kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def run(self): """ Monitors if the config file or plugins are updated. Also outputs the JSON data generated by the plugins, without needing to poll the threads. """ self.run_plugins() while True: # Reload plugins and config if either the config file or plugin ...	[ "def", "run", "(", "self", ")", ":", "self", ".", "run_plugins", "(", ")", "while", "True", ":", "# Reload plugins and config if either the config file or plugin", "# directory are modified.", "if", "self", ".", "_config_mod_time", "!=", "os", ".", "path", ".", "get...	46.941176	19.882353
def side_effect(self, func, args, *kwargs): ''' Wrap side effects for spies. ''' self._spy_side_effect = func self._spy_side_effect_args = args self._spy_side_effect_kwargs = kwargs return self	[ "def", "side_effect", "(", "self", ",", "func", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "self", ".", "_spy_side_effect", "=", "func", "self", ".", "_spy_side_effect_args", "=", "args", "self", ".", "_spy_side_effect_kwargs", "=", "kwargs", "re...	30.5	12.25
def add_resource_context( app: web.Application, module=None, url_prefix: str=None, name_prefix: str=None, make_resource=lambda cls: cls() ): """Context manager which yields a function for adding multiple resources from a given module to an app using `ResourceRouter <aiohttp_utils.routing.ResourceRouter>...	[ "def", "add_resource_context", "(", "app", ":", "web", ".", "Application", ",", "module", "=", "None", ",", "url_prefix", ":", "str", "=", "None", ",", "name_prefix", ":", "str", "=", "None", ",", "make_resource", "=", "lambda", "cls", ":", "cls", "(", ...	36.885714	22.647619
def report(mount): ''' Report on quotas for a specific volume CLI Example: .. code-block:: bash salt '*' quota.report /media/data ''' ret = {mount: {}} ret[mount]['User Quotas'] = _parse_quota(mount, '-u') ret[mount]['Group Quotas'] = _parse_quota(mount, '-g') return ret	[ "def", "report", "(", "mount", ")", ":", "ret", "=", "{", "mount", ":", "{", "}", "}", "ret", "[", "mount", "]", "[", "'User Quotas'", "]", "=", "_parse_quota", "(", "mount", ",", "'-u'", ")", "ret", "[", "mount", "]", "[", "'Group Quotas'", "]", ...	21.785714	23.642857
def conjugate(self): """The element-wise conjugate matrix This is defined only if all the entries in the matrix have a defined conjugate (i.e., they have a `conjugate` method). This is not the case for a matrix of operators. In such a case, only an :meth:`elementwise` :func:`a...	[ "def", "conjugate", "(", "self", ")", ":", "try", ":", "return", "Matrix", "(", "np_conjugate", "(", "self", ".", "matrix", ")", ")", "except", "AttributeError", ":", "raise", "NoConjugateMatrix", "(", "\"Matrix %s contains entries that have no defined \"", "\"conju...	41.444444	21.388889
def get_file_info(hash, context=None): """Returns information about the file, identified by ``hash``. If the `context` (an ident-hash) is supplied, the information returned will be specific to that context. """ if context is None: stmt = _get_sql('get-file-info.sql') args = dict(has...	[ "def", "get_file_info", "(", "hash", ",", "context", "=", "None", ")", ":", "if", "context", "is", "None", ":", "stmt", "=", "_get_sql", "(", "'get-file-info.sql'", ")", "args", "=", "dict", "(", "hash", "=", "hash", ")", "else", ":", "stmt", "=", "_...	34.863636	12.727273
def _parse_scalars(scalars): """Parse the scalars from the YAML file content to a dictionary of ScalarType(s). :return: A dictionary { 'full.scalar.label': ScalarType } """ scalar_dict = {} # Scalars are defined in a fixed two-level hierarchy within the definition file. ...	[ "def", "_parse_scalars", "(", "scalars", ")", ":", "scalar_dict", "=", "{", "}", "# Scalars are defined in a fixed two-level hierarchy within the definition file.", "# The first level contains the category name, while the second level contains the", "# probe name (e.g. \"category.name: probe...	50.045455	24.227273
def split_by_files(self, valid_names:'ItemList')->'ItemLists': "Split the data by using the names in `valid_names` for validation." if isinstance(self.items[0], Path): return self.split_by_valid_func(lambda o: o.name in valid_names) else: return self.split_by_valid_func(lambda o: os.path.basenam...	[ "def", "split_by_files", "(", "self", ",", "valid_names", ":", "'ItemList'", ")", "->", "'ItemLists'", ":", "if", "isinstance", "(", "self", ".", "items", "[", "0", "]", ",", "Path", ")", ":", "return", "self", ".", "split_by_valid_func", "(", "lambda", ...	84.25	44.25
def match_file(apikey, path, metadata=None): """Uses the audioread library to decode an audio file and match it. """ import audioread with audioread.audio_open(path) as f: return match(apikey, iter(f), f.samplerate, int(f.duration), f.channels, metadata)	[ "def", "match_file", "(", "apikey", ",", "path", ",", "metadata", "=", "None", ")", ":", "import", "audioread", "with", "audioread", ".", "audio_open", "(", "path", ")", "as", "f", ":", "return", "match", "(", "apikey", ",", "iter", "(", "f", ")", ",...	41.857143	7.857143
def _instantiateFont(self, path): """ Return a instance of a font object with all the given subclasses """ return self._fontClass(path, libClass=self._libClass, kerningClass=self._kerningClass, groupsClass=self._groupsClass, infoCla...	[ "def", "_instantiateFont", "(", "self", ",", "path", ")", ":", "return", "self", ".", "_fontClass", "(", "path", ",", "libClass", "=", "self", ".", "_libClass", ",", "kerningClass", "=", "self", ".", "_kerningClass", ",", "groupsClass", "=", "self", ".", ...	39.375	5.5
def create_closure_model(cls): """Creates a <Model>Closure model in the same module as the model.""" meta_vals = { 'unique_together': (("parent", "child"),) } if getattr(cls._meta, 'db_table', None): meta_vals['db_table'] = '%sclosure' % getattr(cls._meta, 'db_table') model = type('...	[ "def", "create_closure_model", "(", "cls", ")", ":", "meta_vals", "=", "{", "'unique_together'", ":", "(", "(", "\"parent\"", ",", "\"child\"", ")", ",", ")", "}", "if", "getattr", "(", "cls", ".", "_meta", ",", "'db_table'", ",", "None", ")", ":", "me...	36.173913	14.478261
def make(self, analyte): """ Make filter for specified analyte(s). Filter specified in filt.switches. Parameters ---------- analyte : str or array_like Name or list of names of analytes. Returns ------- array_like boolean...	[ "def", "make", "(", "self", ",", "analyte", ")", ":", "if", "analyte", "is", "None", ":", "analyte", "=", "self", ".", "analytes", "elif", "isinstance", "(", "analyte", ",", "str", ")", ":", "analyte", "=", "[", "analyte", "]", "out", "=", "[", "]"...	24.7	14.233333
def remove_backslash_r(filename, encoding): """ A helpful utility to remove Carriage Return from any file. This will read a file into memory, and overwrite the contents of the original file. TODO: This function may be a liability :param filename: :return: ...	[ "def", "remove_backslash_r", "(", "filename", ",", "encoding", ")", ":", "with", "open", "(", "filename", ",", "'r'", ",", "encoding", "=", "encoding", ",", "newline", "=", "r'\\n'", ")", "as", "filereader", ":", "contents", "=", "filereader", ".", "read",...	30	17.8
def encoded(string, encoding='utf-8'): """Cast string to binary_type. :param string: six.binary_type or six.text_type :param encoding: encoding which the object is forced to :return: six.binary_type """ assert isinstance(string, string_types) or isinstance(string, binary_type) if isinstance...	[ "def", "encoded", "(", "string", ",", "encoding", "=", "'utf-8'", ")", ":", "assert", "isinstance", "(", "string", ",", "string_types", ")", "or", "isinstance", "(", "string", ",", "binary_type", ")", "if", "isinstance", "(", "string", ",", "text_type", ")...	38.611111	17.333333
def __setLock(self, command): """Set lock on requests.""" if command in (TURN_ON, TURN_OFF): self._operation = command elif command in INV_SOURCES: self._operation = SOURCE else: self._operation = ALL self._isLocked = True self._timer =...	[ "def", "__setLock", "(", "self", ",", "command", ")", ":", "if", "command", "in", "(", "TURN_ON", ",", "TURN_OFF", ")", ":", "self", ".", "_operation", "=", "command", "elif", "command", "in", "INV_SOURCES", ":", "self", ".", "_operation", "=", "SOURCE",...	32.3	7.6
def send_worker_queue_message(self, *, batch_id, job_name, entry_point, worker_args, retry_count=0): """Send a message to the `worker_queue` for a worker to execute the requests job Args: batch_id (`str`): Unique ID of the batch the job belongs to job_name (`str`): Non-unique ID...	[ "def", "send_worker_queue_message", "(", "self", ",", "*", ",", "batch_id", ",", "job_name", ",", "entry_point", ",", "worker_args", ",", "retry_count", "=", "0", ")", ":", "try", ":", "job_id", "=", "str", "(", "uuid4", "(", ")", ")", "self", ".", "jo...	40.708333	20.395833
def by_median_household_income(self, lower=-1, upper=2 ** 31, zipcode_type=ZipcodeType.Standard, sort_by=SimpleZipcode.median_household_income.name, ...	[ "def", "by_median_household_income", "(", "self", ",", "lower", "=", "-", "1", ",", "upper", "=", "2", "**", "31", ",", "zipcode_type", "=", "ZipcodeType", ".", "Standard", ",", "sort_by", "=", "SimpleZipcode", ".", "median_household_income", ".", "name", ",...	44.5	14.25
def random(self, num_bytes): """ Get random bytes from YubiHSM. The random data is DRBG_CTR seeded on each startup by a hardware TRNG, so it should be of very good quality. @type num_bytes: integer @return: Bytes with random data @rtype: string @see: L...	[ "def", "random", "(", "self", ",", "num_bytes", ")", ":", "return", "pyhsm", ".", "basic_cmd", ".", "YHSM_Cmd_Random", "(", "self", ".", "stick", ",", "num_bytes", ")", ".", "execute", "(", ")" ]	28.733333	19.4
def _extract(self, in_tile=None, in_data=None, out_tile=None): """Extract data from tile.""" return self.config.output.extract_subset( input_data_tiles=[(in_tile, in_data)], out_tile=out_tile )	[ "def", "_extract", "(", "self", ",", "in_tile", "=", "None", ",", "in_data", "=", "None", ",", "out_tile", "=", "None", ")", ":", "return", "self", ".", "config", ".", "output", ".", "extract_subset", "(", "input_data_tiles", "=", "[", "(", "in_tile", ...	39.333333	13.833333
def do_list(self, arg): """l(ist) [first [,last] \| .] List source code for the current file. Without arguments, list 11 lines around the current line or continue the previous listing. With . as argument, list 11 lines around the current line. With one argument, list 11 lines ...	[ "def", "do_list", "(", "self", ",", "arg", ")", ":", "self", ".", "lastcmd", "=", "'list'", "last", "=", "None", "if", "arg", "and", "arg", "!=", "'.'", ":", "try", ":", "if", "','", "in", "arg", ":", "first", ",", "last", "=", "arg", ".", "spl...	40.469388	15.489796
