kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def old_encode_aes(key, plaintext): """ Utility method to encode some given plaintext with the given key. Important thing to note: This is not a general purpose encryption method - it has specific semantics (see below for details). Takes the given key, pads it to 32 bytes. Then takes the given pla...	[ "def", "old_encode_aes", "(", "key", ",", "plaintext", ")", ":", "# generate 16 cryptographically secure random bytes for our IV (initial value)", "iv", "=", "os", ".", "urandom", "(", "16", ")", "# set up an AES cipher object", "cipher", "=", "AES", ".", "new", "(", ...	46.083333	26.416667
def send_msg_to_webhook( self, json_payload, log_msg ): """todo""" if SILENCE_OVERRIDE: return params = {**json_payload, 'message': log_msg} headers = {'Content-Type': 'application/json'} try: req = requests.post( ...	[ "def", "send_msg_to_webhook", "(", "self", ",", "json_payload", ",", "log_msg", ")", ":", "if", "SILENCE_OVERRIDE", ":", "return", "params", "=", "{", "", "", "json_payload", ",", "'message'", ":", "log_msg", "}", "headers", "=", "{", "'Content-Type'", ":"...	27.931034	17.310345
def diff_flux_threshold(self, skydir, fn, ts_thresh, min_counts): """Compute the differential flux threshold for a point source at position ``skydir`` with spectral parameterization ``fn``. Parameters ---------- skydir : `~astropy.coordinates.SkyCoord` Sky coordinate...	[ "def", "diff_flux_threshold", "(", "self", ",", "skydir", ",", "fn", ",", "ts_thresh", ",", "min_counts", ")", ":", "sig", ",", "bkg", ",", "bkg_fit", "=", "self", ".", "compute_counts", "(", "skydir", ",", "fn", ")", "norms", "=", "irfs", ".", "comput...	37.135135	21.27027
def incr(self, name, amount=1): """自增key的对应的值，当key不存在时则为默认值，否则在基础上自增整数amount :param name: key :param amount: 默认值 :return: 返回自增后的值 """ return self.client.incr(name, amount=amount)	[ "def", "incr", "(", "self", ",", "name", ",", "amount", "=", "1", ")", ":", "return", "self", ".", "client", ".", "incr", "(", "name", ",", "amount", "=", "amount", ")" ]	31.428571	9.571429
def _extract_median(image, mask = slice(None), size = 1, voxelspacing = None): """ Internal, single-image version of `median`. """ # set voxel spacing if voxelspacing is None: voxelspacing = [1.] * image.ndim # determine structure element size in voxel units size = _create_s...	[ "def", "_extract_median", "(", "image", ",", "mask", "=", "slice", "(", "None", ")", ",", "size", "=", "1", ",", "voxelspacing", "=", "None", ")", ":", "# set voxel spacing", "if", "voxelspacing", "is", "None", ":", "voxelspacing", "=", "[", "1.", "]", ...	34.833333	15.833333
def vertex_fingerprints(self): """A fingerprint for each vertex The result is invariant under permutation of the vertex indexes. Vertices that are symmetrically equivalent will get the same fingerprint, e.g. the hydrogens in methane would get the same fingerprint. ...	[ "def", "vertex_fingerprints", "(", "self", ")", ":", "return", "self", ".", "get_vertex_fingerprints", "(", "[", "self", ".", "get_vertex_string", "(", "i", ")", "for", "i", "in", "range", "(", "self", ".", "num_vertices", ")", "]", ",", "[", "self", "."...	43.166667	21.916667
def get_fields_dict(self, row): """ Returns a dict of field name and cleaned value pairs to initialize the model. Beware, it aligns the lists of fields and row values with Nones to allow for adding fields not found in the CSV. Whitespace around the value of the cell is stripped. ...	[ "def", "get_fields_dict", "(", "self", ",", "row", ")", ":", "return", "{", "k", ":", "getattr", "(", "self", ",", "'clean_{}'", ".", "format", "(", "k", ")", ",", "lambda", "x", ":", "x", ")", "(", "v", ".", "strip", "(", ")", "if", "isinstance"...	62.111111	30.555556
def CheckLibWithHeader(context, libs, header, language, call = None, autoadd = 1): # ToDo: accept path for library. Support system header files. """ Another (more sophisticated) test for a library. Checks, if library and header is available for language (may be 'C' or 'CXX'). ...	[ "def", "CheckLibWithHeader", "(", "context", ",", "libs", ",", "header", ",", "language", ",", "call", "=", "None", ",", "autoadd", "=", "1", ")", ":", "# ToDo: accept path for library. Support system header files.", "prog_prefix", ",", "dummy", "=", "createIncludes...	37.863636	19.045455
def mean_samples(data, xcol, ycollist): """Create a sample list that contains the mean of the original list. >>> chart_data.mean_samples([ [1, 10, 15], [2, 5, 10], [3, 8, 33] ], 0, (1, 2)) [(1, 12.5), (2, 7.5), (3, 20.5)] """ out = [] numcol = len(ycollist) try: for elem in data: ...	[ "def", "mean_samples", "(", "data", ",", "xcol", ",", "ycollist", ")", ":", "out", "=", "[", "]", "numcol", "=", "len", "(", "ycollist", ")", "try", ":", "for", "elem", "in", "data", ":", "v", "=", "0", "for", "col", "in", "ycollist", ":", "v", ...	29.157895	19.368421
def add_external_reference_to_entity(self,entity_id, external_ref): """ Adds an external reference to the given entity identifier in the entity layer @type entity_id: string @param entity_id: the entity identifier @param external_ref: an external reference object @type ex...	[ "def", "add_external_reference_to_entity", "(", "self", ",", "entity_id", ",", "external_ref", ")", ":", "if", "self", ".", "entity_layer", "is", "not", "None", ":", "self", ".", "entity_layer", ".", "add_external_reference_to_entity", "(", "entity_id", ",", "exte...	48.5	16.1
def new_state(self): """Generates a state string to be used in authorizations.""" try: self._state = self.state() log.debug("Generated new state %s.", self._state) except TypeError: self._state = self.state log.debug("Re-using previously supplied s...	[ "def", "new_state", "(", "self", ")", ":", "try", ":", "self", ".", "_state", "=", "self", ".", "state", "(", ")", "log", ".", "debug", "(", "\"Generated new state %s.\"", ",", "self", ".", "_state", ")", "except", "TypeError", ":", "self", ".", "_stat...	40.222222	15.555556
def propose_unif(self): """Propose a new live point by sampling uniformly within the unit cube.""" u = self.unitcube.sample(rstate=self.rstate) ax = np.identity(self.npdim) return u, ax	[ "def", "propose_unif", "(", "self", ")", ":", "u", "=", "self", ".", "unitcube", ".", "sample", "(", "rstate", "=", "self", ".", "rstate", ")", "ax", "=", "np", ".", "identity", "(", "self", ".", "npdim", ")", "return", "u", ",", "ax" ]	27.75	16.625
def _predict_forest(model, X, joint_contribution=False): """ For a given RandomForestRegressor, RandomForestClassifier, ExtraTreesRegressor, or ExtraTreesClassifier returns a triple of [prediction, bias and feature_contributions], such that prediction ≈ bias + feature_contributions. """ bias...	[ "def", "_predict_forest", "(", "model", ",", "X", ",", "joint_contribution", "=", "False", ")", ":", "biases", "=", "[", "]", "contributions", "=", "[", "]", "predictions", "=", "[", "]", "if", "joint_contribution", ":", "for", "tree", "in", "model", "."...	31.901961	21.156863
def _parse_arguments(self, method, parameters): """Parse arguments to method, returning a dictionary.""" # TODO: Consider raising an exception if there are extra arguments. arguments = _fetch_arguments(self, method) arg_dict = {} errors = [] for key, properties in parameters: if key i...	[ "def", "_parse_arguments", "(", "self", ",", "method", ",", "parameters", ")", ":", "# TODO: Consider raising an exception if there are extra arguments.", "arguments", "=", "_fetch_arguments", "(", "self", ",", "method", ")", "arg_dict", "=", "{", "}", "errors", "=", ...	33.575758	18.545455
def cookie_attr_value_check(attr_name, attr_value): """ Check cookie attribute value for validity. Return True if value is valid :param attr_name: attribute name to check :param attr_value: attribute value to check :return: bool """ attr_value.encode('us-ascii') return WHTTPCookie.cookie_attr_value_compl...	[ "def", "cookie_attr_value_check", "(", "attr_name", ",", "attr_value", ")", ":", "attr_value", ".", "encode", "(", "'us-ascii'", ")", "return", "WHTTPCookie", ".", "cookie_attr_value_compliance", "[", "attr_name", "]", ".", "match", "(", "attr_value", ")", "is", ...	39.777778	15.888889
def add_stroke(self, new_stroke): """ Update the beam so that it considers `new_stroke`. When a `new_stroke` comes, it can either belong to a symbol for which at least one other stroke was already made or belong to a symbol for which `new_stroke` is the first stroke. Th...	[ "def", "add_stroke", "(", "self", ",", "new_stroke", ")", ":", "global", "single_clf", "if", "len", "(", "self", ".", "hypotheses", ")", "==", "0", ":", "# Don't put this in the constructor!", "self", ".", "hypotheses", "=", "[", "{", "'segmentation'", ":", ...	37.638095	18.704762
def register(classname, cls): """Add a class to the registry of serializer classes. When a class is registered, an entry for both its classname and its full, module-qualified path are added to the registry. Example: :: class MyClass: pass register('MyClass', MyClass) ...	[ "def", "register", "(", "classname", ",", "cls", ")", ":", "# Module where the class is located", "module", "=", "cls", ".", "__module__", "# Full module path to the class", "# e.g. user.schemas.UserSchema", "fullpath", "=", "'.'", ".", "join", "(", "[", "module", ","...	32.358974	17.384615
def _TerminateFlow(rdf_flow, reason=None, flow_state=rdf_flow_objects.Flow.FlowState.ERROR): """Does the actual termination.""" flow_cls = registry.FlowRegistry.FlowClassByName(rdf_flow.flow_class_name) flow_obj = flow_cls(rdf_flow) if not flow_obj.IsRunning(): # Nothi...	[ "def", "_TerminateFlow", "(", "rdf_flow", ",", "reason", "=", "None", ",", "flow_state", "=", "rdf_flow_objects", ".", "Flow", ".", "FlowState", ".", "ERROR", ")", ":", "flow_cls", "=", "registry", ".", "FlowRegistry", ".", "FlowClassByName", "(", "rdf_flow", ...	32.481481	19.518519
def validate_bucket(self): """ Do a quick check to see if the s3 bucket is valid :return: """ s3_check_cmd = "aws s3 ls s3://{} --profile '{}' --region '{}'".format(self.bucket_name, self.aws_project, ...	[ "def", "validate_bucket", "(", "self", ")", ":", "s3_check_cmd", "=", "\"aws s3 ls s3://{} --profile '{}' --region '{}'\"", ".", "format", "(", "self", ".", "bucket_name", ",", "self", ".", "aws_project", ",", "self", ".", "aws_regions", "[", "0", "]", ")", "pri...	47.733333	23.066667
def tracking_error(self, benchmark, ddof=0): """Standard deviation of excess returns. The standard deviation of the differences between a portfolio's returns and its benchmark's returns. [Source: CFA Institute] Also known as: tracking risk; active risk Parameters ...	[ "def", "tracking_error", "(", "self", ",", "benchmark", ",", "ddof", "=", "0", ")", ":", "er", "=", "self", ".", "excess_ret", "(", "benchmark", "=", "benchmark", ")", "return", "er", ".", "anlzd_stdev", "(", "ddof", "=", "ddof", ")" ]	29.173913	19.73913
