1_linear_full_rank", "(", "n", ",", "m", ",", "factor", ",", "target_fnorm1", ",", "target_fnorm2", ")", ":", "def", "func", "(", "params", ",", "vec", ")", ":", "s", "=", "params", ".", "sum", "(", ")", "temp", "=", "2.", "*", "s", "...	28.285714	16.904762
def returnOrderBook(self, currencyPair='all', depth='50'): """Returns the order book for a given market, as well as a sequence number for use with the Push API and an indicator specifying whether the market is frozen. You may set currencyPair to "all" to get the order books of all market...	[ "def", "returnOrderBook", "(", "self", ",", "currencyPair", "=", "'all'", ",", "depth", "=", "'50'", ")", ":", "return", "self", ".", "_public", "(", "'returnOrderBook'", ",", "currencyPair", "=", "currencyPair", ",", "depth", "=", "depth", ")" ]	62	17.285714
def group_primers(self, my_list): """Group elements in list by certain number 'n'""" new_list = [] n = 2 for i in range(0, len(my_list), n): grouped_primers = my_list[i:i + n] forward_primer = grouped_primers[0].split(" ") reverse_primer = grouped_prim...	[ "def", "group_primers", "(", "self", ",", "my_list", ")", ":", "new_list", "=", "[", "]", "n", "=", "2", "for", "i", "in", "range", "(", "0", ",", "len", "(", "my_list", ")", ",", "n", ")", ":", "grouped_primers", "=", "my_list", "[", "i", ":", ...	48.5	18.666667
def info(self, params=None): ''' /v1/account/info GET - account Retrieve information about the current account Link: https://www.vultr.com/api/#account_info ''' params = params if params else dict() return self.request('/v1/account/info', params, 'GET')	[ "def", "info", "(", "self", ",", "params", "=", "None", ")", ":", "params", "=", "params", "if", "params", "else", "dict", "(", ")", "return", "self", ".", "request", "(", "'/v1/account/info'", ",", "params", ",", "'GET'", ")" ]	33.555556	18.444444
def get_request_message(cls, remote_info): # pylint: disable=g-bad-name """Gets request message or container from remote info. Args: remote_info: Instance of protorpc.remote._RemoteMethodInfo corresponding to a method. Returns: Either an instance of the request type from the remote ...	[ "def", "get_request_message", "(", "cls", ",", "remote_info", ")", ":", "# pylint: disable=g-bad-name", "if", "remote_info", "in", "cls", ".", "__remote_info_cache", ":", "return", "cls", ".", "__remote_info_cache", "[", "remote_info", "]", "else", ":", "return", ...	35.666667	21.866667
def perform_edit_extension_draft_operation(self, draft_patch, publisher_name, extension_name, draft_id): """PerformEditExtensionDraftOperation. [Preview API] :param :class:`<ExtensionDraftPatch> <azure.devops.v5_1.gallery.models.ExtensionDraftPatch>` draft_patch: :param str publisher_nam...	[ "def", "perform_edit_extension_draft_operation", "(", "self", ",", "draft_patch", ",", "publisher_name", ",", "extension_name", ",", "draft_id", ")", ":", "route_values", "=", "{", "}", "if", "publisher_name", "is", "not", "None", ":", "route_values", "[", "'publi...	57.826087	24.913043
def cpu_and_memory(programs, items): """Retrieve CPU and memory/core specified in configuration input. """ assert len(items) > 0, "Finding job resources but no items to process" config = items[0]["config"] all_cores = [] all_memory = [] algs = [config_utils.get_algorithm_config(x) for x in i...	[ "def", "cpu_and_memory", "(", "programs", ",", "items", ")", ":", "assert", "len", "(", "items", ")", ">", "0", ",", "\"Finding job resources but no items to process\"", "config", "=", "items", "[", "0", "]", "[", "\"config\"", "]", "all_cores", "=", "[", "]...	39.461538	14.615385
def is_transition_matrix(T, tol=1e-12): r"""Check if the given matrix is a transition matrix. Parameters ---------- T : (M, M) ndarray or scipy.sparse matrix Matrix to check tol : float (optional) Floating point tolerance to check with Returns ------- is_transition_matr...	[ "def", "is_transition_matrix", "(", "T", ",", "tol", "=", "1e-12", ")", ":", "T", "=", "_types", ".", "ensure_ndarray_or_sparse", "(", "T", ",", "ndim", "=", "2", ",", "uniform", "=", "True", ",", "kind", "=", "'numeric'", ")", "if", "_issparse", "(", ...	29.317073	23.804878
def _handle_request(self, request: dict) -> dict: """Processes Alexa requests from skill server and returns responses to Alexa. Args: request: Dict with Alexa request payload and metadata. Returns: result: Alexa formatted or error response. """ request_bo...	[ "def", "_handle_request", "(", "self", ",", "request", ":", "dict", ")", "->", "dict", ":", "request_body", ":", "bytes", "=", "request", "[", "'request_body'", "]", "signature_chain_url", ":", "str", "=", "request", "[", "'signature_chain_url'", "]", "signatu...	43.468085	26.148936
def tensor(self, field_name, tensor_ind): """ Returns the tensor for a given field and tensor index. Parameters ---------- field_name : str the name of the field to load tensor_index : int the index of the tensor Returns ------- :...	[ "def", "tensor", "(", "self", ",", "field_name", ",", "tensor_ind", ")", ":", "if", "tensor_ind", "==", "self", ".", "_tensor_cache_file_num", "[", "field_name", "]", ":", "return", "self", ".", "_tensors", "[", "field_name", "]", "filename", "=", "self", ...	34.545455	16.318182
def first(seq, key=lambda x: bool(x), default=None, apply=lambda x: x): """Give the first value that satisfies the key test. Args: seq (iterable): key (callable): test for each element of iterable default: returned when all elements fail test apply (callable): applied to element...	[ "def", "first", "(", "seq", ",", "key", "=", "lambda", "x", ":", "bool", "(", "x", ")", ",", "default", "=", "None", ",", "apply", "=", "lambda", "x", ":", "x", ")", ":", "return", "next", "(", "(", "apply", "(", "x", ")", "for", "x", "in", ...	36.612903	26.645161
def _init_metadata(self): """stub""" self._learning_objective_id_metadata = { 'element_id': Id(self.my_osid_object_form._authority, self.my_osid_object_form._namespace, 'learning_objective_id'), 'element_label': 'Learning ...	[ "def", "_init_metadata", "(", "self", ")", ":", "self", ".", "_learning_objective_id_metadata", "=", "{", "'element_id'", ":", "Id", "(", "self", ".", "my_osid_object_form", ".", "_authority", ",", "self", ".", "my_osid_object_form", ".", "_namespace", ",", "'le...	39.666667	15.533333
def _call_func_bc(nargs, idx, ops, keys): """ Implements transformation of CALL_FUNCTION bc inst to Rapids expression. The implementation follows definition of behavior defined in https://docs.python.org/3/library/dis.html :param nargs: number of arguments including keyword and positional argum...	[ "def", "_call_func_bc", "(", "nargs", ",", "idx", ",", "ops", ",", "keys", ")", ":", "named_args", "=", "{", "}", "unnamed_args", "=", "[", "]", "args", "=", "[", "]", "# Extract arguments based on calling convention for CALL_FUNCTION_KW", "while", "nargs", ">",...	41.3	17.25
def gatk_filter_rnaseq(vrn_file, data): """ this incorporates filters listed here, dropping clusters of variants within a 35 nucleotide window, high fischer strand values and low quality by depth https://software.broadinstitute.org/gatk/guide/article?id=3891 java -jar GenomeAnalysisTK.jar -T Var...	[ "def", "gatk_filter_rnaseq", "(", "vrn_file", ",", "data", ")", ":", "out_file", "=", "\"%s-filter%s\"", "%", "utils", ".", "splitext_plus", "(", "vrn_file", ")", "if", "not", "file_exists", "(", "out_file", ")", ":", "ref_file", "=", "dd", ".", "get_ref_fil...	51.096774	16.774194
def uniform_partition_fromintv(intv_prod, shape, nodes_on_bdry=False): """Return a partition of an interval product into equally sized cells. Parameters ---------- intv_prod : `IntervalProd` Interval product to be partitioned shape : int or sequence of ints Number of nodes per axis....	[ "def", "uniform_partition_fromintv", "(", "intv_prod", ",", "shape", ",", "nodes_on_bdry", "=", "False", ")", ":", "grid", "=", "uniform_grid_fromintv", "(", "intv_prod", ",", "shape", ",", "nodes_on_bdry", "=", "nodes_on_bdry", ")", "return", "RectPartition", "("...	37.46875	19.390625
def similar(names=None, ids=None, start=0, results=15, buckets=None, limit=False, max_familiarity=None, min_familiarity=None, max_hotttnesss=None, min_hotttnesss=None, seed_catalog=None,artist_start_year_before=None, \ artist_start_year_after=None,artist_end_year_before=None,artist_end_year_afte...	[ "def", "similar", "(", "names", "=", "None", ",", "ids", "=", "None", ",", "start", "=", "0", ",", "results", "=", "15", ",", "buckets", "=", "None", ",", "limit", "=", "False", ",", "max_familiarity", "=", "None", ",", "min_familiarity", "=", "None"...	37.546512	26.988372