def create_random_seq(character, action_metadata, direction, length=8): """Creates a random sequence.""" start = tf.random.uniform([], maxval=action_metadata[1], dtype=tf.int32) return create_seq(character, action_metadata, direction, length, start)	[ "def", "create_random_seq", "(", "character", ",", "action_metadata", ",", "direction", ",", "length", "=", "8", ")", ":", "start", "=", "tf", ".", "random", ".", "uniform", "(", "[", "]", ",", "maxval", "=", "action_metadata", "[", "1", "]", ",", "dty...	63	24.5
def command(cmd): """Execute command and raise an exception upon an error. >>> 'README' in command('ls') True >>> command('nonexistingcommand') #doctest: +ELLIPSIS Traceback (most recent call last): ... SdistCreationError """ status, out = commands.getstatusoutput(cmd)...	[ "def", "command", "(", "cmd", ")", ":", "status", ",", "out", "=", "commands", ".", "getstatusoutput", "(", "cmd", ")", "if", "status", "is", "not", "0", ":", "logger", ".", "error", "(", "\"Something went wrong:\"", ")", "logger", ".", "error", "(", "...	26.470588	16.529412
def convert_shortcut_quick_reply(items): """ support shortcut [{'title':'title', 'payload':'payload'}] """ if items is not None and isinstance(items, list): result = [] for item in items: if isinstance(item, QuickReply): result....	[ "def", "convert_shortcut_quick_reply", "(", "items", ")", ":", "if", "items", "is", "not", "None", "and", "isinstance", "(", "items", ",", "list", ")", ":", "result", "=", "[", "]", "for", "item", "in", "items", ":", "if", "isinstance", "(", "item", ",...	38.8125	15.5625
def load_lines(filename): """ Load a text file as an array of lines. Args: filename: Path to the input file. Returns: An array of strings, each representing an individual line. """ with open(filename, 'r', encoding='utf-8') as f: return [line.rstrip('\n') for line in f...	[ "def", "load_lines", "(", "filename", ")", ":", "with", "open", "(", "filename", ",", "'r'", ",", "encoding", "=", "'utf-8'", ")", "as", "f", ":", "return", "[", "line", ".", "rstrip", "(", "'\\n'", ")", "for", "line", "in", "f", ".", "readlines", ...	24.692308	19.615385
def abspath(myPath): import sys, os """ Get absolute path to resource, works for dev and for PyInstaller """ try: # PyInstaller creates a temp folder and stores path in _MEIPASS base_path = sys._MEIPASS return os.path.join(base_path, os.path.basename(myPath)) except Exception: ...	[ "def", "abspath", "(", "myPath", ")", ":", "import", "sys", ",", "os", "try", ":", "# PyInstaller creates a temp folder and stores path in _MEIPASS", "base_path", "=", "sys", ".", "_MEIPASS", "return", "os", ".", "path", ".", "join", "(", "base_path", ",", "os",...	41.8	18.4
def parse_with_retrieved(self, retrieved): """ Receives in input a dictionary of retrieved nodes. Does all the logic here. """ from aiida.common.exceptions import InvalidOperation import os output_path = None error_path = None try: out...	[ "def", "parse_with_retrieved", "(", "self", ",", "retrieved", ")", ":", "from", "aiida", ".", "common", ".", "exceptions", "import", "InvalidOperation", "import", "os", "output_path", "=", "None", "error_path", "=", "None", "try", ":", "output_path", ",", "err...	31.130435	17.565217
def visit_FunctionDef(self, node): """Visit a function node.""" node = self.get_function_node(node) if node is not None: node._async = False	[ "def", "visit_FunctionDef", "(", "self", ",", "node", ")", ":", "node", "=", "self", ".", "get_function_node", "(", "node", ")", "if", "node", "is", "not", "None", ":", "node", ".", "_async", "=", "False" ]	34.4	6
def generate_certificates(base_dir, *peer_names, pubKeyDir=None, secKeyDir=None, sigKeyDir=None, verkeyDir=None, clean=True): ''' Generate client and server CURVE certificate files''' pubKeyDir = pubKeyDir or 'public_keys' secKeyDir = secKeyDir or 'private...	[ "def", "generate_certificates", "(", "base_dir", ",", "*", "peer_names", ",", "pubKeyDir", "=", "None", ",", "secKeyDir", "=", "None", ",", "sigKeyDir", "=", "None", ",", "verkeyDir", "=", "None", ",", "clean", "=", "True", ")", ":", "pubKeyDir", "=", "p...	39.976744	17
def role_get(name, user=None, host=None, port=None, maintenance_db=None, password=None, runas=None, return_password=False): ''' Return a dict with information about users of a Postgres server. Set return_password to True to get password hash in the result. CLI Example: .. code-block:...	[ "def", "role_get", "(", "name", ",", "user", "=", "None", ",", "host", "=", "None", ",", "port", "=", "None", ",", "maintenance_db", "=", "None", ",", "password", "=", "None", ",", "runas", "=", "None", ",", "return_password", "=", "False", ")", ":",...	33.56	21.32
def is_storage(url, storage=None): """ Check if file is a local file or a storage file. File is considered local if: - URL is a local path. - URL starts by "file://" - a "storage" is provided. Args: url (str): file path or URL storage (str): Storage name. R...	[ "def", "is_storage", "(", "url", ",", "storage", "=", "None", ")", ":", "if", "storage", ":", "return", "True", "split_url", "=", "url", ".", "split", "(", "'://'", ",", "1", ")", "if", "len", "(", "split_url", ")", "==", "2", "and", "split_url", "...	24.090909	16.272727
def define_from_values(cls, xdtu, ydtu, zdtu, xdtu_0, ydtu_0, zdtu_0): """Define class object from from provided values. Parameters ---------- xdtu : float XDTU fits keyword value. ydtu : float YDTU fits keyword value. zdtu : float ZDT...	[ "def", "define_from_values", "(", "cls", ",", "xdtu", ",", "ydtu", ",", "zdtu", ",", "xdtu_0", ",", "ydtu_0", ",", "zdtu_0", ")", ":", "self", "=", "DtuConfiguration", "(", ")", "# define DTU variables", "self", ".", "xdtu", "=", "xdtu", "self", ".", "yd...	26.206897	15.448276
def replay_scope(self, sess): """Enters a replay scope that unsets it at the end.""" current_replay = self.replay(sess) try: self.set_replay(sess, True) yield finally: self.set_replay(sess, current_replay)	[ "def", "replay_scope", "(", "self", ",", "sess", ")", ":", "current_replay", "=", "self", ".", "replay", "(", "sess", ")", "try", ":", "self", ".", "set_replay", "(", "sess", ",", "True", ")", "yield", "finally", ":", "self", ".", "set_replay", "(", ...	29	14
def _load_plugins(self): ''' Sets up all plugins, defaults and settings.py ''' plugins = self.settings['PLUGINS'] self.plugins_dict = {} for key in plugins: # skip loading the plugin if its value is None if plugins[key] is None: co...	[ "def", "_load_plugins", "(", "self", ")", ":", "plugins", "=", "self", ".", "settings", "[", "'PLUGINS'", "]", "self", ".", "plugins_dict", "=", "{", "}", "for", "key", "in", "plugins", ":", "# skip loading the plugin if its value is None", "if", "plugins", "[...	39.166667	17.9
def highres_imu_encode(self, time_usec, xacc, yacc, zacc, xgyro, ygyro, zgyro, xmag, ymag, zmag, abs_pressure, diff_pressure, pressure_alt, temperature, fields_updated): ''' The IMU readings in SI units in NED body frame time_usec : Timestamp (microsecond...	[ "def", "highres_imu_encode", "(", "self", ",", "time_usec", ",", "xacc", ",", "yacc", ",", "zacc", ",", "xgyro", ",", "ygyro", ",", "zgyro", ",", "xmag", ",", "ymag", ",", "zmag", ",", "abs_pressure", ",", "diff_pressure", ",", "pressure_alt", ",", "temp...	80.954545	52.045455
def remove_from_group(self, group, user): """ Remove a user from a group :type user: str :param user: User's email :type group: str :param group: Group name :rtype: dict :return: an empty dictionary """ data = {'group': group, 'user': us...	[ "def", "remove_from_group", "(", "self", ",", "group", ",", "user", ")", ":", "data", "=", "{", "'group'", ":", "group", ",", "'user'", ":", "user", "}", "return", "self", ".", "post", "(", "'removeUserFromGroup'", ",", "data", ")" ]	24.2	14.466667
def log_level(io_handler, level=None, name=None): """ Prints/Changes log level """ # Get the logger logger = logging.getLogger(name) # Normalize the name if not name: name = "Root" if not level: # Level not given: print the logger...	[ "def", "log_level", "(", "io_handler", ",", "level", "=", "None", ",", "name", "=", "None", ")", ":", "# Get the logger", "logger", "=", "logging", ".", "getLogger", "(", "name", ")", "# Normalize the name", "if", "not", "name", ":", "name", "=", "\"Root\"...	32	16.461538
def only_for(theme, redirect_to='/', raise_error=None): """ Decorator for restrict access to views according by list of themes. Params: * ``theme`` - string or list of themes where decorated view must be * ``redirect_to`` - url or name of url pattern for redirect if CURRENT_THEME n...	[ "def", "only_for", "(", "theme", ",", "redirect_to", "=", "'/'", ",", "raise_error", "=", "None", ")", ":", "def", "check_theme", "(", "", "args", ",", "", "*", "kwargs", ")", ":", "if", "isinstance", "(", "theme", ",", "six", ".", "string_types", ...	25.076923	22.205128
def create_sdb(self, name, category_id, owner, description="", user_group_permissions=None, iam_principal_permissions=None): """Create a safe deposit box. You need to refresh your token before the iam role is granted permission to the new safe deposit box. Keyword arguments: ...	[ "def", "create_sdb", "(", "self", ",", "name", ",", "category_id", ",", "owner", ",", "description", "=", "\"\"", ",", "user_group_permissions", "=", "None", ",", "iam_principal_permissions", "=", "None", ")", ":", "# Do some sanity checking", "if", "user_group_pe...	51.384615	25.025641
def execute(self): """ This function Executes the program with set arguments. """ prog_cmd = self.get_cmd().strip() if prog_cmd == '': self.status = 'Failure' debug.log("Error: No program to execute for %s!"%self.name) debug.log(("Could not combine path and arguments into cm...	[ "def", "execute", "(", "self", ")", ":", "prog_cmd", "=", "self", ".", "get_cmd", "(", ")", ".", "strip", "(", ")", "if", "prog_cmd", "==", "''", ":", "self", ".", "status", "=", "'Failure'", "debug", ".", "log", "(", "\"Error: No program to execute for ...	41.775	15.4
def bind(self, args, kwargs): """ Bind arguments and keyword arguments to the encapsulated function. Returns a dictionary of parameters (named according to function parameters) with the values that were bound to each name. """ spec = self._spec resolution = self....	[ "def", "bind", "(", "self", ",", "args", ",", "kwargs", ")", ":", "spec", "=", "self", ".", "_spec", "resolution", "=", "self", ".", "resolve", "(", "args", ",", "kwargs", ")", "params", "=", "dict", "(", "zip", "(", "spec", ".", "args", ",", "re...	37.176471	16.117647