def portfolio_performance(self, verbose=False, risk_free_rate=0.02): """ After optimising, calculate (and optionally print) the performance of the optimal portfolio. Currently calculates expected return, volatility, and the Sharpe ratio. :param verbose: whether performance should be pri...	[ "def", "portfolio_performance", "(", "self", ",", "verbose", "=", "False", ",", "risk_free_rate", "=", "0.02", ")", ":", "return", "base_optimizer", ".", "portfolio_performance", "(", "self", ".", "expected_returns", ",", "self", ".", "cov_matrix", ",", "self", ...	43.65	20.85
def parse(self, raw_sections=None, namespaces=True, strip_comments=True, strip_whitespaces=True, strip_quotation_markers=True, raise_parsing_errors=True): """ Process the file content and extracts the sections / attribut...	[ "def", "parse", "(", "self", ",", "raw_sections", "=", "None", ",", "namespaces", "=", "True", ",", "strip_comments", "=", "True", ",", "strip_whitespaces", "=", "True", ",", "strip_quotation_markers", "=", "True", ",", "raise_parsing_errors", "=", "True", ")"...	49.401575	25.968504
def allVariantAnnotationSets(self): """ Return an iterator over all variant annotation sets in the data repo """ for dataset in self.getDatasets(): for variantSet in dataset.getVariantSets(): for vaSet in variantSet.getVariantAnnotationSets(): ...	[ "def", "allVariantAnnotationSets", "(", "self", ")", ":", "for", "dataset", "in", "self", ".", "getDatasets", "(", ")", ":", "for", "variantSet", "in", "dataset", ".", "getVariantSets", "(", ")", ":", "for", "vaSet", "in", "variantSet", ".", "getVariantAnnot...	37.222222	10.333333
def getFoundIn(self, foundin_name, projectarea_id=None, projectarea_name=None, archived=False): """Get :class:`rtcclient.models.FoundIn` object by its name :param foundin_name: the foundin name :param projectarea_id: the :class:`rtcclient.project_area.ProjectArea` ...	[ "def", "getFoundIn", "(", "self", ",", "foundin_name", ",", "projectarea_id", "=", "None", ",", "projectarea_name", "=", "None", ",", "archived", "=", "False", ")", ":", "self", ".", "log", ".", "debug", "(", "\"Try to get <FoundIn %s>\"", ",", "foundin_name",...	43.75	20.0625
def get_view_nodes_from_indexes(self, indexes): """ Returns the View Nodes from given indexes. :param view: View. :type view: QWidget :param \indexes: Indexes. :type \*indexes: list :return: View nodes. :rtype: dict """ nodes = {} ...	[ "def", "get_view_nodes_from_indexes", "(", "self", ",", "*", "indexes", ")", ":", "nodes", "=", "{", "}", "model", "=", "self", ".", "model", "(", ")", "if", "not", "model", ":", "return", "nodes", "if", "not", "hasattr", "(", "model", ",", "\"get_node...	31.78125	18.28125
def _encode_item(self, item: str) -> str: """ If anonymization is on, an item gets salted and hashed here. :param str item: :return: Hashed item, if anonymization is on; the unmodified item otherwise :rtype: str """ assert item is not None if not self.__r...	[ "def", "_encode_item", "(", "self", ",", "item", ":", "str", ")", "->", "str", ":", "assert", "item", "is", "not", "None", "if", "not", "self", ".", "__redis_conf", "[", "'anonymization'", "]", ":", "return", "item", "connection", "=", "self", ".", "__...	38.222222	15.555556
def _connect(): ''' Return server object used to interact with Jenkins. :return: server object used to interact with Jenkins ''' jenkins_url = __salt__['config.get']('jenkins.url') or \ __salt__['config.get']('jenkins:url') or \ __salt__['pillar.get']('jenkins.url') jenkins_use...	[ "def", "_connect", "(", ")", ":", "jenkins_url", "=", "__salt__", "[", "'config.get'", "]", "(", "'jenkins.url'", ")", "or", "__salt__", "[", "'config.get'", "]", "(", "'jenkins:url'", ")", "or", "__salt__", "[", "'pillar.get'", "]", "(", "'jenkins.url'", ")...	35.458333	21.208333
def authenticate_unless_readonly(f, self, args, kwargs): """authenticate this page unless* readonly view is active. In read-only mode, the notebook list and print view should be accessible without authentication. """ @web.authenticated def auth_f(self, args, *kwargs): ret...	[ "def", "authenticate_unless_readonly", "(", "f", ",", "self", ",", "", "args", ",", "", "", "kwargs", ")", ":", "@", "web", ".", "authenticated", "def", "auth_f", "(", "self", ",", "", "args", ",", "", "", "kwargs", ")", ":", "return", "f", "...	31	14.466667
def update(self): """ rebuild the tree view of the history item tree store :return: """ # with self._update_lock: self._update_lock.acquire() self._store_expansion_state() self.history_tree_store.clear() selected_sm_m = self.model.get_selected_stat...	[ "def", "update", "(", "self", ")", ":", "# with self._update_lock:", "self", ".", "_update_lock", ".", "acquire", "(", ")", "self", ".", "_store_expansion_state", "(", ")", "self", ".", "history_tree_store", ".", "clear", "(", ")", "selected_sm_m", "=", "self"...	50.282051	24.692308
def setto(self, s): """ set j+1...k to string s, readjusting k """ length = len(s) self.b[self.j+1:self.j+1+length] = s self.k = self.j + length	[ "def", "setto", "(", "self", ",", "s", ")", ":", "length", "=", "len", "(", "s", ")", "self", ".", "b", "[", "self", ".", "j", "+", "1", ":", "self", ".", "j", "+", "1", "+", "length", "]", "=", "s", "self", ".", "k", "=", "self", ".", ...	34.4	10
def _get_file_iterator(self, file_obj): """ For given `file_obj` return iterator, which will read the file in `self.read_bs` chunks. Args: file_obj (file): File-like object. Return: iterator: Iterator reading the file-like object in chunks. """ ...	[ "def", "_get_file_iterator", "(", "self", ",", "file_obj", ")", ":", "file_obj", ".", "seek", "(", "0", ")", "return", "iter", "(", "lambda", ":", "file_obj", ".", "read", "(", "self", ".", "read_bs", ")", ",", "''", ")" ]	28	20.571429
def create(self, id): """ Create a new tenant id """ resp = self.client.accounts.create(id=id) self.display(resp)	[ "def", "create", "(", "self", ",", "id", ")", ":", "resp", "=", "self", ".", "client", ".", "accounts", ".", "create", "(", "id", "=", "id", ")", "self", ".", "display", "(", "resp", ")" ]	33.5	10.5
def home_url(): """Get project's home URL based on settings.PROJECT_HOME_NAMESPACE. Returns None if PROJECT_HOME_NAMESPACE is not defined in settings. """ try: return reverse(home_namespace) except Exception: url = home_namespace try: validate_url = URLValidator(...	[ "def", "home_url", "(", ")", ":", "try", ":", "return", "reverse", "(", "home_namespace", ")", "except", "Exception", ":", "url", "=", "home_namespace", "try", ":", "validate_url", "=", "URLValidator", "(", ")", "if", "'://'", "not", "in", "url", ":", "u...	28.588235	14.941176
def _proc_pax(self, tarfile): """Process an extended or global header as described in POSIX.1-2008. """ # Read the header information. buf = tarfile.fileobj.read(self._block(self.size)) # A pax header stores supplemental information for either # the following ...	[ "def", "_proc_pax", "(", "self", ",", "tarfile", ")", ":", "# Read the header information.", "buf", "=", "tarfile", ".", "fileobj", ".", "read", "(", "self", ".", "_block", "(", "self", ".", "size", ")", ")", "# A pax header stores supplemental information for eit...	42.782178	21.039604
def get_dependency_element(self, symbol): """Checks if the specified symbol is the name of one of the methods that this module depends on. If it is, search for the actual code element and return it.""" for depend in self.dependencies: if "." in depend: #We kno...	[ "def", "get_dependency_element", "(", "self", ",", "symbol", ")", ":", "for", "depend", "in", "self", ".", "dependencies", ":", "if", "\".\"", "in", "depend", ":", "#We know the module name and the executable name, easy", "if", "depend", ".", "split", "(", "\".\""...	45.208333	19.291667
def upscale(file_name, scale=1.5, margin_x=0, margin_y=0, suffix='scaled', tempdir=None): """Upscale a PDF to a large size.""" def adjust(page): info = PageMerge().add(page) x1, y1, x2, y2 = info.xobj_box viewrect = (margin_x, margin_y, x2 - x1 - 2 * margin_x, y2 - y1 - 2 * margin_y) ...	[ "def", "upscale", "(", "file_name", ",", "scale", "=", "1.5", ",", "margin_x", "=", "0", ",", "margin_y", "=", "0", ",", "suffix", "=", "'scaled'", ",", "tempdir", "=", "None", ")", ":", "def", "adjust", "(", "page", ")", ":", "info", "=", "PageMer...	38.6	21.4
def solve(self): """ Solve the cross. """ result = Formula(path_actions(a_star_search( ({f: self.cube[f] for f in "LUFDRB"}, self.cube.select_type("edge") & self.cube.has_colour(self.cube["D"].colour)), self.cross_successors, self.cross...	[ "def", "solve", "(", "self", ")", ":", "result", "=", "Formula", "(", "path_actions", "(", "a_star_search", "(", "(", "{", "f", ":", "self", ".", "cube", "[", "f", "]", "for", "f", "in", "\"LUFDRB\"", "}", ",", "self", ".", "cube", ".", "select_typ...	32	14.769231
def find_path_with_profiles(self, conversion_profiles, in_, out): ''' Like find_path, except forces the conversion profiles to be the given conversion profile setting. Useful for "temporarily overriding" the global conversion profiles with your own. ''' original_profiles ...	[ "def", "find_path_with_profiles", "(", "self", ",", "conversion_profiles", ",", "in_", ",", "out", ")", ":", "original_profiles", "=", "dict", "(", "self", ".", "conversion_profiles", ")", "self", ".", "_setup_profiles", "(", "conversion_profiles", ")", "results",...	46.454545	20.272727
def get_dimensions(**kwargs): """ Returns a list of objects describing all the dimensions with all the units. """ dimensions_list = db.DBSession.query(Dimension).options(load_only("id")).all() return_list = [] for dimension in dimensions_list: return_list.append(get_dimension(dimensi...	[ "def", "get_dimensions", "(", "", "", "kwargs", ")", ":", "dimensions_list", "=", "db", ".", "DBSession", ".", "query", "(", "Dimension", ")", ".", "options", "(", "load_only", "(", "\"id\"", ")", ")", ".", "all", "(", ")", "return_list", "=", "[", ...	31.090909	21.090909
def _generate_anchors(base_size, scales, aspect_ratios): """Generate anchor (reference) windows by enumerating aspect ratios X scales wrt a reference (0, 0, base_size - 1, base_size - 1) window. """ anchor = np.array([1, 1, base_size, base_size], dtype=np.float) - 1 anchors = _ratio_enum(anchor, asp...	[ "def", "_generate_anchors", "(", "base_size", ",", "scales", ",", "aspect_ratios", ")", ":", "anchor", "=", "np", ".", "array", "(", "[", "1", ",", "1", ",", "base_size", ",", "base_size", "]", ",", "dtype", "=", "np", ".", "float", ")", "-", "1", ...	46.8	17.8
