kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def init_runner(**kwargs): ''' Initialize the Runner() instance This function will properly initialize both run() and run_async() functions in the same way and return a value instance of Runner. See parameters given to :py:func:`ansible_runner.interface.run` ''' dump_artifacts(kwargs) ...	[ "def", "init_runner", "(", "", "", "kwargs", ")", ":", "dump_artifacts", "(", "kwargs", ")", "debug", "=", "kwargs", ".", "pop", "(", "'debug'", ",", "None", ")", "logfile", "=", "kwargs", ".", "pop", "(", "'logfile'", ",", "None", ")", "if", "not"...	33.947368	23.157895
def add_view(self, row=None, col=None, row_span=1, col_span=1, **kwargs): """ Create a new ViewBox and add it as a child widget. Parameters ---------- row : int The row in which to add the widget (0 is the topmost row) col : int T...	[ "def", "add_view", "(", "self", ",", "row", "=", "None", ",", "col", "=", "None", ",", "row_span", "=", "1", ",", "col_span", "=", "1", ",", "", "", "kwargs", ")", ":", "from", ".", "viewbox", "import", "ViewBox", "view", "=", "ViewBox", "(", "...	37.571429	20.142857
def _add_to_cache(key, value): """ Internal method to add a new key-value to the local cache. :param str key: The new url to add to the cache :param str value: The HTTP response for this key. :returns: void """ if key in _CACHE: _CACHE[key].append(value) else: _CACHE[key]...	[ "def", "_add_to_cache", "(", "key", ",", "value", ")", ":", "if", "key", "in", "_CACHE", ":", "_CACHE", "[", "key", "]", ".", "append", "(", "value", ")", "else", ":", "_CACHE", "[", "key", "]", "=", "[", "_PATTERN", ",", "value", "]", "_CACHE_COUN...	30.083333	12.083333
def writeMultiByte(self, value, charset): """ Writes a multibyte string to the datastream using the specified character set. @type value: C{str} @param value: The string value to be written. @type charset: C{str} @param charset: The string denoting the character ...	[ "def", "writeMultiByte", "(", "self", ",", "value", ",", "charset", ")", ":", "if", "type", "(", "value", ")", "is", "unicode", ":", "value", "=", "value", ".", "encode", "(", "charset", ")", "self", ".", "stream", ".", "write", "(", "value", ")" ]	38.388889	15.944444
def make_query(catalog): """A function to prepare a query """ query = {} request = api.get_request() index = get_search_index_for(catalog) limit = request.form.get("limit") q = request.form.get("q") if len(q) > 0: query[index] = q + "*" else: return None portal_...	[ "def", "make_query", "(", "catalog", ")", ":", "query", "=", "{", "}", "request", "=", "api", ".", "get_request", "(", ")", "index", "=", "get_search_index_for", "(", "catalog", ")", "limit", "=", "request", ".", "form", ".", "get", "(", "\"limit\"", "...	24.083333	15.791667
def GetRootFileEntry(self): """Retrieves the root file entry. Returns: TARFileEntry: file entry. """ path_spec = tar_path_spec.TARPathSpec( location=self.LOCATION_ROOT, parent=self._path_spec.parent) return self.GetFileEntryByPathSpec(path_spec)	[ "def", "GetRootFileEntry", "(", "self", ")", ":", "path_spec", "=", "tar_path_spec", ".", "TARPathSpec", "(", "location", "=", "self", ".", "LOCATION_ROOT", ",", "parent", "=", "self", ".", "_path_spec", ".", "parent", ")", "return", "self", ".", "GetFileEnt...	30.222222	14.222222
def _extract_title(self): """ Extract the title and remove it from the document. If title has already been extracted, this method will do nothing. If removal cannot happen or fails, the document is left untouched. """ if self.title: return for pattern in s...	[ "def", "_extract_title", "(", "self", ")", ":", "if", "self", ".", "title", ":", "return", "for", "pattern", "in", "self", ".", "config", ".", "title", ":", "items", "=", "self", ".", "parsed_tree", ".", "xpath", "(", "pattern", ")", "if", "not", "it...	34.266667	23.616667
