kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def writeToFile(self, f, packed=True): """ Write serialized object to file. :param f: output file :param packed: If true, will pack contents. """ # Get capnproto schema from instance schema = self.getSchema() # Construct new message, otherwise refered to as `proto` proto = schema.n...	[ "def", "writeToFile", "(", "self", ",", "f", ",", "packed", "=", "True", ")", ":", "# Get capnproto schema from instance", "schema", "=", "self", ".", "getSchema", "(", ")", "# Construct new message, otherwise refered to as `proto`", "proto", "=", "schema", ".", "ne...	23.380952	17.095238
def rgbmap_cb(self, rgbmap, channel): """ This method is called when the RGBMap is changed. We update the ColorBar to match. """ if not self.gui_up: return fitsimage = channel.fitsimage if fitsimage != self.fv.getfocus_fitsimage(): return ...	[ "def", "rgbmap_cb", "(", "self", ",", "rgbmap", ",", "channel", ")", ":", "if", "not", "self", ".", "gui_up", ":", "return", "fitsimage", "=", "channel", ".", "fitsimage", "if", "fitsimage", "!=", "self", ".", "fv", ".", "getfocus_fitsimage", "(", ")", ...	32.545455	10
def convert_cityscapes_instance_only( data_dir, out_dir): """Convert from cityscapes format to COCO instance seg format - polygons""" sets = [ 'gtFine_val', 'gtFine_train', 'gtFine_test', # 'gtCoarse_train', # 'gtCoarse_val', # 'gtCoarse_train_extra' ...	[ "def", "convert_cityscapes_instance_only", "(", "data_dir", ",", "out_dir", ")", ":", "sets", "=", "[", "'gtFine_val'", ",", "'gtFine_train'", ",", "'gtFine_test'", ",", "# 'gtCoarse_train',", "# 'gtCoarse_val',", "# 'gtCoarse_train_extra'", "]", "ann_dirs", "=", "[", ...	38.45045	20.027027
def play_human(env): """ Play the environment using keyboard as a human. Args: env (gym.Env): the initialized gym environment to play Returns: None """ # play the game and catch a potential keyboard interrupt try: play(env, fps=env.metadata['video.frames_per_second...	[ "def", "play_human", "(", "env", ")", ":", "# play the game and catch a potential keyboard interrupt", "try", ":", "play", "(", "env", ",", "fps", "=", "env", ".", "metadata", "[", "'video.frames_per_second'", "]", ")", "except", "KeyboardInterrupt", ":", "pass", ...	22.388889	22.277778
def __set_bp(self, aProcess): """ Writes a breakpoint instruction at the target address. @type aProcess: L{Process} @param aProcess: Process object. """ address = self.get_address() self.__previousValue = aProcess.read(address, len(self.bpInstruction)) i...	[ "def", "__set_bp", "(", "self", ",", "aProcess", ")", ":", "address", "=", "self", ".", "get_address", "(", ")", "self", ".", "__previousValue", "=", "aProcess", ".", "read", "(", "address", ",", "len", "(", "self", ".", "bpInstruction", ")", ")", "if"...	40.5	13.214286
def windows_k_distinct(x, k): """Find all largest windows containing exactly k distinct elements :param x: list or string :param k: positive integer :yields: largest intervals [i, j) with len(set(x[i:j])) == k :complexity: `O(\|x\|)` """ dist, i, j = 0, 0, 0 # dist = \|{x[i], .....	[ "def", "windows_k_distinct", "(", "x", ",", "k", ")", ":", "dist", ",", "i", ",", "j", "=", "0", ",", "0", ",", "0", "# dist = \|{x[i], ..., x[j-1]}\|", "occ", "=", "{", "xi", ":", "0", "for", "xi", "in", "x", "}", "# number of occurrences in x[i:j]", "w...	38.217391	17.304348
def __get_bundle(self, io_handler, bundle_id): """ Retrieves the Bundle object with the given bundle ID. Writes errors through the I/O handler if any. :param io_handler: I/O Handler :param bundle_id: String or integer bundle ID :return: The Bundle object matching the giv...	[ "def", "__get_bundle", "(", "self", ",", "io_handler", ",", "bundle_id", ")", ":", "try", ":", "bundle_id", "=", "int", "(", "bundle_id", ")", "return", "self", ".", "_context", ".", "get_bundle", "(", "bundle_id", ")", "except", "(", "TypeError", ",", "...	41.8125	14.6875
def root_item_selected(self, item): """Root item has been selected: expanding it and collapsing others""" if self.show_all_files: return for root_item in self.get_top_level_items(): if root_item is item: self.expandItem(root_item) else: ...	[ "def", "root_item_selected", "(", "self", ",", "item", ")", ":", "if", "self", ".", "show_all_files", ":", "return", "for", "root_item", "in", "self", ".", "get_top_level_items", "(", ")", ":", "if", "root_item", "is", "item", ":", "self", ".", "expandItem...	39.666667	9
def reportPrettyData(root, worker, job, job_types, options): """ print the important bits out. """ out_str = "Batch System: %s\n" % root.batch_system out_str += ("Default Cores: %s Default Memory: %s\n" "Max Cores: %s\n" % ( reportNumber(get(root, "default_cores"), options), ...	[ "def", "reportPrettyData", "(", "root", ",", "worker", ",", "job", ",", "job_types", ",", "options", ")", ":", "out_str", "=", "\"Batch System: %s\\n\"", "%", "root", ".", "batch_system", "out_str", "+=", "(", "\"Default Cores: %s Default Memory: %s\\n\"", "\"Max C...	45.375	18.541667
def advance(self): """Carry out one iteration of Arnoldi.""" if self.iter >= self.maxiter: raise ArgumentError('Maximum number of iterations reached.') if self.invariant: raise ArgumentError('Krylov subspace was found to be invariant ' 'in ...	[ "def", "advance", "(", "self", ")", ":", "if", "self", ".", "iter", ">=", "self", ".", "maxiter", ":", "raise", "ArgumentError", "(", "'Maximum number of iterations reached.'", ")", "if", "self", ".", "invariant", ":", "raise", "ArgumentError", "(", "'Krylov s...	41.045455	16.488636
def create_thread(cls, session, conversation, thread, imported=False): """Create a conversation thread. Please note that threads cannot be added to conversations with 100 threads (or more), if attempted the API will respond with HTTP 412. Args: conversation (helpscout.model...	[ "def", "create_thread", "(", "cls", ",", "session", ",", "conversation", ",", "thread", ",", "imported", "=", "False", ")", ":", "return", "super", "(", "Conversations", ",", "cls", ")", ".", "create", "(", "session", ",", "thread", ",", "endpoint_override...	44.814815	25.888889
def check(self): """ Compare the :func:`os.stat` for the pam_env style environmnt file `path` with the previous result `old_st`, which may be :data:`None` if the previous stat attempt failed. Reload its contents if the file has changed or appeared since last attempt. :re...	[ "def", "check", "(", "self", ")", ":", "st", "=", "self", ".", "_stat", "(", ")", "if", "self", ".", "_st", "==", "st", ":", "return", "self", ".", "_st", "=", "st", "self", ".", "_remove_existing", "(", ")", "if", "st", "is", "None", ":", "LOG...	31.909091	21.454545
def stop(self): """ Stop this instance. :return: None """ instance_status = Instance.InstanceStatus(status='Terminated') xml_content = instance_status.serialize() headers = {'Content-Type': 'application/xml'} self._client.put(self.resource(), xml_conten...	[ "def", "stop", "(", "self", ")", ":", "instance_status", "=", "Instance", ".", "InstanceStatus", "(", "status", "=", "'Terminated'", ")", "xml_content", "=", "instance_status", ".", "serialize", "(", ")", "headers", "=", "{", "'Content-Type'", ":", "'applicati...	27.333333	21.666667
def _ParsePathSpecification( self, knowledge_base, searcher, file_system, path_specification, path_separator): """Parses a file system for a preprocessing attribute. Args: knowledge_base (KnowledgeBase): to fill with preprocessing information. searcher (dfvfs.FileSystemSearcher): file s...	[ "def", "_ParsePathSpecification", "(", "self", ",", "knowledge_base", ",", "searcher", ",", "file_system", ",", "path_specification", ",", "path_separator", ")", ":", "try", ":", "file_entry", "=", "searcher", ".", "GetFileEntryByPathSpec", "(", "path_specification", ...	40.5625	22.09375
def export(self, id, exclude_captures=False): # pylint: disable=invalid-name,redefined-builtin """Export a result. :param id: Result ID as an int. :param exclude_captures: If bool `True`, don't export capture files :rtype: tuple `(io.BytesIO, 'filename')` """ return self...	[ "def", "export", "(", "self", ",", "id", ",", "exclude_captures", "=", "False", ")", ":", "# pylint: disable=invalid-name,redefined-builtin", "return", "self", ".", "service", ".", "export", "(", "self", ".", "base", ",", "id", ",", "params", "=", "{", "'exc...	48.75	24.25
def prop2b(gm, pvinit, dt): """ Given a central mass and the state of massless body at time t_0, this routine determines the state as predicted by a two-body force model at time t_0 + dt. http://naif.jpl.nasa.gov/pub/naif/toolkit_docs/C/cspice/prop2b_c.html :param gm: Gravity of the central ma...	[ "def", "prop2b", "(", "gm", ",", "pvinit", ",", "dt", ")", ":", "gm", "=", "ctypes", ".", "c_double", "(", "gm", ")", "pvinit", "=", "stypes", ".", "toDoubleVector", "(", "pvinit", ")", "dt", "=", "ctypes", ".", "c_double", "(", "dt", ")", "pvprop"...	35.869565	13.956522
def add_eval(self, agent, e, fr=None): """Add or change agent's evaluation of the artifact with given framing information. :param agent: Name of the agent which did the evaluation. :param float e: Evaluation for the artifact. :param object fr: Framing information for the evaluat...	[ "def", "add_eval", "(", "self", ",", "agent", ",", "e", ",", "fr", "=", "None", ")", ":", "self", ".", "_evals", "[", "agent", ".", "name", "]", "=", "e", "self", ".", "_framings", "[", "agent", ".", "name", "]", "=", "fr" ]	40.3	13
def count_sequences(infile): '''Returns the number of sequences in a file''' seq_reader = sequences.file_reader(infile) n = 0 for seq in seq_reader: n += 1 return n	[ "def", "count_sequences", "(", "infile", ")", ":", "seq_reader", "=", "sequences", ".", "file_reader", "(", "infile", ")", "n", "=", "0", "for", "seq", "in", "seq_reader", ":", "n", "+=", "1", "return", "n" ]	26.571429	18.285714
def add_minrmsd_to_ref(self, ref, ref_frame=0, atom_indices=None, precentered=False): r""" Adds the minimum root-mean-square-deviation (minrmsd) with respect to a reference structure to the feature list. Parameters ---------- ref: Reference structure for computing th...	[ "def", "add_minrmsd_to_ref", "(", "self", ",", "ref", ",", "ref_frame", "=", "0", ",", "atom_indices", "=", "None", ",", "precentered", "=", "False", ")", ":", "from", ".", "misc", "import", "MinRmsdFeature", "f", "=", "MinRmsdFeature", "(", "ref", ",", ...	47.28125	29.4375
def searchsorted(arr, N, x): """N is length of arr """ L = 0 R = N-1 done = False m = (L+R)//2 while not done: if arr[m] < x: L = m + 1 elif arr[m] > x: R = m - 1 elif arr[m] == x: done = True m = (L+R)//2 if L>R: ...	[ "def", "searchsorted", "(", "arr", ",", "N", ",", "x", ")", ":", "L", "=", "0", "R", "=", "N", "-", "1", "done", "=", "False", "m", "=", "(", "L", "+", "R", ")", "//", "2", "while", "not", "done", ":", "if", "arr", "[", "m", "]", "<", "...	18.722222	18.611111