def _pin_mongos(self, server): """Pin this session to the given mongos Server.""" self._transaction.sharded = True self._transaction.pinned_address = server.description.address	[ "def", "_pin_mongos", "(", "self", ",", "server", ")", ":", "self", ".", "_transaction", ".", "sharded", "=", "True", "self", ".", "_transaction", ".", "pinned_address", "=", "server", ".", "description", ".", "address" ]	49.25	9.75
def read_ipv6(self, length): """Read Internet Protocol version 6 (IPv6). Structure of IPv6 header [RFC 2460]: 0 1 2 3 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 +-+-+-+-+-+-+-+-+-+-+-+-+-+-...	[ "def", "read_ipv6", "(", "self", ",", "length", ")", ":", "if", "length", "is", "None", ":", "length", "=", "len", "(", "self", ")", "_htet", "=", "self", ".", "_read_ip_hextet", "(", ")", "_plen", "=", "self", ".", "_read_unpack", "(", "2", ")", "...	48.954545	26.651515
def left(self, num=None): """ NOT REQUIRED, BUT EXISTS AS OPPOSITE OF right() """ if num == None: return FlatList([_get_list(self)[0]]) if num <= 0: return Null return FlatList(_get_list(self)[:num])	[ "def", "left", "(", "self", ",", "num", "=", "None", ")", ":", "if", "num", "==", "None", ":", "return", "FlatList", "(", "[", "_get_list", "(", "self", ")", "[", "0", "]", "]", ")", "if", "num", "<=", "0", ":", "return", "Null", "return", "Fla...	26.3	13.9
def plot_fit(self,**kwargs): """ Plots the fit of the model Returns ---------- None (plots data and the fit) """ import matplotlib.pyplot as plt import seaborn as sns figsize = kwargs.get('figsize',(10,7)) if self.latent_variables.estimated is F...	[ "def", "plot_fit", "(", "self", ",", "", "", "kwargs", ")", ":", "import", "matplotlib", ".", "pyplot", "as", "plt", "import", "seaborn", "as", "sns", "figsize", "=", "kwargs", ".", "get", "(", "'figsize'", ",", "(", "10", ",", "7", ")", ")", "if...	36.75	18.291667
def PopEvent(self): """Pops an event from the heap. Returns: tuple: containing: int: event timestamp or None if the heap is empty bytes: serialized event or None if the heap is empty """ try: timestamp, serialized_event = heapq.heappop(self._heap) self.data_size -= l...	[ "def", "PopEvent", "(", "self", ")", ":", "try", ":", "timestamp", ",", "serialized_event", "=", "heapq", ".", "heappop", "(", "self", ".", "_heap", ")", "self", ".", "data_size", "-=", "len", "(", "serialized_event", ")", "return", "timestamp", ",", "se...	24.294118	20.882353
def move_to(self, folder): """Moves the email to the folder specified by the folder parameter. Args: folder: A string containing the folder ID the message should be moved to, or a Folder instance """ if isinstance(folder, Folder): self.move_to(folder.id) ...	[ "def", "move_to", "(", "self", ",", "folder", ")", ":", "if", "isinstance", "(", "folder", ",", "Folder", ")", ":", "self", ".", "move_to", "(", "folder", ".", "id", ")", "else", ":", "self", ".", "_move_to", "(", "folder", ")" ]	31.818182	20.727273
def removecolkeyword(self, columnname, keyword): """Remove a column keyword. It is similar to :func:`removekeyword`. """ if isinstance(keyword, str): self._removekeyword(columnname, keyword, -1) else: self._removekeyword(columnname, '', keyword)	[ "def", "removecolkeyword", "(", "self", ",", "columnname", ",", "keyword", ")", ":", "if", "isinstance", "(", "keyword", ",", "str", ")", ":", "self", ".", "_removekeyword", "(", "columnname", ",", "keyword", ",", "-", "1", ")", "else", ":", "self", "....	30.2	15.8
def stats_evaluation(stats): """Generate an evaluation for the given pylint ``stats``.""" statement = stats.get('statement') error = stats.get('error', 0) warning = stats.get('warning', 0) refactor = stats.get('refactor', 0) convention = stats.get('convention', 0) if not statement or statem...	[ "def", "stats_evaluation", "(", "stats", ")", ":", "statement", "=", "stats", ".", "get", "(", "'statement'", ")", "error", "=", "stats", ".", "get", "(", "'error'", ",", "0", ")", "warning", "=", "stats", ".", "get", "(", "'warning'", ",", "0", ")",...	33.785714	11.5
def translate(self): """Compile the variable lookup.""" ident = self.ident expr = ex_rvalue(VARIABLE_PREFIX + ident) return [expr], set([ident]), set()	[ "def", "translate", "(", "self", ")", ":", "ident", "=", "self", ".", "ident", "expr", "=", "ex_rvalue", "(", "VARIABLE_PREFIX", "+", "ident", ")", "return", "[", "expr", "]", ",", "set", "(", "[", "ident", "]", ")", ",", "set", "(", ")" ]	35.8	9
def parse_cov(cov_table, scaffold2genome): """ calculate genome coverage from scaffold coverage table """ size = {} # size[genome] = genome size mapped = {} # mapped[genome][sample] = mapped bases # parse coverage files for line in open(cov_table): line = line.strip().split('\t') ...	[ "def", "parse_cov", "(", "cov_table", ",", "scaffold2genome", ")", ":", "size", "=", "{", "}", "# size[genome] = genome size", "mapped", "=", "{", "}", "# mapped[genome][sample] = mapped bases", "# parse coverage files", "for", "line", "in", "open", "(", "cov_table", ...	40.473684	9.736842
def gsea_edb_parser(results_path, index=0): """Parse results.edb file stored under edb file folder. :param results_path: the .results file located inside edb folder. :param index: gene_set index of gmt database, used for iterating items. :return: enrichment_term, hit_index,nes, pval, fdr. """ ...	[ "def", "gsea_edb_parser", "(", "results_path", ",", "index", "=", "0", ")", ":", "from", "bs4", "import", "BeautifulSoup", "soup", "=", "BeautifulSoup", "(", "open", "(", "results_path", ")", ",", "features", "=", "'xml'", ")", "tag", "=", "soup", ".", "...	40.133333	14.933333
def to_json(self): """Return a JSON-serializable representation.""" return { 'network': self.network, 'state': self.state, 'nodes': self.node_indices, 'cut': self.cut, }	[ "def", "to_json", "(", "self", ")", ":", "return", "{", "'network'", ":", "self", ".", "network", ",", "'state'", ":", "self", ".", "state", ",", "'nodes'", ":", "self", ".", "node_indices", ",", "'cut'", ":", "self", ".", "cut", ",", "}" ]	29.25	12.75
def write_geno(data, sidx): """ write the geno output formerly used by admixture, still supported by adegenet, perhaps. Also, sNMF still likes .geno. """ ## grab snp and bis data from tmparr start = time.time() tmparrs = os.path.join(data.dirs.outfiles, "tmp-{}.h5".format(data.name)) ...	[ "def", "write_geno", "(", "data", ",", "sidx", ")", ":", "## grab snp and bis data from tmparr", "start", "=", "time", ".", "time", "(", ")", "tmparrs", "=", "os", ".", "path", ".", "join", "(", "data", ".", "dirs", ".", "outfiles", ",", "\"tmp-{}.h5\"", ...	39.849315	23.465753
def parse_backend(backend): """Converts the "backend" into the database connection parameters. It returns a (scheme, host, params) tuple.""" r = urlparse.urlsplit(backend) scheme, host = r.scheme, r.netloc path, query = r.path, r.query if path and not query: query, path = path, '' ...	[ "def", "parse_backend", "(", "backend", ")", ":", "r", "=", "urlparse", ".", "urlsplit", "(", "backend", ")", "scheme", ",", "host", "=", "r", ".", "scheme", ",", "r", ".", "netloc", "path", ",", "query", "=", "r", ".", "path", ",", "r", ".", "qu...	29.789474	13.105263
def threshold_monitor_hidden_threshold_monitor_Memory_high_limit(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") threshold_monitor_hidden = ET.SubElement(config, "threshold-monitor-hidden", xmlns="urn:brocade.com:mgmt:brocade-threshold-monitor") threshol...	[ "def", "threshold_monitor_hidden_threshold_monitor_Memory_high_limit", "(", "self", ",", "", "", "kwargs", ")", ":", "config", "=", "ET", ".", "Element", "(", "\"config\"", ")", "threshold_monitor_hidden", "=", "ET", ".", "SubElement", "(", "config", ",", "\"thr...	53.333333	25.25
def enterEvent(self, event): """ Reimplemented to cancel the hide timer. """ super(CallTipWidget, self).enterEvent(event) self._hide_timer.stop()	[ "def", "enterEvent", "(", "self", ",", "event", ")", ":", "super", "(", "CallTipWidget", ",", "self", ")", ".", "enterEvent", "(", "event", ")", "self", ".", "_hide_timer", ".", "stop", "(", ")" ]	34.6	6.6
def operations(self): """Instance depends on the API version: * 2018-03-31: :class:`Operations<azure.mgmt.containerservice.v2018_03_31.operations.Operations>` * 2018-08-01-preview: :class:`Operations<azure.mgmt.containerservice.v2018_08_01_preview.operations.Operations>` * 2019...	[ "def", "operations", "(", "self", ")", ":", "api_version", "=", "self", ".", "_get_api_version", "(", "'operations'", ")", "if", "api_version", "==", "'2018-03-31'", ":", "from", ".", "v2018_03_31", ".", "operations", "import", "Operations", "as", "OperationClas...	64	35.529412
def query_total_cat_recent(cat_id_arr, label=None, num=8, kind='1'): ''' :param cat_id_arr: list of categories. ['0101', '0102'] :param label: the additional label ''' if label: return MPost.__query_with_label( cat_id_arr, label=label...	[ "def", "query_total_cat_recent", "(", "cat_id_arr", ",", "label", "=", "None", ",", "num", "=", "8", ",", "kind", "=", "'1'", ")", ":", "if", "label", ":", "return", "MPost", ".", "__query_with_label", "(", "cat_id_arr", ",", "label", "=", "label", ",", ...	35.307692	20.538462
def gene_ids(self): """ Return IDs of all genes which overlap this variant. Calling this method is significantly cheaper than calling `Variant.genes()`, which has to issue many more queries to construct each Gene object. """ return self.ensembl.gene_ids_at_locus( ...	[ "def", "gene_ids", "(", "self", ")", ":", "return", "self", ".", "ensembl", ".", "gene_ids_at_locus", "(", "self", ".", "contig", ",", "self", ".", "start", ",", "self", ".", "end", ")" ]	43.875	16.375
def lub(self, other): """ Return the least upper bound for given intervals. :param other: AbstractInterval instance """ return self.__class__( [ max(self.lower, other.lower), max(self.upper, other.upper), ], low...	[ "def", "lub", "(", "self", ",", "other", ")", ":", "return", "self", ".", "__class__", "(", "[", "max", "(", "self", ".", "lower", ",", "other", ".", "lower", ")", ",", "max", "(", "self", ".", "upper", ",", "other", ".", "upper", ")", ",", "]"...	32.214286	18.214286
def _get_auto_rank(self, rank): """Tries to figure out what rank we should use for analyses""" if rank == "auto": # if we're an accessor for a ClassificationsDataFrame, use its _rank property if self.__class__.__name__ == "OneCodexAccessor": return self._rank ...	[ "def", "_get_auto_rank", "(", "self", ",", "rank", ")", ":", "if", "rank", "==", "\"auto\"", ":", "# if we're an accessor for a ClassificationsDataFrame, use its _rank property", "if", "self", ".", "__class__", ".", "__name__", "==", "\"OneCodexAccessor\"", ":", "return...	33.357143	19.071429