def get_bmus(self, activation_map): """Returns Best Matching Units indexes of the activation map. :param activation_map: Activation map computed with self.get_surface_state() :type activation_map: 2D numpy.array :returns: The bmus indexes corresponding to this activation map ...	[ "def", "get_bmus", "(", "self", ",", "activation_map", ")", ":", "Y", ",", "X", "=", "np", ".", "unravel_index", "(", "activation_map", ".", "argmin", "(", "axis", "=", "1", ")", ",", "(", "self", ".", "_n_rows", ",", "self", ".", "_n_columns", ")", ...	40.5	20.642857
def comment_count(self): """ Counts total number of comments on ModelBase object. Comments should always be recorded on ModelBase objects. """ # Get the comment model. comment_model = comments.get_model() modelbase_content_type = ContentType.objects.get(app_label...	[ "def", "comment_count", "(", "self", ")", ":", "# Get the comment model.", "comment_model", "=", "comments", ".", "get_model", "(", ")", "modelbase_content_type", "=", "ContentType", ".", "objects", ".", "get", "(", "app_label", "=", "\"panya\"", ",", "model", "...	42.758621	21.310345
def debug_async(self, conn_id, cmd_name, cmd_args, progress_callback, callback): """Asynchronously complete a named debug command. The command name and arguments are passed to the underlying device adapter and interpreted there. If the command is long running, progress_callback may be ...	[ "def", "debug_async", "(", "self", ",", "conn_id", ",", "cmd_name", ",", "cmd_args", ",", "progress_callback", ",", "callback", ")", ":", "known_commands", "=", "{", "'dump_ram'", ":", "JLinkControlThread", ".", "DUMP_ALL_RAM", ",", "'program_flash'", ":", "JLin...	51.7	32.2
def _replace_auth_key( user, key, enc='ssh-rsa', comment='', options=None, config='.ssh/authorized_keys'): ''' Replace an existing key ''' auth_line = _format_auth_line(key, enc, comment, options or []) lines = [] full = _get_config_file(user, co...	[ "def", "_replace_auth_key", "(", "user", ",", "key", ",", "enc", "=", "'ssh-rsa'", ",", "comment", "=", "''", ",", "options", "=", "None", ",", "config", "=", "'.ssh/authorized_keys'", ")", ":", "auth_line", "=", "_format_auth_line", "(", "key", ",", "enc"...	35.244444	20.577778
def poll(self): """Return the run IDs of the finished jobs Returns ------- list(str) The list of the run IDs of the finished jobs """ clusterids = clusterprocids2clusterids(self.clusterprocids_outstanding) clusterprocid_status_list = query_status_fo...	[ "def", "poll", "(", "self", ")", ":", "clusterids", "=", "clusterprocids2clusterids", "(", "self", ".", "clusterprocids_outstanding", ")", "clusterprocid_status_list", "=", "query_status_for", "(", "clusterids", ")", "# e.g., [['1730126.0', 2], ['1730127.0', 2], ['1730129.1',...	37.470588	25.794118
def tabbar_toggled(self, settings, key, user_data): """If the gconf var use_tabbar be changed, this method will be called and will show/hide the tabbar. """ if settings.get_boolean(key): for n in self.guake.notebook_manager.iter_notebooks(): n.set_property("sh...	[ "def", "tabbar_toggled", "(", "self", ",", "settings", ",", "key", ",", "user_data", ")", ":", "if", "settings", ".", "get_boolean", "(", "key", ")", ":", "for", "n", "in", "self", ".", "guake", ".", "notebook_manager", ".", "iter_notebooks", "(", ")", ...	45.8	11.7
def destroy(name): ''' removes a container [stops a container if it's running and] raises ContainerNotExists exception if the specified name is not created ''' if not exists(name): raise ContainerNotExists("The container (%s) does not exist!" % name) cmd = ['lxc-destroy', '-f', '-...	[ "def", "destroy", "(", "name", ")", ":", "if", "not", "exists", "(", "name", ")", ":", "raise", "ContainerNotExists", "(", "\"The container (%s) does not exist!\"", "%", "name", ")", "cmd", "=", "[", "'lxc-destroy'", ",", "'-f'", ",", "'-n'", ",", "name", ...	39.222222	23.666667
def _compile_arithmetic_expression(self, expr: Expression, scope: Dict[str, TensorFluent], batch_size: Optional[int] = None, noise: Optional[List[tf.Tensor]] = None...	[ "def", "_compile_arithmetic_expression", "(", "self", ",", "expr", ":", "Expression", ",", "scope", ":", "Dict", "[", "str", ",", "TensorFluent", "]", ",", "batch_size", ":", "Optional", "[", "int", "]", "=", "None", ",", "noise", ":", "Optional", "[", "...	37.265306	24.408163
