kejian/codesearchnet-python-rebalanced · Datasets at Hugging Face

text stringlengths 75 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 0.18
def get_project_by_network_id(network_id,**kwargs): """ get a project complexmodel by a network_id """ user_id = kwargs.get('user_id') projects_i = db.DBSession.query(Project).join(ProjectOwner).join(Network, Project.id==Network.project_id).filter( ...	[ "def", "get_project_by_network_id", "(", "network_id", ",", "", "", "kwargs", ")", ":", "user_id", "=", "kwargs", ".", "get", "(", "'user_id'", ")", "projects_i", "=", "db", ".", "DBSession", ".", "query", "(", "Project", ")", ".", "join", "(", "Projec...	41.833333	0.011688
def load_json_dct( dct, record_store=None, schema=None, loader=from_json_compatible ): """ Create a Record instance from a json-compatible dictionary The dictionary values should have types that are json compatible, as if just loaded from a json serialized record string. ...	[ "def", "load_json_dct", "(", "dct", ",", "record_store", "=", "None", ",", "schema", "=", "None", ",", "loader", "=", "from_json_compatible", ")", ":", "if", "schema", "is", "None", ":", "if", "record_store", "is", "None", ":", "record_store", "=", "auto_s...	30.26087	0.000696
def dict_intersection(dict1, dict2, combine=False, combine_op=op.add): r""" Args: dict1 (dict): dict2 (dict): combine (bool): Combines keys only if the values are equal if False else values are combined using combine_op (default = False) combine_op (func): (default = ...	[ "def", "dict_intersection", "(", "dict1", ",", "dict2", ",", "combine", "=", "False", ",", "combine_op", "=", "op", ".", "add", ")", ":", "isect_keys", "=", "set", "(", "dict1", ".", "keys", "(", ")", ")", ".", "intersection", "(", "set", "(", "dict2...	34.581395	0.000654
def expr_stmt(self, lhs, rhs): """ (2.6, 2.7, 3.0, 3.1) expr_stmt: testlist (augassign (yield_expr\|testlist) \| ('=' (yield_expr\|testlist))*) (3.2-) expr_stmt: testlist_star_expr (augassign (yield_expr\|testlist) \| ('=' (yie...	[ "def", "expr_stmt", "(", "self", ",", "lhs", ",", "rhs", ")", ":", "if", "isinstance", "(", "rhs", ",", "ast", ".", "AugAssign", ")", ":", "if", "isinstance", "(", "lhs", ",", "ast", ".", "Tuple", ")", "or", "isinstance", "(", "lhs", ",", "ast", ...	43.12	0.001815
def cluster_elongate(): "Not so applicable for this sample" start_centers = [[1.0, 4.5], [3.1, 2.7]] template_clustering(start_centers, SIMPLE_SAMPLES.SAMPLE_ELONGATE, criterion = splitting_type.BAYESIAN_INFORMATION_CRITERION) template_clustering(start_centers, SIMPLE_SAMPLES.SAMPLE_ELONGATE, criter...	[ "def", "cluster_elongate", "(", ")", ":", "start_centers", "=", "[", "[", "1.0", ",", "4.5", "]", ",", "[", "3.1", ",", "2.7", "]", "]", "template_clustering", "(", "start_centers", ",", "SIMPLE_SAMPLES", ".", "SAMPLE_ELONGATE", ",", "criterion", "=", "spl...	74.8	0.018519
def _match_filter_plot(stream, cccsum, template_names, rawthresh, plotdir, plot_format, i): # pragma: no cover """ Plotting function for match_filter. :param stream: Stream to plot :param cccsum: Cross-correlation sum to plot :param template_names: Template names used :p...	[ "def", "_match_filter_plot", "(", "stream", ",", "cccsum", ",", "template_names", ",", "rawthresh", ",", "plotdir", ",", "plot_format", ",", "i", ")", ":", "# pragma: no cover", "import", "matplotlib", ".", "pyplot", "as", "plt", "plt", ".", "ioff", "(", ")"...	45.371429	0.000617
def display_console(self, request): """Display a standalone shell.""" if 0 not in self.frames: self.frames[0] = _ConsoleFrame(self.console_init_func()) return Response(render_console_html(secret=self.secret), content_type='text/html')	[ "def", "display_console", "(", "self", ",", "request", ")", ":", "if", "0", "not", "in", "self", ".", "frames", ":", "self", ".", "frames", "[", "0", "]", "=", "_ConsoleFrame", "(", "self", ".", "console_init_func", "(", ")", ")", "return", "Response",...	46.166667	0.010638
def get_config_load_path(conf_path=None): """ Return config file load path Priority: 1. conf_path 2. current directory 3. home directory Parameters ---------- conf_path Returns ------- """ if conf_path is None: # test ./andes.conf if o...	[ "def", "get_config_load_path", "(", "conf_path", "=", "None", ")", ":", "if", "conf_path", "is", "None", ":", "# test ./andes.conf", "if", "os", ".", "path", ".", "isfile", "(", "'andes.conf'", ")", ":", "conf_path", "=", "'andes.conf'", "# test ~/andes.conf", ...	22.322581	0.001385
def statement(self) -> Statement: """Parse YANG statement. Raises: EndOfInput: If past the end of input. UnexpectedInput: If no syntactically correct statement is found. """ pref, kw = self.keyword() pres = self.opt_separator() next = self.peek() ...	[ "def", "statement", "(", "self", ")", "->", "Statement", ":", "pref", ",", "kw", "=", "self", ".", "keyword", "(", ")", "pres", "=", "self", ".", "opt_separator", "(", ")", "next", "=", "self", ".", "peek", "(", ")", "if", "next", "==", "\";\"", ...	29.724138	0.002247
def _initialize_memory(self, policy_params): """Initialize temporary and permanent memory. Args: policy_params: Nested tuple of policy parameters with all dimensions set. Initializes the attributes `self._current_episodes`, `self._finished_episodes`, and `self._num_finished_episodes`. The episod...	[ "def", "_initialize_memory", "(", "self", ",", "policy_params", ")", ":", "# We store observation, action, policy parameters, and reward.", "template", "=", "(", "self", ".", "_batch_env", ".", "observ", "[", "0", "]", ",", "self", ".", "_batch_env", ".", "action", ...	46.208333	0.001767
def nearest_neighbors( X, n_neighbors, metric, metric_kwds, angular, random_state, verbose=False ): """Compute the ``n_neighbors`` nearest points for each data point in ``X`` under ``metric``. This may be exact, but more likely is approximated via nearest neighbor descent. Parameters ----------...	[ "def", "nearest_neighbors", "(", "X", ",", "n_neighbors", ",", "metric", ",", "metric_kwds", ",", "angular", ",", "random_state", ",", "verbose", "=", "False", ")", ":", "if", "verbose", ":", "print", "(", "ts", "(", ")", ",", "\"Finding Nearest Neighbors\""...	36.350746	0.001199
def ensure_crossplat_path(path, winroot='C:'): r""" ensure_crossplat_path Args: path (str): Returns: str: crossplat_path Example(DOCTEST): >>> # ENABLE_DOCTEST >>> from utool.util_path import * # NOQA >>> path = r'C:\somedir' >>> cplat_path = ensur...	[ "def", "ensure_crossplat_path", "(", "path", ",", "winroot", "=", "'C:'", ")", ":", "cplat_path", "=", "path", ".", "replace", "(", "'\\\\'", ",", "'/'", ")", "if", "cplat_path", "==", "winroot", ":", "cplat_path", "+=", "'/'", "return", "cplat_path" ]	22.782609	0.001832
def run_cmd(cmd, echo=False, fail_silently=False, **kwargs): r"""Call given command with ``subprocess.call`` function. :param cmd: Command to run. :type cmd: tuple or str :param echo: If enabled show command to call and its output in STDOUT, otherwise hide all output. By default: False ...	[ "def", "run_cmd", "(", "cmd", ",", "echo", "=", "False", ",", "fail_silently", "=", "False", ",", "", "", "kwargs", ")", ":", "out", ",", "err", "=", "None", ",", "None", "if", "echo", ":", "cmd_str", "=", "cmd", "if", "isinstance", "(", "cmd", ...	35.195122	0.000674
def previous(self): """ fetch the chart identified by this chart's previous_id attribute if the previous_id is either null or not present for this chart return None returns the new chart instance on sucess""" try: if self.previous_id: return Ch...	[ "def", "previous", "(", "self", ")", ":", "try", ":", "if", "self", ".", "previous_id", ":", "return", "Chart", "(", "self", ".", "previous_id", ")", "else", ":", "log", ".", "debug", "(", "'attempted to get previous chart, but none was found'", ")", "return",...	43.6	0.010479
def create(host, port, result_converter=None, testcase_converter=None, args=None): """ Function which is called by Icetea to create an instance of the cloud client. This function must exists. This function myust not return None. Either return an instance of Client or raise. """ return SampleClie...	[ "def", "create", "(", "host", ",", "port", ",", "result_converter", "=", "None", ",", "testcase_converter", "=", "None", ",", "args", "=", "None", ")", ":", "return", "SampleClient", "(", "host", ",", "port", ",", "result_converter", ",", "testcase_converter...	53.142857	0.010582
def users_getPresence(self, , user: str, *kwargs) -> SlackResponse: """Gets user presence information. Args: user (str): User to get presence info on. Defaults to the authed user. e.g. 'W1234567890' """ kwargs.update({"user": user}) return self.api_...	[ "def", "users_getPresence", "(", "self", ",", "", ",", "user", ":", "str", ",", "", "*", "kwargs", ")", "->", "SlackResponse", ":", "kwargs", ".", "update", "(", "{", "\"user\"", ":", "user", "}", ")", "return", "self", ".", "api_call", "(", "\"use...	41	0.01061
def _tls_P_hash(secret, seed, req_len, hm): """ Provides the implementation of P_hash function defined in section 5 of RFC 4346 (and section 5 of RFC 5246). Two parameters have been added (hm and req_len): - secret : the key to be used. If RFC 4868 is to be believed, the length must ...	[ "def", "_tls_P_hash", "(", "secret", ",", "seed", ",", "req_len", ",", "hm", ")", ":", "hash_len", "=", "hm", ".", "hash_alg", ".", "hash_len", "n", "=", "(", "req_len", "+", "hash_len", "-", "1", ")", "//", "hash_len", "seed", "=", "bytes_encode", "...	35.366667	0.000917
def cli(env, crt, csr, icc, key, notes): """Add and upload SSL certificate details.""" template = { 'intermediateCertificate': '', 'certificateSigningRequest': '', 'notes': notes, } template['certificate'] = open(crt).read() template['privateKey'] = open(key).read() if c...	[ "def", "cli", "(", "env", ",", "crt", ",", "csr", ",", "icc", ",", "key", ",", "notes", ")", ":", "template", "=", "{", "'intermediateCertificate'", ":", "''", ",", "'certificateSigningRequest'", ":", "''", ",", "'notes'", ":", "notes", ",", "}", "temp...	28.55	0.001695
def print_help(self, session, command=None): """ Prints the available methods and their documentation, or the documentation of the given command. """ if command: # Single command mode if command in self._commands: # Argument is a name space...	[ "def", "print_help", "(", "self", ",", "session", ",", "command", "=", "None", ")", ":", "if", "command", ":", "# Single command mode", "if", "command", "in", "self", ".", "_commands", ":", "# Argument is a name space", "self", ".", "__print_namespace_help", "("...	35.9	0.001085
def timeout_process_add_queue(self, module, cache_time): """ Add a module to the timeout_queue if it is scheduled in the future or if it is due for an update immediately just trigger that. the timeout_queue is a dict with the scheduled time as the key and the value is a list of ...	[ "def", "timeout_process_add_queue", "(", "self", ",", "module", ",", "cache_time", ")", ":", "# If already set to update do nothing", "if", "module", "in", "self", ".", "timeout_update_due", ":", "return", "# remove if already in the queue", "key", "=", "self", ".", "...	42.688889	0.001018