def generic_http_header_parser_for(header_name): """ A parser factory to extract the request id from an HTTP header :return: A parser that can be used to extract the request id from the current request context :rtype: ()->str\|None """ def parser(): request_id = request.headers.get(heade...	[ "def", "generic_http_header_parser_for", "(", "header_name", ")", ":", "def", "parser", "(", ")", ":", "request_id", "=", "request", ".", "headers", ".", "get", "(", "header_name", ",", "''", ")", ".", "strip", "(", ")", "if", "not", "request_id", ":", "...	31.6	21.066667
def register (type, suffixes = [], base_type = None): """ Registers a target type, possibly derived from a 'base-type'. If 'suffixes' are provided, they list all the suffixes that mean a file is of 'type'. Also, the first element gives the suffix to be used when constructing and object of 't...	[ "def", "register", "(", "type", ",", "suffixes", "=", "[", "]", ",", "base_type", "=", "None", ")", ":", "# Type names cannot contain hyphens, because when used as", "# feature-values they will be interpreted as composite features", "# which need to be decomposed.", "if", "__re...	44.140351	22.070175
def ffconvert(fname, limit_states, ff, min_iml=1E-10): """ Convert a fragility function into a numpy array plus a bunch of attributes. :param fname: path to the fragility model file :param limit_states: expected limit states :param ff: fragility function node :returns: a pair (array, dictio...	[ "def", "ffconvert", "(", "fname", ",", "limit_states", ",", "ff", ",", "min_iml", "=", "1E-10", ")", ":", "with", "context", "(", "fname", ",", "ff", ")", ":", "ffs", "=", "ff", "[", "1", ":", "]", "imls", "=", "ff", ".", "imls", "nodamage", "=",...	42.439394	13.924242
def _load_pretrained_tok2vec(nlp, loc): """Load pre-trained weights for the 'token-to-vector' part of the component models, which is typically a CNN. See 'spacy pretrain'. Experimental. """ with loc.open("rb") as file_: weights_data = file_.read() loaded = [] for name, component in nlp.p...	[ "def", "_load_pretrained_tok2vec", "(", "nlp", ",", "loc", ")", ":", "with", "loc", ".", "open", "(", "\"rb\"", ")", "as", "file_", ":", "weights_data", "=", "file_", ".", "read", "(", ")", "loaded", "=", "[", "]", "for", "name", ",", "component", "i...	41.833333	13
def gen_goal(self, y_des): """Generate the goal for path imitation. For rhythmic DMPs the goal is the average of the desired trajectory. y_des np.array: the desired trajectory to follow """ goal = np.zeros(self.dmps) for n in range(self.dmps): ...	[ "def", "gen_goal", "(", "self", ",", "y_des", ")", ":", "goal", "=", "np", ".", "zeros", "(", "self", ".", "dmps", ")", "for", "n", "in", "range", "(", "self", ".", "dmps", ")", ":", "num_idx", "=", "~", "np", ".", "isnan", "(", "y_des", "[", ...	33.4	18.066667
def full_name(self): """ You can get full name of user. :return: str """ full_name = self.first_name if self.last_name: full_name += ' ' + self.last_name return full_name	[ "def", "full_name", "(", "self", ")", ":", "full_name", "=", "self", ".", "first_name", "if", "self", ".", "last_name", ":", "full_name", "+=", "' '", "+", "self", ".", "last_name", "return", "full_name" ]	23	12.2
def init_app(self, app): """Init app with Flask instance. You can also pass the instance of Flask later:: oauth = OAuth() oauth.init_app(app) """ self.app = app app.extensions = getattr(app, 'extensions', {}) app.extensions[self.state_key] = self	[ "def", "init_app", "(", "self", ",", "app", ")", ":", "self", ".", "app", "=", "app", "app", ".", "extensions", "=", "getattr", "(", "app", ",", "'extensions'", ",", "{", "}", ")", "app", ".", "extensions", "[", "self", ".", "state_key", "]", "=", ...	28.181818	15.545455
def get_cycles(graph_dict, vertices=None): """given a dictionary representing an ordered graph (i.e. key are vertices and values is a list of destination vertices representing edges), return a list of detected cycles """ if not graph_dict: return () result = [] if vertices is None: ...	[ "def", "get_cycles", "(", "graph_dict", ",", "vertices", "=", "None", ")", ":", "if", "not", "graph_dict", ":", "return", "(", ")", "result", "=", "[", "]", "if", "vertices", "is", "None", ":", "vertices", "=", "graph_dict", ".", "keys", "(", ")", "f...	34.615385	14.846154
def json(cls, message): """ Print a nice JSON output Args: message: the message to print """ if type(message) is OrderedDict: pprint(dict(message)) else: pprint(message)	[ "def", "json", "(", "cls", ",", "message", ")", ":", "if", "type", "(", "message", ")", "is", "OrderedDict", ":", "pprint", "(", "dict", "(", "message", ")", ")", "else", ":", "pprint", "(", "message", ")" ]	22.272727	15.636364
def dinfdistdown(np, ang, fel, slp, src, statsm, distm, edgecontamination, wg, dist, workingdir=None, mpiexedir=None, exedir=None, log_file=None, runtime_file=None, hostfile=None): """Run D-inf distance down to stream""" in_params = {'-m': '%s %s' % (TauDEM.conv...	[ "def", "dinfdistdown", "(", "np", ",", "ang", ",", "fel", ",", "slp", ",", "src", ",", "statsm", ",", "distm", ",", "edgecontamination", ",", "wg", ",", "dist", ",", "workingdir", "=", "None", ",", "mpiexedir", "=", "None", ",", "exedir", "=", "None"...	63.875	24.9375
def to_datetime(timestamp): """Return datetime object from timestamp.""" return dt.fromtimestamp(time.mktime( time.localtime(int(str(timestamp)[:10]))))	[ "def", "to_datetime", "(", "timestamp", ")", ":", "return", "dt", ".", "fromtimestamp", "(", "time", ".", "mktime", "(", "time", ".", "localtime", "(", "int", "(", "str", "(", "timestamp", ")", "[", ":", "10", "]", ")", ")", ")", ")" ]	41.25	5.75
def new_calendar(self, calendar_name): """ Creates a new calendar :param str calendar_name: name of the new calendar :return: a new Calendar instance :rtype: Calendar """ if not calendar_name: return None url = self.build_url(self._endpoints.get('roo...	[ "def", "new_calendar", "(", "self", ",", "calendar_name", ")", ":", "if", "not", "calendar_name", ":", "return", "None", "url", "=", "self", ".", "build_url", "(", "self", ".", "_endpoints", ".", "get", "(", "'root_calendars'", ")", ")", "response", "=", ...	32.47619	21.666667
def _sizer_add(self, child): "called when adding a control to the window" if self.sizer: if DEBUG: print "adding to sizer:", child.name border = None if not border: border = child.sizer_border flags = child._sizer_flags ...	[ "def", "_sizer_add", "(", "self", ",", "child", ")", ":", "if", "self", ".", "sizer", ":", "if", "DEBUG", ":", "print", "\"adding to sizer:\"", ",", "child", ".", "name", "border", "=", "None", "if", "not", "border", ":", "border", "=", "child", ".", ...	44.111111	14.888889
def _drawContents(self, currentRti=None): """ Draws the attributes of the currentRTI """ table = self.table table.setUpdatesEnabled(False) try: table.clearContents() verticalHeader = table.verticalHeader() verticalHeader.setSectionResizeMode(Qt...	[ "def", "_drawContents", "(", "self", ",", "currentRti", "=", "None", ")", ":", "table", "=", "self", ".", "table", "table", ".", "setUpdatesEnabled", "(", "False", ")", "try", ":", "table", ".", "clearContents", "(", ")", "verticalHeader", "=", "table", ...	39.59375	18.875
def disk_check_size(ctx, param, value): """ Validation callback for disk size parameter.""" if value: # if we've got a prefix if isinstance(value, tuple): val = value[1] else: val = value if val % 1024: raise click.ClickException('Size must be ...	[ "def", "disk_check_size", "(", "ctx", ",", "param", ",", "value", ")", ":", "if", "value", ":", "# if we've got a prefix", "if", "isinstance", "(", "value", ",", "tuple", ")", ":", "val", "=", "value", "[", "1", "]", "else", ":", "val", "=", "value", ...	31.636364	15.909091
def relative_abundance(coverage): """ cov = number of bases / length of genome relative abundance = [(cov) / sum(cov for all genomes)] * 100 """ relative = {} sums = [] for genome in coverage: for cov in coverage[genome]: sums.append(0) break for genome in coverage: index = 0 for cov in coverage[geno...	[ "def", "relative_abundance", "(", "coverage", ")", ":", "relative", "=", "{", "}", "sums", "=", "[", "]", "for", "genome", "in", "coverage", ":", "for", "cov", "in", "coverage", "[", "genome", "]", ":", "sums", ".", "append", "(", "0", ")", "break", ...	22.461538	18.153846
def delete(self): """ Wraps the standard delete() method to catch expected exceptions and raise the appropriate pyrax exceptions. """ try: return super(CloudNetwork, self).delete() except exc.Forbidden as e: # Network is in use raise ex...	[ "def", "delete", "(", "self", ")", ":", "try", ":", "return", "super", "(", "CloudNetwork", ",", "self", ")", ".", "delete", "(", ")", "except", "exc", ".", "Forbidden", "as", "e", ":", "# Network is in use", "raise", "exc", ".", "NetworkInUse", "(", "...	37.2	16.2