def dt_to_struct_time(dt): """ Convert a `datetime.date` or `datetime.datetime` to a `struct_time` representation with zero values for data fields that we cannot always rely on for ancient or far-future dates: tm_wday, tm_yday, tm_isdst NOTE: If it wasn't for the requirement that the extra fields...	[ "def", "dt_to_struct_time", "(", "dt", ")", ":", "if", "isinstance", "(", "dt", ",", "datetime", ")", ":", "return", "struct_time", "(", "[", "dt", ".", "year", ",", "dt", ".", "month", ",", "dt", ".", "day", ",", "dt", ".", "hour", ",", "dt", "....	38.714286	21.666667
async def fetchrow(self, *args, timeout=None): """Execute the statement and return the first row. :param str query: Query text :param args: Query arguments :param float timeout: Optional timeout value in seconds. :return: The first row as a :class:`Record` instance. """...	[ "async", "def", "fetchrow", "(", "self", ",", "*", "args", ",", "timeout", "=", "None", ")", ":", "data", "=", "await", "self", ".", "__bind_execute", "(", "args", ",", "1", ",", "timeout", ")", "if", "not", "data", ":", "return", "None", "return", ...	33.461538	16.307692
def unique(self): """ Return the ``Categorical`` which ``categories`` and ``codes`` are unique. Unused categories are NOT returned. - unordered category: values and categories are sorted by appearance order. - ordered category: values are sorted by appearance order, ca...	[ "def", "unique", "(", "self", ")", ":", "# unlike np.unique, unique1d does not sort", "unique_codes", "=", "unique1d", "(", "self", ".", "codes", ")", "cat", "=", "self", ".", "copy", "(", ")", "# keep nan in codes", "cat", ".", "_codes", "=", "unique_codes", ...	28.036364	20.690909
def cos(duration: int, amp: complex, freq: float = None, phase: float = 0, name: str = None) -> SamplePulse: """Generates cosine wave `SamplePulse`. Applies `left` sampling strategy to generate discrete pulse from continuous function. Args: duration: Duration of pulse. Must be greater than...	[ "def", "cos", "(", "duration", ":", "int", ",", "amp", ":", "complex", ",", "freq", ":", "float", "=", "None", ",", "phase", ":", "float", "=", "0", ",", "name", ":", "str", "=", "None", ")", "->", "SamplePulse", ":", "if", "freq", "is", "None", ...	35.882353	23.764706
def _verify_same_spaces(self): """Verifies that all the envs have the same observation and action space.""" # Pre-conditions: self._envs is initialized. if self._envs is None: raise ValueError("Environments not initialized.") if not isinstance(self._envs, list): tf.logging.warning("Not ch...	[ "def", "_verify_same_spaces", "(", "self", ")", ":", "# Pre-conditions: self._envs is initialized.", "if", "self", ".", "_envs", "is", "None", ":", "raise", "ValueError", "(", "\"Environments not initialized.\"", ")", "if", "not", "isinstance", "(", "self", ".", "_e...	39.810811	21.648649
def sign_transaction(provider: Provider, unsigned: MutableTransaction, key: Kutil) -> Transaction: '''sign transaction with Kutil''' parent_outputs = [find_parent_outputs(provider, i) for i in unsigned.ins] return key.sign_transaction(parent_outputs, unsigned)	[ "def", "sign_transaction", "(", "provider", ":", "Provider", ",", "unsigned", ":", "MutableTransaction", ",", "key", ":", "Kutil", ")", "->", "Transaction", ":", "parent_outputs", "=", "[", "find_parent_outputs", "(", "provider", ",", "i", ")", "for", "i", "...	48.166667	22.5
def alleles_to_retrieve(df): """Alleles to retrieve from genome fasta Get a dict of the genome fasta contig title to a list of blastn results of the allele sequences that must be retrieved from the genome contig. Args: df (pandas.DataFrame): blastn results dataframe Returns: {str:...	[ "def", "alleles_to_retrieve", "(", "df", ")", ":", "contig_blastn_records", "=", "defaultdict", "(", "list", ")", "markers", "=", "df", ".", "marker", ".", "unique", "(", ")", "for", "m", "in", "markers", ":", "dfsub", "=", "df", "[", "df", ".", "marke...	37.090909	22.863636