def default_file_encoder(): """ Get default encoder cwr file :return: """ config = CWRConfiguration() field_configs = config.load_field_config('table') field_configs.update(config.load_field_config('common')) field_values = CWRTables() for entry in field_configs.values(): i...	[ "def", "default_file_encoder", "(", ")", ":", "config", "=", "CWRConfiguration", "(", ")", "field_configs", "=", "config", ".", "load_field_config", "(", "'table'", ")", "field_configs", ".", "update", "(", "config", ".", "load_field_config", "(", "'common'", ")...	30.055556	15.944444
def attribute_value(self, doc: Document, attribute_name: str): """ Access data using attribute name rather than the numeric indices Returns: the value for the attribute """ return doc.cdr_document.get(self.header_translation_table[attribute_name])	[ "def", "attribute_value", "(", "self", ",", "doc", ":", "Document", ",", "attribute_name", ":", "str", ")", ":", "return", "doc", ".", "cdr_document", ".", "get", "(", "self", ".", "header_translation_table", "[", "attribute_name", "]", ")" ]	35.25	22.5
def generate_access_token_from_authorization_code(request, client): """ Generates a new AccessToken from a request with an authorization code. Read the specification: http://tools.ietf.org/html/rfc6749#section-4.1.3 """ authorization_code_value = request.POST.get('code') if not authorization_code_value: ...	[ "def", "generate_access_token_from_authorization_code", "(", "request", ",", "client", ")", ":", "authorization_code_value", "=", "request", ".", "POST", ".", "get", "(", "'code'", ")", "if", "not", "authorization_code_value", ":", "raise", "InvalidRequest", "(", "'...	37.476923	22.384615
def _writeMzmlIndexList(xmlWriter, spectrumIndexList, chromatogramIndexList): """ #TODO: docstring :param xmlWriter: #TODO: docstring :param spectrumIndexList: #TODO: docstring :param chromatogramIndexList: #TODO: docstring """ counts = 0 if spectrumIndexList: counts += 1 if chr...	[ "def", "_writeMzmlIndexList", "(", "xmlWriter", ",", "spectrumIndexList", ",", "chromatogramIndexList", ")", ":", "counts", "=", "0", "if", "spectrumIndexList", ":", "counts", "+=", "1", "if", "chromatogramIndexList", ":", "counts", "+=", "1", "if", "counts", "=...	31	19.28
def update_tabs_text(self): """Update the text from the tabs.""" # This is needed to prevent that hanged consoles make reference # to an index that doesn't exist. See issue 4881 try: for index, fname in enumerate(self.filenames): client = self.clients[in...	[ "def", "update_tabs_text", "(", "self", ")", ":", "# This is needed to prevent that hanged consoles make reference\r", "# to an index that doesn't exist. See issue 4881\r", "try", ":", "for", "index", ",", "fname", "in", "enumerate", "(", "self", ".", "filenames", ")", ":",...	42.357143	17.428571
def remove(self, auto_confirm=False, verbose=False): """Remove paths in ``self.paths`` with confirmation (unless ``auto_confirm`` is True).""" if not self.paths: logger.info( "Can't uninstall '%s'. No files were found to uninstall.", self.dist.project...	[ "def", "remove", "(", "self", ",", "auto_confirm", "=", "False", ",", "verbose", "=", "False", ")", ":", "if", "not", "self", ".", "paths", ":", "logger", ".", "info", "(", "\"Can't uninstall '%s'. No files were found to uninstall.\"", ",", "self", ".", "dist"...	33.866667	21.533333
def terminate(self): """Delete all files created by this index, invalidating `self`. Use with care.""" try: self.id2sims.terminate() except: pass import glob for fname in glob.glob(self.fname + '*'): try: os.remove(fname) ...	[ "def", "terminate", "(", "self", ")", ":", "try", ":", "self", ".", "id2sims", ".", "terminate", "(", ")", "except", ":", "pass", "import", "glob", "for", "fname", "in", "glob", ".", "glob", "(", "self", ".", "fname", "+", "'*'", ")", ":", "try", ...	32.444444	15.611111
def compose_object(self, file_list, destination_file, content_type): """COMPOSE multiple objects together. Using the given list of files, calls the put object with the compose flag. This call merges all the files into the destination file. Args: file_list: list of dicts with the file name. ...	[ "def", "compose_object", "(", "self", ",", "file_list", ",", "destination_file", ",", "content_type", ")", ":", "xml_setting_list", "=", "[", "'<ComposeRequest>'", "]", "for", "meta_data", "in", "file_list", ":", "xml_setting_list", ".", "append", "(", "'<Componen...	36.0625	18.5
def worker_main(self): """ The main function of for the mux process: setup the Mitogen broker thread and ansible_mitogen services, then sleep waiting for the socket connected to the parent to be closed (indicating the parent has died). """ self._setup_master() sel...	[ "def", "worker_main", "(", "self", ")", ":", "self", ".", "_setup_master", "(", ")", "self", ".", "_setup_services", "(", ")", "try", ":", "# Let the parent know our listening socket is ready.", "mitogen", ".", "core", ".", "io_op", "(", "self", ".", "child_sock...	40.227273	22.136364
def superclasses(self, inherited=False): """Iterate over the superclasses of the class. This function is the Python equivalent of the CLIPS class-superclasses command. """ data = clips.data.DataObject(self._env) lib.EnvClassSuperclasses( self._env, self._cl...	[ "def", "superclasses", "(", "self", ",", "inherited", "=", "False", ")", ":", "data", "=", "clips", ".", "data", ".", "DataObject", "(", "self", ".", "_env", ")", "lib", ".", "EnvClassSuperclasses", "(", "self", ".", "_env", ",", "self", ".", "_cls", ...	29.642857	17
def tokenize_akkadian_words(line): """ Operates on a single line of text, returns all words in the line as a tuple in a list. input: "1. isz-pur-ram a-na" output: [("isz-pur-ram", "akkadian"), ("a-na", "akkadian")] :param: line: text string :return: list of tuples: (word, language) """...	[ "def", "tokenize_akkadian_words", "(", "line", ")", ":", "beginning_underscore", "=", "\"_[^_]+(?!_)$\"", "# only match a string if it has a beginning underscore anywhere", "ending_underscore", "=", "\"^(?<!_)[^_]+_\"", "# only match a string if it has an ending underscore anywhere", "tw...	39.644444	16.711111
def start(self, container, instances=None, map_name=None, **kwargs): """ Starts instances for a container configuration. :param container: Container name. :type container: unicode \| str :param instances: Instance names to start. If not specified, will start all instances as spec...	[ "def", "start", "(", "self", ",", "container", ",", "instances", "=", "None", ",", "map_name", "=", "None", ",", "", "", "kwargs", ")", ":", "return", "self", ".", "run_actions", "(", "'start'", ",", "container", ",", "instances", "=", "instances", "...	56.117647	25.411765
def json_files_serializer(objs, status=None): """JSON Files Serializer. :parma objs: A list of:class:`invenio_files_rest.models.ObjectVersion` instances. :param status: A HTTP Status. (Default: ``None``) :returns: A Flask response with JSON data. :rtype: :py:class:`flask.Response`. """ ...	[ "def", "json_files_serializer", "(", "objs", ",", "status", "=", "None", ")", ":", "files", "=", "[", "file_serializer", "(", "obj", ")", "for", "obj", "in", "objs", "]", "return", "make_response", "(", "json", ".", "dumps", "(", "files", ")", ",", "st...	37.454545	12.909091
def to_serializable_value(self): """ Run through all fields of the object and parse the values :return: :rtype: dict """ return { name: field.to_serializable_value() for name, field in self.value.__dict__.items() if isinstance(field, F...	[ "def", "to_serializable_value", "(", "self", ")", ":", "return", "{", "name", ":", "field", ".", "to_serializable_value", "(", ")", "for", "name", ",", "field", "in", "self", ".", "value", ".", "__dict__", ".", "items", "(", ")", "if", "isinstance", "(",...	28.25	17.583333
def get_alert_log(self, current=0, minimum=0, maximum=100, header="", action_key=None): """Get the alert log.""" return self.get_alert(current=current, minimum=mini...	[ "def", "get_alert_log", "(", "self", ",", "current", "=", "0", ",", "minimum", "=", "0", ",", "maximum", "=", "100", ",", "header", "=", "\"\"", ",", "action_key", "=", "None", ")", ":", "return", "self", ".", "get_alert", "(", "current", "=", "curre...	38.230769	6.384615
def get_new_service_instance_stub(service_instance, path, ns=None, version=None): ''' Returns a stub that points to a different path, created from an existing connection. service_instance The Service Instance. path Path of the new stub. ns ...	[ "def", "get_new_service_instance_stub", "(", "service_instance", ",", "path", ",", "ns", "=", "None", ",", "version", "=", "None", ")", ":", "# For python 2.7.9 and later, the default SSL context has more strict", "# connection handshaking rule. We may need turn off the hostname ch...	32.414634	16.902439
def drop_table(self, table): """ Drop a table from the MyDB context. ## Arguments * `table` (str): The name of the table to drop. """ job_id = self.submit("DROP TABLE %s"%table, context="MYDB") status = self.monitor(job_id) if status[0] != 5: ...	[ "def", "drop_table", "(", "self", ",", "table", ")", ":", "job_id", "=", "self", ".", "submit", "(", "\"DROP TABLE %s\"", "%", "table", ",", "context", "=", "\"MYDB\"", ")", "status", "=", "self", ".", "monitor", "(", "job_id", ")", "if", "status", "["...	27.461538	17.923077
def label(self): "Label inherited from items" if self._label: return self._label else: if len(self): label = get_ndmapping_label(self, 'label') return '' if label is None else label else: return ''	[ "def", "label", "(", "self", ")", ":", "if", "self", ".", "_label", ":", "return", "self", ".", "_label", "else", ":", "if", "len", "(", "self", ")", ":", "label", "=", "get_ndmapping_label", "(", "self", ",", "'label'", ")", "return", "''", "if", ...	29.6	16.6
def get_block_height(self, is_full: bool = False) -> int or dict: """ This interface is used to get the decimal block height in current network. Return: the decimal total height of blocks in current network. """ response = self.get_block_count(is_full=True) r...	[ "def", "get_block_height", "(", "self", ",", "is_full", ":", "bool", "=", "False", ")", "->", "int", "or", "dict", ":", "response", "=", "self", ".", "get_block_count", "(", "is_full", "=", "True", ")", "response", "[", "'result'", "]", "-=", "1", "if"...	34.416667	18.416667
def td_waveform_to_fd_waveform(waveform, out=None, length=None, buffer_length=100): """ Convert a time domain into a frequency domain waveform by FFT. As a waveform is assumed to "wrap" in the time domain one must be careful to ensure the waveform goes to 0 at both "bo...	[ "def", "td_waveform_to_fd_waveform", "(", "waveform", ",", "out", "=", "None", ",", "length", "=", "None", ",", "buffer_length", "=", "100", ")", ":", "# Figure out lengths and set out if needed", "if", "out", "is", "None", ":", "if", "length", "is", "None", "...	50.946429	23