def read(self, nml_fname, nml_patch_in=None, patch_fname=None): """Parse a Fortran namelist file and store the contents. >>> parser = f90nml.Parser() >>> data_nml = parser.read('data.nml') """ # For switching based on files versus paths nml_is_path = not hasattr(nml_fnam...	[ "def", "read", "(", "self", ",", "nml_fname", ",", "nml_patch_in", "=", "None", ",", "patch_fname", "=", "None", ")", ":", "# For switching based on files versus paths", "nml_is_path", "=", "not", "hasattr", "(", "nml_fname", ",", "'read'", ")", "patch_is_path", ...	38.139535	0.001189
def _open(self): """ Open the file; get sheets :return: """ if not hasattr(self, '_file'): self._file = self.gc.open(self.name) self.sheet_names = self._file.worksheets()	[ "def", "_open", "(", "self", ")", ":", "if", "not", "hasattr", "(", "self", ",", "'_file'", ")", ":", "self", ".", "_file", "=", "self", ".", "gc", ".", "open", "(", "self", ".", "name", ")", "self", ".", "sheet_names", "=", "self", ".", "_file",...	28.375	0.008547
def encode(msg, strict=False, logger=None, timezone_offset=None): """ Encodes and returns the L{msg<Envelope>} as an AMF stream. @param strict: Enforce strict encoding. Default is C{False}. Specifically header/body lengths will be written correctly, instead of the default 0. Default is `Fal...	[ "def", "encode", "(", "msg", ",", "strict", "=", "False", ",", "logger", "=", "None", ",", "timezone_offset", "=", "None", ")", ":", "stream", "=", "util", ".", "BufferedByteStream", "(", ")", "encoder", "=", "pyamf", ".", "get_encoder", "(", "pyamf", ...	36.418605	0.002488
def posterior_predictive_to_xarray(self): """Convert posterior_predictive samples to xarray.""" posterior = self.posterior posterior_predictive = self.posterior_predictive data = get_draws(posterior, variables=posterior_predictive) return dict_to_dataset(data, library=self.p...	[ "def", "posterior_predictive_to_xarray", "(", "self", ")", ":", "posterior", "=", "self", ".", "posterior", "posterior_predictive", "=", "self", ".", "posterior_predictive", "data", "=", "get_draws", "(", "posterior", ",", "variables", "=", "posterior_predictive", "...	59.5	0.008287
def rm_op(l, name, op): """Remove an opcode. This is used when basing a new Python release off of another one, and there is an opcode that is in the old release that was removed in the new release. We are pretty aggressive about removing traces of the op. """ # opname is an array, so we need to...	[ "def", "rm_op", "(", "l", ",", "name", ",", "op", ")", ":", "# opname is an array, so we need to keep the position in there.", "l", "[", "'opname'", "]", "[", "op", "]", "=", "'<%s>'", "%", "op", "if", "op", "in", "l", "[", "'hasconst'", "]", ":", "l", "...	30.513514	0.012017
def inherit_docstrings(cls): """Class decorator for inheriting docstrings. Automatically inherits base class doc-strings if not present in the derived class. """ @functools.wraps(cls) def _inherit_docstrings(cls): if not isinstance(cls, (type, colorise.compat.ClassType)): r...	[ "def", "inherit_docstrings", "(", "cls", ")", ":", "@", "functools", ".", "wraps", "(", "cls", ")", "def", "_inherit_docstrings", "(", "cls", ")", ":", "if", "not", "isinstance", "(", "cls", ",", "(", "type", ",", "colorise", ".", "compat", ".", "Class...	34.541667	0.001174
def _suggest_semantic_version(s): """ Try to suggest a semantic form for a version for which _suggest_normalized_version couldn't come up with anything. """ result = s.strip().lower() for pat, repl in _REPLACEMENTS: result = pat.sub(repl, result) if not result: result = '0.0....	[ "def", "_suggest_semantic_version", "(", "s", ")", ":", "result", "=", "s", ".", "strip", "(", ")", ".", "lower", "(", ")", "for", "pat", ",", "repl", "in", "_REPLACEMENTS", ":", "result", "=", "pat", ".", "sub", "(", "repl", ",", "result", ")", "i...	29.568182	0.002232
def si_format(value, precision=1, format_str=u'{value} {prefix}', exp_format_str=u'{value}e{expof10}'): ''' Format value to string with SI prefix, using the specified precision. Parameters ---------- value : int, float Input value. precision : int Number of digits ...	[ "def", "si_format", "(", "value", ",", "precision", "=", "1", ",", "format_str", "=", "u'{value} {prefix}'", ",", "exp_format_str", "=", "u'{value}e{expof10}'", ")", ":", "svalue", ",", "expof10", "=", "split", "(", "value", ",", "precision", ")", "value_forma...	31.414894	0.000328
def eig_one_step(current_vector, learning_rate, vector_prod_fn): """Function that performs one step of gd (variant) for min eigen value. Args: current_vector: current estimate of the eigen vector with minimum eigen value. learning_rate: learning rate. vector_prod_fn: function which returns produc...	[ "def", "eig_one_step", "(", "current_vector", ",", "learning_rate", ",", "vector_prod_fn", ")", ":", "grad", "=", "2", "", "vector_prod_fn", "(", "current_vector", ")", "# Current objective = (1/2)v^T (2Mv); v = current_vector", "# grad = 2Mv", "current_objective", "=...	38.923077	0.013878
def find_linked_dynamic_libraries(): """ This function attempts to locate the required link libraries, and returns them as a list of absolute paths. """ with TaskContext("Find the required dynamic libraries") as log: llvm = get_llvm() libs = required_link_libraries() resolved...	[ "def", "find_linked_dynamic_libraries", "(", ")", ":", "with", "TaskContext", "(", "\"Find the required dynamic libraries\"", ")", "as", "log", ":", "llvm", "=", "get_llvm", "(", ")", "libs", "=", "required_link_libraries", "(", ")", "resolved", "=", "[", "]", "...	45.263158	0.001707
def wait_for_instance( vm_=None, data=None, ip_address=None, display_ssh_output=True, call=None, ): ''' Wait for an instance upon creation from the EC2 API, to become available ''' if call == 'function': # Technically this function may be called other ...	[ "def", "wait_for_instance", "(", "vm_", "=", "None", ",", "data", "=", "None", ",", "ip_address", "=", "None", ",", "display_ssh_output", "=", "True", ",", "call", "=", "None", ",", ")", ":", "if", "call", "==", "'function'", ":", "# Technically this funct...	38.533937	0.001374
def getParent(self, returned_properties=None): """Get the parent workitem of this workitem If no parent, None will be returned. :param returned_properties: the returned properties that you want. Refer to :class:`rtcclient.client.RTCClient` for more explanations :return: a :...	[ "def", "getParent", "(", "self", ",", "returned_properties", "=", "None", ")", ":", "parent_tag", "=", "(", "\"rtc_cm:com.ibm.team.workitem.linktype.\"", "\"parentworkitem.parent\"", ")", "rp", "=", "returned_properties", "parent", "=", "(", "self", ".", "rtc_obj", ...	39.576923	0.001898
async def movies(self): '''list of movies in the collection \|force\| \|coro\| Returns ------- list of type :class:`embypy.objects.Movie` ''' items = [] for i in await self.items: if i.type == 'Movie': items.append(i) elif hasattr(i, 'movies'): items....	[ "async", "def", "movies", "(", "self", ")", ":", "items", "=", "[", "]", "for", "i", "in", "await", "self", ".", "items", ":", "if", "i", ".", "type", "==", "'Movie'", ":", "items", ".", "append", "(", "i", ")", "elif", "hasattr", "(", "i", ","...	17.947368	0.008357
def add_all_database_reactions(model, compartments): """Add all reactions from database that occur in given compartments. Args: model: :class:`psamm.metabolicmodel.MetabolicModel`. """ added = set() for rxnid in model.database.reactions: reaction = model.database.get_reaction(rxnid...	[ "def", "add_all_database_reactions", "(", "model", ",", "compartments", ")", ":", "added", "=", "set", "(", ")", "for", "rxnid", "in", "model", ".", "database", ".", "reactions", ":", "reaction", "=", "model", ".", "database", ".", "get_reaction", "(", "rx...	32.176471	0.001776
def schedule_to_array(schedule, events, slots): """Convert a schedule from schedule to array form Parameters ---------- schedule : list or tuple of instances of :py:class:`resources.ScheduledItem` events : list or tuple of :py:class:`resources.Event` instances slots : list or tu...	[ "def", "schedule_to_array", "(", "schedule", ",", "events", ",", "slots", ")", ":", "array", "=", "np", ".", "zeros", "(", "(", "len", "(", "events", ")", ",", "len", "(", "slots", ")", ")", ",", "dtype", "=", "np", ".", "int8", ")", "for", "item...	31.913043	0.001323
def remove_from_role(server_context, role, user_id=None, email=None, container_path=None): """ Remove user/group from security role :param server_context: A LabKey server context. See utils.create_server_context. :param role: (from get_roles) to remove user from :param user_id: to remove permissions...	[ "def", "remove_from_role", "(", "server_context", ",", "role", ",", "user_id", "=", "None", ",", "email", "=", "None", ",", "container_path", "=", "None", ")", ":", "return", "__make_security_role_api_request", "(", "server_context", ",", "'removeAssignment.api'", ...	59	0.008345
def validate_groupby_func(name, args, kwargs, allowed=None): """ 'args' and 'kwargs' should be empty, except for allowed kwargs because all of their necessary parameters are explicitly listed in the function signature """ if allowed is None: allowed = [] kwargs = set(kwargs) - s...	[ "def", "validate_groupby_func", "(", "name", ",", "args", ",", "kwargs", ",", "allowed", "=", "None", ")", ":", "if", "allowed", "is", "None", ":", "allowed", "=", "[", "]", "kwargs", "=", "set", "(", "kwargs", ")", "-", "set", "(", "allowed", ")", ...	31.529412	0.001812
def update_package_files(srcdir, extensions, package_data, packagenames, package_dirs): """ This function is deprecated and maintained for backward compatibility with affiliated packages. Affiliated packages should update their setup.py to use `get_package_info` instead. ""...	[ "def", "update_package_files", "(", "srcdir", ",", "extensions", ",", "package_data", ",", "packagenames", ",", "package_dirs", ")", ":", "info", "=", "get_package_info", "(", "srcdir", ")", "extensions", ".", "extend", "(", "info", "[", "'ext_modules'", "]", ...	41.692308	0.001805
def calc(self, x:Image, args:Any, kwargs:Any)->Image: "Apply to image `x`, wrapping it if necessary." if self._wrap: return getattr(x, self._wrap)(self.func, args, *kwargs) else: return self.func(x, args, **kwargs)	[ "def", "calc", "(", "self", ",", "x", ":", "Image", ",", "", "args", ":", "Any", ",", "", "*", "kwargs", ":", "Any", ")", "->", "Image", ":", "if", "self", ".", "_wrap", ":", "return", "getattr", "(", "x", ",", "self", ".", "_wrap", ")", "(...	62.5	0.039526