def _amIdoneIterating(self, f_k_new, relative_tolerance, iteration, maximum_iterations, print_warning, verbose): """ Convenience function to test whether we are done iterating, same for all iteration types REQUIRED ARGUMENTS f_k_new (array): new free energies f_k (array) : o...	[ "def", "_amIdoneIterating", "(", "self", ",", "f_k_new", ",", "relative_tolerance", ",", "iteration", ",", "maximum_iterations", ",", "print_warning", ",", "verbose", ")", ":", "yesIam", "=", "False", "# Compute change from old to new estimate.", "Delta_f_k", "=", "f_...	42.786885	24.819672
def get_parent_dept_path(self): """Method to get the department list""" self.logger.info("%s\t%s" % (self.request_method, self.request_url)) return self.json_response.get("parentIds", None)	[ "def", "get_parent_dept_path", "(", "self", ")", ":", "self", ".", "logger", ".", "info", "(", "\"%s\\t%s\"", "%", "(", "self", ".", "request_method", ",", "self", ".", "request_url", ")", ")", "return", "self", ".", "json_response", ".", "get", "(", "\"...	53.25	15.25
def visit_Import(self, node): """ Check if imported module exists in MODULES. """ for alias in node.names: current_module = MODULES # Recursive check for submodules for path in alias.name.split('.'): if path not in current_module: r...	[ "def", "visit_Import", "(", "self", ",", "node", ")", ":", "for", "alias", "in", "node", ".", "names", ":", "current_module", "=", "MODULES", "# Recursive check for submodules", "for", "path", "in", "alias", ".", "name", ".", "split", "(", "'.'", ")", ":",...	42.583333	9.833333
def get_environment(self): """ Get environment facts. power and fan are currently not implemented cpu is using 1-minute average cpu hard-coded to cpu0 (i.e. only a single CPU) """ environment = {} cpu_cmd = "show proc cpu" mem_cmd = "show memory s...	[ "def", "get_environment", "(", "self", ")", ":", "environment", "=", "{", "}", "cpu_cmd", "=", "\"show proc cpu\"", "mem_cmd", "=", "\"show memory statistics\"", "temp_cmd", "=", "\"show env temperature status\"", "output", "=", "self", ".", "_send_command", "(", "c...	42.697368	15.697368
def main(custom_commandline=None): """ Main function for esptool custom_commandline - Optional override for default arguments parsing (that uses sys.argv), can be a list of custom arguments as strings. Arguments and their values need to be added as individual items to the list e.g. "-b 115200" thus ...	[ "def", "main", "(", "custom_commandline", "=", "None", ")", ":", "parser", "=", "argparse", ".", "ArgumentParser", "(", "description", "=", "'esptool.py v%s - ESP8266 ROM Bootloader Utility'", "%", "__version__", ",", "prog", "=", "'esptool'", ")", "parser", ".", ...	45.377522	28
def start_transports(self): """start thread transports.""" self.transport = Transport( self.queue, self.batch_size, self.batch_interval, self.session_factory) thread = threading.Thread(target=self.transport.loop) self.threads.append(thread) thread.daemon =...	[ "def", "start_transports", "(", "self", ")", ":", "self", ".", "transport", "=", "Transport", "(", "self", ".", "queue", ",", "self", ".", "batch_size", ",", "self", ".", "batch_interval", ",", "self", ".", "session_factory", ")", "thread", "=", "threading...	37.777778	11.333333
def _combine_arglist(self, args, kwargs): """Combine the default values and the supplied values.""" gmxargs = self.gmxargs.copy() gmxargs.update(self._combineargs(args, *kwargs)) return (), gmxargs	[ "def", "_combine_arglist", "(", "self", ",", "args", ",", "kwargs", ")", ":", "gmxargs", "=", "self", ".", "gmxargs", ".", "copy", "(", ")", "gmxargs", ".", "update", "(", "self", ".", "_combineargs", "(", "", "args", ",", "", "*", "kwargs", ")", ...	45.4	7.2
def UpdateUser(username, password=None, is_admin=False): """Updates the password or privilege-level for a user.""" user_type, password = _GetUserTypeAndPassword( username, password=password, is_admin=is_admin) grr_api = maintenance_utils.InitGRRRootAPI() grr_user = grr_api.GrrUser(username).Get() grr_us...	[ "def", "UpdateUser", "(", "username", ",", "password", "=", "None", ",", "is_admin", "=", "False", ")", ":", "user_type", ",", "password", "=", "_GetUserTypeAndPassword", "(", "username", ",", "password", "=", "password", ",", "is_admin", "=", "is_admin", ")...	51.857143	9.142857
def values(self, corr_plus, corr_cross, snrv, psd, indices, template_plus, template_cross, u_vals, hplus_cross_corr, hpnorm, hcnorm): """ Calculate the chisq at points given by indices. Returns ------- chisq: Array Chisq values, one for each sam...	[ "def", "values", "(", "self", ",", "corr_plus", ",", "corr_cross", ",", "snrv", ",", "psd", ",", "indices", ",", "template_plus", ",", "template_cross", ",", "u_vals", ",", "hplus_cross_corr", ",", "hpnorm", ",", "hcnorm", ")", ":", "if", "self", ".", "d...	45.366667	19.7
def __draw_constant_line(self, value_label_style): "Draw a constant line on the y-axis with the label" value, label, style = value_label_style start = self.transform_output_coordinates((0, value))[1] stop = self.graph_width path = etree.SubElement(self.graph, 'path', { 'd': 'M 0 %(start)s h%(stop)s' % loca...	[ "def", "__draw_constant_line", "(", "self", ",", "value_label_style", ")", ":", "value", ",", "label", ",", "style", "=", "value_label_style", "start", "=", "self", ".", "transform_output_coordinates", "(", "(", "0", ",", "value", ")", ")", "[", "1", "]", ...	34.466667	13.666667
def __complete_info_dict(self, node_info_dict, is_open): # Make pika credentials creds = pika.PlainCredentials( node_info_dict['username'], node_info_dict['password'] ) node_info_dict['credentials'] = creds if 'priority' in node_info_dict and node_info_di...	[ "def", "__complete_info_dict", "(", "self", ",", "node_info_dict", ",", "is_open", ")", ":", "# Make pika credentials", "creds", "=", "pika", ".", "PlainCredentials", "(", "node_info_dict", "[", "'username'", "]", ",", "node_info_dict", "[", "'password'", "]", ")"...	38.540984	20.639344
def write_gphocs(data, sidx): """ write the g-phocs output. This code is hella ugly bcz it's copy/pasted directly from the old loci2gphocs script from pyrad. I figure having it get done the stupid way is better than not having it done at all, at least for the time being. This could probably be sped ...	[ "def", "write_gphocs", "(", "data", ",", "sidx", ")", ":", "outfile", "=", "data", ".", "outfiles", ".", "gphocs", "infile", "=", "data", ".", "outfiles", ".", "loci", "infile", "=", "open", "(", "infile", ")", "outfile", "=", "open", "(", "outfile", ...	42.568966	22.5
def _get_adjtime_timezone(): ''' Return the timezone in /etc/adjtime of the system clock ''' adjtime_file = '/etc/adjtime' if os.path.exists(adjtime_file): cmd = ['tail', '-n', '1', adjtime_file] return __salt__['cmd.run'](cmd, python_shell=False) elif os.path.exists('/dev/rtc'):...	[ "def", "_get_adjtime_timezone", "(", ")", ":", "adjtime_file", "=", "'/etc/adjtime'", "if", "os", ".", "path", ".", "exists", "(", "adjtime_file", ")", ":", "cmd", "=", "[", "'tail'", ",", "'-n'", ",", "'1'", ",", "adjtime_file", "]", "return", "__salt__",...	31.733333	17.6
def convert_exchange_to_compounds(model): """Convert exchange reactions in model to exchange compounds. Only exchange reactions in the extracellular compartment are converted. The extracelluar compartment must be defined for the model. Args: model: :class:`NativeModel`. """ # Build set...	[ "def", "convert_exchange_to_compounds", "(", "model", ")", ":", "# Build set of exchange reactions", "exchanges", "=", "set", "(", ")", "for", "reaction", "in", "model", ".", "reactions", ":", "equation", "=", "reaction", ".", "properties", ".", "get", "(", "'eq...	39.391304	19.826087
def chunks(l, n): """ Yield n successive chunks from l. """ newn = int(len(l) / n) for i in xrange(0, n-1): yield l[inewn:inewn+newn] yield l[n*newn-newn:]	[ "def", "chunks", "(", "l", ",", "n", ")", ":", "newn", "=", "int", "(", "len", "(", "l", ")", "/", "n", ")", "for", "i", "in", "xrange", "(", "0", ",", "n", "-", "1", ")", ":", "yield", "l", "[", "i", "", "newn", ":", "i", "", "newn",...	25.571429	9.857143
def items(self): """ Return a copy of the dictionary's list of (key, value) pairs. """ r = [] for key in self._safe_keys(): try: r.append((key, self[key])) except KeyError: pass return r	[ "def", "items", "(", "self", ")", ":", "r", "=", "[", "]", "for", "key", "in", "self", ".", "_safe_keys", "(", ")", ":", "try", ":", "r", ".", "append", "(", "(", "key", ",", "self", "[", "key", "]", ")", ")", "except", "KeyError", ":", "pass...	29.555556	15
def url(context, view, subdomain=UNSET, args, *kwargs): """ Resolves a URL in a template, using subdomain-based URL resolution. If no subdomain is provided and a ``request`` is in the template context when rendering, the URL will be resolved relative to the current request's subdomain. If no ``re...	[ "def", "url", "(", "context", ",", "view", ",", "subdomain", "=", "UNSET", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "if", "subdomain", "is", "UNSET", ":", "request", "=", "context", ".", "get", "(", "'request'", ")", "if", "request", "i...	39.15625	25.21875