def update(self): """Fetch updated information about devices""" if self.device_time_check(): if not self.in_process: outlets, switches, fans = self.get_devices() self.outlets = helpers.resolve_updates(self.outlets, outlets) self.switches = h...	[ "def", "update", "(", "self", ")", ":", "if", "self", ".", "device_time_check", "(", ")", ":", "if", "not", "self", ".", "in_process", ":", "outlets", ",", "switches", ",", "fans", "=", "self", ".", "get_devices", "(", ")", "self", ".", "outlets", "=...	35.357143	21.857143
def _singleton_method(name): """Return a function to the `name` method on a singleton `coverage` object. The singleton object is created the first time one of these functions is called. """ # Disable pylint msg W0612, because a bunch of variables look unused, but # they're accessed via locals(...	[ "def", "_singleton_method", "(", "name", ")", ":", "# Disable pylint msg W0612, because a bunch of variables look unused, but", "# they're accessed via locals().", "# pylint: disable=W0612", "def", "wrapper", "(", "", "args", ",", "", "*", "kwargs", ")", ":", "\"\"\"Singlet...	31.277778	21.055556
def unregister(self, plugin=None, plugin_file=None): """ Unregister all plugins, or a specific plugin, via an instance, or file (path) containing plugin(s). When this method is called without any arguments then all plugins will be deactivated. :param plugin: Plugin to unregister. ...	[ "def", "unregister", "(", "self", ",", "plugin", "=", "None", ",", "plugin_file", "=", "None", ")", ":", "if", "plugin", "is", "None", "and", "plugin_file", "is", "None", ":", "for", "name", ",", "plugin", "in", "self", ".", "plugins", ".", "items", ...	38.451613	18.967742
def write_shared_locations(self, paths, dry_run=False): """ Write shared location information to the SHARED file in .dist-info. :param paths: A dictionary as described in the documentation for :meth:`shared_locations`. :param dry_run: If True, the action is logged but no file is ...	[ "def", "write_shared_locations", "(", "self", ",", "paths", ",", "dry_run", "=", "False", ")", ":", "shared_path", "=", "os", ".", "path", ".", "join", "(", "self", ".", "path", ",", "'SHARED'", ")", "logger", ".", "info", "(", "'creating %s'", ",", "s...	41.041667	15.375
def load(self, **kwargs): """Method to list the UCS on the system Since this is only fixed in 12.1.0 and up we implemented version check here """ # Check if we are using 12.1.0 version or above when using this method self._is_version_supported_method('12.1.0') n...	[ "def", "load", "(", "self", ",", "", "", "kwargs", ")", ":", "# Check if we are using 12.1.0 version or above when using this method", "self", ".", "_is_version_supported_method", "(", "'12.1.0'", ")", "newinst", "=", "self", ".", "_stamp_out_core", "(", ")", "newin...	30.615385	16.769231
def convert(args, *kargs): """ Wrapper around CountryConverter.convert() Uses the same parameters. This function has the same performance as CountryConverter.convert for one call; for multiple calls it is better to instantiate a common CountryConverter (this avoid loading the source data file mul...	[ "def", "convert", "(", "", "args", ",", "", "*", "kargs", ")", ":", "init", "=", "{", "'country_data'", ":", "COUNTRY_DATA_FILE", ",", "'additional_data'", ":", "None", ",", "'only_UNmember'", ":", "False", ",", "'include_obsolete'", ":", "False", "}", "...	37.177419	23.887097
def make_dataset_header(data, file_format, aminoacids): """Creates the dataset header for NEXUS files from ``#NEXUS`` to ``MATRIX``. Parameters: data (namedtuple): with necessary info for dataset creation. file_format (str): TNT, PHYLIP, NEXUS, FASTA aminoacids (boolean): If ``ami...	[ "def", "make_dataset_header", "(", "data", ",", "file_format", ",", "aminoacids", ")", ":", "if", "aminoacids", ":", "datatype", "=", "'PROTEIN'", "else", ":", "datatype", "=", "'DNA'", "if", "file_format", "in", "[", "'NEXUS'", ",", "'PHYLIP'", ",", "'FASTA...	28.315789	20.184211
def a2bits(chars: str) -> str: """Converts a string to its bits representation as a string of 0's and 1's. >>> a2bits("Hello World!") '010010000110010101101100011011000110111100100000010101110110111101110010011011000110010000100001' """ return bin(reduce(lambda x, y: (x << 8) + y, (ord(c) for c in ...	[ "def", "a2bits", "(", "chars", ":", "str", ")", "->", "str", ":", "return", "bin", "(", "reduce", "(", "lambda", "x", ",", "y", ":", "(", "x", "<<", "8", ")", "+", "y", ",", "(", "ord", "(", "c", ")", "for", "c", "in", "chars", ")", ",", ...	37.888889	25
def get_trace( self, project_id, trace_id, retry=google.api_core.gapic_v1.method.DEFAULT, timeout=google.api_core.gapic_v1.method.DEFAULT, metadata=None, ): """ Gets a single trace by its ID. Example: >>> from google.cloud import t...	[ "def", "get_trace", "(", "self", ",", "project_id", ",", "trace_id", ",", "retry", "=", "google", ".", "api_core", ".", "gapic_v1", ".", "method", ".", "DEFAULT", ",", "timeout", "=", "google", ".", "api_core", ".", "gapic_v1", ".", "method", ".", "DEFAU...	40.114754	22.737705
def launch_instance(instance_name, command, existing_ip=None, cpu=1, mem=4, code_dir=None, setup_command=None): """Launch a GCE instance.""" # Create instance ip = existing_ip or create_instance...	[ "def", "launch_instance", "(", "instance_name", ",", "command", ",", "existing_ip", "=", "None", ",", "cpu", "=", "1", ",", "mem", "=", "4", ",", "code_dir", "=", "None", ",", "setup_command", "=", "None", ")", ":", "# Create instance", "ip", "=", "exist...	32.5	18.642857
def get_outputs(self, out, max_plugins_output_length): """Get check outputs from single output (split perfdata etc). Updates output, perf_data and long_output attributes. :param out: output data of a check :type out: str :param max_output: max plugin data length :type m...	[ "def", "get_outputs", "(", "self", ",", "out", ",", "max_plugins_output_length", ")", ":", "# Squeeze all output after max_plugins_output_length", "out", "=", "out", "[", ":", "max_plugins_output_length", "]", "# manage escaped pipes", "out", "=", "out", ".", "replace",...	42.333333	21.144928
def get_component_id_list(self, system_id): '''get list of component IDs with parameters for a given system ID''' ret = [] for (s,c) in self.mpstate.mav_param_by_sysid.keys(): if s == system_id: ret.append(c) return ret	[ "def", "get_component_id_list", "(", "self", ",", "system_id", ")", ":", "ret", "=", "[", "]", "for", "(", "s", ",", "c", ")", "in", "self", ".", "mpstate", ".", "mav_param_by_sysid", ".", "keys", "(", ")", ":", "if", "s", "==", "system_id", ":", "...	39	18.142857
def _and_join(self, close_group=False): """Combine terms with AND. There must be a term added before using this method. Arguments: close_group (bool): If ``True``, will end the current group and start a new one. If ``False``, will continue current group. ...	[ "def", "_and_join", "(", "self", ",", "close_group", "=", "False", ")", ":", "if", "not", "self", ".", "initialized", ":", "raise", "ValueError", "(", "\"You must add a search term before adding an operator.\"", ")", "else", ":", "self", ".", "_operator", "(", "...	35.590909	23
def sign(self, message): """Signs a message. Args: message: bytes, Message to be signed. Returns: string, The signature of the message for the given key. """ message = _helpers._to_bytes(message, encoding='utf-8') return crypto.sign(self._key, me...	[ "def", "sign", "(", "self", ",", "message", ")", ":", "message", "=", "_helpers", ".", "_to_bytes", "(", "message", ",", "encoding", "=", "'utf-8'", ")", "return", "crypto", ".", "sign", "(", "self", ".", "_key", ",", "message", ",", "'sha256'", ")" ]	29.636364	20.181818
def load_xslt(filename=None, xsl=None): '''Load and compile an XSLT document (specified by filename or string) for repeated use in transforming XML. ''' parser = _get_xmlparser() if filename is not None: xslt_doc = etree.parse(filename, parser=parser) if xsl is not None: xslt_doc...	[ "def", "load_xslt", "(", "filename", "=", "None", ",", "xsl", "=", "None", ")", ":", "parser", "=", "_get_xmlparser", "(", ")", "if", "filename", "is", "not", "None", ":", "xslt_doc", "=", "etree", ".", "parse", "(", "filename", ",", "parser", "=", "...	34.727273	17.090909
def delete(self, req, driver): """Delete a network Delete a specific netowrk with id on special cloud with: :Param req :Type object Request """ response = driver.delete_network(req.params, id) data = { 'action': "delete", 'contro...	[ "def", "delete", "(", "self", ",", "req", ",", "driver", ")", ":", "response", "=", "driver", ".", "delete_network", "(", "req", ".", "params", ",", "id", ")", "data", "=", "{", "'action'", ":", "\"delete\"", ",", "'controller'", ":", "\"network\"", ",...	28.625	14.25
def on_module(self, node): # ():('body',) """Module def.""" out = None for tnode in node.body: out = self.run(tnode) return out	[ "def", "on_module", "(", "self", ",", "node", ")", ":", "# ():('body',)", "out", "=", "None", "for", "tnode", "in", "node", ".", "body", ":", "out", "=", "self", ".", "run", "(", "tnode", ")", "return", "out" ]	28.166667	10.666667
def execCommand(g, command, timeout=10): """ Executes a command by sending it to the rack server Arguments: g : hcam_drivers.globals.Container the Container object of application globals command : (string) the command (see below) Possible commands are: start : s...	[ "def", "execCommand", "(", "g", ",", "command", ",", "timeout", "=", "10", ")", ":", "if", "not", "g", ".", "cpars", "[", "'hcam_server_on'", "]", ":", "g", ".", "clog", ".", "warn", "(", "'execCommand: servers are not active'", ")", "return", "False", "...	32.217391	18.478261
def _easteregg(app=None): """Like the name says. But who knows how it works?""" def bzzzzzzz(gyver): import base64 import zlib return zlib.decompress(base64.b64decode(gyver)).decode('ascii') gyver = u'\n'.join([x + (77 - len(x)) * u' ' for x in bzzzzzzz(b''' eJyFlzuOJDkMRP06xRjymKgD...	[ "def", "_easteregg", "(", "app", "=", "None", ")", ":", "def", "bzzzzzzz", "(", "gyver", ")", ":", "import", "base64", "import", "zlib", "return", "zlib", ".", "decompress", "(", "base64", ".", "b64decode", "(", "gyver", ")", ")", ".", "decode", "(", ...	55.723077	27.692308
def action_cache_reset(): """ Delete all contents from cache folder Then re-generate cached version of all models in the local repo """ printDebug("""The existing cache will be erased and recreated.""") printDebug( """This operation may take several minutes, depending on how man...	[ "def", "action_cache_reset", "(", ")", ":", "printDebug", "(", "\"\"\"The existing cache will be erased and recreated.\"\"\"", ")", "printDebug", "(", "\"\"\"This operation may take several minutes, depending on how many files exist in your local library.\"\"\"", ")", "ONTOSPY_LOCAL_MODELS...	38.428571	19.452381