def hl_table2canvas(self, w, res_dict): """Highlight mask on canvas when user click on table.""" objlist = [] # Remove existing highlight if self.maskhltag: try: self.canvas.delete_object_by_tag(self.maskhltag, redraw=False) except Exception: ...	[ "def", "hl_table2canvas", "(", "self", ",", "w", ",", "res_dict", ")", ":", "objlist", "=", "[", "]", "# Remove existing highlight", "if", "self", ".", "maskhltag", ":", "try", ":", "self", ".", "canvas", ".", "delete_object_by_tag", "(", "self", ".", "mas...	33.833333	0.002395
def getBucketValues(self): """ See the function description in base.py """ # Need to re-create? if self._bucketValues is None: topDownMappingM = self._getTopDownMapping() numBuckets = topDownMappingM.nRows() self._bucketValues = [] for bucketIdx in range(numBuckets): self._b...	[ "def", "getBucketValues", "(", "self", ")", ":", "# Need to re-create?", "if", "self", ".", "_bucketValues", "is", "None", ":", "topDownMappingM", "=", "self", ".", "_getTopDownMapping", "(", ")", "numBuckets", "=", "topDownMappingM", ".", "nRows", "(", ")", "...	33.333333	0.012165
def get_overlapping_ranges(self, collection_link, sorted_ranges): ''' Given the sorted ranges and a collection, Returns the list of overlapping partition key ranges :param str collection_link: The collection link. :param (list of routing_range._Range) sorted_...	[ "def", "get_overlapping_ranges", "(", "self", ",", "collection_link", ",", "sorted_ranges", ")", ":", "# validate if the list is non-overlapping and sorted", "if", "not", "self", ".", "_is_sorted_and_non_overlapping", "(", "sorted_ranges", ")", ":", "raise", "ValueError", ...	49.314815	0.0081
def _build_layers(self, inputs, num_outputs, options): """Process the flattened inputs. Note that dict inputs will be flattened into a vector. To define a model that processes the components separately, use _build_layers_v2(). """ hiddens = options.get("fcnet_hiddens") ...	[ "def", "_build_layers", "(", "self", ",", "inputs", ",", "num_outputs", ",", "options", ")", ":", "hiddens", "=", "options", ".", "get", "(", "\"fcnet_hiddens\"", ")", "activation", "=", "get_activation_fn", "(", "options", ".", "get", "(", "\"fcnet_activation...	36.166667	0.001795
def genfsms(self,meter=None): """Generate FSM images. Requires networkx and GraphViz.""" if (hasattr(self,'allParses')): name=self.getName() import networkx as nx m2int={'w':'0','s':'1'} gs={} gs['weight']=['str_weight'] gs['stress']=['str_stress'] gs['stressweight']=['str_stress','str_weigh...	[ "def", "genfsms", "(", "self", ",", "meter", "=", "None", ")", ":", "if", "(", "hasattr", "(", "self", ",", "'allParses'", ")", ")", ":", "name", "=", "self", ".", "getName", "(", ")", "import", "networkx", "as", "nx", "m2int", "=", "{", "'w'", "...	26.375	0.056585
def isEnabled(self): """ Return whether or not this layer is enabled and can be set as the \ current layer. :sa linkEnabledToCurrent :return <bool> """ if self._linkEnabledToCurrent: addtl = self.isCurrent() e...	[ "def", "isEnabled", "(", "self", ")", ":", "if", "self", ".", "_linkEnabledToCurrent", ":", "addtl", "=", "self", ".", "isCurrent", "(", ")", "else", ":", "addtl", "=", "True", "return", "self", ".", "_enabled", "and", "addtl" ]	23.875	0.015113
def get(self, url, params=None, headers=None, content=None, form_content=None): # type: (str, Optional[Dict[str, str]], Optional[Dict[str, str]], Any, Optional[Dict[str, Any]]) -> ClientRequest """Create a GET request object. :param str url: The request URL. :param dict params: Request ...	[ "def", "get", "(", "self", ",", "url", ",", "params", "=", "None", ",", "headers", "=", "None", ",", "content", "=", "None", ",", "form_content", "=", "None", ")", ":", "# type: (str, Optional[Dict[str, str]], Optional[Dict[str, str]], Any, Optional[Dict[str, Any]]) -...	46.5	0.008787
def summary(self, key, column="C1", timeoutSecs=10, **kwargs): ''' Return the summary for a single column for a single Frame in the h2o cluster. ''' params_dict = { # 'offset': 0, # 'len': 100 } h2o_methods.check_params_update_kwargs(params_dict, kwargs, 'summary', True) ...	[ "def", "summary", "(", "self", ",", "key", ",", "column", "=", "\"C1\"", ",", "timeoutSecs", "=", "10", ",", "", "", "kwargs", ")", ":", "params_dict", "=", "{", "# 'offset': 0,", "# 'len': 100", "}", "h2o_methods", ".", "check_params_update_kwargs", "(", ...	38.307692	0.013725
def render(self, content = None, settings): """ Perform widget rendering, but do not print anything. """ (content, settings) = self.get_setup(content, settings) return self._render(content, **settings)	[ "def", "render", "(", "self", ",", "content", "=", "None", ",", "", "", "settings", ")", ":", "(", "content", ",", "settings", ")", "=", "self", ".", "get_setup", "(", "content", ",", "", "", "settings", ")", "return", "self", ".", "_render", "...	40	0.016327
def oneup(self, window_name, object_name, iterations): """ Press scrollbar up with number of iterations @param window_name: Window name to type in, either full name, LDTP's name convention, or a Unix glob. @type window_name: string @param object_name: Object name to type...	[ "def", "oneup", "(", "self", ",", "window_name", ",", "object_name", ",", "iterations", ")", ":", "if", "not", "self", ".", "verifyscrollbarvertical", "(", "window_name", ",", "object_name", ")", ":", "raise", "LdtpServerException", "(", "'Object not vertical scro...	37.151515	0.00159
def sens_batmon_encode(self, temperature, voltage, current, SoC, batterystatus, serialnumber, hostfetcontrol, cellvoltage1, cellvoltage2, cellvoltage3, cellvoltage4, cellvoltage5, cellvoltage6): ''' Battery pack monitoring data for Li-Ion batteries temperature ...	[ "def", "sens_batmon_encode", "(", "self", ",", "temperature", ",", "voltage", ",", "current", ",", "SoC", ",", "batterystatus", ",", "serialnumber", ",", "hostfetcontrol", ",", "cellvoltage1", ",", "cellvoltage2", ",", "cellvoltage3", ",", "cellvoltage4", ",", "...	83.7	0.010041
def setup_temp_logger(log_level='error'): ''' Setup the temporary console logger ''' if is_temp_logging_configured(): logging.getLogger(__name__).warning( 'Temporary logging is already configured' ) return if log_level is None: log_level = 'warning' ...	[ "def", "setup_temp_logger", "(", "log_level", "=", "'error'", ")", ":", "if", "is_temp_logging_configured", "(", ")", ":", "logging", ".", "getLogger", "(", "__name__", ")", ".", "warning", "(", "'Temporary logging is already configured'", ")", "return", "if", "lo...	29.25	0.000636
def run_drop_tables(_): ''' Running the script. ''' print('--') drop_the_table(TabPost) drop_the_table(TabTag) drop_the_table(TabMember) drop_the_table(TabWiki) drop_the_table(TabLink) drop_the_table(TabEntity) drop_the_table(TabPostHist) drop_the_table(TabWikiHist) ...	[ "def", "run_drop_tables", "(", "_", ")", ":", "print", "(", "'--'", ")", "drop_the_table", "(", "TabPost", ")", "drop_the_table", "(", "TabTag", ")", "drop_the_table", "(", "TabMember", ")", "drop_the_table", "(", "TabWiki", ")", "drop_the_table", "(", "TabLin...	24.545455	0.001783
def miller_rabin(n, k): """Run the Miller-Rabin test on n with at most k iterations Arguments: n (int): number whose primality is to be tested k (int): maximum number of iterations to run Returns: bool: If n is prime, then True is returned. Otherwise, False is returned, exc...	[ "def", "miller_rabin", "(", "n", ",", "k", ")", ":", "assert", "n", ">", "3", "# find r and d such that n-1 = 2^r × d", "d", "=", "n", "-", "1", "r", "=", "0", "while", "d", "%", "2", "==", "0", ":", "d", "//=", "2", "r", "+=", "1", "assert", "n"...	26.5	0.000958
def set_static_ip(iface, addr, gateway=None, append=False): ''' Set static IP configuration on a Windows NIC iface The name of the interface to manage addr IP address with subnet length (ex. ``10.1.2.3/24``). The :mod:`ip.get_subnet_length <salt.modules.win_ip.get_subnet_length...	[ "def", "set_static_ip", "(", "iface", ",", "addr", ",", "gateway", "=", "None", ",", "append", "=", "False", ")", ":", "def", "_find_addr", "(", "iface", ",", "addr", ",", "timeout", "=", "1", ")", ":", "ip", ",", "cidr", "=", "addr", ".", "rsplit"...	32.555556	0.001104
def _get_quantiles(self, X, width, quantiles, modelmat=None, lp=None, prediction=False, xform=True, term=-1): """ estimate prediction intervals for LinearGAM Parameters ---------- X : array input data of shape (n_samples, m_features) wi...	[ "def", "_get_quantiles", "(", "self", ",", "X", ",", "width", ",", "quantiles", ",", "modelmat", "=", "None", ",", "lp", "=", "None", ",", "prediction", "=", "False", ",", "xform", "=", "True", ",", "term", "=", "-", "1", ")", ":", "if", "quantiles...	38.402597	0.001978
def owner_type(self, value): """Set ``owner_type`` to the given value. In addition: * Update the internal type of the ``owner`` field. * Update the value of the ``owner`` field if a value is already set. """ self._owner_type = value if value == 'User': ...	[ "def", "owner_type", "(", "self", ",", "value", ")", ":", "self", ".", "_owner_type", "=", "value", "if", "value", "==", "'User'", ":", "self", ".", "_fields", "[", "'owner'", "]", "=", "entity_fields", ".", "OneToOneField", "(", "User", ")", "if", "ha...	38.333333	0.001885
def get_objects(self): """ Return a list of all content objects in this distribution. :rtype: list of :class:`boto.cloudfront.object.Object` :return: The content objects """ bucket = self._get_bucket() objs = [] for key in bucket: objs...	[ "def", "get_objects", "(", "self", ")", ":", "bucket", "=", "self", ".", "_get_bucket", "(", ")", "objs", "=", "[", "]", "for", "key", "in", "bucket", ":", "objs", ".", "append", "(", "key", ")", "return", "objs" ]	28.416667	0.008523
def ensure_traj(traj): r"""Makes sure that traj is a trajectory (array of float) """ if is_float_matrix(traj) or is_bool_matrix(traj): return traj elif is_float_vector(traj): return traj[:,None] else: try: arr = np.array(traj) arr = ensure_dtype_float...	[ "def", "ensure_traj", "(", "traj", ")", ":", "if", "is_float_matrix", "(", "traj", ")", "or", "is_bool_matrix", "(", "traj", ")", ":", "return", "traj", "elif", "is_float_vector", "(", "traj", ")", ":", "return", "traj", "[", ":", ",", "None", "]", "el...	36.45	0.008021
def EMetaclass(cls): """Class decorator for creating PyEcore metaclass.""" superclass = cls.__bases__ if not issubclass(cls, EObject): sclasslist = list(superclass) if object in superclass: index = sclasslist.index(object) sclasslist.insert(index, EObject) ...	[ "def", "EMetaclass", "(", "cls", ")", ":", "superclass", "=", "cls", ".", "__bases__", "if", "not", "issubclass", "(", "cls", ",", "EObject", ")", ":", "sclasslist", "=", "list", "(", "superclass", ")", "if", "object", "in", "superclass", ":", "index", ...	35.772727	0.001238
def del_edges(self, edges, args, *kwargs): """ Removes edges from the graph. Takes optional arguments for ``DictGraph.del_edge``. Arguments: - edges(iterable) Sequence of edges to be removed from the ``DictGraph``. """ ...	[ "def", "del_edges", "(", "self", ",", "edges", ",", "", "args", ",", "", "", "kwargs", ")", ":", "for", "edge", "in", "edges", ":", "self", ".", "del_edge", "(", "edge", ",", "", "args", ",", "", "", "kwargs", ")" ]	29.153846	0.017903