def __get_concurrency_maps(self, states, session=None): """ Get the concurrency maps. :param states: List of states to query for :type states: list[airflow.utils.state.State] :return: A map from (dag_id, task_id) to # of task instances and a map from (dag_id, task_id) t...	[ "def", "__get_concurrency_maps", "(", "self", ",", "states", ",", "session", "=", "None", ")", ":", "TI", "=", "models", ".", "TaskInstance", "ti_concurrency_query", "=", "(", "session", ".", "query", "(", "TI", ".", "task_id", ",", "TI", ".", "dag_id", ...	36.88	12.96
def build_module(project, env=None): '''Build project script as module''' from pyspider.libs import base_handler assert 'name' in project, 'need name of project' assert 'script' in project, 'need script of project' if env is None: env = {} # fix for old non-p...	[ "def", "build_module", "(", "project", ",", "env", "=", "None", ")", ":", "from", "pyspider", ".", "libs", "import", "base_handler", "assert", "'name'", "in", "project", ",", "'need name of project'", "assert", "'script'", "in", "project", ",", "'need script of ...	36.892857	18.357143
def invoke_hook_spout_ack(self, message_id, complete_latency_ns): """invoke task hooks for every time spout acks a tuple :type message_id: str :param message_id: message id to which an acked tuple was anchored :type complete_latency_ns: float :param complete_latency_ns: complete latency in nano sec...	[ "def", "invoke_hook_spout_ack", "(", "self", ",", "message_id", ",", "complete_latency_ns", ")", ":", "if", "len", "(", "self", ".", "task_hooks", ")", ">", "0", ":", "spout_ack_info", "=", "SpoutAckInfo", "(", "message_id", "=", "message_id", ",", "spout_task...	47	17.066667
def run(self): """Run command.""" onnx_script = os.path.realpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "tools/mypy-onnx.py")) returncode = subprocess.call([sys.executable, onnx_script]) sys.exit(returncode)	[ "def", "run", "(", "self", ")", ":", "onnx_script", "=", "os", ".", "path", ".", "realpath", "(", "os", ".", "path", ".", "join", "(", "os", ".", "path", ".", "dirname", "(", "os", ".", "path", ".", "abspath", "(", "__file__", ")", ")", ",", "\...	50.6	28.6
def _iter_module_files(): """This iterates over all relevant Python files. It goes through all loaded files from modules, all files in folders of already loaded modules as well as all files reachable through a package. """ # The list call is necessary on Python 3 in case the module # dictionary...	[ "def", "_iter_module_files", "(", ")", ":", "# The list call is necessary on Python 3 in case the module", "# dictionary modifies during iteration.", "for", "module", "in", "list", "(", "sys", ".", "modules", ".", "values", "(", ")", ")", ":", "if", "module", "is", "N...	39.045455	12.681818
def get_vnetwork_vswitches_output_vnetwork_vswitches_name(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") get_vnetwork_vswitches = ET.Element("get_vnetwork_vswitches") config = get_vnetwork_vswitches output = ET.SubElement(get_vnetwork_vswitches,...	[ "def", "get_vnetwork_vswitches_output_vnetwork_vswitches_name", "(", "self", ",", "", "", "kwargs", ")", ":", "config", "=", "ET", ".", "Element", "(", "\"config\"", ")", "get_vnetwork_vswitches", "=", "ET", ".", "Element", "(", "\"get_vnetwork_vswitches\"", ")", ...	44.461538	15.923077
def _strongly_connected_subgraph(counts, weight=1, verbose=True): """Trim a transition count matrix down to its maximal strongly ergodic subgraph. From the counts matrix, we define a graph where there exists a directed edge between two nodes, `i` and `j` if `counts[i][j] > weight`. We then find the...	[ "def", "_strongly_connected_subgraph", "(", "counts", ",", "weight", "=", "1", ",", "verbose", "=", "True", ")", ":", "n_states_input", "=", "counts", ".", "shape", "[", "0", "]", "n_components", ",", "component_assignments", "=", "csgraph", ".", "connected_co...	43.308824	22.897059
def gff(args): """ %prog gff *.gff Draw exons for genes based on gff files. Each gff file should contain only one gene, and only the "mRNA" and "CDS" feature will be drawn on the canvas. """ align_choices = ("left", "center", "right") p = OptionParser(gff.__doc__) p.add_option("--align"...	[ "def", "gff", "(", "args", ")", ":", "align_choices", "=", "(", "\"left\"", ",", "\"center\"", ",", "\"right\"", ")", "p", "=", "OptionParser", "(", "gff", ".", "__doc__", ")", "p", ".", "add_option", "(", "\"--align\"", ",", "default", "=", "\"left\"", ...	31.266667	21.088889
def _token_auth(self): """Add ThreatConnect Token Auth to Session.""" return TcExTokenAuth( self, self.args.tc_token, self.args.tc_token_expires, self.args.tc_api_path, self.tcex.log, )	[ "def", "_token_auth", "(", "self", ")", ":", "return", "TcExTokenAuth", "(", "self", ",", "self", ".", "args", ".", "tc_token", ",", "self", ".", "args", ".", "tc_token_expires", ",", "self", ".", "args", ".", "tc_api_path", ",", "self", ".", "tcex", "...	29	12.555556
def from_environment_or_defaults(cls, environment=None): """Create a Run object taking values from the local environment where possible. The run ID comes from WANDB_RUN_ID or is randomly generated. The run mode ("dryrun", or "run") comes from WANDB_MODE or defaults to "dryrun". The run ...	[ "def", "from_environment_or_defaults", "(", "cls", ",", "environment", "=", "None", ")", ":", "if", "environment", "is", "None", ":", "environment", "=", "os", ".", "environ", "run_id", "=", "environment", ".", "get", "(", "env", ".", "RUN_ID", ")", "resum...	44.690476	17.690476
def _compute_equations(self, x, verbose=False): '''Compute the values and the normals (gradients) of active constraints. Arguments: \| ``x`` -- The unknowns. ''' # compute the error and the normals. normals = [] values = [] signs = [] error ...	[ "def", "_compute_equations", "(", "self", ",", "x", ",", "verbose", "=", "False", ")", ":", "# compute the error and the normals.", "normals", "=", "[", "]", "values", "=", "[", "]", "signs", "=", "[", "]", "error", "=", "0.0", "if", "verbose", ":", "pri...	35.195122	13.146341
def calculate_angle_bw_tangents(self, base_step, cumulative=False, masked=False): """To calculate angle (Radian) between two tangent vectors of global helical axis. Parameters ---------- base_step : 1D list List of two base-steps for which angle will be calculated. ...	[ "def", "calculate_angle_bw_tangents", "(", "self", ",", "base_step", ",", "cumulative", "=", "False", ",", "masked", "=", "False", ")", ":", "if", "(", "len", "(", "base_step", ")", "!=", "2", ")", ":", "raise", "ValueError", "(", "\"See, documentation for s...	41.868852	26.016393
def _basic_auth_str(username, password): """Returns a Basic Auth string.""" authstr = 'Basic ' + to_native_string( b64encode(('%s:%s' % (username, password)).encode('latin1')).strip() ) return authstr	[ "def", "_basic_auth_str", "(", "username", ",", "password", ")", ":", "authstr", "=", "'Basic '", "+", "to_native_string", "(", "b64encode", "(", "(", "'%s:%s'", "%", "(", "username", ",", "password", ")", ")", ".", "encode", "(", "'latin1'", ")", ")", "...	27.375	21.875
def apply(self, flag_set: AbstractSet[Flag], operand: AbstractSet[Flag]) \ -> FrozenSet[Flag]: """Apply the flag operation on the two sets, returning the result. Args: flag_set: The flag set being operated on. operand: The flags to use as the operand. """ ...	[ "def", "apply", "(", "self", ",", "flag_set", ":", "AbstractSet", "[", "Flag", "]", ",", "operand", ":", "AbstractSet", "[", "Flag", "]", ")", "->", "FrozenSet", "[", "Flag", "]", ":", "if", "self", "==", "FlagOp", ".", "ADD", ":", "return", "frozens...	36.266667	14.2
def read_eeprom_calibration(self, temperature=False): # use default values for temperature, EEPROM values are usually not calibrated and random '''Reading EEPROM calibration for power regulators and temperature ''' header = self.get_format() if header == self.HEADER_V1: data...	[ "def", "read_eeprom_calibration", "(", "self", ",", "temperature", "=", "False", ")", ":", "# use default values for temperature, EEPROM values are usually not calibrated and random", "header", "=", "self", ".", "get_format", "(", ")", "if", "header", "==", "self", ".", ...	68.258065	33.354839
def _set(self, path, value, build_dir=''): """Create and set a node by path This creates a node from a filename or pandas DataFrame. If `value` is a filename, it must be relative to `build_dir`. `value` is stored as the export path. `build_dir` defaults to the current dire...	[ "def", "_set", "(", "self", ",", "path", ",", "value", ",", "build_dir", "=", "''", ")", ":", "assert", "isinstance", "(", "path", ",", "list", ")", "and", "len", "(", "path", ")", ">", "0", "if", "isinstance", "(", "value", ",", "pd", ".", "Data...	45.018182	26.345455