def get_table_options(self, connection, table_name, schema, **kw): """ Return a dictionary of options specified when the table of the given name was created. Overrides interface :meth:`~sqlalchemy.engine.Inspector.get_table_options`. """ def keyfunc(column): ...	[ "def", "get_table_options", "(", "self", ",", "connection", ",", "table_name", ",", "schema", ",", "", "", "kw", ")", ":", "def", "keyfunc", "(", "column", ")", ":", "num", "=", "int", "(", "column", ".", "sortkey", ")", "# If sortkey is interleaved, col...	43.121212	15.909091
def toner_status(self, filter_supported: bool = True) -> Dict[str, Any]: """Return the state of all toners cartridges.""" toner_status = {} for color in self.COLOR_NAMES: try: toner_stat = self.data.get( '{}_{}'.format(SyncThru.TONER, color),...	[ "def", "toner_status", "(", "self", ",", "filter_supported", ":", "bool", "=", "True", ")", "->", "Dict", "[", "str", ",", "Any", "]", ":", "toner_status", "=", "{", "}", "for", "color", "in", "self", ".", "COLOR_NAMES", ":", "try", ":", "toner_stat", ...	43.5	13.714286
def generate_license(template, context): """ Generate a license by extracting variables from the template and replacing them with the corresponding values in the given context. """ out = StringIO() content = template.getvalue() for key in extract_vars(template): if key not in context...	[ "def", "generate_license", "(", "template", ",", "context", ")", ":", "out", "=", "StringIO", "(", ")", "content", "=", "template", ".", "getvalue", "(", ")", "for", "key", "in", "extract_vars", "(", "template", ")", ":", "if", "key", "not", "in", "con...	43.461538	16.307692
def create_component(self, name, description=None): """ Create a sub component in the business component. :param name: The new component's name. :param description: The new component's description. :returns: The created component. """ new_comp = Component(name,...	[ "def", "create_component", "(", "self", ",", "name", ",", "description", "=", "None", ")", ":", "new_comp", "=", "Component", "(", "name", ",", "self", ".", "gl", ",", "description", "=", "description", ")", "new_comp", ".", "set_parent_path", "(", "self",...	32.142857	15.857143
def get_file_annotate(self, path): """ Returns a generator of four element tuples with lineno, sha, changeset lazy loader and line TODO: This function now uses os underlying 'git' command which is generally not good. Should be replaced with algorithm iterating commit...	[ "def", "get_file_annotate", "(", "self", ",", "path", ")", ":", "cmd", "=", "'blame -l --root -r %s -- \"%s\"'", "%", "(", "self", ".", "id", ",", "path", ")", "# -l ==> outputs long shas (and we need all 40 characters)", "# --root ==> doesn't put '^' character for bounde...	44.263158	20.473684
def inverse(self): """ Inverts image (all nonzeros become zeros and vice verse) Returns ------- :obj:`BinaryImage` inverse of this binary image """ data = np.zeros(self.shape).astype(np.uint8) ind = np.where(self.data == 0) data[ind[0], ind[1],...	[ "def", "inverse", "(", "self", ")", ":", "data", "=", "np", ".", "zeros", "(", "self", ".", "shape", ")", ".", "astype", "(", "np", ".", "uint8", ")", "ind", "=", "np", ".", "where", "(", "self", ".", "data", "==", "0", ")", "data", "[", "ind...	34.636364	10.727273
def update_frame(self, key, ranges=None): """ Update the internal state of the Plot to represent the given key tuple (where integers represent frames). Returns this state. """ ranges = self.compute_ranges(self.layout, key, ranges) for r, c in self.coords: ...	[ "def", "update_frame", "(", "self", ",", "key", ",", "ranges", "=", "None", ")", ":", "ranges", "=", "self", ".", "compute_ranges", "(", "self", ".", "layout", ",", "key", ",", "ranges", ")", "for", "r", ",", "c", "in", "self", ".", "coords", ":", ...	38.5	11.5
def iter_options(grouped_choices, cutoff=None, cutoff_text=None): """ Helper function for options and option groups in templates. """ class StartOptionGroup(object): start_option_group = True end_option_group = False def __init__(self, label): self.label = label ...	[ "def", "iter_options", "(", "grouped_choices", ",", "cutoff", "=", "None", ",", "cutoff_text", "=", "None", ")", ":", "class", "StartOptionGroup", "(", "object", ")", ":", "start_option_group", "=", "True", "end_option_group", "=", "False", "def", "__init__", ...	30.688889	16.955556
def xcorr(x1,x2,Nlags): """ r12, k = xcorr(x1,x2,Nlags), r12 and k are ndarray's Compute the energy normalized cross correlation between the sequences x1 and x2. If x1 = x2 the cross correlation is the autocorrelation. The number of lags sets how many lags to return centered about zero """ K...	[ "def", "xcorr", "(", "x1", ",", "x2", ",", "Nlags", ")", ":", "K", "=", "2", "*", "(", "int", "(", "np", ".", "floor", "(", "len", "(", "x1", ")", "/", "2", ")", ")", ")", "X1", "=", "fft", ".", "fft", "(", "x1", "[", ":", "K", "]", "...	37.941176	13.588235
def parse_cache(self, full_df): """ Format the cached data model into a dictionary of DataFrames and a criteria map DataFrame. Parameters ---------- full_df : DataFrame result of self.get_dm_offline() Returns ---------- data_model : d...	[ "def", "parse_cache", "(", "self", ",", "full_df", ")", ":", "data_model", "=", "{", "}", "levels", "=", "[", "'specimens'", ",", "'samples'", ",", "'sites'", ",", "'locations'", ",", "'ages'", ",", "'measurements'", ",", "'criteria'", ",", "'contribution'",...	35.192308	17.192308
def list_dataset_uris(cls, base_uri, config_path): """Return list containing URIs with base URI.""" storage_account_name = generous_parse_uri(base_uri).netloc blobservice = get_blob_service(storage_account_name, config_path) containers = blobservice.list_containers(include_metadata=True...	[ "def", "list_dataset_uris", "(", "cls", ",", "base_uri", ",", "config_path", ")", ":", "storage_account_name", "=", "generous_parse_uri", "(", "base_uri", ")", ".", "netloc", "blobservice", "=", "get_blob_service", "(", "storage_account_name", ",", "config_path", ")...	33.833333	18.166667
def github_belspec_files(spec_dir, force: bool = False): """Get belspec files from Github repo Args: spec_dir: directory to store the BEL Specification and derived files force: force update of BEL Specifications from Github - skipped if local files less than 1 day old """ if not force...	[ "def", "github_belspec_files", "(", "spec_dir", ",", "force", ":", "bool", "=", "False", ")", ":", "if", "not", "force", ":", "dtnow", "=", "datetime", ".", "datetime", ".", "utcnow", "(", ")", "delta", "=", "datetime", ".", "timedelta", "(", "1", ")",...	36.956522	25.391304
def _parse_sod_segment(self, fptr): """Parse the SOD (start-of-data) segment. Parameters ---------- fptr : file Open file object. Returns ------- SODSegment The current SOD segment. """ offset = fptr.tell() - 2 len...	[ "def", "_parse_sod_segment", "(", "self", ",", "fptr", ")", ":", "offset", "=", "fptr", ".", "tell", "(", ")", "-", "2", "length", "=", "0", "return", "SODsegment", "(", "length", ",", "offset", ")" ]	20.823529	18.117647
def _verifyDiscoveredServices(self, claimed_id, services, to_match_endpoints): """See @L{_discoverAndVerify}""" # Search the services resulting from discovery to find one # that matches the information from the assertion failure_messages = [] fo...	[ "def", "_verifyDiscoveredServices", "(", "self", ",", "claimed_id", ",", "services", ",", "to_match_endpoints", ")", ":", "# Search the services resulting from discovery to find one", "# that matches the information from the assertion", "failure_messages", "=", "[", "]", "for", ...	43.923077	17.538462
def send(self, packet, recalculate_checksum=True): """ Injects a packet into the network stack. Recalculates the checksum before sending unless recalculate_checksum=False is passed. The injected packet may be one received from recv(), or a modified version, or a completely new packet. ...	[ "def", "send", "(", "self", ",", "packet", ",", "recalculate_checksum", "=", "True", ")", ":", "if", "recalculate_checksum", ":", "packet", ".", "recalculate_checksums", "(", ")", "send_len", "=", "c_uint", "(", "0", ")", "if", "PY2", ":", "# .from_buffer(me...	39.057143	23
def month_crumb(date): """ Crumb for a month. """ year = date.strftime('%Y') month = date.strftime('%m') month_text = DateFormat(date).format('F').capitalize() return Crumb(month_text, reverse('zinnia:entry_archive_month', args=[year, month]))	[ "def", "month_crumb", "(", "date", ")", ":", "year", "=", "date", ".", "strftime", "(", "'%Y'", ")", "month", "=", "date", ".", "strftime", "(", "'%m'", ")", "month_text", "=", "DateFormat", "(", "date", ")", ".", "format", "(", "'F'", ")", ".", "c...	33.333333	12.888889
def widths_in_range_mm( self, minwidth=EMIR_MINIMUM_SLITLET_WIDTH_MM, maxwidth=EMIR_MAXIMUM_SLITLET_WIDTH_MM ): """Return list of slitlets which width is within given range Parameters ---------- minwidth : float Minimum slit width (mm)...	[ "def", "widths_in_range_mm", "(", "self", ",", "minwidth", "=", "EMIR_MINIMUM_SLITLET_WIDTH_MM", ",", "maxwidth", "=", "EMIR_MAXIMUM_SLITLET_WIDTH_MM", ")", ":", "list_ok", "=", "[", "]", "for", "i", "in", "range", "(", "EMIR_NBARS", ")", ":", "slitlet_ok", "=",...	26.068966	19.62069
def get_canonical_transaction(self, transaction_hash: Hash32) -> BaseTransaction: """ Returns the requested transaction as specified by the transaction hash from the canonical chain. Raises TransactionNotFound if no transaction with the specified hash is found in the main chain....	[ "def", "get_canonical_transaction", "(", "self", ",", "transaction_hash", ":", "Hash32", ")", "->", "BaseTransaction", ":", "(", "block_num", ",", "index", ")", "=", "self", ".", "chaindb", ".", "get_transaction_index", "(", "transaction_hash", ")", "VM_class", ...	37.192308	22.576923
def _releaseId(self, msgId): """ Release message ID to the pool. @param msgId: message ID, no longer on the wire @type msgId: C{str} """ self._uuids.append(msgId) if len(self._uuids) > 2 * self.UUID_POOL_GEN_SIZE: self._uuids[-self.UUID_POOL_GEN_SIZE:...	[ "def", "_releaseId", "(", "self", ",", "msgId", ")", ":", "self", ".", "_uuids", ".", "append", "(", "msgId", ")", "if", "len", "(", "self", ".", "_uuids", ")", ">", "2", "*", "self", ".", "UUID_POOL_GEN_SIZE", ":", "self", ".", "_uuids", "[", "-",...	31.7	12.1