def _stderr_raw(self, s): """Writes the string to stdout""" print(s, end='', file=sys.stderr) sys.stderr.flush()	[ "def", "_stderr_raw", "(", "self", ",", "s", ")", ":", "print", "(", "s", ",", "end", "=", "''", ",", "file", "=", "sys", ".", "stderr", ")", "sys", ".", "stderr", ".", "flush", "(", ")" ]	33.25	0.014706
def deserialize_dataframe(reader, data_type_id): """ Deserialize a dataframe. Parameters ---------- reader : file File-like object to read from. Must be opened in binary mode. data_type_id : dict Serialization format of the raw data. See the azureml.DataTypeIds class for...	[ "def", "deserialize_dataframe", "(", "reader", ",", "data_type_id", ")", ":", "_not_none", "(", "'reader'", ",", "reader", ")", "_not_none_or_empty", "(", "'data_type_id'", ",", "data_type_id", ")", "serializer", "=", "_SERIALIZERS", ".", "get", "(", "data_type_id...	26.875	0.001497
def deposit_fetcher(record_uuid, data): """Fetch a deposit identifier. :param record_uuid: Record UUID. :param data: Record content. :returns: A :class:`invenio_pidstore.fetchers.FetchedPID` that contains data['_deposit']['id'] as pid_value. """ return FetchedPID( provider=Depos...	[ "def", "deposit_fetcher", "(", "record_uuid", ",", "data", ")", ":", "return", "FetchedPID", "(", "provider", "=", "DepositProvider", ",", "pid_type", "=", "DepositProvider", ".", "pid_type", ",", "pid_value", "=", "str", "(", "data", "[", "'_deposit'", "]", ...	31.923077	0.002342
def get_info(self): """ Get info for all filters. """ out = '' for k in sorted(self.components.keys()): out += '{:s}: {:s}'.format(k, self.info[k]) + '\n' return(out)	[ "def", "get_info", "(", "self", ")", ":", "out", "=", "''", "for", "k", "in", "sorted", "(", "self", ".", "components", ".", "keys", "(", ")", ")", ":", "out", "+=", "'{:s}: {:s}'", ".", "format", "(", "k", ",", "self", ".", "info", "[", "k", "...	27.375	0.00885
def undo(self): """Undo the last cluster assignment operation. Returns ------- up : UpdateInfo instance of the changes done by this operation. """ _, _, undo_state = self._undo_stack.back() # Retrieve the initial spike_cluster structure. spike_clusters...	[ "def", "undo", "(", "self", ")", ":", "_", ",", "_", ",", "undo_state", "=", "self", ".", "_undo_stack", ".", "back", "(", ")", "# Retrieve the initial spike_cluster structure.", "spike_clusters_new", "=", "self", ".", "_spike_clusters_base", ".", "copy", "(", ...	33.34375	0.001821
def print_tree(editor, file=sys.stdout, print_blocks=False, return_list=False): """ Prints the editor fold tree to stdout, for debugging purpose. :param editor: CodeEditor instance. :param file: file handle where the tree will be printed. Default is stdout. :param print_blocks: True to print all bl...	[ "def", "print_tree", "(", "editor", ",", "file", "=", "sys", ".", "stdout", ",", "print_blocks", "=", "False", ",", "return_list", "=", "False", ")", ":", "output_list", "=", "[", "]", "block", "=", "editor", ".", "document", "(", ")", ".", "firstBlock...	38.428571	0.000725
def gather(params, indices, dtype=tf.float32): """Version of tf.gather that works faster on tpu.""" if not is_xla_compiled(): return tf.gather(params, indices) vocab_size = params.get_shape().as_list()[0] indices_flat = tf.reshape(indices, [-1]) out = tf.matmul(tf.one_hot(indices_flat, vocab_size, dtype=d...	[ "def", "gather", "(", "params", ",", "indices", ",", "dtype", "=", "tf", ".", "float32", ")", ":", "if", "not", "is_xla_compiled", "(", ")", ":", "return", "tf", ".", "gather", "(", "params", ",", "indices", ")", "vocab_size", "=", "params", ".", "ge...	43.777778	0.0199
def physical_pins(self, function): """ Return the physical pins supporting the specified function as tuples of ``(header, pin_number)`` where header is a string specifying the header containing the pin_number. Note that the return value is a :class:`set` which is not indexa...	[ "def", "physical_pins", "(", "self", ",", "function", ")", ":", "return", "{", "(", "header", ",", "pin", ".", "number", ")", "for", "(", "header", ",", "info", ")", "in", "self", ".", "headers", ".", "items", "(", ")", "for", "pin", "in", "info", ...	43.473684	0.00237
def get_submodules(app, module): """Get all submodules without packages for the given module/package :param app: the sphinx app :type app: :class:`sphinx.application.Sphinx` :param module: the module to query or module path :type module: module \| str :returns: list of module names excluding pac...	[ "def", "get_submodules", "(", "app", ",", "module", ")", ":", "submodules", "=", "_get_submodules", "(", "app", ",", "module", ")", "return", "[", "name", "for", "name", ",", "ispkg", "in", "submodules", "if", "not", "ispkg", "]" ]	36	0.002083
def create(cls, service=None, endpoint=None, data=None, args, *kwargs): """ Create an integration within the scope of an service. Make sure that they should reasonably be able to query with an service or endpoint that knows about an service. """ cls.validate(data) ...	[ "def", "create", "(", "cls", ",", "service", "=", "None", ",", "endpoint", "=", "None", ",", "data", "=", "None", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "cls", ".", "validate", "(", "data", ")", "if", "service", "is", "None", "and",...	43.777778	0.002484
def label_to_latex(text): # pylint: disable=anomalous-backslash-in-string r"""Convert text into a latex-passable representation. This method just escapes the following reserved LaTeX characters: % \ _ ~ &, whilst trying to avoid doubly-escaping already escaped characters Parameters -------...	[ "def", "label_to_latex", "(", "text", ")", ":", "# pylint: disable=anomalous-backslash-in-string", "if", "text", "is", "None", ":", "return", "''", "out", "=", "[", "]", "x", "=", "None", "# loop over matches in reverse order and replace", "for", "m", "in", "re_late...	26.255319	0.000781
def init_app(self, app): """Initialize the `app` for use with this :class:`~flask_mysqldb.MySQL` class. This is called automatically if `app` is passed to :meth:`~MySQL.__init__`. :param flask.Flask app: the application to configure for use with this :class:`~flask_m...	[ "def", "init_app", "(", "self", ",", "app", ")", ":", "app", ".", "config", ".", "setdefault", "(", "'MYSQL_HOST'", ",", "'localhost'", ")", "app", ".", "config", ".", "setdefault", "(", "'MYSQL_USER'", ",", "None", ")", "app", ".", "config", ".", "set...	43.6	0.001795
def handle_import(self, options): """ Gets the posts from either the provided URL or the path if it is local. """ url = options.get("url") if url is None: raise CommandError("Usage is import_wordpress %s" % self.args) try: import feedparse...	[ "def", "handle_import", "(", "self", ",", "options", ")", ":", "url", "=", "options", ".", "get", "(", "\"url\"", ")", "if", "url", "is", "None", ":", "raise", "CommandError", "(", "\"Usage is import_wordpress %s\"", "%", "self", ".", "args", ")", "try", ...	45.261538	0.000665
def fix_objective_as_constraint(model, fraction=1, bound=None, name='fixed_objective_{}'): """Fix current objective as an additional constraint. When adding constraints to a model, such as done in pFBA which minimizes total flux, these constraints can become too powerful, ...	[ "def", "fix_objective_as_constraint", "(", "model", ",", "fraction", "=", "1", ",", "bound", "=", "None", ",", "name", "=", "'fixed_objective_{}'", ")", ":", "fix_objective_name", "=", "name", ".", "format", "(", "model", ".", "objective", ".", "name", ")", ...	39.73913	0.000534
def exit_if_path_exists(self): """ Exit early if the path cannot be found. """ if os.path.exists(self.output_path): ui.error(c.MESSAGES["path_exists"], self.output_path) sys.exit(1)	[ "def", "exit_if_path_exists", "(", "self", ")", ":", "if", "os", ".", "path", ".", "exists", "(", "self", ".", "output_path", ")", ":", "ui", ".", "error", "(", "c", ".", "MESSAGES", "[", "\"path_exists\"", "]", ",", "self", ".", "output_path", ")", ...	33	0.008439
def searchNs(self, doc, nameSpace): """Search a Ns registered under a given name space for a document. recurse on the parents until it finds the defined namespace or return None otherwise. @nameSpace can be None, this is a search for the default namespace. We don't allow ...	[ "def", "searchNs", "(", "self", ",", "doc", ",", "nameSpace", ")", ":", "if", "doc", "is", "None", ":", "doc__o", "=", "None", "else", ":", "doc__o", "=", "doc", ".", "_o", "ret", "=", "libxml2mod", ".", "xmlSearchNs", "(", "doc__o", ",", "self", "...	52.071429	0.008086
def propose(self, current, r): """Generates a random sample from the discrete probability distribution and returns its value, the log of the probability of sampling that value and the log of the probability of sampling the current value (passed in). """ stay = (r.uniform(0, 1) < self.kernel) if ...	[ "def", "propose", "(", "self", ",", "current", ",", "r", ")", ":", "stay", "=", "(", "r", ".", "uniform", "(", "0", ",", "1", ")", "<", "self", ".", "kernel", ")", "if", "stay", ":", "logKernel", "=", "numpy", ".", "log", "(", "self", ".", "k...	43.875	0.018131
def shrink(self, index, target, body=None, params=None): """ The shrink index API allows you to shrink an existing index into a new index with fewer primary shards. The number of primary shards in the target index must be a factor of the shards in the source index. For example an...	[ "def", "shrink", "(", "self", ",", "index", ",", "target", ",", "body", "=", "None", ",", "params", "=", "None", ")", ":", "for", "param", "in", "(", "index", ",", "target", ")", ":", "if", "param", "in", "SKIP_IN_PATH", ":", "raise", "ValueError", ...	56.678571	0.002478
def namedb_preorder_insert( cur, preorder_rec ): """ Add a name or namespace preorder record, if it doesn't exist already. DO NOT CALL THIS DIRECTLY. """ preorder_row = copy.deepcopy( preorder_rec ) assert 'preorder_hash' in preorder_row, "BUG: missing preorder_hash" try: pre...	[ "def", "namedb_preorder_insert", "(", "cur", ",", "preorder_rec", ")", ":", "preorder_row", "=", "copy", ".", "deepcopy", "(", "preorder_rec", ")", "assert", "'preorder_hash'", "in", "preorder_row", ",", "\"BUG: missing preorder_hash\"", "try", ":", "preorder_query", ...	31.75	0.019878
def get_base_url(self, request): """ Creates base url string. :param request: OGC-type request with specified bounding box, cloud coverage for specific product. :type request: OgcRequest or GeopediaRequest :return: base string for url to Sentinel Hub's OGC service for this product. ...	[ "def", "get_base_url", "(", "self", ",", "request", ")", ":", "url", "=", "self", ".", "base_url", "+", "request", ".", "service_type", ".", "value", "# These 2 lines are temporal and will be removed after the use of uswest url wont be required anymore:", "if", "hasattr", ...	61.470588	0.009425