def _get_local_files(self, path): """Returns a dictionary of all the files under a path.""" if not path: raise ValueError("No path specified") files = defaultdict(lambda: None) path_len = len(path) + 1 for root, dirs, filenames in os.walk(path): for name i...	[ "def", "_get_local_files", "(", "self", ",", "path", ")", ":", "if", "not", "path", ":", "raise", "ValueError", "(", "\"No path specified\"", ")", "files", "=", "defaultdict", "(", "lambda", ":", "None", ")", "path_len", "=", "len", "(", "path", ")", "+"...	41.636364	10.454545
def show_keyword_help(cur, arg): """ Call the built-in "show <command>", to display help for an SQL keyword. :param cur: cursor :param arg: string :return: list """ keyword = arg.strip('"').strip("'") query = "help '{0}'".format(keyword) log.debug(query) cur.execute(query) if...	[ "def", "show_keyword_help", "(", "cur", ",", "arg", ")", ":", "keyword", "=", "arg", ".", "strip", "(", "'\"'", ")", ".", "strip", "(", "\"'\"", ")", "query", "=", "\"help '{0}'\"", ".", "format", "(", "keyword", ")", "log", ".", "debug", "(", "query...	33.375	14.625
def pathFromHere_walk(self, astr_startPath = '/'): """ Return a list of paths from "here" in the stree, using the internal cd() to walk the path space. :return: a list of paths from "here" """ self.l_lwd = [] self.treeWalk(startPath ...	[ "def", "pathFromHere_walk", "(", "self", ",", "astr_startPath", "=", "'/'", ")", ":", "self", ".", "l_lwd", "=", "[", "]", "self", ".", "treeWalk", "(", "startPath", "=", "astr_startPath", ",", "f", "=", "self", ".", "lwd", ")", "return", "self", ".", ...	33.545455	16.818182
def _init_append(self): """ Initializes file on 'a' mode. """ if self._content_length: # Adjust size if content length specified with _handle_azure_exception(): self._resize( content_length=self._content_length, **self._client_k...	[ "def", "_init_append", "(", "self", ")", ":", "if", "self", ".", "_content_length", ":", "# Adjust size if content length specified", "with", "_handle_azure_exception", "(", ")", ":", "self", ".", "_resize", "(", "content_length", "=", "self", ".", "_content_length"...	34	12.923077
def get_bounds(locations, lonlat=False): """ Computes the bounds of the object in the form [[lat_min, lon_min], [lat_max, lon_max]] """ bounds = [[None, None], [None, None]] for point in iter_coords(locations): bounds = [ [ none_min(bounds[0][0], point[0]), ...	[ "def", "get_bounds", "(", "locations", ",", "lonlat", "=", "False", ")", ":", "bounds", "=", "[", "[", "None", ",", "None", "]", ",", "[", "None", ",", "None", "]", "]", "for", "point", "in", "iter_coords", "(", "locations", ")", ":", "bounds", "="...	27.52381	14.285714
def is_iso8601(instance: str): """Validates ISO8601 format""" if not isinstance(instance, str): return True return ISO8601.match(instance) is not None	[ "def", "is_iso8601", "(", "instance", ":", "str", ")", ":", "if", "not", "isinstance", "(", "instance", ",", "str", ")", ":", "return", "True", "return", "ISO8601", ".", "match", "(", "instance", ")", "is", "not", "None" ]	33.2	8
def restart(self, container, instances=None, map_name=None, **kwargs): """ Restarts instances for a container configuration. :param container: Container name. :type container: unicode \| str :param instances: Instance names to stop. If not specified, will restart all instances as...	[ "def", "restart", "(", "self", ",", "container", ",", "instances", "=", "None", ",", "map_name", "=", "None", ",", "", "", "kwargs", ")", ":", "return", "self", ".", "run_actions", "(", "'restart'", ",", "container", ",", "instances", "=", "instances",...	56.764706	25.823529
def _merge_parameters(self, other_trajectory, remove_duplicates=False, trial_parameter_name=None, ignore_data=()): """Merges parameters from the other trajectory into the current one. The explored parameters in the current trajectory are directly enla...	[ "def", "_merge_parameters", "(", "self", ",", "other_trajectory", ",", "remove_duplicates", "=", "False", ",", "trial_parameter_name", "=", "None", ",", "ignore_data", "=", "(", ")", ")", ":", "if", "trial_parameter_name", ":", "if", "remove_duplicates", ":", "s...	48.293578	27.720183
def pre_disconnect(self, sid, namespace): """Put the client in the to-be-disconnected list. This allows the client data structures to be present while the disconnect handler is invoked, but still recognize the fact that the client is soon going away. """ if namespace not...	[ "def", "pre_disconnect", "(", "self", ",", "sid", ",", "namespace", ")", ":", "if", "namespace", "not", "in", "self", ".", "pending_disconnect", ":", "self", ".", "pending_disconnect", "[", "namespace", "]", "=", "[", "]", "self", ".", "pending_disconnect", ...	44.6	15
def profiler(self): """Creates a dictionary from the profile scheme(s)""" # Initialise variables profiledata = defaultdict(make_dict) profileset = set() # supplementalset = '' genedict = {} # Find all the unique profiles to use with a set for sample in sel...	[ "def", "profiler", "(", "self", ")", ":", "# Initialise variables", "profiledata", "=", "defaultdict", "(", "make_dict", ")", "profileset", "=", "set", "(", ")", "# supplementalset = ''", "genedict", "=", "{", "}", "# Find all the unique profiles to use with a set", "...	54.377049	21.672131
def _get_all_constants(): """ Get list of all uppercase, non-private globals (doesn't start with ``_``). Returns: list: Uppercase names defined in `globals()` (variables from this \ module). """ return [ key for key in globals().keys() if all([ not ...	[ "def", "_get_all_constants", "(", ")", ":", "return", "[", "key", "for", "key", "in", "globals", "(", ")", ".", "keys", "(", ")", "if", "all", "(", "[", "not", "key", ".", "startswith", "(", "\"_\"", ")", ",", "# publicly accesible", "key", ".", "upp...	31.625	23.125
def validate_relation_data(self, sentry_unit, relation, expected): """Validate actual relation data based on expected relation data.""" actual = sentry_unit.relation(relation[0], relation[1]) return self._validate_dict_data(expected, actual)	[ "def", "validate_relation_data", "(", "self", ",", "sentry_unit", ",", "relation", ",", "expected", ")", ":", "actual", "=", "sentry_unit", ".", "relation", "(", "relation", "[", "0", "]", ",", "relation", "[", "1", "]", ")", "return", "self", ".", "_val...	65.5	16.5
def register_add_user_command(self, add_user_func): """ Add the add-user command to the parser and call add_user_func(project_name, user_full_name, auth_role) when chosen. :param add_user_func: func Called when this option is chosen: upload_func(project_name, user_full_name, auth_role). ...	[ "def", "register_add_user_command", "(", "self", ",", "add_user_func", ")", ":", "description", "=", "\"Gives user permission to access a remote project.\"", "add_user_parser", "=", "self", ".", "subparsers", ".", "add_parser", "(", "'add-user'", ",", "description", "=", ...	61.642857	29.928571
def string_to_identity(identity_str): """Parse string into Identity dictionary.""" m = _identity_regexp.match(identity_str) result = m.groupdict() log.debug('parsed identity: %s', result) return {k: v for k, v in result.items() if v}	[ "def", "string_to_identity", "(", "identity_str", ")", ":", "m", "=", "_identity_regexp", ".", "match", "(", "identity_str", ")", "result", "=", "m", ".", "groupdict", "(", ")", "log", ".", "debug", "(", "'parsed identity: %s'", ",", "result", ")", "return",...	41.333333	5.666667
def _addPolylineToElements(self): """Creates a new Polyline element that will be used for future movement/drawing. The old one (if filled) will be stored on the movement stack. """ if (len(self._pointsOfPolyline) > 1): s = '' for point in self._pointsOfPolyline: ...	[ "def", "_addPolylineToElements", "(", "self", ")", ":", "if", "(", "len", "(", "self", ".", "_pointsOfPolyline", ")", ">", "1", ")", ":", "s", "=", "''", "for", "point", "in", "self", ".", "_pointsOfPolyline", ":", "s", "+=", "str", "(", "point", ")"...	52.615385	18.461538
def decode(self, X, lengths=None, algorithm=None): """Find most likely state sequence corresponding to ``X``. Parameters ---------- X : array-like, shape (n_samples, n_features) Feature matrix of individual samples. lengths : array-like of integers, shape (n_sequenc...	[ "def", "decode", "(", "self", ",", "X", ",", "lengths", "=", "None", ",", "algorithm", "=", "None", ")", ":", "check_is_fitted", "(", "self", ",", "\"startprob_\"", ")", "self", ".", "_check", "(", ")", "algorithm", "=", "algorithm", "or", "self", ".",...	33.407407	19.981481
def pop(self): """ Pop the frame at the top of the stack. @return: The popped frame, else None. @rtype: L{Frame} """ if len(self.stack): popped = self.stack.pop() #log.debug('pop: (%s)\n%s', Repr(popped), Repr(self.stack)) return ...	[ "def", "pop", "(", "self", ")", ":", "if", "len", "(", "self", ".", "stack", ")", ":", "popped", "=", "self", ".", "stack", ".", "pop", "(", ")", "#log.debug('pop: (%s)\\n%s', Repr(popped), Repr(self.stack))", "return", "popped", "else", ":", "#log.debug('stac...	29.571429	13.571429
def _get_warped_mean(self, mean, std, pred_init=None, deg_gauss_hermite=20): """ Calculate the warped mean by using Gauss-Hermite quadrature. """ gh_samples, gh_weights = np.polynomial.hermite.hermgauss(deg_gauss_hermite) gh_samples = gh_samples[:, None] gh_weights = gh_w...	[ "def", "_get_warped_mean", "(", "self", ",", "mean", ",", "std", ",", "pred_init", "=", "None", ",", "deg_gauss_hermite", "=", "20", ")", ":", "gh_samples", ",", "gh_weights", "=", "np", ".", "polynomial", ".", "hermite", ".", "hermgauss", "(", "deg_gauss_...	52.625	19.875
def export_model(self, format, file_name=None): """Save the assembled model in a modeling formalism other than PySB. For more details on exporting PySB models, see http://pysb.readthedocs.io/en/latest/modules/export/index.html Parameters ---------- format : str ...	[ "def", "export_model", "(", "self", ",", "format", ",", "file_name", "=", "None", ")", ":", "# Handle SBGN as special case", "if", "format", "==", "'sbgn'", ":", "exp_str", "=", "export_sbgn", "(", "self", ".", "model", ")", "elif", "format", "==", "'kappa_i...	37.840909	20
def prepare_parameters(self, multi_row_parameters): """ Attribute sql parameters with meta data for a prepared statement. Make some basic checks that at least the number of parameters is correct. :param multi_row_parameters: A list/tuple containing list/tuples of parameters (for multiple rows) ...	[ "def", "prepare_parameters", "(", "self", ",", "multi_row_parameters", ")", ":", "self", ".", "_multi_row_parameters", "=", "multi_row_parameters", "self", ".", "_num_rows", "=", "len", "(", "multi_row_parameters", ")", "self", ".", "_iter_row_count", "=", "0", "r...	60	25