def user_topic_ids(user): """Retrieve the list of topics IDs a user has access to.""" if user.is_super_admin() or user.is_read_only_user(): query = sql.select([models.TOPICS]) else: query = (sql.select([models.JOINS_TOPICS_TEAMS.c.topic_id]) .select_from( ...	[ "def", "user_topic_ids", "(", "user", ")", ":", "if", "user", ".", "is_super_admin", "(", ")", "or", "user", ".", "is_read_only_user", "(", ")", ":", "query", "=", "sql", ".", "select", "(", "[", "models", ".", "TOPICS", "]", ")", "else", ":", "query...	51.058824	27.352941
def run_interactive_command(command, env=None, **kwargs): """ Runs a command interactively, reusing the current stdin, stdout and stderr Args: command(list of str): args of the command to execute, including the command itself as command[0] as `['ls', '-l']` env(dict of str:str):...	[ "def", "run_interactive_command", "(", "command", ",", "env", "=", "None", ",", "", "", "kwargs", ")", ":", "command_result", "=", "_run_command", "(", "command", "=", "command", ",", "out_pipe", "=", "sys", ".", "stdout", ",", "err_pipe", "=", "sys", ...	32.375	21.708333
def restart(ctx, job_name, data, open_notebook, env, message, gpu, cpu, gpup, cpup, command): """ Restart a finished job as a new job. """ # Error early if more than one --env is passed. Then get the first/only # --env out of the list so all other operations work normally (they don't # expect an...	[ "def", "restart", "(", "ctx", ",", "job_name", ",", "data", ",", "open_notebook", ",", "env", ",", "message", ",", "gpu", ",", "cpu", ",", "gpup", ",", "cpup", ",", "command", ")", ":", "# Error early if more than one --env is passed. Then get the first/only", "...	29.774194	22.935484
def macro_network(): """A network of micro elements which has greater integrated information after coarse graining to a macro scale. """ tpm = np.array([[0.3, 0.3, 0.3, 0.3], [0.3, 0.3, 0.3, 0.3], [0.3, 0.3, 0.3, 0.3], [0.3, 0.3, 1.0, 1.0], ...	[ "def", "macro_network", "(", ")", ":", "tpm", "=", "np", ".", "array", "(", "[", "[", "0.3", ",", "0.3", ",", "0.3", ",", "0.3", "]", ",", "[", "0.3", ",", "0.3", ",", "0.3", ",", "0.3", "]", ",", "[", "0.3", ",", "0.3", ",", "0.3", ",", ...	40.952381	2.761905
def _RunAndWaitForVFSFileUpdate(self, path): """Runs a flow on the client, and waits for it to finish.""" client_id = rdf_client.GetClientURNFromPath(path) # If we're not actually in a directory on a client, no need to run a flow. if client_id is None: return flow_utils.UpdateVFSFileAndWait...	[ "def", "_RunAndWaitForVFSFileUpdate", "(", "self", ",", "path", ")", ":", "client_id", "=", "rdf_client", ".", "GetClientURNFromPath", "(", "path", ")", "# If we're not actually in a directory on a client, no need to run a flow.", "if", "client_id", "is", "None", ":", "re...	30.357143	19.357143
def url(url_pattern, view, kwargs=None, name=None): """ This is replacement for ``django.conf.urls.url`` function. This url auto calls ``as_view`` method for Class based views and resolves URLPattern objects. If ``name`` is not specified it will try to guess it. :param url_pattern: string with...	[ "def", "url", "(", "url_pattern", ",", "view", ",", "kwargs", "=", "None", ",", "name", "=", "None", ")", ":", "# Special handling for included view", "if", "isinstance", "(", "url_pattern", ",", "URLPattern", ")", "and", "isinstance", "(", "view", ",", "tup...	33.607143	21.035714
def apply_refactor(self, call_id, payload): """Apply a refactor depending on its type.""" supported_refactorings = ["Rename", "InlineLocal", "AddImport", "OrganizeImports"] if payload["refactorType"]["typehint"] in supported_refactorings: diff_filepath = payload["diff"] ...	[ "def", "apply_refactor", "(", "self", ",", "call_id", ",", "payload", ")", ":", "supported_refactorings", "=", "[", "\"Rename\"", ",", "\"InlineLocal\"", ",", "\"AddImport\"", ",", "\"OrganizeImports\"", "]", "if", "payload", "[", "\"refactorType\"", "]", "[", "...	53.684211	19.421053
def make_list(default_symbol_list, len_list_to_print): ''' provide the list of symbols to use according for the list of species/arrays to plot. Parameters ---------- default_symbol_list : list Symbols that the user choose to use. len_list_to_print : integer len of list of sp...	[ "def", "make_list", "(", "default_symbol_list", ",", "len_list_to_print", ")", ":", "symbol_used", "=", "[", "]", "for", "i", "in", "range", "(", "len_list_to_print", ")", ":", "symbol_used", ".", "append", "(", "default_symbol_list", "[", "sc", ".", "mod", ...	26.421053	23.263158
def remove_shared_folder(self, name): """Removes the global shared folder with the given name previously created by :py:func:`create_shared_folder` from the collection of shared folders and stops sharing it. In the current implementation, this operation is not implement...	[ "def", "remove_shared_folder", "(", "self", ",", "name", ")", ":", "if", "not", "isinstance", "(", "name", ",", "basestring", ")", ":", "raise", "TypeError", "(", "\"name can only be an instance of type basestring\"", ")", "self", ".", "_call", "(", "\"removeShare...	37.875	16.9375
def _add_content_type(self, partname, content_type): """ Add a content type for the part with partname and content_type, using a default or override as appropriate. """ ext = partname.ext if (ext.lower(), content_type) in default_content_types: self._defau...	[ "def", "_add_content_type", "(", "self", ",", "partname", ",", "content_type", ")", ":", "ext", "=", "partname", ".", "ext", "if", "(", "ext", ".", "lower", "(", ")", ",", "content_type", ")", "in", "default_content_types", ":", "self", ".", "_defaults", ...	40.1	14.1
def __rv_french(self, word, vowels): """ Return the region RV that is used by the French stemmer. If the word begins with two vowels, RV is the region after the third letter. Otherwise, it is the region after the first vowel not at the beginning of the word, or the end of the wo...	[ "def", "__rv_french", "(", "self", ",", "word", ",", "vowels", ")", ":", "rv", "=", "\"\"", "if", "len", "(", "word", ")", ">=", "2", ":", "if", "(", "word", ".", "startswith", "(", "(", "\"par\"", ",", "\"col\"", ",", "\"tap\"", ")", ")", "or", ...	39.558824	19.441176
def _from_cfg(self, cfg): """ Initialize CFBlanket from a CFG instance. :param cfg: A CFG instance. :return: None """ # Let's first add all functions first for func in cfg.kb.functions.values(): self.add_function(func) self._mark_unknowns...	[ "def", "_from_cfg", "(", "self", ",", "cfg", ")", ":", "# Let's first add all functions first", "for", "func", "in", "cfg", ".", "kb", ".", "functions", ".", "values", "(", ")", ":", "self", ".", "add_function", "(", "func", ")", "self", ".", "_mark_unknow...	23.846154	14.769231
def model_to_dict(model, sort=False): """Convert model to a dict. Parameters ---------- model : cobra.Model The model to reformulate as a dict. sort : bool, optional Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model. Return...	[ "def", "model_to_dict", "(", "model", ",", "sort", "=", "False", ")", ":", "obj", "=", "OrderedDict", "(", ")", "obj", "[", "\"metabolites\"", "]", "=", "list", "(", "map", "(", "metabolite_to_dict", ",", "model", ".", "metabolites", ")", ")", "obj", "...	33.166667	19.888889
def serial_send(self, args): '''send some bytes''' mav = self.master.mav flags = 0 if self.locked: flags \|= mavutil.mavlink.SERIAL_CONTROL_FLAG_EXCLUSIVE if self.serial_settings.timeout != 0: flags \|= mavutil.mavlink.SERIAL_CONTROL_FLAG_RESPOND if ...	[ "def", "serial_send", "(", "self", ",", "args", ")", ":", "mav", "=", "self", ".", "master", ".", "mav", "flags", "=", "0", "if", "self", ".", "locked", ":", "flags", "\|=", "mavutil", ".", "mavlink", ".", "SERIAL_CONTROL_FLAG_EXCLUSIVE", "if", "self", ...	39.857143	14.333333
def random_ucast_ip(): """ Function to generate a random unicast ip address :return: A unicast IP Address """ first_octet = str(__random.randrange(1, 224)) def get_other_octetes(): return str(__random.randrange(0, 255)) return '{first_octet}.{second_octet}.{third_octe...	[ "def", "random_ucast_ip", "(", ")", ":", "first_octet", "=", "str", "(", "__random", ".", "randrange", "(", "1", ",", "224", ")", ")", "def", "get_other_octetes", "(", ")", ":", "return", "str", "(", "__random", ".", "randrange", "(", "0", ",", "255", ...	43.125	30.375
def parse_result(line): """ Parse the result line of a phenomizer request. Arguments: line (str): A raw output line from phenomizer Returns: result (dict): A dictionary with the phenomizer info: { 'p_value': float, 'gene_symbols': l...	[ "def", "parse_result", "(", "line", ")", ":", "if", "line", ".", "startswith", "(", "\"Problem\"", ")", ":", "raise", "RuntimeError", "(", "\"Login credentials seems to be wrong\"", ")", "result", "=", "{", "'p_value'", ":", "None", ",", "'gene_symbols'", ":", ...	24.931034	19.862069
def bunkers_storm_motion(pressure, u, v, heights): r"""Calculate the Bunkers right-mover and left-mover storm motions and sfc-6km mean flow. Uses the storm motion calculation from [Bunkers2000]_. Parameters ---------- pressure : array-like Pressure from sounding u : array-like ...	[ "def", "bunkers_storm_motion", "(", "pressure", ",", "u", ",", "v", ",", "heights", ")", ":", "# mean wind from sfc-6km", "wind_mean", "=", "concatenate", "(", "mean_pressure_weighted", "(", "pressure", ",", "u", ",", "v", ",", "heights", "=", "heights", ",", ...	37.037037	24.259259
def processing_blocks(self): """Return the a JSON dict encoding the PBs known to SDP.""" pb_list = ProcessingBlockList() # TODO(BMo) realtime, offline etc. return json.dumps(dict(active=pb_list.active, completed=pb_list.completed, ...	[ "def", "processing_blocks", "(", "self", ")", ":", "pb_list", "=", "ProcessingBlockList", "(", ")", "# TODO(BMo) realtime, offline etc.", "return", "json", ".", "dumps", "(", "dict", "(", "active", "=", "pb_list", ".", "active", ",", "completed", "=", "pb_list",...	49.142857	9
def get_abs_filename_with_sub_path(sub_path, filename): """ 生成当前路径下一级路径某文件的完整文件名； :param: * sub_path: (string) 下一级的某路径名称 * filename: (string) 下一级路径的某个文件名 :returns: * 返回类型 (tuple)，有两个值，第一个为 flag，第二个为文件名，说明见下 * flag: (bool) 如果文件存在，返回 True，文件不存在...	[ "def", "get_abs_filename_with_sub_path", "(", "sub_path", ",", "filename", ")", ":", "try", ":", "cur_path", "=", "pathlib", ".", "Path", ".", "cwd", "(", ")", "abs_filename", "=", "cur_path", "/", "pathlib", ".", "Path", "(", "sub_path", ")", "/", "filena...	29.54717	21.358491