def create_table(self, model): """Create model and table in database. >> migrator.create_table(model) """ self.orm[model._meta.table_name] = model model._meta.database = self.database self.ops.append(model.create_table) return model	[ "def", "create_table", "(", "self", ",", "model", ")", ":", "self", ".", "orm", "[", "model", ".", "_meta", ".", "table_name", "]", "=", "model", "model", ".", "_meta", ".", "database", "=", "self", ".", "database", "self", ".", "ops", ".", "append",...	31.222222	9.555556
def set_server_setting(settings, server=_DEFAULT_SERVER): ''' Set the value of the setting for the SMTP virtual server. .. note:: The setting names are case-sensitive. :param str settings: A dictionary of the setting names and their values. :param str server: The SMTP server name. :r...	[ "def", "set_server_setting", "(", "settings", ",", "server", "=", "_DEFAULT_SERVER", ")", ":", "if", "not", "settings", ":", "_LOG", ".", "warning", "(", "'No settings provided'", ")", "return", "False", "# Some fields are formatted like '{data}'. Salt tries to convert th...	38.898551	27.217391
def create(self, store_id, product_id, data): """ Add a new image to the product. :param store_id: The store id. :type store_id: :py:class:`str` :param product_id: The id for the product of a store. :type product_id: :py:class:`str` :param data: The request body ...	[ "def", "create", "(", "self", ",", "store_id", ",", "product_id", ",", "data", ")", ":", "self", ".", "store_id", "=", "store_id", "self", ".", "product_id", "=", "product_id", "if", "'id'", "not", "in", "data", ":", "raise", "KeyError", "(", "'The produ...	35.481481	14.222222
def has_option(self, section, option): """Checks for the existence of a given option in a given section. Args: section (str): name of section option (str): name of option Returns: bool: whether the option exists in the given section """ if se...	[ "def", "has_option", "(", "self", ",", "section", ",", "option", ")", ":", "if", "section", "not", "in", "self", ".", "sections", "(", ")", ":", "return", "False", "else", ":", "option", "=", "self", ".", "optionxform", "(", "option", ")", "return", ...	30.866667	14.066667
def normalise_correlation_coefficient(image_tile_dict, transformed_array, template, normed_tolerance=1): """As above, but for when the correlation coefficient matching method is used """ template_mean = np.mean(template) template_minus_mean = template - template_mean template_norm = np.linalg.norm(t...	[ "def", "normalise_correlation_coefficient", "(", "image_tile_dict", ",", "transformed_array", ",", "template", ",", "normed_tolerance", "=", "1", ")", ":", "template_mean", "=", "np", ".", "mean", "(", "template", ")", "template_minus_mean", "=", "template", "-", ...	74.923077	37.692308
def _kernel_versions_debian(): ''' Last installed kernel name, for Debian based systems. Returns: List with possible names of last installed kernel as they are probably interpreted in output of `uname -a` command. ''' kernel_get_selections = __salt__['cmd.run']('dpkg --get-s...	[ "def", "_kernel_versions_debian", "(", ")", ":", "kernel_get_selections", "=", "__salt__", "[", "'cmd.run'", "]", "(", "'dpkg --get-selections linux-image-*'", ")", "kernels", "=", "[", "]", "kernel_versions", "=", "[", "]", "for", "line", "in", "kernel_get_selectio...	33.444444	24.111111
def from_json(cls, json): """Deserialize from json. Args: json: a dict of json compatible fields. Returns: a KeyRanges object. Raises: ValueError: if the json is invalid. """ if json["name"] in _KEYRANGES_CLASSES: return _KEYRANGES_CLASSES[json["name"]].from_json(json)...	[ "def", "from_json", "(", "cls", ",", "json", ")", ":", "if", "json", "[", "\"name\"", "]", "in", "_KEYRANGES_CLASSES", ":", "return", "_KEYRANGES_CLASSES", "[", "json", "[", "\"name\"", "]", "]", ".", "from_json", "(", "json", ")", "raise", "ValueError", ...	23.466667	18.133333
def next_down(x, context=None): """next_down(x): return the greatest representable float that's strictly less than x. This operation is quiet: flags are not affected. """ x = BigFloat._implicit_convert(x) # make sure we don't alter any flags with _saved_flags(): with (context if c...	[ "def", "next_down", "(", "x", ",", "context", "=", "None", ")", ":", "x", "=", "BigFloat", ".", "_implicit_convert", "(", "x", ")", "# make sure we don't alter any flags", "with", "_saved_flags", "(", ")", ":", "with", "(", "context", "if", "context", "is", ...	32	15.461538
def generate_form(args): """Generate form.""" form_name = args.get('<form>') logger.info('Start generating form.') _generate_form(form_name) logger.info('Finish generating form.')	[ "def", "generate_form", "(", "args", ")", ":", "form_name", "=", "args", ".", "get", "(", "'<form>'", ")", "logger", ".", "info", "(", "'Start generating form.'", ")", "_generate_form", "(", "form_name", ")", "logger", ".", "info", "(", "'Finish generating for...	32.333333	6
def __parse_fc_data(fc_data): """Parse the forecast data from the json section.""" fc = [] for day in fc_data: fcdata = { CONDITION: __cond_from_desc( __get_str( day, __WEATHERDESCRIPTION) ), TEMPERATURE: __g...	[ "def", "__parse_fc_data", "(", "fc_data", ")", ":", "fc", "=", "[", "]", "for", "day", "in", "fc_data", ":", "fcdata", "=", "{", "CONDITION", ":", "__cond_from_desc", "(", "__get_str", "(", "day", ",", "__WEATHERDESCRIPTION", ")", ")", ",", "TEMPERATURE", ...	38.703704	16.481481
def reverse(self, request, view_name): """ Returns the URL of this tenant. """ http_type = 'https://' if request.is_secure() else 'http://' domain = get_current_site(request).domain url = ''.join((http_type, self.schema_name, '.', domain, reverse(view_name))) r...	[ "def", "reverse", "(", "self", ",", "request", ",", "view_name", ")", ":", "http_type", "=", "'https://'", "if", "request", ".", "is_secure", "(", ")", "else", "'http://'", "domain", "=", "get_current_site", "(", "request", ")", ".", "domain", "url", "=", ...	29	20.636364
def _checkSetupNeeded(self, message): """Check an id_res message to see if it is a checkid_immediate cancel response. @raises SetupNeededError: if it is a checkid_immediate cancellation """ # In OpenID 1, we check to see if this is a cancel from # immediate mode by the p...	[ "def", "_checkSetupNeeded", "(", "self", ",", "message", ")", ":", "# In OpenID 1, we check to see if this is a cancel from", "# immediate mode by the presence of the user_setup_url", "# parameter.", "if", "message", ".", "isOpenID1", "(", ")", ":", "user_setup_url", "=", "me...	43.230769	15.615385
def nested_to_ring(nested_index, nside): """ Convert a HEALPix 'nested' index to a HEALPix 'ring' index Parameters ---------- nested_index : int or `~numpy.ndarray` Healpix index using the 'nested' ordering nside : int or `~numpy.ndarray` Number of pixels along the side of each ...	[ "def", "nested_to_ring", "(", "nested_index", ",", "nside", ")", ":", "nside", "=", "np", ".", "asarray", "(", "nside", ",", "dtype", "=", "np", ".", "intc", ")", "return", "_core", ".", "nested_to_ring", "(", "nested_index", ",", "nside", ")" ]	27.8	18.6
async def status(dev: Device): """Display status information.""" power = await dev.get_power() click.echo(click.style("%s" % power, bold=power)) vol = await dev.get_volume_information() click.echo(vol.pop()) play_info = await dev.get_play_info() if not play_info.is_idle: click.echo...	[ "async", "def", "status", "(", "dev", ":", "Device", ")", ":", "power", "=", "await", "dev", ".", "get_power", "(", ")", "click", ".", "echo", "(", "click", ".", "style", "(", "\"%s\"", "%", "power", ",", "bold", "=", "power", ")", ")", "vol", "=...	28.714286	15.428571
def create_field(field_info): """ Create a field by field info dict. """ field_type = field_info.get('type') if field_type not in FIELDS_NAME_MAP: raise ValueError(_('not support this field: {}').format(field_type)) field_class = FIELDS_NAME_MAP.get(field_type) params = dict(field_in...	[ "def", "create_field", "(", "field_info", ")", ":", "field_type", "=", "field_info", ".", "get", "(", "'type'", ")", "if", "field_type", "not", "in", "FIELDS_NAME_MAP", ":", "raise", "ValueError", "(", "_", "(", "'not support this field: {}'", ")", ".", "forma...	34.272727	8.090909
def get_signature(self, base_commit=None): """Get the signature of the current state of the repository TODO right now `get_signature` is an effectful process in that it adds all untracked file to staging. This is the only way to get accruate diff on new files. This is ok because we only...	[ "def", "get_signature", "(", "self", ",", "base_commit", "=", "None", ")", ":", "if", "base_commit", "is", "None", ":", "base_commit", "=", "'HEAD'", "self", ".", "run", "(", "'add'", ",", "'-A'", ",", "self", ".", "path", ")", "sha", "=", "self", "....	33.785714	18.571429