def cli(wio, send): ''' Sends a UDP command to the wio device. \b DOES: Support "VERSION", "SCAN", "Blank?", "DEBUG", "ENDEBUG: 1", "ENDEBUG: 0" "APCFG: AP\\tPWDs\\tTOKENs\\tSNs\\tSERVER_Domains\\tXSERVER_Domain\\t\\r\\n", Note: 1. Ensure your device is Configure Mode. ...	[ "def", "cli", "(", "wio", ",", "send", ")", ":", "command", "=", "send", "click", ".", "echo", "(", "\"UDP command: {}\"", ".", "format", "(", "command", ")", ")", "result", "=", "udp", ".", "common_send", "(", "command", ")", "if", "result", "is", "...	27.173913	23.782609
def _options_browser(cfg, ret_config, defaults, virtualname, options): """ Iterator generating all duples ```option name -> value``` @see :func:`get_returner_options` """ for option in options: # default place for the option in the config value = _fetch_option(cfg, ret_config, vir...	[ "def", "_options_browser", "(", "cfg", ",", "ret_config", ",", "defaults", ",", "virtualname", ",", "options", ")", ":", "for", "option", "in", "options", ":", "# default place for the option in the config", "value", "=", "_fetch_option", "(", "cfg", ",", "ret_con...	28.72	21.36
def lookup(self, nick): """Looks for the most recent paste by a given nick. Returns the uid or None""" query = dict(nick=nick) order = [('time', pymongo.DESCENDING)] recs = self.db.pastes.find(query).sort(order).limit(1) try: return next(recs)['uid'] e...	[ "def", "lookup", "(", "self", ",", "nick", ")", ":", "query", "=", "dict", "(", "nick", "=", "nick", ")", "order", "=", "[", "(", "'time'", ",", "pymongo", ".", "DESCENDING", ")", "]", "recs", "=", "self", ".", "db", ".", "pastes", ".", "find", ...	34.8	12.1
def ignore_import_warnings_for_related_fields(orig_method, self, node): """ Replaces the leave_module method on the VariablesChecker class to prevent unused-import warnings which are caused by the ForeignKey and OneToOneField transformations. By replacing the nodes in the AST with their type rather ...	[ "def", "ignore_import_warnings_for_related_fields", "(", "orig_method", ",", "self", ",", "node", ")", ":", "consumer", "=", "self", ".", "_to_consume", "[", "0", "]", "# pylint: disable=W0212", "# we can disable this warning ('Access to a protected member _to_consume of a clie...	46.666667	27.481481
def pulse_train(time, start, duration, repeat_time, end): """ Implements vensim's PULSE TRAIN function In range [-inf, start) returns 0 In range [start + n * repeat_time, start + n * repeat_time + duration) return 1 In range [start + n * repeat_time + duration, start + (n+1) * repeat_time) return 0 ...	[ "def", "pulse_train", "(", "time", ",", "start", ",", "duration", ",", "repeat_time", ",", "end", ")", ":", "t", "=", "time", "(", ")", "if", "start", "<=", "t", "<", "end", ":", "return", "1", "if", "(", "t", "-", "start", ")", "%", "repeat_time...	37	22.583333
def get_storage_info(self, human=False): """ Get storage info :param bool human: whether return human-readable size :return: total and used storage :rtype: dict """ res = self._req_get_storage_info() if human: res['total'] = humanize.naturals...	[ "def", "get_storage_info", "(", "self", ",", "human", "=", "False", ")", ":", "res", "=", "self", ".", "_req_get_storage_info", "(", ")", "if", "human", ":", "res", "[", "'total'", "]", "=", "humanize", ".", "naturalsize", "(", "res", "[", "'total'", "...	30.642857	17.928571
def delete_view(self, query_criteria=None, uid='_all_users'): ''' a method to delete a view associated with a user design doc :param query_criteria: [optional] dictionary with valid jsonmodel query criteria :param uid: [optional] string with uid of design document to up...	[ "def", "delete_view", "(", "self", ",", "query_criteria", "=", "None", ",", "uid", "=", "'_all_users'", ")", ":", "# https://developer.couchbase.com/documentation/mobile/1.5/references/sync-gateway/admin-rest-api/index.html#/query/delete__db___design__ddoc_", "title", "=", "'%s.del...	40.94382	26.247191
def calc_frip(self, input_bam, input_bed, threads=4): """ Calculate fraction of reads in peaks. A file of with a pool of sequencing reads and a file with peak call regions define the operation that will be performed. Thread count for samtools can be specified as well. :...	[ "def", "calc_frip", "(", "self", ",", "input_bam", ",", "input_bed", ",", "threads", "=", "4", ")", ":", "cmd", "=", "self", ".", "simple_frip", "(", "input_bam", ",", "input_bed", ",", "threads", ")", "return", "subprocess", ".", "check_output", "(", "c...	46	20.533333
def is_new_namespace_preorder( self, namespace_id_hash, lastblock=None ): """ Given a namespace preorder hash, determine whether or not is is unseen before. """ if lastblock is None: lastblock = self.lastblock preorder = namedb_get_namespace_preorder( self.db, names...	[ "def", "is_new_namespace_preorder", "(", "self", ",", "namespace_id_hash", ",", "lastblock", "=", "None", ")", ":", "if", "lastblock", "is", "None", ":", "lastblock", "=", "self", ".", "lastblock", "preorder", "=", "namedb_get_namespace_preorder", "(", "self", "...	35.916667	20.583333
def _items(self): """Extract a list of (key, value) pairs, suitable for our __init__.""" for name in self.declarations: yield name, self.declarations[name] for subkey, value in self.contexts[name].items(): yield self.join(name, subkey), value	[ "def", "_items", "(", "self", ")", ":", "for", "name", "in", "self", ".", "declarations", ":", "yield", "name", ",", "self", ".", "declarations", "[", "name", "]", "for", "subkey", ",", "value", "in", "self", ".", "contexts", "[", "name", "]", ".", ...	48.833333	10.833333
def syslog(server, enable=True, host=None, admin_username=None, admin_password=None, module=None): ''' Configure syslog remote logging, by default syslog will automatically be enabled if a server is specified. However, if you want to disable syslog you will need to specify a server followed b...	[ "def", "syslog", "(", "server", ",", "enable", "=", "True", ",", "host", "=", "None", ",", "admin_username", "=", "None", ",", "admin_password", "=", "None", ",", "module", "=", "None", ")", ":", "if", "enable", "and", "__execute_cmd", "(", "'config -g c...	43.6875	20.75
def profile_detail(request, username, template_name=userena_settings.USERENA_PROFILE_DETAIL_TEMPLATE, extra_context=None, **kwargs): """ Detailed view of an user. :param username: String of the username of which the profile should be viewed. :param template_name: String represe...	[ "def", "profile_detail", "(", "request", ",", "username", ",", "template_name", "=", "userena_settings", ".", "USERENA_PROFILE_DETAIL_TEMPLATE", ",", "extra_context", "=", "None", ",", "", "", "kwargs", ")", ":", "user", "=", "get_object_or_404", "(", "get_user_...	35.375	21.9375
def from_string(string): """Return the mnemonic represented by the given string. """ mnemonics = { # Arithmetic Instructions "add": ReilMnemonic.ADD, "sub": ReilMnemonic.SUB, "mul": ReilMnemonic.MUL, "div": ReilMnemonic.DIV, ...	[ "def", "from_string", "(", "string", ")", ":", "mnemonics", "=", "{", "# Arithmetic Instructions", "\"add\"", ":", "ReilMnemonic", ".", "ADD", ",", "\"sub\"", ":", "ReilMnemonic", ".", "SUB", ",", "\"mul\"", ":", "ReilMnemonic", ".", "MUL", ",", "\"div\"", "...	29.435897	10.410256
def sweepCrossValidation(self): """ sweepCrossValidation() will go through each of the crossvalidation input/targets. The crossValidationCorpus is a list of dictionaries of input/targets referenced by layername. Example: ({"input": [0.0, 0.1], "output": [1.0]}, {"input": [0.5, 0....	[ "def", "sweepCrossValidation", "(", "self", ")", ":", "# get learning value and then turn it off", "oldLearning", "=", "self", ".", "learning", "self", ".", "learning", "=", "0", "tssError", "=", "0.0", "totalCorrect", "=", "0", "totalCount", "=", "0", "totalPCorr...	47.736842	16.578947
def spanning_2d_grid(length): """ Generate a square lattice with auxiliary nodes for spanning detection Parameters ---------- length : int Number of nodes in one dimension, excluding the auxiliary nodes. Returns ------- networkx.Graph A square lattice graph with auxilia...	[ "def", "spanning_2d_grid", "(", "length", ")", ":", "ret", "=", "nx", ".", "grid_2d_graph", "(", "length", "+", "2", ",", "length", ")", "for", "i", "in", "range", "(", "length", ")", ":", "# side 0", "ret", ".", "node", "[", "(", "0", ",", "i", ...	20.571429	24.685714
def _weight_by_hue(self): """ Returns a list of (hue, ranges, total weight, normalized total weight)-tuples. ColorTheme is made up out of (color, range, weight) tuples. For consistency with XML-output in the old Prism format (i.e. <color>s made up of <shade>s) we need a group ...	[ "def", "_weight_by_hue", "(", "self", ")", ":", "grouped", "=", "{", "}", "weights", "=", "[", "]", "for", "clr", ",", "rng", ",", "weight", "in", "self", ".", "ranges", ":", "h", "=", "clr", ".", "nearest_hue", "(", "primary", "=", "False", ")", ...	39.606061	19.787879
def run(self): """Run find_route_functions_taint_args on each CFG.""" function_cfgs = list() for _ in self.cfg_list: function_cfgs.extend(self.find_route_functions_taint_args()) self.cfg_list.extend(function_cfgs)	[ "def", "run", "(", "self", ")", ":", "function_cfgs", "=", "list", "(", ")", "for", "_", "in", "self", ".", "cfg_list", ":", "function_cfgs", ".", "extend", "(", "self", ".", "find_route_functions_taint_args", "(", ")", ")", "self", ".", "cfg_list", ".",...	42	13.333333
def list(self, prefix='', delimiter='', filter_function=None, max_results=1, previous_key=''): ''' a method to list keys in the collection :param prefix: string with prefix value to filter results :param delimiter: string with value results must not contain (after prefix) ...	[ "def", "list", "(", "self", ",", "prefix", "=", "''", ",", "delimiter", "=", "''", ",", "filter_function", "=", "None", ",", "max_results", "=", "1", ",", "previous_key", "=", "''", ")", ":", "title", "=", "'%s.list'", "%", "self", ".", "__class__", ...	41.848739	22.436975
def read_dependencies(filename): """Read in the dependencies from the virtualenv requirements file. """ dependencies = [] filepath = os.path.join('requirements', filename) with open(filepath, 'r') as stream: for line in stream: package = line.strip().split('#')[0].strip() ...	[ "def", "read_dependencies", "(", "filename", ")", ":", "dependencies", "=", "[", "]", "filepath", "=", "os", ".", "path", ".", "join", "(", "'requirements'", ",", "filename", ")", "with", "open", "(", "filepath", ",", "'r'", ")", "as", "stream", ":", "...	35.75	12.333333
def inv_std_norm_cdf(x): """ Inverse cumulative standard Gaussian distribution Based on Winitzki, S. (2008) """ z = 2x -1 ln1z2 = np.log(1-z2) a = 8(np.pi -3)/(3np.pi(4-np.pi)) b = 2/(np.pi * a) + ln1z2/2 inv_erf = np.sign(z) * np.sqrt( np.sqrt(b**2 - ln1z2/a) - b ) return ...	[ "def", "inv_std_norm_cdf", "(", "x", ")", ":", "z", "=", "2", "", "x", "-", "1", "ln1z2", "=", "np", ".", "log", "(", "1", "-", "z", "", "2", ")", "a", "=", "8", "", "(", "np", ".", "pi", "-", "3", ")", "/", "(", "3", "*", "np", "...	30	10.909091