def str_variants(store, institute_obj, case_obj, variants_query, page=1, per_page=50): """Pre-process list of STR variants.""" # Nothing unique to STRs on this level. Inheritance? return variants(store, institute_obj, case_obj, variants_query, page, per_page)	[ "def", "str_variants", "(", "store", ",", "institute_obj", ",", "case_obj", ",", "variants_query", ",", "page", "=", "1", ",", "per_page", "=", "50", ")", ":", "# Nothing unique to STRs on this level. Inheritance?", "return", "variants", "(", "store", ",", "instit...	67	0.01107
def get_recent_comments(number=5, template='zinnia/tags/comments_recent.html'): """ Return the most recent comments. """ # Using map(smart_text... fix bug related to issue #8554 entry_published_pks = map(smart_text, Entry.published.values_list('id', flat=True)) cont...	[ "def", "get_recent_comments", "(", "number", "=", "5", ",", "template", "=", "'zinnia/tags/comments_recent.html'", ")", ":", "# Using map(smart_text... fix bug related to issue #8554", "entry_published_pks", "=", "map", "(", "smart_text", ",", "Entry", ".", "published", "...	40.277778	0.001348
def escape(s, quote=False): """Replace special characters "&", "<" and ">" to HTML-safe sequences. If the optional flag `quote` is `True`, the quotation mark character (") is also translated. There is a special handling for `None` which escapes to an empty string. :param s: the string to escape. ...	[ "def", "escape", "(", "s", ",", "quote", "=", "False", ")", ":", "if", "s", "is", "None", ":", "return", "''", "elif", "hasattr", "(", "s", ",", "'__html__'", ")", ":", "return", "s", ".", "__html__", "(", ")", "elif", "not", "isinstance", "(", "...	33.3	0.00146
def CacheStorage_deleteEntry(self, cacheId, request): """ Function path: CacheStorage.deleteEntry Domain: CacheStorage Method name: deleteEntry Parameters: Required arguments: 'cacheId' (type: CacheId) -> Id of cache where the entry will be deleted. 'request' (type: string) -> URL spec of ...	[ "def", "CacheStorage_deleteEntry", "(", "self", ",", "cacheId", ",", "request", ")", ":", "assert", "isinstance", "(", "request", ",", "(", "str", ",", ")", ")", ",", "\"Argument 'request' must be of type '['str']'. Received type: '%s'\"", "%", "type", "(", "request...	32.45	0.043413
def inverse_transform(self, maps): """ This function transforms from component masses and cartesian spins to mass-weighted spin parameters perpendicular with the angular momentum. Parameters ---------- maps : a mapping object Returns ------- out : dict ...	[ "def", "inverse_transform", "(", "self", ",", "maps", ")", ":", "# convert", "out", "=", "{", "}", "xi1", "=", "conversions", ".", "primary_xi", "(", "maps", "[", "parameters", ".", "mass1", "]", ",", "maps", "[", "parameters", ".", "mass2", "]", ",", ...	44.754717	0.001238
def get_ft_names(mod, include_inner=False)->List[str]: "Return all the functions of module `mod`." # If the module has an attribute __all__, it picks those. # Otherwise, it returns all the functions defined inside a module. fn_names = [] for elt_name in get_exports(mod): elt = getattr(mod,el...	[ "def", "get_ft_names", "(", "mod", ",", "include_inner", "=", "False", ")", "->", "List", "[", "str", "]", ":", "# If the module has an attribute __all__, it picks those.", "# Otherwise, it returns all the functions defined inside a module.", "fn_names", "=", "[", "]", "for...	45.2	0.015168
def upsert_acl(cursor, uuid_, permissions): """Given a ``uuid`` and a set of permissions given as a tuple of ``uid`` and ``permission``, upsert them into the database. """ if not isinstance(permissions, (list, set, tuple,)): raise TypeError("``permissions`` is an invalid type: {}" ...	[ "def", "upsert_acl", "(", "cursor", ",", "uuid_", ",", "permissions", ")", ":", "if", "not", "isinstance", "(", "permissions", ",", "(", "list", ",", "set", ",", "tuple", ",", ")", ")", ":", "raise", "TypeError", "(", "\"``permissions`` is an invalid type: {...	33.192308	0.001126
def times_to_ms(h=0, m=0, s=0, ms=0): """ Convert hours, minutes, seconds to milliseconds. Arguments may be positive or negative, int or float, need not be normalized (``s=120`` is okay). Returns: Number of milliseconds (rounded to int). """ ms += s * 1000 ms += m ...	[ "def", "times_to_ms", "(", "h", "=", "0", ",", "m", "=", "0", ",", "s", "=", "0", ",", "ms", "=", "0", ")", ":", "ms", "+=", "s", "", "1000", "ms", "+=", "m", "", "60000", "ms", "+=", "h", "*", "3600000", "return", "int", "(", "round", ...	24.066667	0.010667
def _antenna_uvw(uvw, antenna1, antenna2, chunks, nr_of_antenna): """ numba implementation of antenna_uvw """ if antenna1.ndim != 1: raise ValueError("antenna1 shape should be (row,)") if antenna2.ndim != 1: raise ValueError("antenna2 shape should be (row,)") if uvw.ndim != 2 or uvw.s...	[ "def", "_antenna_uvw", "(", "uvw", ",", "antenna1", ",", "antenna2", ",", "chunks", ",", "nr_of_antenna", ")", ":", "if", "antenna1", ".", "ndim", "!=", "1", ":", "raise", "ValueError", "(", "\"antenna1 shape should be (row,)\"", ")", "if", "antenna2", ".", ...	29.694444	0.000906
def opt_pagesize(self, pagesize): """ Get or set the page size of the query output """ if pagesize != "auto": pagesize = int(pagesize) self.conf["pagesize"] = pagesize	[ "def", "opt_pagesize", "(", "self", ",", "pagesize", ")", ":", "if", "pagesize", "!=", "\"auto\"", ":", "pagesize", "=", "int", "(", "pagesize", ")", "self", ".", "conf", "[", "\"pagesize\"", "]", "=", "pagesize" ]	39.8	0.009852
def request_id(self, request_id): """ Sets the request_id of this ErrorResponse. Request ID. :param request_id: The request_id of this ErrorResponse. :type: str """ if request_id is not None and not re.search('^[A-Za-z0-9]{32}', request_id): raise Val...	[ "def", "request_id", "(", "self", ",", "request_id", ")", ":", "if", "request_id", "is", "not", "None", "and", "not", "re", ".", "search", "(", "'^[A-Za-z0-9]{32}'", ",", "request_id", ")", ":", "raise", "ValueError", "(", "\"Invalid value for `request_id`, must...	37.333333	0.008715
def find_mutant_amino_acid_interval( cdna_sequence, cdna_first_codon_offset, cdna_variant_start_offset, cdna_variant_end_offset, n_ref, n_amino_acids): """ Parameters ---------- cdna_sequence : skbio.DNA or str cDNA sequence found in RNAseq data ...	[ "def", "find_mutant_amino_acid_interval", "(", "cdna_sequence", ",", "cdna_first_codon_offset", ",", "cdna_variant_start_offset", ",", "cdna_variant_end_offset", ",", "n_ref", ",", "n_amino_acids", ")", ":", "cdna_alt_nucleotides", "=", "cdna_sequence", "[", "cdna_variant_sta...	38.586957	0.001099
def accession(auth, label, project=None): ''' Get the Accession ID for any Experiment label. Example: >>> import yaxil >>> auth = yaxil.XnatAuth(url='...', username='...', password='...') >>> yaxil.accession(auth, 'AB1234C') u'XNAT_E00001' :param auth: XNAT authenticati...	[ "def", "accession", "(", "auth", ",", "label", ",", "project", "=", "None", ")", ":", "return", "list", "(", "experiments", "(", "auth", ",", "label", ",", "project", ")", ")", "[", "0", "]", ".", "id" ]	28.85	0.001678
def _evaluate(self,x,y): ''' Returns the level of the interpolated function at each value in x,y. Only called internally by HARKinterpolator2D.__call__ (etc). ''' x_pos, y_pos = self.findSector(x,y) alpha, beta = self.findCoords(x,y,x_pos,y_pos) # Calculate the f...	[ "def", "_evaluate", "(", "self", ",", "x", ",", "y", ")", ":", "x_pos", ",", "y_pos", "=", "self", ".", "findSector", "(", "x", ",", "y", ")", "alpha", ",", "beta", "=", "self", ".", "findCoords", "(", "x", ",", "y", ",", "x_pos", ",", "y_pos",...	41.066667	0.028571
def delete_object(self, id): """Deletes the object with the given ID from the graph.""" return self.request( "{0}/{1}".format(self.version, id), method="DELETE" )	[ "def", "delete_object", "(", "self", ",", "id", ")", ":", "return", "self", ".", "request", "(", "\"{0}/{1}\"", ".", "format", "(", "self", ".", "version", ",", "id", ")", ",", "method", "=", "\"DELETE\"", ")" ]	38.8	0.010101
def gpg_download_key( key_id, key_server, config_dir=None ): """ Download a GPG key from a key server. Do not import it into any keyrings. Return the ASCII-armored key """ config_dir = get_config_dir( config_dir ) tmpdir = make_gpg_tmphome( prefix="download", config_dir=config_dir ) gpg...	[ "def", "gpg_download_key", "(", "key_id", ",", "key_server", ",", "config_dir", "=", "None", ")", ":", "config_dir", "=", "get_config_dir", "(", "config_dir", ")", "tmpdir", "=", "make_gpg_tmphome", "(", "prefix", "=", "\"download\"", ",", "config_dir", "=", "...	30.333333	0.021302
def list_tar (archive, compression, cmd, verbosity, interactive): """List a TAR archive.""" cmdlist = [cmd, '-n'] add_star_opts(cmdlist, compression, verbosity) cmdlist.append("file=%s" % archive) return cmdlist	[ "def", "list_tar", "(", "archive", ",", "compression", ",", "cmd", ",", "verbosity", ",", "interactive", ")", ":", "cmdlist", "=", "[", "cmd", ",", "'-n'", "]", "add_star_opts", "(", "cmdlist", ",", "compression", ",", "verbosity", ")", "cmdlist", ".", "...	37.666667	0.008658
def modify_number_pattern(number_pattern, **kwargs): """Modifies a number pattern by specified keyword arguments.""" params = ['pattern', 'prefix', 'suffix', 'grouping', 'int_prec', 'frac_prec', 'exp_prec', 'exp_plus'] for param in params: if param in kwargs: continue ...	[ "def", "modify_number_pattern", "(", "number_pattern", ",", "", "", "kwargs", ")", ":", "params", "=", "[", "'pattern'", ",", "'prefix'", ",", "'suffix'", ",", "'grouping'", ",", "'int_prec'", ",", "'frac_prec'", ",", "'exp_prec'", ",", "'exp_plus'", "]", ...	44	0.002475
def saveDirectory(alias): """save a directory to a certain alias/nickname""" if not settings.platformCompatible(): return False dataFile = open(settings.getDataFile(), "wb") currentDirectory = os.path.abspath(".") directory = {alias : currentDirectory} pickle.dump(directory, dataFile) speech.success(alias + " ...	[ "def", "saveDirectory", "(", "alias", ")", ":", "if", "not", "settings", ".", "platformCompatible", "(", ")", ":", "return", "False", "dataFile", "=", "open", "(", "settings", ".", "getDataFile", "(", ")", ",", "\"wb\"", ")", "currentDirectory", "=", "os",...	44.1	0.026667
def calculate_fuzzy_chi(alpha, square_map, right_eigenvectors): """Calculate the membership matrix (chi) from parameters alpha. Parameters ---------- alpha : ndarray Parameters of objective function (e.g. flattened A) square_map : ndarray Mapping from square indices (i,j) to flat in...	[ "def", "calculate_fuzzy_chi", "(", "alpha", ",", "square_map", ",", "right_eigenvectors", ")", ":", "# Convert parameter vector into matrix A", "A", "=", "to_square", "(", "alpha", ",", "square_map", ")", "# Make A feasible.", "A", "=", "fill_A", "(", "A", ",", "r...	31.1	0.00104