def cancel(self): """Cancel a running :meth:`iterconsume` session.""" for consumer_tag in self._open_consumers.values(): try: self.backend.cancel(consumer_tag) except KeyError: pass self._open_consumers.clear()

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35.375

13.75

def run_tfba(self, reaction): """Run FBA and tFBA on model.""" solver = self._get_solver(integer=True) p = fluxanalysis.FluxBalanceProblem(self._mm, solver) start_time = time.time() p.add_thermodynamic() try: p.maximize(reaction) except fluxanalysi...

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28.6

19.4

def _wrap_ele(self, block, view, frag, extra_data=None): """ Does the guts of the wrapping the same way for both xblocks and asides. Their wrappers provide other info in extra_data which gets put into the dom data- attrs. """ wrapped = Fragment() data = { 'usa...

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40.119048

22.404762

def twenty_five_neurons_mix_stimulated(): "Object allocation" "If M = 0 then only object will be allocated" params = pcnn_parameters(); params.AF = 0.1; params.AL = 0.0; params.AT = 0.7; params.VF = 1.0; params.VL = 1.0; params.VT = 10.0; params.M = 0.0; ...

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33.222222

18.444444

def dtrajs(self): """ get discrete trajectories """ if not self._estimated: self.logger.info("not yet parametrized, running now.") self.parametrize() return self._chain[-1].dtrajs

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37

11.833333

def tlv_parse(data): """ Parses a bytestring of TLV values into a dict with the tags as keys.""" parsed = {} while data: t, l, data = ord_byte(data[0]), ord_byte(data[1]), data[2:] parsed[t], data = data[:l], data[l:] return parsed

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36.714286

17.714286

def reset_spyder(self): """ Quit and reset Spyder and then Restart application. """ answer = QMessageBox.warning(self, _("Warning"), _("Spyder will restart and reset to default settings: <br><br>" "Do you want to continue?"), QMessageBox.Ye...

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40.7

10.7

def find_first_wt_parent(self, with_ip=False): """ Recursively looks at the part_of parent ancestry line (ignoring pooled_from parents) and returns a parent Biosample ID if its wild_type attribute is True. Args: with_ip: `bool`. True means to restrict the search to the firs...

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46.074074

24.074074

async def result(self) -> T: """\ Wait for the task's termination; either the result is returned or a raised exception is reraised. If an event is sent before the task terminates, an `EventException` is raised with the event as argument. """ try: event = await self.re...

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43.666667

18.944444

def _from_record(data): """ Infer a BigQuery table schema from a list of fields or a dictionary. The typeof the elements is used. For a list, the field names are simply 'Column1', 'Column2', etc. Args: data: The list of fields or dictionary. Returns: A list of dictionaries containing fi...

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37.882353

21.176471

def copy_path(self): """Return a copy of the current path. :returns: A list of ``(path_operation, coordinates)`` tuples of a :ref:`PATH_OPERATION` string and a tuple of floats coordinates whose content depends on the operation type: * :obj:`M...

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37.6

17.3

def get_photos_info(photoset_id): """Request the photos information with the photoset id :param photoset_id: The photoset id of flickr :type photoset_id: str :return: photos information :rtype: list """ args = _get_request_args( 'flickr.photosets.getPhotos', photoset_id=phot...

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29.764706

12.764706

def _spawn_thread(self, target): """ Create a thread """ t = Thread(target=target) t.daemon = True t.start() return t

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25.333333

13.166667

def _is_url_like_archive(url): # type: (str) -> bool """Return whether the URL looks like an archive. """ filename = Link(url).filename for bad_ext in ARCHIVE_EXTENSIONS: if filename.endswith(bad_ext): return True return False

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29.111111

8.555556

def geo_haystack(self, name, bucket_size): """ Create a Haystack index. See: http://www.mongodb.org/display/DOCS/Geospatial+Haystack+Indexing :param name: Name of the indexed column :param bucket_size: Size of the haystack buckets (see mongo docs) """ self.c...

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41.1

16

def GetDateRange(self): """Return the range over which this ServicePeriod is valid. The range includes exception dates that add service outside of (start_date, end_date), but doesn't shrink the range if exception dates take away service at the edges of the range. Returns: A tuple of "YYYYMMD...

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31.962963

20.555556

def getVersionString(): """ Function return string with version information. It is performed by use one of three procedures: git describe, file in .git dir and file __VERSION__. """ version_string = None try: version_string = subprocess.check_output(['git', 'describe']) except: ...

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35.393939

20.30303

def unified_load(namespace, subclasses=None, recurse=False): """Provides a unified interface to both the module and class loaders, finding modules by default or classes if given a ``subclasses`` parameter. """ if subclasses is not None: return ClassLoader(recurse=recurse).load(namespace, subcla...

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44.333333

22.333333

def _lmder1_linear_full_rank(n, m, factor, target_fnorm1, target_fnorm2): """A full-rank linear function (lmder test #1)""" def func(params, vec): s = params.sum() temp = 2. * s / m + 1 vec[:] = -temp vec[:params.size] += params def jac(params, jac): # jac.shape = (...

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28.285714

16.904762

def returnOrderBook(self, currencyPair='all', depth='50'): """Returns the order book for a given market, as well as a sequence number for use with the Push API and an indicator specifying whether the market is frozen. You may set currencyPair to "all" to get the order books of all market...

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62

17.285714

def group_primers(self, my_list): """Group elements in list by certain number 'n'""" new_list = [] n = 2 for i in range(0, len(my_list), n): grouped_primers = my_list[i:i + n] forward_primer = grouped_primers[0].split(" ") reverse_primer = grouped_prim...

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48.5

18.666667

def info(self, params=None): ''' /v1/account/info GET - account Retrieve information about the current account Link: https://www.vultr.com/api/#account_info ''' params = params if params else dict() return self.request('/v1/account/info', params, 'GET')

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33.555556

18.444444

def get_request_message(cls, remote_info): # pylint: disable=g-bad-name """Gets request message or container from remote info. Args: remote_info: Instance of protorpc.remote._RemoteMethodInfo corresponding to a method. Returns: Either an instance of the request type from the remote ...

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35.666667

21.866667

def perform_edit_extension_draft_operation(self, draft_patch, publisher_name, extension_name, draft_id): """PerformEditExtensionDraftOperation. [Preview API] :param :class:`<ExtensionDraftPatch> <azure.devops.v5_1.gallery.models.ExtensionDraftPatch>` draft_patch: :param str publisher_nam...

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57.826087

24.913043

def cpu_and_memory(programs, items): """Retrieve CPU and memory/core specified in configuration input. """ assert len(items) > 0, "Finding job resources but no items to process" config = items[0]["config"] all_cores = [] all_memory = [] algs = [config_utils.get_algorithm_config(x) for x in i...

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39.461538

14.615385

def is_transition_matrix(T, tol=1e-12): r"""Check if the given matrix is a transition matrix. Parameters ---------- T : (M, M) ndarray or scipy.sparse matrix Matrix to check tol : float (optional) Floating point tolerance to check with Returns ------- is_transition_matr...