def get_font_glyph_data(font): """Return information for each glyph in a font""" from fontbakery.constants import (PlatformID, WindowsEncodingID) font_data = [] try: subtable = font['cmap'].getcmap(PlatformID.WINDOWS, ...	[ "def", "get_font_glyph_data", "(", "font", ")", ":", "from", "fontbakery", ".", "constants", "import", "(", "PlatformID", ",", "WindowsEncodingID", ")", "font_data", "=", "[", "]", "try", ":", "subtable", "=", "font", "[", "'cmap'", "]", ".", "getcmap", "(...	33.2	17.366667
async def install_mediaroom_protocol(responses_callback, box_ip=None): """Install an asyncio protocol to process NOTIFY messages.""" from . import version _LOGGER.debug(version) loop = asyncio.get_event_loop() mediaroom_protocol = MediaroomProtocol(responses_callback, box_ip) sock = create_so...	[ "async", "def", "install_mediaroom_protocol", "(", "responses_callback", ",", "box_ip", "=", "None", ")", ":", "from", ".", "import", "version", "_LOGGER", ".", "debug", "(", "version", ")", "loop", "=", "asyncio", ".", "get_event_loop", "(", ")", "mediaroom_p...	30.285714	25.5
def add_object(self, object): """Add object to db session. Only for session-centric object-database mappers.""" if object.id is None: object.get_id() self.db.engine.save(object)	[ "def", "add_object", "(", "self", ",", "object", ")", ":", "if", "object", ".", "id", "is", "None", ":", "object", ".", "get_id", "(", ")", "self", ".", "db", ".", "engine", ".", "save", "(", "object", ")" ]	41.8	8
def dist_abs(self, src, tar): """Return the bag distance between two strings. Parameters ---------- src : str Source string for comparison tar : str Target string for comparison Returns ------- int Bag distance ...	[ "def", "dist_abs", "(", "self", ",", "src", ",", "tar", ")", ":", "if", "tar", "==", "src", ":", "return", "0", "elif", "not", "src", ":", "return", "len", "(", "tar", ")", "elif", "not", "tar", ":", "return", "len", "(", "src", ")", "src_bag", ...	22.111111	19
def convert_type(d, intype, outtype, convert_list=True, in_place=True): """ convert all values of one type to another Parameters ---------- d : dict intype : type_class outtype : type_class convert_list : bool whether to convert instances inside lists and tuples in_place : bool ...	[ "def", "convert_type", "(", "d", ",", "intype", ",", "outtype", ",", "convert_list", "=", "True", ",", "in_place", "=", "True", ")", ":", "if", "not", "in_place", ":", "out_dict", "=", "copy", ".", "deepcopy", "(", "d", ")", "else", ":", "out_dict", ...	24.068493	19.054795
def plot(self, title='TimeMoc', view=(None, None)): """ Plot the TimeMoc in a time window. This method uses interactive matplotlib. The user can move its mouse through the plot to see the time (at the mouse position). Parameters ---------- title : str, optional ...	[ "def", "plot", "(", "self", ",", "title", "=", "'TimeMoc'", ",", "view", "=", "(", "None", ",", "None", ")", ")", ":", "from", "matplotlib", ".", "colors", "import", "LinearSegmentedColormap", "import", "matplotlib", ".", "pyplot", "as", "plt", "if", "se...	33.571429	24.5
def from_custom_template(cls, searchpath, name): """ Factory function for creating a subclass of ``Styler`` with a custom template and Jinja environment. Parameters ---------- searchpath : str or list Path or paths of directories containing the templates ...	[ "def", "from_custom_template", "(", "cls", ",", "searchpath", ",", "name", ")", ":", "loader", "=", "ChoiceLoader", "(", "[", "FileSystemLoader", "(", "searchpath", ")", ",", "cls", ".", "loader", ",", "]", ")", "class", "MyStyler", "(", "cls", ")", ":",...	29	18.703704
def _extents(self): """A (left, top, width, height) tuple describing range extents. Note this is normalized to accommodate the various orderings of the corner cells provided on construction, which may be in any of four configurations such as (top-left, bottom-right), (bottom-lef...	[ "def", "_extents", "(", "self", ")", ":", "def", "start_and_size", "(", "idx", ",", "other_idx", ")", ":", "\"\"\"Return beginning and length of range based on two indexes.\"\"\"", "return", "min", "(", "idx", ",", "other_idx", ")", ",", "abs", "(", "idx", "-", ...	41.388889	19.722222
def get_root_path(obj): """ Get file path for object and returns its dirname """ try: filename = os.path.abspath(obj.__globals__['__file__']) except (KeyError, AttributeError): if getattr(obj, '__wrapped__', None): # decorator package has been used in view ret...	[ "def", "get_root_path", "(", "obj", ")", ":", "try", ":", "filename", "=", "os", ".", "path", ".", "abspath", "(", "obj", ".", "__globals__", "[", "'__file__'", "]", ")", "except", "(", "KeyError", ",", "AttributeError", ")", ":", "if", "getattr", "(",...	35	9.833333
def rename(self, node): """ Translate a rename node into SQLQuery. :param node: a treebrd node :return: a SQLQuery object for the tree rooted at node """ child_object = self.translate(node.child) from_block = '({child}) AS {name}({attributes})'.format( ...	[ "def", "rename", "(", "self", ",", "node", ")", ":", "child_object", "=", "self", ".", "translate", "(", "node", ".", "child", ")", "from_block", "=", "'({child}) AS {name}({attributes})'", ".", "format", "(", "child", "=", "child_object", ".", "to_sql", "("...	43.909091	13.181818
def get_collection(self, url): """ Pages through an object collection from the bitbucket API. Returns an iterator that lazily goes through all the 'values' of all the pages in the collection. """ url = self.BASE_API2 + url while url is not None: response = self.get_da...	[ "def", "get_collection", "(", "self", ",", "url", ")", ":", "url", "=", "self", ".", "BASE_API2", "+", "url", "while", "url", "is", "not", "None", ":", "response", "=", "self", ".", "get_data", "(", "url", ")", "for", "value", "in", "response", "[", ...	43.6	7.7
def _TypecheckDecorator(subject=None, **kwargs): """Dispatches type checks based on what the subject is. Functions or methods are annotated directly. If this method is called with keyword arguments only, return a decorator. """ if subject is None: return _TypecheckDecoratorFactory(kwargs) elif inspect....	[ "def", "_TypecheckDecorator", "(", "subject", "=", "None", ",", "", "", "kwargs", ")", ":", "if", "subject", "is", "None", ":", "return", "_TypecheckDecoratorFactory", "(", "kwargs", ")", "elif", "inspect", ".", "isfunction", "(", "subject", ")", "or", "...	36.666667	16.666667
def predict(self, dataset, output_type='cluster_id', verbose=True): """ Return predicted cluster label for instances in the new 'dataset'. K-means predictions are made by assigning each new instance to the closest cluster center. Parameters ---------- dataset : S...	[ "def", "predict", "(", "self", ",", "dataset", ",", "output_type", "=", "'cluster_id'", ",", "verbose", "=", "True", ")", ":", "## Validate the input dataset.", "_tkutl", ".", "_raise_error_if_not_sframe", "(", "dataset", ",", "\"dataset\"", ")", "_tkutl", ".", ...	38.0375	23.5875
def clear(self): """Clear current state.""" # Adapted from http://stackoverflow.com/a/13103617/1198772 for i in reversed(list(range(self.extra_keywords_layout.count()))): self.extra_keywords_layout.itemAt(i).widget().setParent(None) self.widgets_dict = OrderedDict()	[ "def", "clear", "(", "self", ")", ":", "# Adapted from http://stackoverflow.com/a/13103617/1198772", "for", "i", "in", "reversed", "(", "list", "(", "range", "(", "self", ".", "extra_keywords_layout", ".", "count", "(", ")", ")", ")", ")", ":", "self", ".", ...	50.833333	19.833333
def _override_runner(runner): """ Context manager that monkey patches `bonobo.run` function with our current command logic. :param runner: the callable that will handle the `run()` logic. """ import bonobo _get_argument_parser = bonobo.util.environ.get_argument_parser _run = bonobo.run ...	[ "def", "_override_runner", "(", "runner", ")", ":", "import", "bonobo", "_get_argument_parser", "=", "bonobo", ".", "util", ".", "environ", ".", "get_argument_parser", "_run", "=", "bonobo", ".", "run", "try", ":", "# Original get_argument_parser would create or updat...	37	26.916667
def post(self, request, bot_id, format=None): """ Add a new state --- serializer: StateSerializer responseMessages: - code: 401 message: Not authenticated - code: 400 message: Not valid request """ return super(S...	[ "def", "post", "(", "self", ",", "request", ",", "bot_id", ",", "format", "=", "None", ")", ":", "return", "super", "(", "StateList", ",", "self", ")", ".", "post", "(", "request", ",", "bot_id", ",", "format", ")" ]	29.5	11
def redispatch(obj, device_type, session_prep=True): """Dynamically change Netmiko object's class to proper class. Generally used with terminal_server device_type when you need to redispatch after interacting with terminal server. """ new_class = ssh_dispatcher(device_type) obj.device_type = de...	[ "def", "redispatch", "(", "obj", ",", "device_type", ",", "session_prep", "=", "True", ")", ":", "new_class", "=", "ssh_dispatcher", "(", "device_type", ")", "obj", ".", "device_type", "=", "device_type", "obj", ".", "__class__", "=", "new_class", "if", "ses...	37.181818	15.181818
def INIT(self): """INIT state. [:rfc:`2131#section-4.4.1`]:: The client SHOULD wait a random time between one and ten seconds to desynchronize the use of DHCP at startup .. todo:: - The initial delay is implemented, but probably is not in other ...	[ "def", "INIT", "(", "self", ")", ":", "# NOTE: in case INIT is reached from other state, initialize attributes", "# reset all variables.", "logger", ".", "debug", "(", "'In state: INIT'", ")", "if", "self", ".", "current_state", "is", "not", "STATE_PREINIT", ":", "self", ...	39.939394	17.121212
def update(self, data): """Updates the object information based on live data, if there were any changes made. Any changes will be automatically applied to the object, but will not be automatically persisted. You must manually call `db.session.add(ami)` on the object. Args: d...	[ "def", "update", "(", "self", ",", "data", ")", ":", "updated", "=", "self", ".", "set_property", "(", "'description'", ",", "data", ".", "description", ")", "updated", "\|=", "self", ".", "set_property", "(", "'state'", ",", "data", ".", "state", ")", ...	36.888889	20.962963
def get_gene_leaves(graph) -> Iterable[BaseEntity]: """Iterate over all genes who have only one connection, that's a transcription to its RNA. :param pybel.BELGraph graph: A BEL graph """ for node in get_nodes_by_function(graph, GENE): if graph.in_degree(node) != 0: continue ...	[ "def", "get_gene_leaves", "(", "graph", ")", "->", "Iterable", "[", "BaseEntity", "]", ":", "for", "node", "in", "get_nodes_by_function", "(", "graph", ",", "GENE", ")", ":", "if", "graph", ".", "in_degree", "(", "node", ")", "!=", "0", ":", "continue", ...	30.375	16.6875