def task_done(self): """Mark a task as done.""" with self._lock: unfinished = self._unfinished_tasks - 1 if unfinished < 0: raise RuntimeError('task_done() called too many times') elif unfinished == 0: self._alldone.notify() ...	[ "def", "task_done", "(", "self", ")", ":", "with", "self", ".", "_lock", ":", "unfinished", "=", "self", ".", "_unfinished_tasks", "-", "1", "if", "unfinished", "<", "0", ":", "raise", "RuntimeError", "(", "'task_done() called too many times'", ")", "elif", ...	38.666667	11.555556
def tupleize( rows, alphabetize_columns=getattr( settings, 'ALPHABETIZE_COLUMNS', False)): """Also alphabetizes columns and returns a tuple of tuples""" # define a blank list as our return object l = [] for r in rows: row = [] row = list(r.val...	[ "def", "tupleize", "(", "rows", ",", "alphabetize_columns", "=", "getattr", "(", "settings", ",", "'ALPHABETIZE_COLUMNS'", ",", "False", ")", ")", ":", "# define a blank list as our return object\r", "l", "=", "[", "]", "for", "r", "in", "rows", ":", "row", "=...	22.227273	19.590909
def stats_tube(self, tube: str) -> Stats: """Returns tube statistics. :param tube: The tube to return statistics for. """ return self._stats_cmd(b'stats-tube %b' % tube.encode('ascii'))	[ "def", "stats_tube", "(", "self", ",", "tube", ":", "str", ")", "->", "Stats", ":", "return", "self", ".", "_stats_cmd", "(", "b'stats-tube %b'", "%", "tube", ".", "encode", "(", "'ascii'", ")", ")" ]	35.5	14.5
def docSetRootElement(self, doc): """Set the root element of the document (doc->children is a list containing possibly comments, PIs, etc ...). """ if doc is None: doc__o = None else: doc__o = doc._o ret = libxml2mod.xmlDocSetRootElement(doc__o, self._o) if ret is None...	[ "def", "docSetRootElement", "(", "self", ",", "doc", ")", ":", "if", "doc", "is", "None", ":", "doc__o", "=", "None", "else", ":", "doc__o", "=", "doc", ".", "_o", "ret", "=", "libxml2mod", ".", "xmlDocSetRootElement", "(", "doc__o", ",", "self", ".", ...	42.111111	8.444444
def is_draft_version(self): """ Return if this version is the draft version of a layer """ pub_ver = getattr(self, 'published_version', None) latest_ver = getattr(self, 'latest_version', None) this_ver = getattr(self, 'this_version', None) return this_ver and latest_ver and (this...	[ "def", "is_draft_version", "(", "self", ")", ":", "pub_ver", "=", "getattr", "(", "self", ",", "'published_version'", ",", "None", ")", "latest_ver", "=", "getattr", "(", "self", ",", "'latest_version'", ",", "None", ")", "this_ver", "=", "getattr", "(", "...	60.333333	19.666667
def to_bool(x): """"Converts to a boolean in a semantically meaningful way.""" if isinstance(x, bool): return x elif isinstance(x, str): return False if x.lower() in _FALSES else True else: return bool(x)	[ "def", "to_bool", "(", "x", ")", ":", "if", "isinstance", "(", "x", ",", "bool", ")", ":", "return", "x", "elif", "isinstance", "(", "x", ",", "str", ")", ":", "return", "False", "if", "x", ".", "lower", "(", ")", "in", "_FALSES", "else", "True",...	29.625	17.125
def execute_fragment_under_context(self, ctx, start_label, end_label): ''' just like run but returns if moved outside of the specified fragment # 4 different exectution results # 0=normal, 1=return, 2=jump_outside, 3=errors # execute_fragment_under_context returns: ...	[ "def", "execute_fragment_under_context", "(", "self", ",", "ctx", ",", "start_label", ",", "end_label", ")", ":", "old_curr_ctx", "=", "self", ".", "current_ctx", "self", ".", "ctx_depth", "+=", "1", "old_stack_len", "=", "len", "(", "ctx", ".", "stack", ")"...	45.655172	14.689655
def delete_chat_photo(chat_id, **kwargs): """ Use this method to delete a chat photo. Photos can't be changed for private chats. The bot must be an administrator in the chat for this to work and must have the appropriate admin rights. :param chat_id: Unique identifier for the target chat or username of...	[ "def", "delete_chat_photo", "(", "chat_id", ",", "", "", "kwargs", ")", ":", "# required args", "params", "=", "dict", "(", "chat_id", "=", "chat_id", ")", "return", "TelegramBotRPCRequest", "(", "'deleteChatPhoto'", ",", "params", "=", "params", ",", "on_re...	47.642857	31.5
def create_key(file_): """ Create a key and save it into ``file_``. Note that ``file`` must be opened in binary mode. """ pkey = crypto.PKey() pkey.generate_key(crypto.TYPE_RSA, 2048) file_.write(crypto.dump_privatekey(crypto.FILETYPE_PEM, pkey)) file_.flush()	[ "def", "create_key", "(", "file_", ")", ":", "pkey", "=", "crypto", ".", "PKey", "(", ")", "pkey", ".", "generate_key", "(", "crypto", ".", "TYPE_RSA", ",", "2048", ")", "file_", ".", "write", "(", "crypto", ".", "dump_privatekey", "(", "crypto", ".", ...	25.818182	16.727273
def create_embedded_class(self, method): """ Build the estimator class. Returns ------- :return : string The built class as string. """ temp_class = self.temp('embedded.class') return temp_class.format(class_name=self.class_name, ...	[ "def", "create_embedded_class", "(", "self", ",", "method", ")", ":", "temp_class", "=", "self", ".", "temp", "(", "'embedded.class'", ")", "return", "temp_class", ".", "format", "(", "class_name", "=", "self", ".", "class_name", ",", "method_name", "=", "se...	33.307692	15.307692
def get_doc_lengths(self): ''' Returns a list of document lengths in words Returns ------- np.array ''' idx_to_delete_list = self._build_term_index_list(True, self._get_non_unigrams()) unigram_X, _ = self._get_X_after_delete_terms(idx_to_delete_list) ...	[ "def", "get_doc_lengths", "(", "self", ")", ":", "idx_to_delete_list", "=", "self", ".", "_build_term_index_list", "(", "True", ",", "self", ".", "_get_non_unigrams", "(", ")", ")", "unigram_X", ",", "_", "=", "self", ".", "_get_X_after_delete_terms", "(", "id...	31.363636	25.363636
def rm_job(name): ''' Remove the specified job from the server. CLI Example: .. code-block:: bash salt chronos-minion-id chronos.rm_job my-job ''' response = salt.utils.http.query( "{0}/scheduler/job/{1}".format(_base_url(), name), method='DELETE', ) return Tru...	[ "def", "rm_job", "(", "name", ")", ":", "response", "=", "salt", ".", "utils", ".", "http", ".", "query", "(", "\"{0}/scheduler/job/{1}\"", ".", "format", "(", "_base_url", "(", ")", ",", "name", ")", ",", "method", "=", "'DELETE'", ",", ")", "return",...	20.466667	24.2
def _aggregations_config(self): """Load aggregation configurations.""" result = {} for ep in iter_entry_points( group=self.entry_point_group_aggs): for cfg in ep.load()(): if cfg['aggregation_name'] not in self.enabled_aggregations: ...	[ "def", "_aggregations_config", "(", "self", ")", ":", "result", "=", "{", "}", "for", "ep", "in", "iter_entry_points", "(", "group", "=", "self", ".", "entry_point_group_aggs", ")", ":", "for", "cfg", "in", "ep", ".", "load", "(", ")", "(", ")", ":", ...	46.111111	17.555556
def __chopStringDict(self, data): '''Returns a dictionary of the provided raw service/host check string.''' r = {} d = data.split('\t') for item in d: item_parts = item.split('::') if len(item_parts) == 2: (name, value) = item_parts e...	[ "def", "__chopStringDict", "(", "self", ",", "data", ")", ":", "r", "=", "{", "}", "d", "=", "data", ".", "split", "(", "'\\t'", ")", "for", "item", "in", "d", ":", "item_parts", "=", "item", ".", "split", "(", "'::'", ")", "if", "len", "(", "i...	33.064516	20.419355
def run(self): ''' Execute the runner sequence ''' # Print documentation only if self.opts.get('doc', False): self.print_docs() else: return self._run_runner()	[ "def", "run", "(", "self", ")", ":", "# Print documentation only", "if", "self", ".", "opts", ".", "get", "(", "'doc'", ",", "False", ")", ":", "self", ".", "print_docs", "(", ")", "else", ":", "return", "self", ".", "_run_runner", "(", ")" ]	24.777778	15.222222
def tile_coord(self, xtile, ytile, zoom): """ This returns the NW-corner of the square. Use the function with xtile+1 and/or ytile+1 to get the other corners. With xtile+0.5 & ytile+0.5 it will return the center of the tile. http://wiki.openstreetmap.org/wiki/Slippy_map_tilenames...	[ "def", "tile_coord", "(", "self", ",", "xtile", ",", "ytile", ",", "zoom", ")", ":", "assert", "self", ".", "tile_srid", "==", "3857", ",", "'Custom tile projection not supported yet'", "n", "=", "2.0", "*", "zoom", "lon_deg", "=", "xtile", "/", "n", "",...	49.538462	17.846154
def ilike_helper(default): """Helper function that performs an `ilike` query if a string value is passed, otherwise the normal default operation.""" @functools.wraps(default) def wrapped(x, y): # String values should use ILIKE queries. if isinstance(y, six.string_types) and not isinstanc...	[ "def", "ilike_helper", "(", "default", ")", ":", "@", "functools", ".", "wraps", "(", "default", ")", "def", "wrapped", "(", "x", ",", "y", ")", ":", "# String values should use ILIKE queries.", "if", "isinstance", "(", "y", ",", "six", ".", "string_types", ...	39.727273	13.545455
def _strategy(codes, context): """ Convert SRE regex parse tree to strategy that generates strings matching that regex represented by that parse tree. `codes` is either a list of SRE regex elements representations or a particular element representation. Each element is a tuple of element code (as s...	[ "def", "_strategy", "(", "codes", ",", "context", ")", ":", "if", "not", "isinstance", "(", "codes", ",", "tuple", ")", ":", "# List of codes", "strategies", "=", "[", "]", "i", "=", "0", "while", "i", "<", "len", "(", "codes", ")", ":", "if", "cod...	36.225	20.2875
def fastaAlignmentRead(fasta, mapFn=(lambda x : x), l=None): """ reads in columns of multiple alignment and returns them iteratively """ if l is None: l = _getMultiFastaOffsets(fasta) else: l = l[:] seqNo = len(l) for i in xrange(0, seqNo): j = open(fasta, 'r') ...	[ "def", "fastaAlignmentRead", "(", "fasta", ",", "mapFn", "=", "(", "lambda", "x", ":", "x", ")", ",", "l", "=", "None", ")", ":", "if", "l", "is", "None", ":", "l", "=", "_getMultiFastaOffsets", "(", "fasta", ")", "else", ":", "l", "=", "l", "[",...	30.709677	14.322581
def _update_data_dict(self, data_dict, back_or_front): """ Adds spct if relevant, adds service """ data_dict['back_or_front'] = back_or_front # The percentage of used sessions based on 'scur' and 'slim' if 'slim' in data_dict and 'scur' in data_dict: try: ...	[ "def", "_update_data_dict", "(", "self", ",", "data_dict", ",", "back_or_front", ")", ":", "data_dict", "[", "'back_or_front'", "]", "=", "back_or_front", "# The percentage of used sessions based on 'scur' and 'slim'", "if", "'slim'", "in", "data_dict", "and", "'scur'", ...	41.727273	15