def download_current_dataset(self, dest_path=".", dest_filename=None, unzip=True, tournament=1): """Download dataset for the current active round. Args: dest_path (str, optional): destination folder, defaults to `.` dest_filename (str, optional):...	[ "def", "download_current_dataset", "(", "self", ",", "dest_path", "=", "\".\"", ",", "dest_filename", "=", "None", ",", "unzip", "=", "True", ",", "tournament", "=", "1", ")", ":", "# set up download path", "if", "dest_filename", "is", "None", ":", "round_numb...	38.152174	20.369565
def conv_cy(self, cy_cl): """Convert cycles (cy/CL) to other units, such as FLOP/s or It/s.""" if not isinstance(cy_cl, PrefixedUnit): cy_cl = PrefixedUnit(cy_cl, '', 'cy/CL') clock = self.machine['clock'] element_size = self.kernel.datatypes_size[self.kernel.datatype] ...	[ "def", "conv_cy", "(", "self", ",", "cy_cl", ")", ":", "if", "not", "isinstance", "(", "cy_cl", ",", "PrefixedUnit", ")", ":", "cy_cl", "=", "PrefixedUnit", "(", "cy_cl", ",", "''", ",", "'cy/CL'", ")", "clock", "=", "self", ".", "machine", "[", "'cl...	41.947368	12.789474
def compute_disagg(sitecol, sources, cmaker, iml4, trti, bin_edges, oqparam, monitor): # see https://bugs.launchpad.net/oq-engine/+bug/1279247 for an explanation # of the algorithm used """ :param sitecol: a :class:`openquake.hazardlib.site.SiteCollection` instance :param ...	[ "def", "compute_disagg", "(", "sitecol", ",", "sources", ",", "cmaker", ",", "iml4", ",", "trti", ",", "bin_edges", ",", "oqparam", ",", "monitor", ")", ":", "# see https://bugs.launchpad.net/oq-engine/+bug/1279247 for an explanation", "# of the algorithm used", "result",...	38.756098	14.609756
def create_shortcuts(self): """Create shortcuts for ipyconsole.""" inspect = config_shortcut(self._control.inspect_current_object, context='Console', name='Inspect current object', parent=self) clear_console = config_shortcut(se...	[ "def", "create_shortcuts", "(", "self", ")", ":", "inspect", "=", "config_shortcut", "(", "self", ".", "_control", ".", "inspect_current_object", ",", "context", "=", "'Console'", ",", "name", "=", "'Inspect current object'", ",", "parent", "=", "self", ")", "...	63.785714	27.357143
def get_int_or_uuid(value): """Check if a value is valid as UUID or an integer. This method is mainly used to convert floating IP id to the appropriate type. For floating IP id, integer is used in Nova's original implementation, but UUID is used in Neutron based one. """ try: uuid.UUID(...	[ "def", "get_int_or_uuid", "(", "value", ")", ":", "try", ":", "uuid", ".", "UUID", "(", "value", ")", "return", "value", "except", "(", "ValueError", ",", "AttributeError", ")", ":", "return", "int", "(", "value", ")" ]	33.583333	17.75
def add_plugin_filepaths(self, filepaths, except_blacklisted=True): """ Adds `filepaths` to the `self.plugin_filepaths`. Recommend passing in absolute filepaths. Method will attempt to convert to absolute paths if they are not already. `filepaths` can be a single object or an it...	[ "def", "add_plugin_filepaths", "(", "self", ",", "filepaths", ",", "except_blacklisted", "=", "True", ")", ":", "filepaths", "=", "util", ".", "to_absolute_paths", "(", "filepaths", ")", "if", "except_blacklisted", ":", "filepaths", "=", "util", ".", "remove_fro...	41.117647	19.823529
def alter_zero_tip_allowed_states(tree, feature): """ Alters the bottom-up likelihood arrays for zero-distance tips to make sure they do not contradict with other zero-distance tip siblings. :param tree: ete3.Tree, the tree of interest :param feature: str, character for which the likelihood is alte...	[ "def", "alter_zero_tip_allowed_states", "(", "tree", ",", "feature", ")", ":", "zero_parent2tips", "=", "defaultdict", "(", "list", ")", "allowed_state_feature", "=", "get_personalized_feature_name", "(", "feature", ",", "ALLOWED_STATES", ")", "for", "tip", "in", "t...	41.2	21.1