def writeToFile(self, f, packed=True): """ Write serialized object to file. :param f: output file :param packed: If true, will pack contents. """ # Get capnproto schema from instance schema = self.getSchema() # Construct new message, otherwise refered to as `proto` proto = schema.n...

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def rgbmap_cb(self, rgbmap, channel): """ This method is called when the RGBMap is changed. We update the ColorBar to match. """ if not self.gui_up: return fitsimage = channel.fitsimage if fitsimage != self.fv.getfocus_fitsimage(): return ...

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def convert_cityscapes_instance_only( data_dir, out_dir): """Convert from cityscapes format to COCO instance seg format - polygons""" sets = [ 'gtFine_val', 'gtFine_train', 'gtFine_test', # 'gtCoarse_train', # 'gtCoarse_val', # 'gtCoarse_train_extra' ...

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def play_human(env): """ Play the environment using keyboard as a human. Args: env (gym.Env): the initialized gym environment to play Returns: None """ # play the game and catch a potential keyboard interrupt try: play(env, fps=env.metadata['video.frames_per_second...

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def __set_bp(self, aProcess): """ Writes a breakpoint instruction at the target address. @type aProcess: L{Process} @param aProcess: Process object. """ address = self.get_address() self.__previousValue = aProcess.read(address, len(self.bpInstruction)) i...

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def windows_k_distinct(x, k): """Find all largest windows containing exactly k distinct elements :param x: list or string :param k: positive integer :yields: largest intervals [i, j) with len(set(x[i:j])) == k :complexity: `O(|x|)` """ dist, i, j = 0, 0, 0 # dist = |{x[i], .....

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def __get_bundle(self, io_handler, bundle_id): """ Retrieves the Bundle object with the given bundle ID. Writes errors through the I/O handler if any. :param io_handler: I/O Handler :param bundle_id: String or integer bundle ID :return: The Bundle object matching the giv...

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def root_item_selected(self, item): """Root item has been selected: expanding it and collapsing others""" if self.show_all_files: return for root_item in self.get_top_level_items(): if root_item is item: self.expandItem(root_item) else: ...

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def reportPrettyData(root, worker, job, job_types, options): """ print the important bits out. """ out_str = "Batch System: %s\n" % root.batch_system out_str += ("Default Cores: %s Default Memory: %s\n" "Max Cores: %s\n" % ( reportNumber(get(root, "default_cores"), options), ...

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def advance(self): """Carry out one iteration of Arnoldi.""" if self.iter >= self.maxiter: raise ArgumentError('Maximum number of iterations reached.') if self.invariant: raise ArgumentError('Krylov subspace was found to be invariant ' 'in ...

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def create_thread(cls, session, conversation, thread, imported=False): """Create a conversation thread. Please note that threads cannot be added to conversations with 100 threads (or more), if attempted the API will respond with HTTP 412. Args: conversation (helpscout.model...

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def check(self): """ Compare the :func:`os.stat` for the pam_env style environmnt file `path` with the previous result `old_st`, which may be :data:`None` if the previous stat attempt failed. Reload its contents if the file has changed or appeared since last attempt. :re...

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def stop(self): """ Stop this instance. :return: None """ instance_status = Instance.InstanceStatus(status='Terminated') xml_content = instance_status.serialize() headers = {'Content-Type': 'application/xml'} self._client.put(self.resource(), xml_conten...

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def _ParsePathSpecification( self, knowledge_base, searcher, file_system, path_specification, path_separator): """Parses a file system for a preprocessing attribute. Args: knowledge_base (KnowledgeBase): to fill with preprocessing information. searcher (dfvfs.FileSystemSearcher): file s...

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def export(self, id, exclude_captures=False): # pylint: disable=invalid-name,redefined-builtin """Export a result. :param id: Result ID as an int. :param exclude_captures: If bool `True`, don't export capture files :rtype: tuple `(io.BytesIO, 'filename')` """ return self...

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def prop2b(gm, pvinit, dt): """ Given a central mass and the state of massless body at time t_0, this routine determines the state as predicted by a two-body force model at time t_0 + dt. http://naif.jpl.nasa.gov/pub/naif/toolkit_docs/C/cspice/prop2b_c.html :param gm: Gravity of the central ma...

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35.869565

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def add_eval(self, agent, e, fr=None): """Add or change agent's evaluation of the artifact with given framing information. :param agent: Name of the agent which did the evaluation. :param float e: Evaluation for the artifact. :param object fr: Framing information for the evaluat...