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29.317073

23.804878

def _handle_request(self, request: dict) -> dict: """Processes Alexa requests from skill server and returns responses to Alexa. Args: request: Dict with Alexa request payload and metadata. Returns: result: Alexa formatted or error response. """ request_bo...

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43.468085

26.148936

def tensor(self, field_name, tensor_ind): """ Returns the tensor for a given field and tensor index. Parameters ---------- field_name : str the name of the field to load tensor_index : int the index of the tensor Returns ------- :...

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34.545455

16.318182

def first(seq, key=lambda x: bool(x), default=None, apply=lambda x: x): """Give the first value that satisfies the key test. Args: seq (iterable): key (callable): test for each element of iterable default: returned when all elements fail test apply (callable): applied to element...

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36.612903

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def _init_metadata(self): """stub""" self._learning_objective_id_metadata = { 'element_id': Id(self.my_osid_object_form._authority, self.my_osid_object_form._namespace, 'learning_objective_id'), 'element_label': 'Learning ...

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def _call_func_bc(nargs, idx, ops, keys): """ Implements transformation of CALL_FUNCTION bc inst to Rapids expression. The implementation follows definition of behavior defined in https://docs.python.org/3/library/dis.html :param nargs: number of arguments including keyword and positional argum...

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def gatk_filter_rnaseq(vrn_file, data): """ this incorporates filters listed here, dropping clusters of variants within a 35 nucleotide window, high fischer strand values and low quality by depth https://software.broadinstitute.org/gatk/guide/article?id=3891 java -jar GenomeAnalysisTK.jar -T Var...

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def uniform_partition_fromintv(intv_prod, shape, nodes_on_bdry=False): """Return a partition of an interval product into equally sized cells. Parameters ---------- intv_prod : `IntervalProd` Interval product to be partitioned shape : int or sequence of ints Number of nodes per axis....

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def similar(names=None, ids=None, start=0, results=15, buckets=None, limit=False, max_familiarity=None, min_familiarity=None, max_hotttnesss=None, min_hotttnesss=None, seed_catalog=None,artist_start_year_before=None, \ artist_start_year_after=None,artist_end_year_before=None,artist_end_year_afte...

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def generic_http_header_parser_for(header_name): """ A parser factory to extract the request id from an HTTP header :return: A parser that can be used to extract the request id from the current request context :rtype: ()->str|None """ def parser(): request_id = request.headers.get(heade...

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def register (type, suffixes = [], base_type = None): """ Registers a target type, possibly derived from a 'base-type'. If 'suffixes' are provided, they list all the suffixes that mean a file is of 'type'. Also, the first element gives the suffix to be used when constructing and object of 't...

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def ffconvert(fname, limit_states, ff, min_iml=1E-10): """ Convert a fragility function into a numpy array plus a bunch of attributes. :param fname: path to the fragility model file :param limit_states: expected limit states :param ff: fragility function node :returns: a pair (array, dictio...

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def _load_pretrained_tok2vec(nlp, loc): """Load pre-trained weights for the 'token-to-vector' part of the component models, which is typically a CNN. See 'spacy pretrain'. Experimental. """ with loc.open("rb") as file_: weights_data = file_.read() loaded = [] for name, component in nlp.p...

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def gen_goal(self, y_des): """Generate the goal for path imitation. For rhythmic DMPs the goal is the average of the desired trajectory. y_des np.array: the desired trajectory to follow """ goal = np.zeros(self.dmps) for n in range(self.dmps): ...

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def full_name(self): """ You can get full name of user. :return: str """ full_name = self.first_name if self.last_name: full_name += ' ' + self.last_name return full_name

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def init_app(self, app): """Init app with Flask instance. You can also pass the instance of Flask later:: oauth = OAuth() oauth.init_app(app) """ self.app = app app.extensions = getattr(app, 'extensions', {}) app.extensions[self.state_key] = self

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def get_cycles(graph_dict, vertices=None): """given a dictionary representing an ordered graph (i.e. key are vertices and values is a list of destination vertices representing edges), return a list of detected cycles """ if not graph_dict: return () result = [] if vertices is None: ...

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def json(cls, message): """ Print a nice JSON output Args: message: the message to print """ if type(message) is OrderedDict: pprint(dict(message)) else: pprint(message)

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def dinfdistdown(np, ang, fel, slp, src, statsm, distm, edgecontamination, wg, dist, workingdir=None, mpiexedir=None, exedir=None, log_file=None, runtime_file=None, hostfile=None): """Run D-inf distance down to stream""" in_params = {'-m': '%s %s' % (TauDEM.conv...

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def to_datetime(timestamp): """Return datetime object from timestamp.""" return dt.fromtimestamp(time.mktime( time.localtime(int(str(timestamp)[:10]))))

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def new_calendar(self, calendar_name): """ Creates a new calendar :param str calendar_name: name of the new calendar :return: a new Calendar instance :rtype: Calendar """ if not calendar_name: return None url = self.build_url(self._endpoints.get('roo...

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def _sizer_add(self, child): "called when adding a control to the window" if self.sizer: if DEBUG: print "adding to sizer:", child.name border = None if not border: border = child.sizer_border flags = child._sizer_flags ...

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def _drawContents(self, currentRti=None): """ Draws the attributes of the currentRTI """ table = self.table table.setUpdatesEnabled(False) try: table.clearContents() verticalHeader = table.verticalHeader() verticalHeader.setSectionResizeMode(Qt...

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def disk_check_size(ctx, param, value): """ Validation callback for disk size parameter.""" if value: # if we've got a prefix if isinstance(value, tuple): val = value[1] else: val = value if val % 1024: raise click.ClickException('Size must be ...

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def relative_abundance(coverage): """ cov = number of bases / length of genome relative abundance = [(cov) / sum(cov for all genomes)] * 100 """ relative = {} sums = [] for genome in coverage: for cov in coverage[genome]: sums.append(0) break for genome in coverage: index = 0 for cov in coverage[geno...

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def delete(self): """ Wraps the standard delete() method to catch expected exceptions and raise the appropriate pyrax exceptions. """ try: return super(CloudNetwork, self).delete() except exc.Forbidden as e: # Network is in use raise ex...

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def _amIdoneIterating(self, f_k_new, relative_tolerance, iteration, maximum_iterations, print_warning, verbose): """ Convenience function to test whether we are done iterating, same for all iteration types REQUIRED ARGUMENTS f_k_new (array): new free energies f_k (array) : o...

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def get_parent_dept_path(self): """Method to get the department list""" self.logger.info("%s\t%s" % (self.request_method, self.request_url)) return self.json_response.get("parentIds", None)

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def visit_Import(self, node): """ Check if imported module exists in MODULES. """ for alias in node.names: current_module = MODULES # Recursive check for submodules for path in alias.name.split('.'): if path not in current_module: r...

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def get_environment(self): """ Get environment facts. power and fan are currently not implemented cpu is using 1-minute average cpu hard-coded to cpu0 (i.e. only a single CPU) """ environment = {} cpu_cmd = "show proc cpu" mem_cmd = "show memory s...

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def main(custom_commandline=None): """ Main function for esptool custom_commandline - Optional override for default arguments parsing (that uses sys.argv), can be a list of custom arguments as strings. Arguments and their values need to be added as individual items to the list e.g. "-b 115200" thus ...

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def start_transports(self): """start thread transports.""" self.transport = Transport( self.queue, self.batch_size, self.batch_interval, self.session_factory) thread = threading.Thread(target=self.transport.loop) self.threads.append(thread) thread.daemon =...

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def _combine_arglist(self, args, kwargs): """Combine the default values and the supplied values.""" gmxargs = self.gmxargs.copy() gmxargs.update(self._combineargs(*args, **kwargs)) return (), gmxargs

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45.4

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def UpdateUser(username, password=None, is_admin=False): """Updates the password or privilege-level for a user.""" user_type, password = _GetUserTypeAndPassword( username, password=password, is_admin=is_admin) grr_api = maintenance_utils.InitGRRRootAPI() grr_user = grr_api.GrrUser(username).Get() grr_us...

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def values(self, corr_plus, corr_cross, snrv, psd, indices, template_plus, template_cross, u_vals, hplus_cross_corr, hpnorm, hcnorm): """ Calculate the chisq at points given by indices. Returns ------- chisq: Array Chisq values, one for each sam...

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45.366667

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def __draw_constant_line(self, value_label_style): "Draw a constant line on the y-axis with the label" value, label, style = value_label_style start = self.transform_output_coordinates((0, value))[1] stop = self.graph_width path = etree.SubElement(self.graph, 'path', { 'd': 'M 0 %(start)s h%(stop)s' % loca...

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def __complete_info_dict(self, node_info_dict, is_open): # Make pika credentials creds = pika.PlainCredentials( node_info_dict['username'], node_info_dict['password'] ) node_info_dict['credentials'] = creds if 'priority' in node_info_dict and node_info_di...

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38.540984

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def write_gphocs(data, sidx): """ write the g-phocs output. This code is hella ugly bcz it's copy/pasted directly from the old loci2gphocs script from pyrad. I figure having it get done the stupid way is better than not having it done at all, at least for the time being. This could probably be sped ...