def from_json(self, document): """Create a model database object from a given Json document. Parameters ---------- document : JSON Json representation of the object Returns ModelHandle """ # The timestamp is optional (e.g., in cases where mod...	[ "def", "from_json", "(", "self", ",", "document", ")", ":", "# The timestamp is optional (e.g., in cases where model definitions are", "# loaded from file).", "if", "'timestamp'", "in", "document", ":", "timestamp", "=", "datetime", ".", "datetime", ".", "strptime", "(", ...	31.464286	16.75
def parse_json_feed_file(filename: str) -> JSONFeed: """Parse a JSON feed from a local json file.""" with open(filename) as f: try: root = json.load(f) except json.decoder.JSONDecodeError: raise FeedJSONError('Not a valid JSON document') return parse_json_feed(root)	[ "def", "parse_json_feed_file", "(", "filename", ":", "str", ")", "->", "JSONFeed", ":", "with", "open", "(", "filename", ")", "as", "f", ":", "try", ":", "root", "=", "json", ".", "load", "(", "f", ")", "except", "json", ".", "decoder", ".", "JSONDec...	34.555556	14.666667
def with_dependencies(cls, model_expr, dependency_model, init_kwargs): """ Initiate a model whose components depend on another model. For example:: >>> x, y, z = variables('x, y, z') >>> dependency_model = Model({y: x2}) >>> model_dict = {z: y**2} >>>...	[ "def", "with_dependencies", "(", "cls", ",", "model_expr", ",", "dependency_model", ",", "", "", "init_kwargs", ")", ":", "model", "=", "cls", "(", "model_expr", ",", "", "", "init_kwargs", ")", "# Initiate model instance.", "if", "any", "(", "var", "in"...	54.795918	22.387755
def _clean_text(text): """ Clean up a multiple-line, potentially multiple-paragraph text string. This is used to extract the first paragraph of a string and eliminate line breaks and indentation. Lines will be joined together by a single space. :param text: The text string to clean up. It is...	[ "def", "_clean_text", "(", "text", ")", ":", "desc", "=", "[", "]", "for", "line", "in", "(", "text", "or", "''", ")", ".", "strip", "(", ")", ".", "split", "(", "'\\n'", ")", ":", "# Clean up the line...", "line", "=", "line", ".", "strip", "(", ...	26.88	21.84
def add_bonds(self, neighbors, center, color=None, opacity=None, radius=0.1): """ Adds bonds for a site. Args: neighbors: Neighbors of the site. center: The site in the center for all bonds. color: Color of the tubes representing the bonds ...	[ "def", "add_bonds", "(", "self", ",", "neighbors", ",", "center", ",", "color", "=", "None", ",", "opacity", "=", "None", ",", "radius", "=", "0.1", ")", ":", "points", "=", "vtk", ".", "vtkPoints", "(", ")", "points", ".", "InsertPoint", "(", "0", ...	33.928571	14.02381
def _get_file(src): """ Return content from local or remote file. """ try: if '://' in src or src[0:2] == '//': # Most likely this is remote file response = urllib2.urlopen(src) return response.read() else: with open(src, 'rb') as fh: return f...	[ "def", "_get_file", "(", "src", ")", ":", "try", ":", "if", "'://'", "in", "src", "or", "src", "[", "0", ":", "2", "]", "==", "'//'", ":", "# Most likely this is remote file", "response", "=", "urllib2", ".", "urlopen", "(", "src", ")", "return", "resp...	38	16.636364
def _get_pypirc_command(self): """ Get the distutils command for interacting with PyPI configurations. :return: the command. """ from distutils.core import Distribution from distutils.config import PyPIRCCommand d = Distribution() return PyPIRCCommand(d)	[ "def", "_get_pypirc_command", "(", "self", ")", ":", "from", "distutils", ".", "core", "import", "Distribution", "from", "distutils", ".", "config", "import", "PyPIRCCommand", "d", "=", "Distribution", "(", ")", "return", "PyPIRCCommand", "(", "d", ")" ]	34.444444	10.666667
def main(args, prog_name): """ main entry point for the script. :param args: the arguments for this script, as a list of string. Should already have had things like the script name stripped. That is, if there are no args provided, this should be an empty list. """ ...	[ "def", "main", "(", "args", ",", "prog_name", ")", ":", "# get options and arguments", "ui", "=", "getUI", "(", "args", ",", "prog_name", ")", "if", "ui", ".", "optionIsSet", "(", "\"test\"", ")", ":", "# just run unit tests", "unittest", ".", "main", "(", ...	31.510638	20.148936