def get_project_by_network_id(network_id,**kwargs): """ get a project complexmodel by a network_id """ user_id = kwargs.get('user_id') projects_i = db.DBSession.query(Project).join(ProjectOwner).join(Network, Project.id==Network.project_id).filter( ...

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def load_json_dct( dct, record_store=None, schema=None, loader=from_json_compatible ): """ Create a Record instance from a json-compatible dictionary The dictionary values should have types that are json compatible, as if just loaded from a json serialized record string. ...

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def dict_intersection(dict1, dict2, combine=False, combine_op=op.add): r""" Args: dict1 (dict): dict2 (dict): combine (bool): Combines keys only if the values are equal if False else values are combined using combine_op (default = False) combine_op (func): (default = ...

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def cluster_elongate(): "Not so applicable for this sample" start_centers = [[1.0, 4.5], [3.1, 2.7]] template_clustering(start_centers, SIMPLE_SAMPLES.SAMPLE_ELONGATE, criterion = splitting_type.BAYESIAN_INFORMATION_CRITERION) template_clustering(start_centers, SIMPLE_SAMPLES.SAMPLE_ELONGATE, criter...

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def _match_filter_plot(stream, cccsum, template_names, rawthresh, plotdir, plot_format, i): # pragma: no cover """ Plotting function for match_filter. :param stream: Stream to plot :param cccsum: Cross-correlation sum to plot :param template_names: Template names used :p...

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def display_console(self, request): """Display a standalone shell.""" if 0 not in self.frames: self.frames[0] = _ConsoleFrame(self.console_init_func()) return Response(render_console_html(secret=self.secret), content_type='text/html')

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def get_config_load_path(conf_path=None): """ Return config file load path Priority: 1. conf_path 2. current directory 3. home directory Parameters ---------- conf_path Returns ------- """ if conf_path is None: # test ./andes.conf if o...

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def statement(self) -> Statement: """Parse YANG statement. Raises: EndOfInput: If past the end of input. UnexpectedInput: If no syntactically correct statement is found. """ pref, kw = self.keyword() pres = self.opt_separator() next = self.peek() ...

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def _initialize_memory(self, policy_params): """Initialize temporary and permanent memory. Args: policy_params: Nested tuple of policy parameters with all dimensions set. Initializes the attributes `self._current_episodes`, `self._finished_episodes`, and `self._num_finished_episodes`. The episod...

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def nearest_neighbors( X, n_neighbors, metric, metric_kwds, angular, random_state, verbose=False ): """Compute the ``n_neighbors`` nearest points for each data point in ``X`` under ``metric``. This may be exact, but more likely is approximated via nearest neighbor descent. Parameters ----------...

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def ensure_crossplat_path(path, winroot='C:'): r""" ensure_crossplat_path Args: path (str): Returns: str: crossplat_path Example(DOCTEST): >>> # ENABLE_DOCTEST >>> from utool.util_path import * # NOQA >>> path = r'C:\somedir' >>> cplat_path = ensur...

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def run_cmd(cmd, echo=False, fail_silently=False, **kwargs): r"""Call given command with ``subprocess.call`` function. :param cmd: Command to run. :type cmd: tuple or str :param echo: If enabled show command to call and its output in STDOUT, otherwise hide all output. By default: False ...

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def previous(self): """ fetch the chart identified by this chart's previous_id attribute if the previous_id is either null or not present for this chart return None returns the new chart instance on sucess""" try: if self.previous_id: return Ch...

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def create(host, port, result_converter=None, testcase_converter=None, args=None): """ Function which is called by Icetea to create an instance of the cloud client. This function must exists. This function myust not return None. Either return an instance of Client or raise. """ return SampleClie...

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def users_getPresence(self, *, user: str, **kwargs) -> SlackResponse: """Gets user presence information. Args: user (str): User to get presence info on. Defaults to the authed user. e.g. 'W1234567890' """ kwargs.update({"user": user}) return self.api_...

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def _tls_P_hash(secret, seed, req_len, hm): """ Provides the implementation of P_hash function defined in section 5 of RFC 4346 (and section 5 of RFC 5246). Two parameters have been added (hm and req_len): - secret : the key to be used. If RFC 4868 is to be believed, the length must ...