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42.568966

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def _get_adjtime_timezone(): ''' Return the timezone in /etc/adjtime of the system clock ''' adjtime_file = '/etc/adjtime' if os.path.exists(adjtime_file): cmd = ['tail', '-n', '1', adjtime_file] return __salt__['cmd.run'](cmd, python_shell=False) elif os.path.exists('/dev/rtc'):...

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31.733333

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def convert_exchange_to_compounds(model): """Convert exchange reactions in model to exchange compounds. Only exchange reactions in the extracellular compartment are converted. The extracelluar compartment must be defined for the model. Args: model: :class:`NativeModel`. """ # Build set...

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def chunks(l, n): """ Yield n successive chunks from l. """ newn = int(len(l) / n) for i in xrange(0, n-1): yield l[i*newn:i*newn+newn] yield l[n*newn-newn:]

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def items(self): """ Return a copy of the dictionary's list of (key, value) pairs. """ r = [] for key in self._safe_keys(): try: r.append((key, self[key])) except KeyError: pass return r

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def url(context, view, subdomain=UNSET, *args, **kwargs): """ Resolves a URL in a template, using subdomain-based URL resolution. If no subdomain is provided and a ``request`` is in the template context when rendering, the URL will be resolved relative to the current request's subdomain. If no ``re...

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def __get_concurrency_maps(self, states, session=None): """ Get the concurrency maps. :param states: List of states to query for :type states: list[airflow.utils.state.State] :return: A map from (dag_id, task_id) to # of task instances and a map from (dag_id, task_id) t...

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36.88

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def build_module(project, env=None): '''Build project script as module''' from pyspider.libs import base_handler assert 'name' in project, 'need name of project' assert 'script' in project, 'need script of project' if env is None: env = {} # fix for old non-p...

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def invoke_hook_spout_ack(self, message_id, complete_latency_ns): """invoke task hooks for every time spout acks a tuple :type message_id: str :param message_id: message id to which an acked tuple was anchored :type complete_latency_ns: float :param complete_latency_ns: complete latency in nano sec...

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def run(self): """Run command.""" onnx_script = os.path.realpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "tools/mypy-onnx.py")) returncode = subprocess.call([sys.executable, onnx_script]) sys.exit(returncode)

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def _iter_module_files(): """This iterates over all relevant Python files. It goes through all loaded files from modules, all files in folders of already loaded modules as well as all files reachable through a package. """ # The list call is necessary on Python 3 in case the module # dictionary...

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def get_vnetwork_vswitches_output_vnetwork_vswitches_name(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") get_vnetwork_vswitches = ET.Element("get_vnetwork_vswitches") config = get_vnetwork_vswitches output = ET.SubElement(get_vnetwork_vswitches,...

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def _strongly_connected_subgraph(counts, weight=1, verbose=True): """Trim a transition count matrix down to its maximal strongly ergodic subgraph. From the counts matrix, we define a graph where there exists a directed edge between two nodes, `i` and `j` if `counts[i][j] > weight`. We then find the...

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def gff(args): """ %prog gff *.gff Draw exons for genes based on gff files. Each gff file should contain only one gene, and only the "mRNA" and "CDS" feature will be drawn on the canvas. """ align_choices = ("left", "center", "right") p = OptionParser(gff.__doc__) p.add_option("--align"...

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def _token_auth(self): """Add ThreatConnect Token Auth to Session.""" return TcExTokenAuth( self, self.args.tc_token, self.args.tc_token_expires, self.args.tc_api_path, self.tcex.log, )

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def from_environment_or_defaults(cls, environment=None): """Create a Run object taking values from the local environment where possible. The run ID comes from WANDB_RUN_ID or is randomly generated. The run mode ("dryrun", or "run") comes from WANDB_MODE or defaults to "dryrun". The run ...

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def _compute_equations(self, x, verbose=False): '''Compute the values and the normals (gradients) of active constraints. Arguments: | ``x`` -- The unknowns. ''' # compute the error and the normals. normals = [] values = [] signs = [] error ...

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def calculate_angle_bw_tangents(self, base_step, cumulative=False, masked=False): """To calculate angle (Radian) between two tangent vectors of global helical axis. Parameters ---------- base_step : 1D list List of two base-steps for which angle will be calculated. ...

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def _basic_auth_str(username, password): """Returns a Basic Auth string.""" authstr = 'Basic ' + to_native_string( b64encode(('%s:%s' % (username, password)).encode('latin1')).strip() ) return authstr

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def apply(self, flag_set: AbstractSet[Flag], operand: AbstractSet[Flag]) \ -> FrozenSet[Flag]: """Apply the flag operation on the two sets, returning the result. Args: flag_set: The flag set being operated on. operand: The flags to use as the operand. """ ...

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def read_eeprom_calibration(self, temperature=False): # use default values for temperature, EEPROM values are usually not calibrated and random '''Reading EEPROM calibration for power regulators and temperature ''' header = self.get_format() if header == self.HEADER_V1: data...

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def _set(self, path, value, build_dir=''): """Create and set a node by path This creates a node from a filename or pandas DataFrame. If `value` is a filename, it must be relative to `build_dir`. `value` is stored as the export path. `build_dir` defaults to the current dire...

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def create_table(self, model): """Create model and table in database. >> migrator.create_table(model) """ self.orm[model._meta.table_name] = model model._meta.database = self.database self.ops.append(model.create_table) return model

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def set_server_setting(settings, server=_DEFAULT_SERVER): ''' Set the value of the setting for the SMTP virtual server. .. note:: The setting names are case-sensitive. :param str settings: A dictionary of the setting names and their values. :param str server: The SMTP server name. :r...

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def create(self, store_id, product_id, data): """ Add a new image to the product. :param store_id: The store id. :type store_id: :py:class:`str` :param product_id: The id for the product of a store. :type product_id: :py:class:`str` :param data: The request body ...

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def has_option(self, section, option): """Checks for the existence of a given option in a given section. Args: section (str): name of section option (str): name of option Returns: bool: whether the option exists in the given section """ if se...

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def normalise_correlation_coefficient(image_tile_dict, transformed_array, template, normed_tolerance=1): """As above, but for when the correlation coefficient matching method is used """ template_mean = np.mean(template) template_minus_mean = template - template_mean template_norm = np.linalg.norm(t...

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def _kernel_versions_debian(): ''' Last installed kernel name, for Debian based systems. Returns: List with possible names of last installed kernel as they are probably interpreted in output of `uname -a` command. ''' kernel_get_selections = __salt__['cmd.run']('dpkg --get-s...

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def from_json(cls, json): """Deserialize from json. Args: json: a dict of json compatible fields. Returns: a KeyRanges object. Raises: ValueError: if the json is invalid. """ if json["name"] in _KEYRANGES_CLASSES: return _KEYRANGES_CLASSES[json["name"]].from_json(json)...

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def next_down(x, context=None): """next_down(x): return the greatest representable float that's strictly less than x. This operation is quiet: flags are not affected. """ x = BigFloat._implicit_convert(x) # make sure we don't alter any flags with _saved_flags(): with (context if c...

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def generate_form(args): """Generate form.""" form_name = args.get('<form>') logger.info('Start generating form.') _generate_form(form_name) logger.info('Finish generating form.')

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def __parse_fc_data(fc_data): """Parse the forecast data from the json section.""" fc = [] for day in fc_data: fcdata = { CONDITION: __cond_from_desc( __get_str( day, __WEATHERDESCRIPTION) ), TEMPERATURE: __g...

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def reverse(self, request, view_name): """ Returns the URL of this tenant. """ http_type = 'https://' if request.is_secure() else 'http://' domain = get_current_site(request).domain url = ''.join((http_type, self.schema_name, '.', domain, reverse(view_name))) r...

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def _checkSetupNeeded(self, message): """Check an id_res message to see if it is a checkid_immediate cancel response. @raises SetupNeededError: if it is a checkid_immediate cancellation """ # In OpenID 1, we check to see if this is a cancel from # immediate mode by the p...

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def nested_to_ring(nested_index, nside): """ Convert a HEALPix 'nested' index to a HEALPix 'ring' index Parameters ---------- nested_index : int or `~numpy.ndarray` Healpix index using the 'nested' ordering nside : int or `~numpy.ndarray` Number of pixels along the side of each ...

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async def status(dev: Device): """Display status information.""" power = await dev.get_power() click.echo(click.style("%s" % power, bold=power)) vol = await dev.get_volume_information() click.echo(vol.pop()) play_info = await dev.get_play_info() if not play_info.is_idle: click.echo...

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def create_field(field_info): """ Create a field by field info dict. """ field_type = field_info.get('type') if field_type not in FIELDS_NAME_MAP: raise ValueError(_('not support this field: {}').format(field_type)) field_class = FIELDS_NAME_MAP.get(field_type) params = dict(field_in...

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def get_signature(self, base_commit=None): """Get the signature of the current state of the repository TODO right now `get_signature` is an effectful process in that it adds all untracked file to staging. This is the only way to get accruate diff on new files. This is ok because we only...

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