def run(self): """ Monitors if the config file or plugins are updated. Also outputs the JSON data generated by the plugins, without needing to poll the threads. """ self.run_plugins() while True: # Reload plugins and config if either the config file or plugin ...

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def side_effect(self, func, *args, **kwargs): ''' Wrap side effects for spies. ''' self._spy_side_effect = func self._spy_side_effect_args = args self._spy_side_effect_kwargs = kwargs return self

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def add_resource_context( app: web.Application, module=None, url_prefix: str=None, name_prefix: str=None, make_resource=lambda cls: cls() ): """Context manager which yields a function for adding multiple resources from a given module to an app using `ResourceRouter <aiohttp_utils.routing.ResourceRouter>...

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def report(mount): ''' Report on quotas for a specific volume CLI Example: .. code-block:: bash salt '*' quota.report /media/data ''' ret = {mount: {}} ret[mount]['User Quotas'] = _parse_quota(mount, '-u') ret[mount]['Group Quotas'] = _parse_quota(mount, '-g') return ret

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21.785714

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def conjugate(self): """The element-wise conjugate matrix This is defined only if all the entries in the matrix have a defined conjugate (i.e., they have a `conjugate` method). This is *not* the case for a matrix of operators. In such a case, only an :meth:`elementwise` :func:`a...

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41.444444

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def get_file_info(hash, context=None): """Returns information about the file, identified by ``hash``. If the `context` (an ident-hash) is supplied, the information returned will be specific to that context. """ if context is None: stmt = _get_sql('get-file-info.sql') args = dict(has...

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def _parse_scalars(scalars): """Parse the scalars from the YAML file content to a dictionary of ScalarType(s). :return: A dictionary { 'full.scalar.label': ScalarType } """ scalar_dict = {} # Scalars are defined in a fixed two-level hierarchy within the definition file. ...

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def split_by_files(self, valid_names:'ItemList')->'ItemLists': "Split the data by using the names in `valid_names` for validation." if isinstance(self.items[0], Path): return self.split_by_valid_func(lambda o: o.name in valid_names) else: return self.split_by_valid_func(lambda o: os.path.basenam...

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84.25

44.25

def match_file(apikey, path, metadata=None): """Uses the audioread library to decode an audio file and match it. """ import audioread with audioread.audio_open(path) as f: return match(apikey, iter(f), f.samplerate, int(f.duration), f.channels, metadata)

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41.857143

7.857143

def _instantiateFont(self, path): """ Return a instance of a font object with all the given subclasses """ return self._fontClass(path, libClass=self._libClass, kerningClass=self._kerningClass, groupsClass=self._groupsClass, infoCla...

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39.375

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def create_closure_model(cls): """Creates a <Model>Closure model in the same module as the model.""" meta_vals = { 'unique_together': (("parent", "child"),) } if getattr(cls._meta, 'db_table', None): meta_vals['db_table'] = '%sclosure' % getattr(cls._meta, 'db_table') model = type('...

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36.173913

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def make(self, analyte): """ Make filter for specified analyte(s). Filter specified in filt.switches. Parameters ---------- analyte : str or array_like Name or list of names of analytes. Returns ------- array_like boolean...

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24.7

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def remove_backslash_r(filename, encoding): """ A helpful utility to remove Carriage Return from any file. This will read a file into memory, and overwrite the contents of the original file. TODO: This function may be a liability :param filename: :return: ...

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30

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def encoded(string, encoding='utf-8'): """Cast string to binary_type. :param string: six.binary_type or six.text_type :param encoding: encoding which the object is forced to :return: six.binary_type """ assert isinstance(string, string_types) or isinstance(string, binary_type) if isinstance...

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38.611111

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def __setLock(self, command): """Set lock on requests.""" if command in (TURN_ON, TURN_OFF): self._operation = command elif command in INV_SOURCES: self._operation = SOURCE else: self._operation = ALL self._isLocked = True self._timer =...

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32.3

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def send_worker_queue_message(self, *, batch_id, job_name, entry_point, worker_args, retry_count=0): """Send a message to the `worker_queue` for a worker to execute the requests job Args: batch_id (`str`): Unique ID of the batch the job belongs to job_name (`str`): Non-unique ID...

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40.708333

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def by_median_household_income(self, lower=-1, upper=2 ** 31, zipcode_type=ZipcodeType.Standard, sort_by=SimpleZipcode.median_household_income.name, ...

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44.5

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def random(self, num_bytes): """ Get random bytes from YubiHSM. The random data is DRBG_CTR seeded on each startup by a hardware TRNG, so it should be of very good quality. @type num_bytes: integer @return: Bytes with random data @rtype: string @see: L...

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28.733333

19.4

def _extract(self, in_tile=None, in_data=None, out_tile=None): """Extract data from tile.""" return self.config.output.extract_subset( input_data_tiles=[(in_tile, in_data)], out_tile=out_tile )

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39.333333

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def do_list(self, arg): """l(ist) [first [,last] | .] List source code for the current file. Without arguments, list 11 lines around the current line or continue the previous listing. With . as argument, list 11 lines around the current line. With one argument, list 11 lines ...