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def cli(env, crt, csr, icc, key, notes): """Add and upload SSL certificate details.""" template = { 'intermediateCertificate': '', 'certificateSigningRequest': '', 'notes': notes, } template['certificate'] = open(crt).read() template['privateKey'] = open(key).read() if c...

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def print_help(self, session, command=None): """ Prints the available methods and their documentation, or the documentation of the given command. """ if command: # Single command mode if command in self._commands: # Argument is a name space...

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def timeout_process_add_queue(self, module, cache_time): """ Add a module to the timeout_queue if it is scheduled in the future or if it is due for an update immediately just trigger that. the timeout_queue is a dict with the scheduled time as the key and the value is a list of ...

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def read(self, nml_fname, nml_patch_in=None, patch_fname=None): """Parse a Fortran namelist file and store the contents. >>> parser = f90nml.Parser() >>> data_nml = parser.read('data.nml') """ # For switching based on files versus paths nml_is_path = not hasattr(nml_fnam...

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def _open(self): """ Open the file; get sheets :return: """ if not hasattr(self, '_file'): self._file = self.gc.open(self.name) self.sheet_names = self._file.worksheets()

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def encode(msg, strict=False, logger=None, timezone_offset=None): """ Encodes and returns the L{msg<Envelope>} as an AMF stream. @param strict: Enforce strict encoding. Default is C{False}. Specifically header/body lengths will be written correctly, instead of the default 0. Default is `Fal...

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def posterior_predictive_to_xarray(self): """Convert posterior_predictive samples to xarray.""" posterior = self.posterior posterior_predictive = self.posterior_predictive data = get_draws(posterior, variables=posterior_predictive) return dict_to_dataset(data, library=self.p...

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def rm_op(l, name, op): """Remove an opcode. This is used when basing a new Python release off of another one, and there is an opcode that is in the old release that was removed in the new release. We are pretty aggressive about removing traces of the op. """ # opname is an array, so we need to...

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def inherit_docstrings(cls): """Class decorator for inheriting docstrings. Automatically inherits base class doc-strings if not present in the derived class. """ @functools.wraps(cls) def _inherit_docstrings(cls): if not isinstance(cls, (type, colorise.compat.ClassType)): r...

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def _suggest_semantic_version(s): """ Try to suggest a semantic form for a version for which _suggest_normalized_version couldn't come up with anything. """ result = s.strip().lower() for pat, repl in _REPLACEMENTS: result = pat.sub(repl, result) if not result: result = '0.0....

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def si_format(value, precision=1, format_str=u'{value} {prefix}', exp_format_str=u'{value}e{expof10}'): ''' Format value to string with SI prefix, using the specified precision. Parameters ---------- value : int, float Input value. precision : int Number of digits ...

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def eig_one_step(current_vector, learning_rate, vector_prod_fn): """Function that performs one step of gd (variant) for min eigen value. Args: current_vector: current estimate of the eigen vector with minimum eigen value. learning_rate: learning rate. vector_prod_fn: function which returns produc...

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def find_linked_dynamic_libraries(): """ This function attempts to locate the required link libraries, and returns them as a list of absolute paths. """ with TaskContext("Find the required dynamic libraries") as log: llvm = get_llvm() libs = required_link_libraries() resolved...

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def wait_for_instance( vm_=None, data=None, ip_address=None, display_ssh_output=True, call=None, ): ''' Wait for an instance upon creation from the EC2 API, to become available ''' if call == 'function': # Technically this function may be called other ...

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def getParent(self, returned_properties=None): """Get the parent workitem of this workitem If no parent, None will be returned. :param returned_properties: the returned properties that you want. Refer to :class:`rtcclient.client.RTCClient` for more explanations :return: a :...

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async def movies(self): '''list of movies in the collection |force| |coro| Returns ------- list of type :class:`embypy.objects.Movie` ''' items = [] for i in await self.items: if i.type == 'Movie': items.append(i) elif hasattr(i, 'movies'): items....

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def add_all_database_reactions(model, compartments): """Add all reactions from database that occur in given compartments. Args: model: :class:`psamm.metabolicmodel.MetabolicModel`. """ added = set() for rxnid in model.database.reactions: reaction = model.database.get_reaction(rxnid...

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def schedule_to_array(schedule, events, slots): """Convert a schedule from schedule to array form Parameters ---------- schedule : list or tuple of instances of :py:class:`resources.ScheduledItem` events : list or tuple of :py:class:`resources.Event` instances slots : list or tu...

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def remove_from_role(server_context, role, user_id=None, email=None, container_path=None): """ Remove user/group from security role :param server_context: A LabKey server context. See utils.create_server_context. :param role: (from get_roles) to remove user from :param user_id: to remove permissions...

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def validate_groupby_func(name, args, kwargs, allowed=None): """ 'args' and 'kwargs' should be empty, except for allowed kwargs because all of their necessary parameters are explicitly listed in the function signature """ if allowed is None: allowed = [] kwargs = set(kwargs) - s...

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def update_package_files(srcdir, extensions, package_data, packagenames, package_dirs): """ This function is deprecated and maintained for backward compatibility with affiliated packages. Affiliated packages should update their setup.py to use `get_package_info` instead. ""...

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def calc(self, x:Image, *args:Any, **kwargs:Any)->Image: "Apply to image `x`, wrapping it if necessary." if self._wrap: return getattr(x, self._wrap)(self.func, *args, **kwargs) else: return self.func(x, *args, **kwargs)

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def hl_table2canvas(self, w, res_dict): """Highlight mask on canvas when user click on table.""" objlist = [] # Remove existing highlight if self.maskhltag: try: self.canvas.delete_object_by_tag(self.maskhltag, redraw=False) except Exception: ...

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def getBucketValues(self): """ See the function description in base.py """ # Need to re-create? if self._bucketValues is None: topDownMappingM = self._getTopDownMapping() numBuckets = topDownMappingM.nRows() self._bucketValues = [] for bucketIdx in range(numBuckets): self._b...

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def get_overlapping_ranges(self, collection_link, sorted_ranges): ''' Given the sorted ranges and a collection, Returns the list of overlapping partition key ranges :param str collection_link: The collection link. :param (list of routing_range._Range) sorted_...

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def _build_layers(self, inputs, num_outputs, options): """Process the flattened inputs. Note that dict inputs will be flattened into a vector. To define a model that processes the components separately, use _build_layers_v2(). """ hiddens = options.get("fcnet_hiddens") ...

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def genfsms(self,meter=None): """Generate FSM images. Requires networkx and GraphViz.""" if (hasattr(self,'allParses')): name=self.getName() import networkx as nx m2int={'w':'0','s':'1'} gs={} gs['weight']=['str_weight'] gs['stress']=['str_stress'] gs['stressweight']=['str_stress','str_weigh...

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def isEnabled(self): """ Return whether or not this layer is enabled and can be set as the \ current layer. :sa linkEnabledToCurrent :return <bool> """ if self._linkEnabledToCurrent: addtl = self.isCurrent() e...

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def get(self, url, params=None, headers=None, content=None, form_content=None): # type: (str, Optional[Dict[str, str]], Optional[Dict[str, str]], Any, Optional[Dict[str, Any]]) -> ClientRequest """Create a GET request object. :param str url: The request URL. :param dict params: Request ...

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def summary(self, key, column="C1", timeoutSecs=10, **kwargs): ''' Return the summary for a single column for a single Frame in the h2o cluster. ''' params_dict = { # 'offset': 0, # 'len': 100 } h2o_methods.check_params_update_kwargs(params_dict, kwargs, 'summary', True) ...

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def render(self, content = None, **settings): """ Perform widget rendering, but do not print anything. """ (content, settings) = self.get_setup(content, **settings) return self._render(content, **settings)

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def oneup(self, window_name, object_name, iterations): """ Press scrollbar up with number of iterations @param window_name: Window name to type in, either full name, LDTP's name convention, or a Unix glob. @type window_name: string @param object_name: Object name to type...

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def sens_batmon_encode(self, temperature, voltage, current, SoC, batterystatus, serialnumber, hostfetcontrol, cellvoltage1, cellvoltage2, cellvoltage3, cellvoltage4, cellvoltage5, cellvoltage6): ''' Battery pack monitoring data for Li-Ion batteries temperature ...

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def setup_temp_logger(log_level='error'): ''' Setup the temporary console logger ''' if is_temp_logging_configured(): logging.getLogger(__name__).warning( 'Temporary logging is already configured' ) return if log_level is None: log_level = 'warning' ...

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def run_drop_tables(_): ''' Running the script. ''' print('--') drop_the_table(TabPost) drop_the_table(TabTag) drop_the_table(TabMember) drop_the_table(TabWiki) drop_the_table(TabLink) drop_the_table(TabEntity) drop_the_table(TabPostHist) drop_the_table(TabWikiHist) ...

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def miller_rabin(n, k): """Run the Miller-Rabin test on n with at most k iterations Arguments: n (int): number whose primality is to be tested k (int): maximum number of iterations to run Returns: bool: If n is prime, then True is returned. Otherwise, False is returned, exc...

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def set_static_ip(iface, addr, gateway=None, append=False): ''' Set static IP configuration on a Windows NIC iface The name of the interface to manage addr IP address with subnet length (ex. ``10.1.2.3/24``). The :mod:`ip.get_subnet_length <salt.modules.win_ip.get_subnet_length...

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def _get_quantiles(self, X, width, quantiles, modelmat=None, lp=None, prediction=False, xform=True, term=-1): """ estimate prediction intervals for LinearGAM Parameters ---------- X : array input data of shape (n_samples, m_features) wi...

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def owner_type(self, value): """Set ``owner_type`` to the given value. In addition: * Update the internal type of the ``owner`` field. * Update the value of the ``owner`` field if a value is already set. """ self._owner_type = value if value == 'User': ...

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def get_objects(self): """ Return a list of all content objects in this distribution. :rtype: list of :class:`boto.cloudfront.object.Object` :return: The content objects """ bucket = self._get_bucket() objs = [] for key in bucket: objs...

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def ensure_traj(traj): r"""Makes sure that traj is a trajectory (array of float) """ if is_float_matrix(traj) or is_bool_matrix(traj): return traj elif is_float_vector(traj): return traj[:,None] else: try: arr = np.array(traj) arr = ensure_dtype_float...

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def EMetaclass(cls): """Class decorator for creating PyEcore metaclass.""" superclass = cls.__bases__ if not issubclass(cls, EObject): sclasslist = list(superclass) if object in superclass: index = sclasslist.index(object) sclasslist.insert(index, EObject) ...