def swaggerize_response(response, op): """ Delegate handling the Swagger concerns of the response to bravado-core. :type response: :class:`pyramid.response.Response` :type op: :class:`bravado_core.operation.Operation` """ response_spec = get_response_spec(response.status_int, op) bravado_co...	[ "def", "swaggerize_response", "(", "response", ",", "op", ")", ":", "response_spec", "=", "get_response_spec", "(", "response", ".", "status_int", ",", "op", ")", "bravado_core", ".", "response", ".", "validate_response", "(", "response_spec", ",", "op", ",", ...	40.2	15.2
def convert_shaders(convert, shaders): """ Modify shading code so that we can write code once and make it run "everywhere". """ # New version of the shaders out = [] if convert == 'es2': for isfragment, shader in enumerate(shaders): has_version = False has_prec...	[ "def", "convert_shaders", "(", "convert", ",", "shaders", ")", ":", "# New version of the shaders", "out", "=", "[", "]", "if", "convert", "==", "'es2'", ":", "for", "isfragment", ",", "shader", "in", "enumerate", "(", "shaders", ")", ":", "has_version", "="...	35.118644	15.711864
def bam2mat(args): """ %prog bam2mat input.bam Convert bam file to .mat format, which is simply numpy 2D array. Important parameter is the resolution, which is the cell size. Small cell size lead to more fine-grained heatmap, but leads to large .mat size and slower plotting. """ import ...	[ "def", "bam2mat", "(", "args", ")", ":", "import", "pysam", "from", "jcvi", ".", "utils", ".", "cbook", "import", "percentage", "p", "=", "OptionParser", "(", "bam2mat", ".", "__doc__", ")", "p", ".", "add_option", "(", "\"--resolution\"", ",", "default", ...	33.24	19.9
def system_monitor_cid_card_threshold_down_threshold(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") system_monitor = ET.SubElement(config, "system-monitor", xmlns="urn:brocade.com:mgmt:brocade-system-monitor") cid_card = ET.SubElement(system_monitor, "c...	[ "def", "system_monitor_cid_card_threshold_down_threshold", "(", "self", ",", "", "", "kwargs", ")", ":", "config", "=", "ET", ".", "Element", "(", "\"config\"", ")", "system_monitor", "=", "ET", ".", "SubElement", "(", "config", ",", "\"system-monitor\"", ",",...	49.416667	21.333333
def _bor16(ins): ''' Pops top 2 operands out of the stack, and performs 1st operand OR (bitwise) 2nd operand (top of the stack), pushes result (16 bit in HL). 16 bit un/signed version Optimizations: If any of the operators are constants: Returns either 0 or the oth...	[ "def", "_bor16", "(", "ins", ")", ":", "op1", ",", "op2", "=", "tuple", "(", "ins", ".", "quad", "[", "2", ":", "]", ")", "if", "_int_ops", "(", "op1", ",", "op2", ")", "is", "not", "None", ":", "op1", ",", "op2", "=", "_int_ops", "(", "op1",...	26.71875	18.15625
def converter(type_name): """Get a given converter by name, or raise an exception.""" converter = TYPES.get(type_name) if converter is None: raise ConverterError('Unknown converter: %r' % type_name) return converter()	[ "def", "converter", "(", "type_name", ")", ":", "converter", "=", "TYPES", ".", "get", "(", "type_name", ")", "if", "converter", "is", "None", ":", "raise", "ConverterError", "(", "'Unknown converter: %r'", "%", "type_name", ")", "return", "converter", "(", ...	39.333333	12.833333
def get_version_from_unpacked_sdist(path): """Assume path points to unpacked source distribution and get version.""" # This is a condensed version of the relevant code in pkginfo 1.4.1 try: with open(os.path.join(path, 'PKG-INFO')) as f: data = f.read() except IOError: # Coul...	[ "def", "get_version_from_unpacked_sdist", "(", "path", ")", ":", "# This is a condensed version of the relevant code in pkginfo 1.4.1", "try", ":", "with", "open", "(", "os", ".", "path", ".", "join", "(", "path", ",", "'PKG-INFO'", ")", ")", "as", "f", ":", "data...	37.928571	16.857143
def alignment(self, align): '''Sets the alignment of the printer. Args: align: desired alignment. Options are 'left', 'center', 'right', and 'justified'. Anything else will throw an error. Returns: None Raises: RuntimeError: Invali...	[ "def", "alignment", "(", "self", ",", "align", ")", ":", "if", "align", "==", "'left'", ":", "align", "=", "'0'", "elif", "align", "==", "'center'", ":", "align", "=", "'1'", "elif", "align", "==", "'right'", ":", "align", "=", "'2'", "elif", "align"...	30.090909	19.818182
def modify_parameter_group(self, name, parameters=None): """ Modify a parameter group for your account. :type name: string :param name: The name of the new parameter group :type parameters: list of :class:`boto.rds.parametergroup.Parameter` :param parameters: The new pa...	[ "def", "modify_parameter_group", "(", "self", ",", "name", ",", "parameters", "=", "None", ")", ":", "params", "=", "{", "'DBParameterGroupName'", ":", "name", "}", "for", "i", "in", "range", "(", "0", ",", "len", "(", "parameters", ")", ")", ":", "par...	38.368421	15.842105
def jpath_parse_c(jpath): """ Caching variant of :py:func:`jpath_parse` function. Same arguments and return value. For performance reasons thee is no copying and all returned values are references to internal cache. Treat the returned values as read only, or suffer the consequences. """ ...	[ "def", "jpath_parse_c", "(", "jpath", ")", ":", "if", "not", "jpath", "in", "_JPATH_CACHE", ":", "_JPATH_CACHE", "[", "jpath", "]", "=", "jpath_parse", "(", "jpath", ")", "return", "_JPATH_CACHE", "[", "jpath", "]" ]	34.916667	19.416667
def _get_value(self, var): """Return value of variable in solution.""" return self._problem._p.getVarByName(self._problem._variables[var]).x	[ "def", "_get_value", "(", "self", ",", "var", ")", ":", "return", "self", ".", "_problem", ".", "_p", ".", "getVarByName", "(", "self", ".", "_problem", ".", "_variables", "[", "var", "]", ")", ".", "x" ]	51.333333	17
def shrink_patch(patch_path, target_file): """ Shrinks a patch on patch_path to contain only changes for target_file. :param patch_path: path to the shrinked patch file :param target_file: filename of a file of which changes should be kept :return: True if the is a section containing changes for ta...	[ "def", "shrink_patch", "(", "patch_path", ",", "target_file", ")", ":", "logging", ".", "debug", "(", "\"Shrinking patch file %s to keep only %s changes.\"", ",", "patch_path", ",", "target_file", ")", "shrinked_lines", "=", "[", "]", "patch_file", "=", "None", "try...	34.575	18.325
def clear(self): """"Removes all elements from the collection and resets the error handling """ self.bad = False self.errors = {} self._collection.clear()	[ "def", "clear", "(", "self", ")", ":", "self", ".", "bad", "=", "False", "self", ".", "errors", "=", "{", "}", "self", ".", "_collection", ".", "clear", "(", ")" ]	31.5	10.666667
def validate_schema(schema_name): """Validate the JSON against a required schema_name.""" def decorator(f): @wraps(f) def wrapper(args, *kw): instance = args[0] try: instance.validator(instance.schemas[schema_name]).validate(request.get_json()) ...	[ "def", "validate_schema", "(", "schema_name", ")", ":", "def", "decorator", "(", "f", ")", ":", "@", "wraps", "(", "f", ")", "def", "wrapper", "(", "", "args", ",", "", "*", "kw", ")", ":", "instance", "=", "args", "[", "0", "]", "try", ":", ...	45.052632	18.473684
def wrapped_help_text(wrapped_func): """Decorator to pass through the documentation from a wrapped function. """ def decorator(wrapper_func): """The decorator. Parameters ---------- f : callable The wrapped function. """ wrapper_func.__doc__ = ('...	[ "def", "wrapped_help_text", "(", "wrapped_func", ")", ":", "def", "decorator", "(", "wrapper_func", ")", ":", "\"\"\"The decorator.\n\n Parameters\n ----------\n f : callable\n The wrapped function.\n\n \"\"\"", "wrapper_func", ".", "__doc__", "...	29.1875	16.3125
def ParCalculate(systems,calc,cleanup=True,block=True,prefix="Calc_"): ''' Run calculators in parallel for all systems. Calculators are executed in isolated processes and directories. The resulting objects are returned in the list (one per input system). ''' if type(systems) != type([]) : ...	[ "def", "ParCalculate", "(", "systems", ",", "calc", ",", "cleanup", "=", "True", ",", "block", "=", "True", ",", "prefix", "=", "\"Calc_\"", ")", ":", "if", "type", "(", "systems", ")", "!=", "type", "(", "[", "]", ")", ":", "sysl", "=", "[", "sy...	33.016667	19.65
def setCenterLineColor(self, color): """ Sets the color for the center line. :return <QColor> """ palette = self.palette() palette.setColor(palette.GridCenterline, QColor(color))	[ "def", "setCenterLineColor", "(", "self", ",", "color", ")", ":", "palette", "=", "self", ".", "palette", "(", ")", "palette", ".", "setColor", "(", "palette", ".", "GridCenterline", ",", "QColor", "(", "color", ")", ")" ]	29	10.25
def get_data(n_samples=100): """Get synthetic classification data with n_samples samples.""" X, y = make_classification( n_samples=n_samples, n_features=N_FEATURES, n_classes=N_CLASSES, random_state=0, ) X = X.astype(np.float32) return X, y	[ "def", "get_data", "(", "n_samples", "=", "100", ")", ":", "X", ",", "y", "=", "make_classification", "(", "n_samples", "=", "n_samples", ",", "n_features", "=", "N_FEATURES", ",", "n_classes", "=", "N_CLASSES", ",", "random_state", "=", "0", ",", ")", "...	28.3	14.4
def visit_any_conditionnal(self, node1, node2): """ Set and restore the in_cond variable before visiting subnode. Compute correct dependencies on a value as both branch are possible path. """ true_naming = false_naming = None try: tmp = self.naming....	[ "def", "visit_any_conditionnal", "(", "self", ",", "node1", ",", "node2", ")", ":", "true_naming", "=", "false_naming", "=", "None", "try", ":", "tmp", "=", "self", ".", "naming", ".", "copy", "(", ")", "for", "expr", "in", "node1", ":", "self", ".", ...	28.55814	15.44186
def insertUnorderedList(self): """ Inserts an ordered list into the editor. """ cursor = self.editor().textCursor() currlist = cursor.currentList() new_style = QTextListFormat.ListDisc indent = 1 if currlist: format = currlis...	[ "def", "insertUnorderedList", "(", "self", ")", ":", "cursor", "=", "self", ".", "editor", "(", ")", ".", "textCursor", "(", ")", "currlist", "=", "cursor", ".", "currentList", "(", ")", "new_style", "=", "QTextListFormat", ".", "ListDisc", "indent", "=", ...	32.296296	11.703704
def timethis(what): """"Utility function for making simple benchmarks (calculates time calls). It can be used either as a context manager or as a decorator. """ @contextlib.contextmanager def benchmark(): timer = time.clock if sys.platform == "win32" else time.time start = timer() ...	[ "def", "timethis", "(", "what", ")", ":", "@", "contextlib", ".", "contextmanager", "def", "benchmark", "(", ")", ":", "timer", "=", "time", ".", "clock", "if", "sys", ".", "platform", "==", "\"win32\"", "else", "time", ".", "time", "start", "=", "time...	30.35	15.6