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40.469388

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def create_random_seq(character, action_metadata, direction, length=8): """Creates a random sequence.""" start = tf.random.uniform([], maxval=action_metadata[1], dtype=tf.int32) return create_seq(character, action_metadata, direction, length, start)

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63

24.5

def command(cmd): """Execute command and raise an exception upon an error. >>> 'README' in command('ls') True >>> command('nonexistingcommand') #doctest: +ELLIPSIS Traceback (most recent call last): ... SdistCreationError """ status, out = commands.getstatusoutput(cmd)...

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26.470588

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def convert_shortcut_quick_reply(items): """ support shortcut [{'title':'title', 'payload':'payload'}] """ if items is not None and isinstance(items, list): result = [] for item in items: if isinstance(item, QuickReply): result....

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38.8125

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def load_lines(filename): """ Load a text file as an array of lines. Args: filename: Path to the input file. Returns: An array of strings, each representing an individual line. """ with open(filename, 'r', encoding='utf-8') as f: return [line.rstrip('\n') for line in f...

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24.692308

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def abspath(myPath): import sys, os """ Get absolute path to resource, works for dev and for PyInstaller """ try: # PyInstaller creates a temp folder and stores path in _MEIPASS base_path = sys._MEIPASS return os.path.join(base_path, os.path.basename(myPath)) except Exception: ...

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41.8

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def parse_with_retrieved(self, retrieved): """ Receives in input a dictionary of retrieved nodes. Does all the logic here. """ from aiida.common.exceptions import InvalidOperation import os output_path = None error_path = None try: out...

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31.130435

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def visit_FunctionDef(self, node): """Visit a function node.""" node = self.get_function_node(node) if node is not None: node._async = False

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34.4

6

def generate_certificates(base_dir, *peer_names, pubKeyDir=None, secKeyDir=None, sigKeyDir=None, verkeyDir=None, clean=True): ''' Generate client and server CURVE certificate files''' pubKeyDir = pubKeyDir or 'public_keys' secKeyDir = secKeyDir or 'private...

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39.976744

17

def role_get(name, user=None, host=None, port=None, maintenance_db=None, password=None, runas=None, return_password=False): ''' Return a dict with information about users of a Postgres server. Set return_password to True to get password hash in the result. CLI Example: .. code-block:...

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33.56

21.32

def is_storage(url, storage=None): """ Check if file is a local file or a storage file. File is considered local if: - URL is a local path. - URL starts by "file://" - a "storage" is provided. Args: url (str): file path or URL storage (str): Storage name. R...

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24.090909

16.272727

def define_from_values(cls, xdtu, ydtu, zdtu, xdtu_0, ydtu_0, zdtu_0): """Define class object from from provided values. Parameters ---------- xdtu : float XDTU fits keyword value. ydtu : float YDTU fits keyword value. zdtu : float ZDT...

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26.206897

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def replay_scope(self, sess): """Enters a replay scope that unsets it at the end.""" current_replay = self.replay(sess) try: self.set_replay(sess, True) yield finally: self.set_replay(sess, current_replay)

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29

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def _load_plugins(self): ''' Sets up all plugins, defaults and settings.py ''' plugins = self.settings['PLUGINS'] self.plugins_dict = {} for key in plugins: # skip loading the plugin if its value is None if plugins[key] is None: co...

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39.166667

17.9

def highres_imu_encode(self, time_usec, xacc, yacc, zacc, xgyro, ygyro, zgyro, xmag, ymag, zmag, abs_pressure, diff_pressure, pressure_alt, temperature, fields_updated): ''' The IMU readings in SI units in NED body frame time_usec : Timestamp (microsecond...

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80.954545

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def remove_from_group(self, group, user): """ Remove a user from a group :type user: str :param user: User's email :type group: str :param group: Group name :rtype: dict :return: an empty dictionary """ data = {'group': group, 'user': us...

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24.2

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def log_level(io_handler, level=None, name=None): """ Prints/Changes log level """ # Get the logger logger = logging.getLogger(name) # Normalize the name if not name: name = "Root" if not level: # Level not given: print the logger...

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32

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def only_for(theme, redirect_to='/', raise_error=None): """ Decorator for restrict access to views according by list of themes. Params: * ``theme`` - string or list of themes where decorated view must be * ``redirect_to`` - url or name of url pattern for redirect if CURRENT_THEME n...

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25.076923

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def create_sdb(self, name, category_id, owner, description="", user_group_permissions=None, iam_principal_permissions=None): """Create a safe deposit box. You need to refresh your token before the iam role is granted permission to the new safe deposit box. Keyword arguments: ...

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51.384615

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def execute(self): """ This function Executes the program with set arguments. """ prog_cmd = self.get_cmd().strip() if prog_cmd == '': self.status = 'Failure' debug.log("Error: No program to execute for %s!"%self.name) debug.log(("Could not combine path and arguments into cm...

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41.775

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def bind(self, args, kwargs): """ Bind arguments and keyword arguments to the encapsulated function. Returns a dictionary of parameters (named according to function parameters) with the values that were bound to each name. """ spec = self._spec resolution = self....

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def _pin_mongos(self, server): """Pin this session to the given mongos Server.""" self._transaction.sharded = True self._transaction.pinned_address = server.description.address

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49.25

9.75

def read_ipv6(self, length): """Read Internet Protocol version 6 (IPv6). Structure of IPv6 header [RFC 2460]: 0 1 2 3 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 +-+-+-+-+-+-+-+-+-+-+-+-+-+-...

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48.954545

26.651515

def left(self, num=None): """ NOT REQUIRED, BUT EXISTS AS OPPOSITE OF right() """ if num == None: return FlatList([_get_list(self)[0]]) if num <= 0: return Null return FlatList(_get_list(self)[:num])

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26.3

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def plot_fit(self,**kwargs): """ Plots the fit of the model Returns ---------- None (plots data and the fit) """ import matplotlib.pyplot as plt import seaborn as sns figsize = kwargs.get('figsize',(10,7)) if self.latent_variables.estimated is F...

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36.75

18.291667

def PopEvent(self): """Pops an event from the heap. Returns: tuple: containing: int: event timestamp or None if the heap is empty bytes: serialized event or None if the heap is empty """ try: timestamp, serialized_event = heapq.heappop(self._heap) self.data_size -= l...

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def move_to(self, folder): """Moves the email to the folder specified by the folder parameter. Args: folder: A string containing the folder ID the message should be moved to, or a Folder instance """ if isinstance(folder, Folder): self.move_to(folder.id) ...

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31.818182

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def removecolkeyword(self, columnname, keyword): """Remove a column keyword. It is similar to :func:`removekeyword`. """ if isinstance(keyword, str): self._removekeyword(columnname, keyword, -1) else: self._removekeyword(columnname, '', keyword)

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30.2

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def stats_evaluation(stats): """Generate an evaluation for the given pylint ``stats``.""" statement = stats.get('statement') error = stats.get('error', 0) warning = stats.get('warning', 0) refactor = stats.get('refactor', 0) convention = stats.get('convention', 0) if not statement or statem...

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33.785714

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def translate(self): """Compile the variable lookup.""" ident = self.ident expr = ex_rvalue(VARIABLE_PREFIX + ident) return [expr], set([ident]), set()

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35.8

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def parse_cov(cov_table, scaffold2genome): """ calculate genome coverage from scaffold coverage table """ size = {} # size[genome] = genome size mapped = {} # mapped[genome][sample] = mapped bases # parse coverage files for line in open(cov_table): line = line.strip().split('\t') ...

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40.473684

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def gsea_edb_parser(results_path, index=0): """Parse results.edb file stored under **edb** file folder. :param results_path: the .results file located inside edb folder. :param index: gene_set index of gmt database, used for iterating items. :return: enrichment_term, hit_index,nes, pval, fdr. """ ...

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40.133333

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def to_json(self): """Return a JSON-serializable representation.""" return { 'network': self.network, 'state': self.state, 'nodes': self.node_indices, 'cut': self.cut, }

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29.25

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def write_geno(data, sidx): """ write the geno output formerly used by admixture, still supported by adegenet, perhaps. Also, sNMF still likes .geno. """ ## grab snp and bis data from tmparr start = time.time() tmparrs = os.path.join(data.dirs.outfiles, "tmp-{}.h5".format(data.name)) ...

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39.849315

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def parse_backend(backend): """Converts the "backend" into the database connection parameters. It returns a (scheme, host, params) tuple.""" r = urlparse.urlsplit(backend) scheme, host = r.scheme, r.netloc path, query = r.path, r.query if path and not query: query, path = path, '' ...

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29.789474

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def threshold_monitor_hidden_threshold_monitor_Memory_high_limit(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") threshold_monitor_hidden = ET.SubElement(config, "threshold-monitor-hidden", xmlns="urn:brocade.com:mgmt:brocade-threshold-monitor") threshol...

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53.333333

25.25

def enterEvent(self, event): """ Reimplemented to cancel the hide timer. """ super(CallTipWidget, self).enterEvent(event) self._hide_timer.stop()

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34.6

6.6

def operations(self): """Instance depends on the API version: * 2018-03-31: :class:`Operations<azure.mgmt.containerservice.v2018_03_31.operations.Operations>` * 2018-08-01-preview: :class:`Operations<azure.mgmt.containerservice.v2018_08_01_preview.operations.Operations>` * 2019...

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64

35.529412

def query_total_cat_recent(cat_id_arr, label=None, num=8, kind='1'): ''' :param cat_id_arr: list of categories. ['0101', '0102'] :param label: the additional label ''' if label: return MPost.__query_with_label( cat_id_arr, label=label...

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35.307692

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def gene_ids(self): """ Return IDs of all genes which overlap this variant. Calling this method is significantly cheaper than calling `Variant.genes()`, which has to issue many more queries to construct each Gene object. """ return self.ensembl.gene_ids_at_locus( ...

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43.875

16.375

def lub(self, other): """ Return the least upper bound for given intervals. :param other: AbstractInterval instance """ return self.__class__( [ max(self.lower, other.lower), max(self.upper, other.upper), ], low...

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32.214286

18.214286

def _get_auto_rank(self, rank): """Tries to figure out what rank we should use for analyses""" if rank == "auto": # if we're an accessor for a ClassificationsDataFrame, use its _rank property if self.__class__.__name__ == "OneCodexAccessor": return self._rank ...