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40.3

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def count_sequences(infile): '''Returns the number of sequences in a file''' seq_reader = sequences.file_reader(infile) n = 0 for seq in seq_reader: n += 1 return n

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def add_minrmsd_to_ref(self, ref, ref_frame=0, atom_indices=None, precentered=False): r""" Adds the minimum root-mean-square-deviation (minrmsd) with respect to a reference structure to the feature list. Parameters ---------- ref: Reference structure for computing th...

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def searchsorted(arr, N, x): """N is length of arr """ L = 0 R = N-1 done = False m = (L+R)//2 while not done: if arr[m] < x: L = m + 1 elif arr[m] > x: R = m - 1 elif arr[m] == x: done = True m = (L+R)//2 if L>R: ...

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18.722222

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def default_file_encoder(): """ Get default encoder cwr file :return: """ config = CWRConfiguration() field_configs = config.load_field_config('table') field_configs.update(config.load_field_config('common')) field_values = CWRTables() for entry in field_configs.values(): i...

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def attribute_value(self, doc: Document, attribute_name: str): """ Access data using attribute name rather than the numeric indices Returns: the value for the attribute """ return doc.cdr_document.get(self.header_translation_table[attribute_name])

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def generate_access_token_from_authorization_code(request, client): """ Generates a new AccessToken from a request with an authorization code. Read the specification: http://tools.ietf.org/html/rfc6749#section-4.1.3 """ authorization_code_value = request.POST.get('code') if not authorization_code_value: ...

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def _writeMzmlIndexList(xmlWriter, spectrumIndexList, chromatogramIndexList): """ #TODO: docstring :param xmlWriter: #TODO: docstring :param spectrumIndexList: #TODO: docstring :param chromatogramIndexList: #TODO: docstring """ counts = 0 if spectrumIndexList: counts += 1 if chr...

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def update_tabs_text(self): """Update the text from the tabs.""" # This is needed to prevent that hanged consoles make reference # to an index that doesn't exist. See issue 4881 try: for index, fname in enumerate(self.filenames): client = self.clients[in...

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def remove(self, auto_confirm=False, verbose=False): """Remove paths in ``self.paths`` with confirmation (unless ``auto_confirm`` is True).""" if not self.paths: logger.info( "Can't uninstall '%s'. No files were found to uninstall.", self.dist.project...

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def terminate(self): """Delete all files created by this index, invalidating `self`. Use with care.""" try: self.id2sims.terminate() except: pass import glob for fname in glob.glob(self.fname + '*'): try: os.remove(fname) ...

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def compose_object(self, file_list, destination_file, content_type): """COMPOSE multiple objects together. Using the given list of files, calls the put object with the compose flag. This call merges all the files into the destination file. Args: file_list: list of dicts with the file name. ...

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def worker_main(self): """ The main function of for the mux process: setup the Mitogen broker thread and ansible_mitogen services, then sleep waiting for the socket connected to the parent to be closed (indicating the parent has died). """ self._setup_master() sel...

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def superclasses(self, inherited=False): """Iterate over the superclasses of the class. This function is the Python equivalent of the CLIPS class-superclasses command. """ data = clips.data.DataObject(self._env) lib.EnvClassSuperclasses( self._env, self._cl...

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def tokenize_akkadian_words(line): """ Operates on a single line of text, returns all words in the line as a tuple in a list. input: "1. isz-pur-ram a-na" output: [("isz-pur-ram", "akkadian"), ("a-na", "akkadian")] :param: line: text string :return: list of tuples: (word, language) """...

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def start(self, container, instances=None, map_name=None, **kwargs): """ Starts instances for a container configuration. :param container: Container name. :type container: unicode | str :param instances: Instance names to start. If not specified, will start all instances as spec...

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def json_files_serializer(objs, status=None): """JSON Files Serializer. :parma objs: A list of:class:`invenio_files_rest.models.ObjectVersion` instances. :param status: A HTTP Status. (Default: ``None``) :returns: A Flask response with JSON data. :rtype: :py:class:`flask.Response`. """ ...

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def to_serializable_value(self): """ Run through all fields of the object and parse the values :return: :rtype: dict """ return { name: field.to_serializable_value() for name, field in self.value.__dict__.items() if isinstance(field, F...

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def get_alert_log(self, current=0, minimum=0, maximum=100, header="", action_key=None): """Get the alert log.""" return self.get_alert(current=current, minimum=mini...

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def get_new_service_instance_stub(service_instance, path, ns=None, version=None): ''' Returns a stub that points to a different path, created from an existing connection. service_instance The Service Instance. path Path of the new stub. ns ...

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def drop_table(self, table): """ Drop a table from the MyDB context. ## Arguments * `table` (str): The name of the table to drop. """ job_id = self.submit("DROP TABLE %s"%table, context="MYDB") status = self.monitor(job_id) if status[0] != 5: ...

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def label(self): "Label inherited from items" if self._label: return self._label else: if len(self): label = get_ndmapping_label(self, 'label') return '' if label is None else label else: return ''

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def get_block_height(self, is_full: bool = False) -> int or dict: """ This interface is used to get the decimal block height in current network. Return: the decimal total height of blocks in current network. """ response = self.get_block_count(is_full=True) r...

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def td_waveform_to_fd_waveform(waveform, out=None, length=None, buffer_length=100): """ Convert a time domain into a frequency domain waveform by FFT. As a waveform is assumed to "wrap" in the time domain one must be careful to ensure the waveform goes to 0 at both "bo...

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def _get_local_files(self, path): """Returns a dictionary of all the files under a path.""" if not path: raise ValueError("No path specified") files = defaultdict(lambda: None) path_len = len(path) + 1 for root, dirs, filenames in os.walk(path): for name i...

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def show_keyword_help(cur, arg): """ Call the built-in "show <command>", to display help for an SQL keyword. :param cur: cursor :param arg: string :return: list """ keyword = arg.strip('"').strip("'") query = "help '{0}'".format(keyword) log.debug(query) cur.execute(query) if...

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def pathFromHere_walk(self, astr_startPath = '/'): """ Return a list of paths from "here" in the stree, using the internal cd() to walk the path space. :return: a list of paths from "here" """ self.l_lwd = [] self.treeWalk(startPath ...

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def _init_append(self): """ Initializes file on 'a' mode. """ if self._content_length: # Adjust size if content length specified with _handle_azure_exception(): self._resize( content_length=self._content_length, **self._client_k...

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def get_bounds(locations, lonlat=False): """ Computes the bounds of the object in the form [[lat_min, lon_min], [lat_max, lon_max]] """ bounds = [[None, None], [None, None]] for point in iter_coords(locations): bounds = [ [ none_min(bounds[0][0], point[0]), ...

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def is_iso8601(instance: str): """Validates ISO8601 format""" if not isinstance(instance, str): return True return ISO8601.match(instance) is not None

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def restart(self, container, instances=None, map_name=None, **kwargs): """ Restarts instances for a container configuration. :param container: Container name. :type container: unicode | str :param instances: Instance names to stop. If not specified, will restart all instances as...

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def _merge_parameters(self, other_trajectory, remove_duplicates=False, trial_parameter_name=None, ignore_data=()): """Merges parameters from the other trajectory into the current one. The explored parameters in the current trajectory are directly enla...

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def pre_disconnect(self, sid, namespace): """Put the client in the to-be-disconnected list. This allows the client data structures to be present while the disconnect handler is invoked, but still recognize the fact that the client is soon going away. """ if namespace not...

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def profiler(self): """Creates a dictionary from the profile scheme(s)""" # Initialise variables profiledata = defaultdict(make_dict) profileset = set() # supplementalset = '' genedict = {} # Find all the unique profiles to use with a set for sample in sel...

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54.377049

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def _get_all_constants(): """ Get list of all uppercase, non-private globals (doesn't start with ``_``). Returns: list: Uppercase names defined in `globals()` (variables from this \ module). """ return [ key for key in globals().keys() if all([ not ...

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def validate_relation_data(self, sentry_unit, relation, expected): """Validate actual relation data based on expected relation data.""" actual = sentry_unit.relation(relation[0], relation[1]) return self._validate_dict_data(expected, actual)

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def register_add_user_command(self, add_user_func): """ Add the add-user command to the parser and call add_user_func(project_name, user_full_name, auth_role) when chosen. :param add_user_func: func Called when this option is chosen: upload_func(project_name, user_full_name, auth_role). ...

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61.642857

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def string_to_identity(identity_str): """Parse string into Identity dictionary.""" m = _identity_regexp.match(identity_str) result = m.groupdict() log.debug('parsed identity: %s', result) return {k: v for k, v in result.items() if v}

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def _addPolylineToElements(self): """Creates a new Polyline element that will be used for future movement/drawing. The old one (if filled) will be stored on the movement stack. """ if (len(self._pointsOfPolyline) > 1): s = '' for point in self._pointsOfPolyline: ...

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def decode(self, X, lengths=None, algorithm=None): """Find most likely state sequence corresponding to ``X``. Parameters ---------- X : array-like, shape (n_samples, n_features) Feature matrix of individual samples. lengths : array-like of integers, shape (n_sequenc...

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def pop(self): """ Pop the frame at the top of the stack. @return: The popped frame, else None. @rtype: L{Frame} """ if len(self.stack): popped = self.stack.pop() #log.debug('pop: (%s)\n%s', Repr(popped), Repr(self.stack)) return ...

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def _get_warped_mean(self, mean, std, pred_init=None, deg_gauss_hermite=20): """ Calculate the warped mean by using Gauss-Hermite quadrature. """ gh_samples, gh_weights = np.polynomial.hermite.hermgauss(deg_gauss_hermite) gh_samples = gh_samples[:, None] gh_weights = gh_w...

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def export_model(self, format, file_name=None): """Save the assembled model in a modeling formalism other than PySB. For more details on exporting PySB models, see http://pysb.readthedocs.io/en/latest/modules/export/index.html Parameters ---------- format : str ...

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def prepare_parameters(self, multi_row_parameters): """ Attribute sql parameters with meta data for a prepared statement. Make some basic checks that at least the number of parameters is correct. :param multi_row_parameters: A list/tuple containing list/tuples of parameters (for multiple rows) ...