def old_encode_aes(key, plaintext): """ Utility method to encode some given plaintext with the given key. Important thing to note: This is not a general purpose encryption method - it has specific semantics (see below for details). Takes the given key, pads it to 32 bytes. Then takes the given pla...

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def send_msg_to_webhook( self, json_payload, log_msg ): """todo""" if SILENCE_OVERRIDE: return params = {**json_payload, 'message': log_msg} headers = {'Content-Type': 'application/json'} try: req = requests.post( ...

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def diff_flux_threshold(self, skydir, fn, ts_thresh, min_counts): """Compute the differential flux threshold for a point source at position ``skydir`` with spectral parameterization ``fn``. Parameters ---------- skydir : `~astropy.coordinates.SkyCoord` Sky coordinate...

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def incr(self, name, amount=1): """自增key的对应的值，当key不存在时则为默认值，否则在基础上自增整数amount :param name: key :param amount: 默认值 :return: 返回自增后的值 """ return self.client.incr(name, amount=amount)

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def _extract_median(image, mask = slice(None), size = 1, voxelspacing = None): """ Internal, single-image version of `median`. """ # set voxel spacing if voxelspacing is None: voxelspacing = [1.] * image.ndim # determine structure element size in voxel units size = _create_s...

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def vertex_fingerprints(self): """A fingerprint for each vertex The result is invariant under permutation of the vertex indexes. Vertices that are symmetrically equivalent will get the same fingerprint, e.g. the hydrogens in methane would get the same fingerprint. ...

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def get_fields_dict(self, row): """ Returns a dict of field name and cleaned value pairs to initialize the model. Beware, it aligns the lists of fields and row values with Nones to allow for adding fields not found in the CSV. Whitespace around the value of the cell is stripped. ...

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def CheckLibWithHeader(context, libs, header, language, call = None, autoadd = 1): # ToDo: accept path for library. Support system header files. """ Another (more sophisticated) test for a library. Checks, if library and header is available for language (may be 'C' or 'CXX'). ...

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def mean_samples(data, xcol, ycollist): """Create a sample list that contains the mean of the original list. >>> chart_data.mean_samples([ [1, 10, 15], [2, 5, 10], [3, 8, 33] ], 0, (1, 2)) [(1, 12.5), (2, 7.5), (3, 20.5)] """ out = [] numcol = len(ycollist) try: for elem in data: ...

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def add_external_reference_to_entity(self,entity_id, external_ref): """ Adds an external reference to the given entity identifier in the entity layer @type entity_id: string @param entity_id: the entity identifier @param external_ref: an external reference object @type ex...

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def new_state(self): """Generates a state string to be used in authorizations.""" try: self._state = self.state() log.debug("Generated new state %s.", self._state) except TypeError: self._state = self.state log.debug("Re-using previously supplied s...

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def propose_unif(self): """Propose a new live point by sampling *uniformly* within the unit cube.""" u = self.unitcube.sample(rstate=self.rstate) ax = np.identity(self.npdim) return u, ax

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def _predict_forest(model, X, joint_contribution=False): """ For a given RandomForestRegressor, RandomForestClassifier, ExtraTreesRegressor, or ExtraTreesClassifier returns a triple of [prediction, bias and feature_contributions], such that prediction ≈ bias + feature_contributions. """ bias...

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def _parse_arguments(self, method, parameters): """Parse arguments to method, returning a dictionary.""" # TODO: Consider raising an exception if there are extra arguments. arguments = _fetch_arguments(self, method) arg_dict = {} errors = [] for key, properties in parameters: if key i...

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def cookie_attr_value_check(attr_name, attr_value): """ Check cookie attribute value for validity. Return True if value is valid :param attr_name: attribute name to check :param attr_value: attribute value to check :return: bool """ attr_value.encode('us-ascii') return WHTTPCookie.cookie_attr_value_compl...

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def add_stroke(self, new_stroke): """ Update the beam so that it considers `new_stroke`. When a `new_stroke` comes, it can either belong to a symbol for which at least one other stroke was already made or belong to a symbol for which `new_stroke` is the first stroke. Th...

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def register(classname, cls): """Add a class to the registry of serializer classes. When a class is registered, an entry for both its classname and its full, module-qualified path are added to the registry. Example: :: class MyClass: pass register('MyClass', MyClass) ...

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def _TerminateFlow(rdf_flow, reason=None, flow_state=rdf_flow_objects.Flow.FlowState.ERROR): """Does the actual termination.""" flow_cls = registry.FlowRegistry.FlowClassByName(rdf_flow.flow_class_name) flow_obj = flow_cls(rdf_flow) if not flow_obj.IsRunning(): # Nothi...