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def del_edges(self, edges, *args, **kwargs): """ Removes edges from the graph. Takes optional arguments for ``DictGraph.del_edge``. Arguments: - edges(iterable) Sequence of edges to be removed from the ``DictGraph``. """ ...

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def _stderr_raw(self, s): """Writes the string to stdout""" print(s, end='', file=sys.stderr) sys.stderr.flush()

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def deserialize_dataframe(reader, data_type_id): """ Deserialize a dataframe. Parameters ---------- reader : file File-like object to read from. Must be opened in binary mode. data_type_id : dict Serialization format of the raw data. See the azureml.DataTypeIds class for...

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def deposit_fetcher(record_uuid, data): """Fetch a deposit identifier. :param record_uuid: Record UUID. :param data: Record content. :returns: A :class:`invenio_pidstore.fetchers.FetchedPID` that contains data['_deposit']['id'] as pid_value. """ return FetchedPID( provider=Depos...

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def get_info(self): """ Get info for all filters. """ out = '' for k in sorted(self.components.keys()): out += '{:s}: {:s}'.format(k, self.info[k]) + '\n' return(out)

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def undo(self): """Undo the last cluster assignment operation. Returns ------- up : UpdateInfo instance of the changes done by this operation. """ _, _, undo_state = self._undo_stack.back() # Retrieve the initial spike_cluster structure. spike_clusters...

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def print_tree(editor, file=sys.stdout, print_blocks=False, return_list=False): """ Prints the editor fold tree to stdout, for debugging purpose. :param editor: CodeEditor instance. :param file: file handle where the tree will be printed. Default is stdout. :param print_blocks: True to print all bl...

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def gather(params, indices, dtype=tf.float32): """Version of tf.gather that works faster on tpu.""" if not is_xla_compiled(): return tf.gather(params, indices) vocab_size = params.get_shape().as_list()[0] indices_flat = tf.reshape(indices, [-1]) out = tf.matmul(tf.one_hot(indices_flat, vocab_size, dtype=d...

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def physical_pins(self, function): """ Return the physical pins supporting the specified *function* as tuples of ``(header, pin_number)`` where *header* is a string specifying the header containing the *pin_number*. Note that the return value is a :class:`set` which is not indexa...

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def get_submodules(app, module): """Get all submodules without packages for the given module/package :param app: the sphinx app :type app: :class:`sphinx.application.Sphinx` :param module: the module to query or module path :type module: module | str :returns: list of module names excluding pac...

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def create(cls, service=None, endpoint=None, data=None, *args, **kwargs): """ Create an integration within the scope of an service. Make sure that they should reasonably be able to query with an service or endpoint that knows about an service. """ cls.validate(data) ...

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def label_to_latex(text): # pylint: disable=anomalous-backslash-in-string r"""Convert text into a latex-passable representation. This method just escapes the following reserved LaTeX characters: % \ _ ~ &, whilst trying to avoid doubly-escaping already escaped characters Parameters -------...

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def init_app(self, app): """Initialize the `app` for use with this :class:`~flask_mysqldb.MySQL` class. This is called automatically if `app` is passed to :meth:`~MySQL.__init__`. :param flask.Flask app: the application to configure for use with this :class:`~flask_m...

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def handle_import(self, options): """ Gets the posts from either the provided URL or the path if it is local. """ url = options.get("url") if url is None: raise CommandError("Usage is import_wordpress %s" % self.args) try: import feedparse...

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def fix_objective_as_constraint(model, fraction=1, bound=None, name='fixed_objective_{}'): """Fix current objective as an additional constraint. When adding constraints to a model, such as done in pFBA which minimizes total flux, these constraints can become too powerful, ...

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def exit_if_path_exists(self): """ Exit early if the path cannot be found. """ if os.path.exists(self.output_path): ui.error(c.MESSAGES["path_exists"], self.output_path) sys.exit(1)

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def searchNs(self, doc, nameSpace): """Search a Ns registered under a given name space for a document. recurse on the parents until it finds the defined namespace or return None otherwise. @nameSpace can be None, this is a search for the default namespace. We don't allow ...

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def propose(self, current, r): """Generates a random sample from the discrete probability distribution and returns its value, the log of the probability of sampling that value and the log of the probability of sampling the current value (passed in). """ stay = (r.uniform(0, 1) < self.kernel) if ...

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def shrink(self, index, target, body=None, params=None): """ The shrink index API allows you to shrink an existing index into a new index with fewer primary shards. The number of primary shards in the target index must be a factor of the shards in the source index. For example an...

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def namedb_preorder_insert( cur, preorder_rec ): """ Add a name or namespace preorder record, if it doesn't exist already. DO NOT CALL THIS DIRECTLY. """ preorder_row = copy.deepcopy( preorder_rec ) assert 'preorder_hash' in preorder_row, "BUG: missing preorder_hash" try: pre...

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def get_base_url(self, request): """ Creates base url string. :param request: OGC-type request with specified bounding box, cloud coverage for specific product. :type request: OgcRequest or GeopediaRequest :return: base string for url to Sentinel Hub's OGC service for this product. ...

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def str_variants(store, institute_obj, case_obj, variants_query, page=1, per_page=50): """Pre-process list of STR variants.""" # Nothing unique to STRs on this level. Inheritance? return variants(store, institute_obj, case_obj, variants_query, page, per_page)

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def get_recent_comments(number=5, template='zinnia/tags/comments_recent.html'): """ Return the most recent comments. """ # Using map(smart_text... fix bug related to issue #8554 entry_published_pks = map(smart_text, Entry.published.values_list('id', flat=True)) cont...

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def escape(s, quote=False): """Replace special characters "&", "<" and ">" to HTML-safe sequences. If the optional flag `quote` is `True`, the quotation mark character (") is also translated. There is a special handling for `None` which escapes to an empty string. :param s: the string to escape. ...

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def CacheStorage_deleteEntry(self, cacheId, request): """ Function path: CacheStorage.deleteEntry Domain: CacheStorage Method name: deleteEntry Parameters: Required arguments: 'cacheId' (type: CacheId) -> Id of cache where the entry will be deleted. 'request' (type: string) -> URL spec of ...

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def inverse_transform(self, maps): """ This function transforms from component masses and cartesian spins to mass-weighted spin parameters perpendicular with the angular momentum. Parameters ---------- maps : a mapping object Returns ------- out : dict ...

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def get_ft_names(mod, include_inner=False)->List[str]: "Return all the functions of module `mod`." # If the module has an attribute __all__, it picks those. # Otherwise, it returns all the functions defined inside a module. fn_names = [] for elt_name in get_exports(mod): elt = getattr(mod,el...

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def upsert_acl(cursor, uuid_, permissions): """Given a ``uuid`` and a set of permissions given as a tuple of ``uid`` and ``permission``, upsert them into the database. """ if not isinstance(permissions, (list, set, tuple,)): raise TypeError("``permissions`` is an invalid type: {}" ...

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def times_to_ms(h=0, m=0, s=0, ms=0): """ Convert hours, minutes, seconds to milliseconds. Arguments may be positive or negative, int or float, need not be normalized (``s=120`` is okay). Returns: Number of milliseconds (rounded to int). """ ms += s * 1000 ms += m ...

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def _antenna_uvw(uvw, antenna1, antenna2, chunks, nr_of_antenna): """ numba implementation of antenna_uvw """ if antenna1.ndim != 1: raise ValueError("antenna1 shape should be (row,)") if antenna2.ndim != 1: raise ValueError("antenna2 shape should be (row,)") if uvw.ndim != 2 or uvw.s...

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def opt_pagesize(self, pagesize): """ Get or set the page size of the query output """ if pagesize != "auto": pagesize = int(pagesize) self.conf["pagesize"] = pagesize

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def request_id(self, request_id): """ Sets the request_id of this ErrorResponse. Request ID. :param request_id: The request_id of this ErrorResponse. :type: str """ if request_id is not None and not re.search('^[A-Za-z0-9]{32}', request_id): raise Val...

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def find_mutant_amino_acid_interval( cdna_sequence, cdna_first_codon_offset, cdna_variant_start_offset, cdna_variant_end_offset, n_ref, n_amino_acids): """ Parameters ---------- cdna_sequence : skbio.DNA or str cDNA sequence found in RNAseq data ...

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def accession(auth, label, project=None): ''' Get the Accession ID for any Experiment label. Example: >>> import yaxil >>> auth = yaxil.XnatAuth(url='...', username='...', password='...') >>> yaxil.accession(auth, 'AB1234C') u'XNAT_E00001' :param auth: XNAT authenticati...

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def _evaluate(self,x,y): ''' Returns the level of the interpolated function at each value in x,y. Only called internally by HARKinterpolator2D.__call__ (etc). ''' x_pos, y_pos = self.findSector(x,y) alpha, beta = self.findCoords(x,y,x_pos,y_pos) # Calculate the f...

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def delete_object(self, id): """Deletes the object with the given ID from the graph.""" return self.request( "{0}/{1}".format(self.version, id), method="DELETE" )

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38.8

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def gpg_download_key( key_id, key_server, config_dir=None ): """ Download a GPG key from a key server. Do not import it into any keyrings. Return the ASCII-armored key """ config_dir = get_config_dir( config_dir ) tmpdir = make_gpg_tmphome( prefix="download", config_dir=config_dir ) gpg...

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def list_tar (archive, compression, cmd, verbosity, interactive): """List a TAR archive.""" cmdlist = [cmd, '-n'] add_star_opts(cmdlist, compression, verbosity) cmdlist.append("file=%s" % archive) return cmdlist

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def modify_number_pattern(number_pattern, **kwargs): """Modifies a number pattern by specified keyword arguments.""" params = ['pattern', 'prefix', 'suffix', 'grouping', 'int_prec', 'frac_prec', 'exp_prec', 'exp_plus'] for param in params: if param in kwargs: continue ...

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def saveDirectory(alias): """save a directory to a certain alias/nickname""" if not settings.platformCompatible(): return False dataFile = open(settings.getDataFile(), "wb") currentDirectory = os.path.abspath(".") directory = {alias : currentDirectory} pickle.dump(directory, dataFile) speech.success(alias + " ...

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def calculate_fuzzy_chi(alpha, square_map, right_eigenvectors): """Calculate the membership matrix (chi) from parameters alpha. Parameters ---------- alpha : ndarray Parameters of objective function (e.g. flattened A) square_map : ndarray Mapping from square indices (i,j) to flat in...

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