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60

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def cli(wio, send): ''' Sends a UDP command to the wio device. \b DOES: Support "VERSION", "SCAN", "Blank?", "DEBUG", "ENDEBUG: 1", "ENDEBUG: 0" "APCFG: AP\\tPWDs\\tTOKENs\\tSNs\\tSERVER_Domains\\tXSERVER_Domain\\t\\r\\n", Note: 1. Ensure your device is Configure Mode. ...

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27.173913

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def _options_browser(cfg, ret_config, defaults, virtualname, options): """ Iterator generating all duples ```option name -> value``` @see :func:`get_returner_options` """ for option in options: # default place for the option in the config value = _fetch_option(cfg, ret_config, vir...

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28.72

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def lookup(self, nick): """Looks for the most recent paste by a given nick. Returns the uid or None""" query = dict(nick=nick) order = [('time', pymongo.DESCENDING)] recs = self.db.pastes.find(query).sort(order).limit(1) try: return next(recs)['uid'] e...

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34.8

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def ignore_import_warnings_for_related_fields(orig_method, self, node): """ Replaces the leave_module method on the VariablesChecker class to prevent unused-import warnings which are caused by the ForeignKey and OneToOneField transformations. By replacing the nodes in the AST with their type rather ...

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46.666667

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def pulse_train(time, start, duration, repeat_time, end): """ Implements vensim's PULSE TRAIN function In range [-inf, start) returns 0 In range [start + n * repeat_time, start + n * repeat_time + duration) return 1 In range [start + n * repeat_time + duration, start + (n+1) * repeat_time) return 0 ...

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def get_storage_info(self, human=False): """ Get storage info :param bool human: whether return human-readable size :return: total and used storage :rtype: dict """ res = self._req_get_storage_info() if human: res['total'] = humanize.naturals...

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30.642857

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def delete_view(self, query_criteria=None, uid='_all_users'): ''' a method to delete a view associated with a user design doc :param query_criteria: [optional] dictionary with valid jsonmodel query criteria :param uid: [optional] string with uid of design document to up...

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40.94382

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def calc_frip(self, input_bam, input_bed, threads=4): """ Calculate fraction of reads in peaks. A file of with a pool of sequencing reads and a file with peak call regions define the operation that will be performed. Thread count for samtools can be specified as well. :...

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46

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def is_new_namespace_preorder( self, namespace_id_hash, lastblock=None ): """ Given a namespace preorder hash, determine whether or not is is unseen before. """ if lastblock is None: lastblock = self.lastblock preorder = namedb_get_namespace_preorder( self.db, names...

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35.916667

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def _items(self): """Extract a list of (key, value) pairs, suitable for our __init__.""" for name in self.declarations: yield name, self.declarations[name] for subkey, value in self.contexts[name].items(): yield self.join(name, subkey), value

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48.833333

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def syslog(server, enable=True, host=None, admin_username=None, admin_password=None, module=None): ''' Configure syslog remote logging, by default syslog will automatically be enabled if a server is specified. However, if you want to disable syslog you will need to specify a server followed b...

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43.6875

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def profile_detail(request, username, template_name=userena_settings.USERENA_PROFILE_DETAIL_TEMPLATE, extra_context=None, **kwargs): """ Detailed view of an user. :param username: String of the username of which the profile should be viewed. :param template_name: String represe...

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def from_string(string): """Return the mnemonic represented by the given string. """ mnemonics = { # Arithmetic Instructions "add": ReilMnemonic.ADD, "sub": ReilMnemonic.SUB, "mul": ReilMnemonic.MUL, "div": ReilMnemonic.DIV, ...

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def sweepCrossValidation(self): """ sweepCrossValidation() will go through each of the crossvalidation input/targets. The crossValidationCorpus is a list of dictionaries of input/targets referenced by layername. Example: ({"input": [0.0, 0.1], "output": [1.0]}, {"input": [0.5, 0....

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def spanning_2d_grid(length): """ Generate a square lattice with auxiliary nodes for spanning detection Parameters ---------- length : int Number of nodes in one dimension, excluding the auxiliary nodes. Returns ------- networkx.Graph A square lattice graph with auxilia...

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def _weight_by_hue(self): """ Returns a list of (hue, ranges, total weight, normalized total weight)-tuples. ColorTheme is made up out of (color, range, weight) tuples. For consistency with XML-output in the old Prism format (i.e. <color>s made up of <shade>s) we need a group ...

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def run(self): """Run find_route_functions_taint_args on each CFG.""" function_cfgs = list() for _ in self.cfg_list: function_cfgs.extend(self.find_route_functions_taint_args()) self.cfg_list.extend(function_cfgs)

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def list(self, prefix='', delimiter='', filter_function=None, max_results=1, previous_key=''): ''' a method to list keys in the collection :param prefix: string with prefix value to filter results :param delimiter: string with value results must not contain (after prefix) ...

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41.848739

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def read_dependencies(filename): """Read in the dependencies from the virtualenv requirements file. """ dependencies = [] filepath = os.path.join('requirements', filename) with open(filepath, 'r') as stream: for line in stream: package = line.strip().split('#')[0].strip() ...

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35.75

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def inv_std_norm_cdf(x): """ Inverse cumulative standard Gaussian distribution Based on Winitzki, S. (2008) """ z = 2*x -1 ln1z2 = np.log(1-z**2) a = 8*(np.pi -3)/(3*np.pi*(4-np.pi)) b = 2/(np.pi * a) + ln1z2/2 inv_erf = np.sign(z) * np.sqrt( np.sqrt(b**2 - ln1z2/a) - b ) return ...

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def get_font_glyph_data(font): """Return information for each glyph in a font""" from fontbakery.constants import (PlatformID, WindowsEncodingID) font_data = [] try: subtable = font['cmap'].getcmap(PlatformID.WINDOWS, ...

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async def install_mediaroom_protocol(responses_callback, box_ip=None): """Install an asyncio protocol to process NOTIFY messages.""" from . import version _LOGGER.debug(version) loop = asyncio.get_event_loop() mediaroom_protocol = MediaroomProtocol(responses_callback, box_ip) sock = create_so...

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30.285714

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def add_object(self, object): """Add object to db session. Only for session-centric object-database mappers.""" if object.id is None: object.get_id() self.db.engine.save(object)

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41.8

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def dist_abs(self, src, tar): """Return the bag distance between two strings. Parameters ---------- src : str Source string for comparison tar : str Target string for comparison Returns ------- int Bag distance ...

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def convert_type(d, intype, outtype, convert_list=True, in_place=True): """ convert all values of one type to another Parameters ---------- d : dict intype : type_class outtype : type_class convert_list : bool whether to convert instances inside lists and tuples in_place : bool ...

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def plot(self, title='TimeMoc', view=(None, None)): """ Plot the TimeMoc in a time window. This method uses interactive matplotlib. The user can move its mouse through the plot to see the time (at the mouse position). Parameters ---------- title : str, optional ...

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33.571429

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def from_custom_template(cls, searchpath, name): """ Factory function for creating a subclass of ``Styler`` with a custom template and Jinja environment. Parameters ---------- searchpath : str or list Path or paths of directories containing the templates ...

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29

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def _extents(self): """A (left, top, width, height) tuple describing range extents. Note this is normalized to accommodate the various orderings of the corner cells provided on construction, which may be in any of four configurations such as (top-left, bottom-right), (bottom-lef...

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41.388889

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def get_root_path(obj): """ Get file path for object and returns its dirname """ try: filename = os.path.abspath(obj.__globals__['__file__']) except (KeyError, AttributeError): if getattr(obj, '__wrapped__', None): # decorator package has been used in view ret...

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35

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def rename(self, node): """ Translate a rename node into SQLQuery. :param node: a treebrd node :return: a SQLQuery object for the tree rooted at node """ child_object = self.translate(node.child) from_block = '({child}) AS {name}({attributes})'.format( ...

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43.909091

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def get_collection(self, url): """ Pages through an object collection from the bitbucket API. Returns an iterator that lazily goes through all the 'values' of all the pages in the collection. """ url = self.BASE_API2 + url while url is not None: response = self.get_da...

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43.6

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def _TypecheckDecorator(subject=None, **kwargs): """Dispatches type checks based on what the subject is. Functions or methods are annotated directly. If this method is called with keyword arguments only, return a decorator. """ if subject is None: return _TypecheckDecoratorFactory(kwargs) elif inspect....

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36.666667

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def predict(self, dataset, output_type='cluster_id', verbose=True): """ Return predicted cluster label for instances in the new 'dataset'. K-means predictions are made by assigning each new instance to the closest cluster center. Parameters ---------- dataset : S...

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38.0375

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def clear(self): """Clear current state.""" # Adapted from http://stackoverflow.com/a/13103617/1198772 for i in reversed(list(range(self.extra_keywords_layout.count()))): self.extra_keywords_layout.itemAt(i).widget().setParent(None) self.widgets_dict = OrderedDict()

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50.833333

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def _override_runner(runner): """ Context manager that monkey patches `bonobo.run` function with our current command logic. :param runner: the callable that will handle the `run()` logic. """ import bonobo _get_argument_parser = bonobo.util.environ.get_argument_parser _run = bonobo.run ...

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37

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def post(self, request, bot_id, format=None): """ Add a new state --- serializer: StateSerializer responseMessages: - code: 401 message: Not authenticated - code: 400 message: Not valid request """ return super(S...

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29.5

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def redispatch(obj, device_type, session_prep=True): """Dynamically change Netmiko object's class to proper class. Generally used with terminal_server device_type when you need to redispatch after interacting with terminal server. """ new_class = ssh_dispatcher(device_type) obj.device_type = de...

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37.181818

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def INIT(self): """INIT state. [:rfc:`2131#section-4.4.1`]:: The client SHOULD wait a random time between one and ten seconds to desynchronize the use of DHCP at startup .. todo:: - The initial delay is implemented, but probably is not in other ...

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def update(self, data): """Updates the object information based on live data, if there were any changes made. Any changes will be automatically applied to the object, but will not be automatically persisted. You must manually call `db.session.add(ami)` on the object. Args: d...

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36.888889

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def get_gene_leaves(graph) -> Iterable[BaseEntity]: """Iterate over all genes who have only one connection, that's a transcription to its RNA. :param pybel.BELGraph graph: A BEL graph """ for node in get_nodes_by_function(graph, GENE): if graph.in_degree(node) != 0: continue ...

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30.375

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