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def validate_bucket(self): """ Do a quick check to see if the s3 bucket is valid :return: """ s3_check_cmd = "aws s3 ls s3://{} --profile '{}' --region '{}'".format(self.bucket_name, self.aws_project, ...

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def tracking_error(self, benchmark, ddof=0): """Standard deviation of excess returns. The standard deviation of the differences between a portfolio's returns and its benchmark's returns. [Source: CFA Institute] Also known as: tracking risk; active risk Parameters ...

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def portfolio_performance(self, verbose=False, risk_free_rate=0.02): """ After optimising, calculate (and optionally print) the performance of the optimal portfolio. Currently calculates expected return, volatility, and the Sharpe ratio. :param verbose: whether performance should be pri...

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def parse(self, raw_sections=None, namespaces=True, strip_comments=True, strip_whitespaces=True, strip_quotation_markers=True, raise_parsing_errors=True): """ Process the file content and extracts the sections / attribut...

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def allVariantAnnotationSets(self): """ Return an iterator over all variant annotation sets in the data repo """ for dataset in self.getDatasets(): for variantSet in dataset.getVariantSets(): for vaSet in variantSet.getVariantAnnotationSets(): ...

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def getFoundIn(self, foundin_name, projectarea_id=None, projectarea_name=None, archived=False): """Get :class:`rtcclient.models.FoundIn` object by its name :param foundin_name: the foundin name :param projectarea_id: the :class:`rtcclient.project_area.ProjectArea` ...

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def get_view_nodes_from_indexes(self, *indexes): """ Returns the View Nodes from given indexes. :param view: View. :type view: QWidget :param \*indexes: Indexes. :type \*indexes: list :return: View nodes. :rtype: dict """ nodes = {} ...

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def _encode_item(self, item: str) -> str: """ If anonymization is on, an item gets salted and hashed here. :param str item: :return: Hashed item, if anonymization is on; the unmodified item otherwise :rtype: str """ assert item is not None if not self.__r...

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def _connect(): ''' Return server object used to interact with Jenkins. :return: server object used to interact with Jenkins ''' jenkins_url = __salt__['config.get']('jenkins.url') or \ __salt__['config.get']('jenkins:url') or \ __salt__['pillar.get']('jenkins.url') jenkins_use...

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def authenticate_unless_readonly(f, self, *args, **kwargs): """authenticate this page *unless* readonly view is active. In read-only mode, the notebook list and print view should be accessible without authentication. """ @web.authenticated def auth_f(self, *args, **kwargs): ret...

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def update(self): """ rebuild the tree view of the history item tree store :return: """ # with self._update_lock: self._update_lock.acquire() self._store_expansion_state() self.history_tree_store.clear() selected_sm_m = self.model.get_selected_stat...

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def setto(self, s): """ set j+1...k to string s, readjusting k """ length = len(s) self.b[self.j+1:self.j+1+length] = s self.k = self.j + length

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34.4

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def _get_file_iterator(self, file_obj): """ For given `file_obj` return iterator, which will read the file in `self.read_bs` chunks. Args: file_obj (file): File-like object. Return: iterator: Iterator reading the file-like object in chunks. """ ...

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28

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def create(self, id): """ Create a new tenant id """ resp = self.client.accounts.create(id=id) self.display(resp)

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33.5

10.5

def home_url(): """Get project's home URL based on settings.PROJECT_HOME_NAMESPACE. Returns None if PROJECT_HOME_NAMESPACE is not defined in settings. """ try: return reverse(home_namespace) except Exception: url = home_namespace try: validate_url = URLValidator(...

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def _proc_pax(self, tarfile): """Process an extended or global header as described in POSIX.1-2008. """ # Read the header information. buf = tarfile.fileobj.read(self._block(self.size)) # A pax header stores supplemental information for either # the following ...

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42.782178

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def get_dependency_element(self, symbol): """Checks if the specified symbol is the name of one of the methods that this module depends on. If it is, search for the actual code element and return it.""" for depend in self.dependencies: if "." in depend: #We kno...

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45.208333

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def upscale(file_name, scale=1.5, margin_x=0, margin_y=0, suffix='scaled', tempdir=None): """Upscale a PDF to a large size.""" def adjust(page): info = PageMerge().add(page) x1, y1, x2, y2 = info.xobj_box viewrect = (margin_x, margin_y, x2 - x1 - 2 * margin_x, y2 - y1 - 2 * margin_y) ...

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38.6

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def solve(self): """ Solve the cross. """ result = Formula(path_actions(a_star_search( ({f: self.cube[f] for f in "LUFDRB"}, self.cube.select_type("edge") & self.cube.has_colour(self.cube["D"].colour)), self.cross_successors, self.cross...

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def find_path_with_profiles(self, conversion_profiles, in_, out): ''' Like find_path, except forces the conversion profiles to be the given conversion profile setting. Useful for "temporarily overriding" the global conversion profiles with your own. ''' original_profiles ...

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def get_dimensions(**kwargs): """ Returns a list of objects describing all the dimensions with all the units. """ dimensions_list = db.DBSession.query(Dimension).options(load_only("id")).all() return_list = [] for dimension in dimensions_list: return_list.append(get_dimension(dimensi...

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31.090909

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def _generate_anchors(base_size, scales, aspect_ratios): """Generate anchor (reference) windows by enumerating aspect ratios X scales wrt a reference (0, 0, base_size - 1, base_size - 1) window. """ anchor = np.array([1, 1, base_size, base_size], dtype=np.float) - 1 anchors = _ratio_enum(anchor, asp...

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46.8

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def update(self): """Fetch updated information about devices""" if self.device_time_check(): if not self.in_process: outlets, switches, fans = self.get_devices() self.outlets = helpers.resolve_updates(self.outlets, outlets) self.switches = h...

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35.357143

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def _singleton_method(name): """Return a function to the `name` method on a singleton `coverage` object. The singleton object is created the first time one of these functions is called. """ # Disable pylint msg W0612, because a bunch of variables look unused, but # they're accessed via locals(...

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def unregister(self, plugin=None, plugin_file=None): """ Unregister all plugins, or a specific plugin, via an instance, or file (path) containing plugin(s). When this method is called without any arguments then all plugins will be deactivated. :param plugin: Plugin to unregister. ...

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def write_shared_locations(self, paths, dry_run=False): """ Write shared location information to the SHARED file in .dist-info. :param paths: A dictionary as described in the documentation for :meth:`shared_locations`. :param dry_run: If True, the action is logged but no file is ...

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def load(self, **kwargs): """Method to list the UCS on the system Since this is only fixed in 12.1.0 and up we implemented version check here """ # Check if we are using 12.1.0 version or above when using this method self._is_version_supported_method('12.1.0') n...

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def convert(*args, **kargs): """ Wrapper around CountryConverter.convert() Uses the same parameters. This function has the same performance as CountryConverter.convert for one call; for multiple calls it is better to instantiate a common CountryConverter (this avoid loading the source data file mul...

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37.177419

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def make_dataset_header(data, file_format, aminoacids): """Creates the dataset header for NEXUS files from ``#NEXUS`` to ``MATRIX``. Parameters: data (namedtuple): with necessary info for dataset creation. file_format (str): TNT, PHYLIP, NEXUS, FASTA aminoacids (boolean): If ``ami...

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28.315789

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def a2bits(chars: str) -> str: """Converts a string to its bits representation as a string of 0's and 1's. >>> a2bits("Hello World!") '010010000110010101101100011011000110111100100000010101110110111101110010011011000110010000100001' """ return bin(reduce(lambda x, y: (x << 8) + y, (ord(c) for c in ...

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37.888889

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def get_trace( self, project_id, trace_id, retry=google.api_core.gapic_v1.method.DEFAULT, timeout=google.api_core.gapic_v1.method.DEFAULT, metadata=None, ): """ Gets a single trace by its ID. Example: >>> from google.cloud import t...

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40.114754

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def launch_instance(instance_name, command, existing_ip=None, cpu=1, mem=4, code_dir=None, setup_command=None): """Launch a GCE instance.""" # Create instance ip = existing_ip or create_instance...

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32.5

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def get_outputs(self, out, max_plugins_output_length): """Get check outputs from single output (split perfdata etc). Updates output, perf_data and long_output attributes. :param out: output data of a check :type out: str :param max_output: max plugin data length :type m...

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42.333333

21.144928

def get_component_id_list(self, system_id): '''get list of component IDs with parameters for a given system ID''' ret = [] for (s,c) in self.mpstate.mav_param_by_sysid.keys(): if s == system_id: ret.append(c) return ret

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39

18.142857

def _and_join(self, close_group=False): """Combine terms with AND. There must be a term added before using this method. Arguments: close_group (bool): If ``True``, will end the current group and start a new one. If ``False``, will continue current group. ...

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35.590909

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def sign(self, message): """Signs a message. Args: message: bytes, Message to be signed. Returns: string, The signature of the message for the given key. """ message = _helpers._to_bytes(message, encoding='utf-8') return crypto.sign(self._key, me...

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29.636364

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def load_xslt(filename=None, xsl=None): '''Load and compile an XSLT document (specified by filename or string) for repeated use in transforming XML. ''' parser = _get_xmlparser() if filename is not None: xslt_doc = etree.parse(filename, parser=parser) if xsl is not None: xslt_doc...

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def delete(self, req, driver): """Delete a network Delete a specific netowrk with id on special cloud with: :Param req :Type object Request """ response = driver.delete_network(req.params, id) data = { 'action': "delete", 'contro...

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28.625

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def on_module(self, node): # ():('body',) """Module def.""" out = None for tnode in node.body: out = self.run(tnode) return out

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28.166667

10.666667

def execCommand(g, command, timeout=10): """ Executes a command by sending it to the rack server Arguments: g : hcam_drivers.globals.Container the Container object of application globals command : (string) the command (see below) Possible commands are: start : s...

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32.217391

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def _easteregg(app=None): """Like the name says. But who knows how it works?""" def bzzzzzzz(gyver): import base64 import zlib return zlib.decompress(base64.b64decode(gyver)).decode('ascii') gyver = u'\n'.join([x + (77 - len(x)) * u' ' for x in bzzzzzzz(b''' eJyFlzuOJDkMRP06xRjymKgD...