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33.357143

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def get_table_options(self, connection, table_name, schema, **kw): """ Return a dictionary of options specified when the table of the given name was created. Overrides interface :meth:`~sqlalchemy.engine.Inspector.get_table_options`. """ def keyfunc(column): ...

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43.121212

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def toner_status(self, filter_supported: bool = True) -> Dict[str, Any]: """Return the state of all toners cartridges.""" toner_status = {} for color in self.COLOR_NAMES: try: toner_stat = self.data.get( '{}_{}'.format(SyncThru.TONER, color),...

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43.5

13.714286

def generate_license(template, context): """ Generate a license by extracting variables from the template and replacing them with the corresponding values in the given context. """ out = StringIO() content = template.getvalue() for key in extract_vars(template): if key not in context...

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43.461538

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def create_component(self, name, description=None): """ Create a sub component in the business component. :param name: The new component's name. :param description: The new component's description. :returns: The created component. """ new_comp = Component(name,...

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32.142857

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def get_file_annotate(self, path): """ Returns a generator of four element tuples with lineno, sha, changeset lazy loader and line TODO: This function now uses os underlying 'git' command which is generally not good. Should be replaced with algorithm iterating commit...

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44.263158

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def inverse(self): """ Inverts image (all nonzeros become zeros and vice verse) Returns ------- :obj:`BinaryImage` inverse of this binary image """ data = np.zeros(self.shape).astype(np.uint8) ind = np.where(self.data == 0) data[ind[0], ind[1],...

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34.636364

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def update_frame(self, key, ranges=None): """ Update the internal state of the Plot to represent the given key tuple (where integers represent frames). Returns this state. """ ranges = self.compute_ranges(self.layout, key, ranges) for r, c in self.coords: ...

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38.5

11.5

def iter_options(grouped_choices, cutoff=None, cutoff_text=None): """ Helper function for options and option groups in templates. """ class StartOptionGroup(object): start_option_group = True end_option_group = False def __init__(self, label): self.label = label ...

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30.688889

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def xcorr(x1,x2,Nlags): """ r12, k = xcorr(x1,x2,Nlags), r12 and k are ndarray's Compute the energy normalized cross correlation between the sequences x1 and x2. If x1 = x2 the cross correlation is the autocorrelation. The number of lags sets how many lags to return centered about zero """ K...

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37.941176

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def parse_cache(self, full_df): """ Format the cached data model into a dictionary of DataFrames and a criteria map DataFrame. Parameters ---------- full_df : DataFrame result of self.get_dm_offline() Returns ---------- data_model : d...

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35.192308

17.192308

def list_dataset_uris(cls, base_uri, config_path): """Return list containing URIs with base URI.""" storage_account_name = generous_parse_uri(base_uri).netloc blobservice = get_blob_service(storage_account_name, config_path) containers = blobservice.list_containers(include_metadata=True...

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33.833333

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def github_belspec_files(spec_dir, force: bool = False): """Get belspec files from Github repo Args: spec_dir: directory to store the BEL Specification and derived files force: force update of BEL Specifications from Github - skipped if local files less than 1 day old """ if not force...

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36.956522

25.391304

def _parse_sod_segment(self, fptr): """Parse the SOD (start-of-data) segment. Parameters ---------- fptr : file Open file object. Returns ------- SODSegment The current SOD segment. """ offset = fptr.tell() - 2 len...

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20.823529

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def _verifyDiscoveredServices(self, claimed_id, services, to_match_endpoints): """See @L{_discoverAndVerify}""" # Search the services resulting from discovery to find one # that matches the information from the assertion failure_messages = [] fo...

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43.923077

17.538462

def send(self, packet, recalculate_checksum=True): """ Injects a packet into the network stack. Recalculates the checksum before sending unless recalculate_checksum=False is passed. The injected packet may be one received from recv(), or a modified version, or a completely new packet. ...

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39.057143

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def month_crumb(date): """ Crumb for a month. """ year = date.strftime('%Y') month = date.strftime('%m') month_text = DateFormat(date).format('F').capitalize() return Crumb(month_text, reverse('zinnia:entry_archive_month', args=[year, month]))

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33.333333

12.888889

def widths_in_range_mm( self, minwidth=EMIR_MINIMUM_SLITLET_WIDTH_MM, maxwidth=EMIR_MAXIMUM_SLITLET_WIDTH_MM ): """Return list of slitlets which width is within given range Parameters ---------- minwidth : float Minimum slit width (mm)...

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26.068966

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def get_canonical_transaction(self, transaction_hash: Hash32) -> BaseTransaction: """ Returns the requested transaction as specified by the transaction hash from the canonical chain. Raises TransactionNotFound if no transaction with the specified hash is found in the main chain....

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def _releaseId(self, msgId): """ Release message ID to the pool. @param msgId: message ID, no longer on the wire @type msgId: C{str} """ self._uuids.append(msgId) if len(self._uuids) > 2 * self.UUID_POOL_GEN_SIZE: self._uuids[-self.UUID_POOL_GEN_SIZE:...

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31.7

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def task_done(self): """Mark a task as done.""" with self._lock: unfinished = self._unfinished_tasks - 1 if unfinished < 0: raise RuntimeError('task_done() called too many times') elif unfinished == 0: self._alldone.notify() ...

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38.666667

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def tupleize( rows, alphabetize_columns=getattr( settings, 'ALPHABETIZE_COLUMNS', False)): """Also alphabetizes columns and returns a tuple of tuples""" # define a blank list as our return object l = [] for r in rows: row = [] row = list(r.val...

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22.227273

19.590909

def stats_tube(self, tube: str) -> Stats: """Returns tube statistics. :param tube: The tube to return statistics for. """ return self._stats_cmd(b'stats-tube %b' % tube.encode('ascii'))

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35.5

14.5

def docSetRootElement(self, doc): """Set the root element of the document (doc->children is a list containing possibly comments, PIs, etc ...). """ if doc is None: doc__o = None else: doc__o = doc._o ret = libxml2mod.xmlDocSetRootElement(doc__o, self._o) if ret is None...

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42.111111

8.444444

def is_draft_version(self): """ Return if this version is the draft version of a layer """ pub_ver = getattr(self, 'published_version', None) latest_ver = getattr(self, 'latest_version', None) this_ver = getattr(self, 'this_version', None) return this_ver and latest_ver and (this...

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60.333333

19.666667

def to_bool(x): """"Converts to a boolean in a semantically meaningful way.""" if isinstance(x, bool): return x elif isinstance(x, str): return False if x.lower() in _FALSES else True else: return bool(x)

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29.625

17.125

def execute_fragment_under_context(self, ctx, start_label, end_label): ''' just like run but returns if moved outside of the specified fragment # 4 different exectution results # 0=normal, 1=return, 2=jump_outside, 3=errors # execute_fragment_under_context returns: ...

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45.655172

14.689655

def delete_chat_photo(chat_id, **kwargs): """ Use this method to delete a chat photo. Photos can't be changed for private chats. The bot must be an administrator in the chat for this to work and must have the appropriate admin rights. :param chat_id: Unique identifier for the target chat or username of...

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47.642857

31.5

def create_key(file_): """ Create a key and save it into ``file_``. Note that ``file`` must be opened in binary mode. """ pkey = crypto.PKey() pkey.generate_key(crypto.TYPE_RSA, 2048) file_.write(crypto.dump_privatekey(crypto.FILETYPE_PEM, pkey)) file_.flush()

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25.818182

16.727273

def create_embedded_class(self, method): """ Build the estimator class. Returns ------- :return : string The built class as string. """ temp_class = self.temp('embedded.class') return temp_class.format(class_name=self.class_name, ...

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33.307692

15.307692

def get_doc_lengths(self): ''' Returns a list of document lengths in words Returns ------- np.array ''' idx_to_delete_list = self._build_term_index_list(True, self._get_non_unigrams()) unigram_X, _ = self._get_X_after_delete_terms(idx_to_delete_list) ...

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31.363636

25.363636

def rm_job(name): ''' Remove the specified job from the server. CLI Example: .. code-block:: bash salt chronos-minion-id chronos.rm_job my-job ''' response = salt.utils.http.query( "{0}/scheduler/job/{1}".format(_base_url(), name), method='DELETE', ) return Tru...

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20.466667

24.2

def _aggregations_config(self): """Load aggregation configurations.""" result = {} for ep in iter_entry_points( group=self.entry_point_group_aggs): for cfg in ep.load()(): if cfg['aggregation_name'] not in self.enabled_aggregations: ...

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46.111111

17.555556

def __chopStringDict(self, data): '''Returns a dictionary of the provided raw service/host check string.''' r = {} d = data.split('\t') for item in d: item_parts = item.split('::') if len(item_parts) == 2: (name, value) = item_parts e...

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33.064516

20.419355

def run(self): ''' Execute the runner sequence ''' # Print documentation only if self.opts.get('doc', False): self.print_docs() else: return self._run_runner()

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24.777778

15.222222

def tile_coord(self, xtile, ytile, zoom): """ This returns the NW-corner of the square. Use the function with xtile+1 and/or ytile+1 to get the other corners. With xtile+0.5 & ytile+0.5 it will return the center of the tile. http://wiki.openstreetmap.org/wiki/Slippy_map_tilenames...

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49.538462

17.846154

def ilike_helper(default): """Helper function that performs an `ilike` query if a string value is passed, otherwise the normal default operation.""" @functools.wraps(default) def wrapped(x, y): # String values should use ILIKE queries. if isinstance(y, six.string_types) and not isinstanc...

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39.727273

13.545455

def _strategy(codes, context): """ Convert SRE regex parse tree to strategy that generates strings matching that regex represented by that parse tree. `codes` is either a list of SRE regex elements representations or a particular element representation. Each element is a tuple of element code (as s...

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36.225

20.2875

def fastaAlignmentRead(fasta, mapFn=(lambda x : x), l=None): """ reads in columns of multiple alignment and returns them iteratively """ if l is None: l = _getMultiFastaOffsets(fasta) else: l = l[:] seqNo = len(l) for i in xrange(0, seqNo): j = open(fasta, 'r') ...

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30.709677

14.322581

def _update_data_dict(self, data_dict, back_or_front): """ Adds spct if relevant, adds service """ data_dict['back_or_front'] = back_or_front # The percentage of used sessions based on 'scur' and 'slim' if 'slim' in data_dict and 'scur' in data_dict: try: ...

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41.727273

15