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55.723077

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def action_cache_reset(): """ Delete all contents from cache folder Then re-generate cached version of all models in the local repo """ printDebug("""The existing cache will be erased and recreated.""") printDebug( """This operation may take several minutes, depending on how man...

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def user_topic_ids(user): """Retrieve the list of topics IDs a user has access to.""" if user.is_super_admin() or user.is_read_only_user(): query = sql.select([models.TOPICS]) else: query = (sql.select([models.JOINS_TOPICS_TEAMS.c.topic_id]) .select_from( ...

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51.058824

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def run_interactive_command(command, env=None, **kwargs): """ Runs a command interactively, reusing the current stdin, stdout and stderr Args: command(list of str): args of the command to execute, including the command itself as command[0] as `['ls', '-l']` env(dict of str:str):...

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def restart(ctx, job_name, data, open_notebook, env, message, gpu, cpu, gpup, cpup, command): """ Restart a finished job as a new job. """ # Error early if more than one --env is passed. Then get the first/only # --env out of the list so all other operations work normally (they don't # expect an...

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29.774194

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def macro_network(): """A network of micro elements which has greater integrated information after coarse graining to a macro scale. """ tpm = np.array([[0.3, 0.3, 0.3, 0.3], [0.3, 0.3, 0.3, 0.3], [0.3, 0.3, 0.3, 0.3], [0.3, 0.3, 1.0, 1.0], ...

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40.952381

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def _RunAndWaitForVFSFileUpdate(self, path): """Runs a flow on the client, and waits for it to finish.""" client_id = rdf_client.GetClientURNFromPath(path) # If we're not actually in a directory on a client, no need to run a flow. if client_id is None: return flow_utils.UpdateVFSFileAndWait...

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30.357143

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def url(url_pattern, view, kwargs=None, name=None): """ This is replacement for ``django.conf.urls.url`` function. This url auto calls ``as_view`` method for Class based views and resolves URLPattern objects. If ``name`` is not specified it will try to guess it. :param url_pattern: string with...

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def apply_refactor(self, call_id, payload): """Apply a refactor depending on its type.""" supported_refactorings = ["Rename", "InlineLocal", "AddImport", "OrganizeImports"] if payload["refactorType"]["typehint"] in supported_refactorings: diff_filepath = payload["diff"] ...

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def make_list(default_symbol_list, len_list_to_print): ''' provide the list of symbols to use according for the list of species/arrays to plot. Parameters ---------- default_symbol_list : list Symbols that the user choose to use. len_list_to_print : integer len of list of sp...

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def remove_shared_folder(self, name): """Removes the global shared folder with the given name previously created by :py:func:`create_shared_folder` from the collection of shared folders and stops sharing it. In the current implementation, this operation is not implement...

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def _add_content_type(self, partname, content_type): """ Add a content type for the part with *partname* and *content_type*, using a default or override as appropriate. """ ext = partname.ext if (ext.lower(), content_type) in default_content_types: self._defau...

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40.1

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def __rv_french(self, word, vowels): """ Return the region RV that is used by the French stemmer. If the word begins with two vowels, RV is the region after the third letter. Otherwise, it is the region after the first vowel not at the beginning of the word, or the end of the wo...

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39.558824

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def _from_cfg(self, cfg): """ Initialize CFBlanket from a CFG instance. :param cfg: A CFG instance. :return: None """ # Let's first add all functions first for func in cfg.kb.functions.values(): self.add_function(func) self._mark_unknowns...

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def model_to_dict(model, sort=False): """Convert model to a dict. Parameters ---------- model : cobra.Model The model to reformulate as a dict. sort : bool, optional Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model. Return...

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def serial_send(self, args): '''send some bytes''' mav = self.master.mav flags = 0 if self.locked: flags |= mavutil.mavlink.SERIAL_CONTROL_FLAG_EXCLUSIVE if self.serial_settings.timeout != 0: flags |= mavutil.mavlink.SERIAL_CONTROL_FLAG_RESPOND if ...

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def random_ucast_ip(): """ Function to generate a random unicast ip address :return: A unicast IP Address """ first_octet = str(__random.randrange(1, 224)) def get_other_octetes(): return str(__random.randrange(0, 255)) return '{first_octet}.{second_octet}.{third_octe...

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def parse_result(line): """ Parse the result line of a phenomizer request. Arguments: line (str): A raw output line from phenomizer Returns: result (dict): A dictionary with the phenomizer info: { 'p_value': float, 'gene_symbols': l...

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def bunkers_storm_motion(pressure, u, v, heights): r"""Calculate the Bunkers right-mover and left-mover storm motions and sfc-6km mean flow. Uses the storm motion calculation from [Bunkers2000]_. Parameters ---------- pressure : array-like Pressure from sounding u : array-like ...

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def processing_blocks(self): """Return the a JSON dict encoding the PBs known to SDP.""" pb_list = ProcessingBlockList() # TODO(BMo) realtime, offline etc. return json.dumps(dict(active=pb_list.active, completed=pb_list.completed, ...

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def get_abs_filename_with_sub_path(sub_path, filename): """ 生成当前路径下一级路径某文件的完整文件名； :param: * sub_path: (string) 下一级的某路径名称 * filename: (string) 下一级路径的某个文件名 :returns: * 返回类型 (tuple)，有两个值，第一个为 flag，第二个为文件名，说明见下 * flag: (bool) 如果文件存在，返回 True，文件不存在...

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def swaggerize_response(response, op): """ Delegate handling the Swagger concerns of the response to bravado-core. :type response: :class:`pyramid.response.Response` :type op: :class:`bravado_core.operation.Operation` """ response_spec = get_response_spec(response.status_int, op) bravado_co...

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def convert_shaders(convert, shaders): """ Modify shading code so that we can write code once and make it run "everywhere". """ # New version of the shaders out = [] if convert == 'es2': for isfragment, shader in enumerate(shaders): has_version = False has_prec...

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def bam2mat(args): """ %prog bam2mat input.bam Convert bam file to .mat format, which is simply numpy 2D array. Important parameter is the resolution, which is the cell size. Small cell size lead to more fine-grained heatmap, but leads to large .mat size and slower plotting. """ import ...

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33.24

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def system_monitor_cid_card_threshold_down_threshold(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") system_monitor = ET.SubElement(config, "system-monitor", xmlns="urn:brocade.com:mgmt:brocade-system-monitor") cid_card = ET.SubElement(system_monitor, "c...

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49.416667

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def _bor16(ins): ''' Pops top 2 operands out of the stack, and performs 1st operand OR (bitwise) 2nd operand (top of the stack), pushes result (16 bit in HL). 16 bit un/signed version Optimizations: If any of the operators are constants: Returns either 0 or the oth...

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def converter(type_name): """Get a given converter by name, or raise an exception.""" converter = TYPES.get(type_name) if converter is None: raise ConverterError('Unknown converter: %r' % type_name) return converter()

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39.333333

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def get_version_from_unpacked_sdist(path): """Assume path points to unpacked source distribution and get version.""" # This is a condensed version of the relevant code in pkginfo 1.4.1 try: with open(os.path.join(path, 'PKG-INFO')) as f: data = f.read() except IOError: # Coul...

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def alignment(self, align): '''Sets the alignment of the printer. Args: align: desired alignment. Options are 'left', 'center', 'right', and 'justified'. Anything else will throw an error. Returns: None Raises: RuntimeError: Invali...

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30.090909

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def modify_parameter_group(self, name, parameters=None): """ Modify a parameter group for your account. :type name: string :param name: The name of the new parameter group :type parameters: list of :class:`boto.rds.parametergroup.Parameter` :param parameters: The new pa...

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38.368421

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def jpath_parse_c(jpath): """ Caching variant of :py:func:`jpath_parse` function. Same arguments and return value. For performance reasons thee is no copying and all returned values are references to internal cache. Treat the returned values as read only, or suffer the consequences. """ ...

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34.916667

19.416667

def _get_value(self, var): """Return value of variable in solution.""" return self._problem._p.getVarByName(self._problem._variables[var]).x

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51.333333

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def shrink_patch(patch_path, target_file): """ Shrinks a patch on patch_path to contain only changes for target_file. :param patch_path: path to the shrinked patch file :param target_file: filename of a file of which changes should be kept :return: True if the is a section containing changes for ta...

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34.575

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def clear(self): """"Removes all elements from the collection and resets the error handling """ self.bad = False self.errors = {} self._collection.clear()

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31.5

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def validate_schema(schema_name): """Validate the JSON against a required schema_name.""" def decorator(f): @wraps(f) def wrapper(*args, **kw): instance = args[0] try: instance.validator(instance.schemas[schema_name]).validate(request.get_json()) ...

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def wrapped_help_text(wrapped_func): """Decorator to pass through the documentation from a wrapped function. """ def decorator(wrapper_func): """The decorator. Parameters ---------- f : callable The wrapped function. """ wrapper_func.__doc__ = ('...

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29.1875

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def ParCalculate(systems,calc,cleanup=True,block=True,prefix="Calc_"): ''' Run calculators in parallel for all systems. Calculators are executed in isolated processes and directories. The resulting objects are returned in the list (one per input system). ''' if type(systems) != type([]) : ...

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33.016667

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def setCenterLineColor(self, color): """ Sets the color for the center line. :return <QColor> """ palette = self.palette() palette.setColor(palette.GridCenterline, QColor(color))

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29

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def get_data(n_samples=100): """Get synthetic classification data with n_samples samples.""" X, y = make_classification( n_samples=n_samples, n_features=N_FEATURES, n_classes=N_CLASSES, random_state=0, ) X = X.astype(np.float32) return X, y

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28.3

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def visit_any_conditionnal(self, node1, node2): """ Set and restore the in_cond variable before visiting subnode. Compute correct dependencies on a value as both branch are possible path. """ true_naming = false_naming = None try: tmp = self.naming....

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28.55814

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def insertUnorderedList(self): """ Inserts an ordered list into the editor. """ cursor = self.editor().textCursor() currlist = cursor.currentList() new_style = QTextListFormat.ListDisc indent = 1 if currlist: format = currlis...

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32.296296

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def timethis(what): """"Utility function for making simple benchmarks (calculates time calls). It can be used either as a context manager or as a decorator. """ @contextlib.contextmanager def benchmark(): timer = time.clock if sys.platform == "win32" else time.time start = timer() ...

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30.35

15.6