def flush(self): """Flush file contents to 'disk'.""" self._check_open_file() if self.allow_update and not self.is_stream: contents = self._io.getvalue() if self._append: self._sync_io() old_contents = (self.file_object.byte_contents ...	[ "def", "flush", "(", "self", ")", ":", "self", ".", "_check_open_file", "(", ")", "if", "self", ".", "allow_update", "and", "not", "self", ".", "is_stream", ":", "contents", "=", "self", ".", "_io", ".", "getvalue", "(", ")", "if", "self", ".", "_app...	42.807692	14.269231
def show(self, delete_after=20, scale=10, border=None, color='#000', background='#fff'): # pragma: no cover """\ Displays this QR code. This method is mainly intended for debugging purposes. This method saves the output of the :py:meth:`png` method (by default wit...	[ "def", "show", "(", "self", ",", "delete_after", "=", "20", ",", "scale", "=", "10", ",", "border", "=", "None", ",", "color", "=", "'#000'", ",", "background", "=", "'#fff'", ")", ":", "# pragma: no cover", "import", "os", "import", "time", "import", ...	34.960784	20.784314
def _log(code, message, level, domain): """Call this to add an entry in the journal""" entry = LogEntry(level, domain, code, message) Logger.journal.append(entry) if Logger.silent: return if level >= Logger._verbosity: _print_entry(entry)	[ "def", "_log", "(", "code", ",", "message", ",", "level", ",", "domain", ")", ":", "entry", "=", "LogEntry", "(", "level", ",", "domain", ",", "code", ",", "message", ")", "Logger", ".", "journal", ".", "append", "(", "entry", ")", "if", "Logger", ...	29.5	14.7
def acquire_discharge(self, cav, payload): ''' Request a discharge macaroon from the caveat location as an HTTP URL. @param cav Third party {pymacaroons.Caveat} to be discharged. @param payload External caveat data {bytes}. @return The acquired macaroon {macaroonbakery.Macaroon} ...	[ "def", "acquire_discharge", "(", "self", ",", "cav", ",", "payload", ")", ":", "resp", "=", "self", ".", "_acquire_discharge_with_token", "(", "cav", ",", "payload", ",", "None", ")", "# TODO Fabrice what is the other http response possible ??", "if", "resp", ".", ...	46	18.411765
def forward(self, is_train=False, kwargs): """Calculate the outputs specified by the bound symbol. Parameters ---------- is_train: bool, optional Whether this forward is for evaluation purpose. If True, a backward call is expected to follow. kwargs ...	[ "def", "forward", "(", "self", ",", "is_train", "=", "False", ",", "", "", "kwargs", ")", ":", "if", "len", "(", "kwargs", ")", "!=", "0", ":", "arg_dict", "=", "self", ".", "arg_dict", "for", "name", ",", "array", "in", "kwargs", ".", "items", ...	40.95	19.6
def _build_response(data, renderer=None): """ Build a response using the renderer from the data :return: """ if isinstance(data, Response) or isinstance(data, BaseResponse): return data if not renderer: raise AttributeError(" Renderer is required") if isinstance(data, dict) o...	[ "def", "_build_response", "(", "data", ",", "renderer", "=", "None", ")", ":", "if", "isinstance", "(", "data", ",", "Response", ")", "or", "isinstance", "(", "data", ",", "BaseResponse", ")", ":", "return", "data", "if", "not", "renderer", ":", "raise",...	34.1	12.5
def defaultBuilder(value, nt): """Reasonably sensible default handling of put builder """ if callable(value): def logbuilder(V): try: value(V) except: _log.exception("Error in Builder") raise # will be logged again retu...	[ "def", "defaultBuilder", "(", "value", ",", "nt", ")", ":", "if", "callable", "(", "value", ")", ":", "def", "logbuilder", "(", "V", ")", ":", "try", ":", "value", "(", "V", ")", "except", ":", "_log", ".", "exception", "(", "\"Error in Builder\"", "...	29.68	14.44
def set_minimum_level(self, level=0, stdoutFlag=True, fileFlag=True): """ Set the minimum logging level. All levels below the minimum will be ignored at logging. :Parameters: #. level (None, number, str): The minimum level of logging. If None, minimum level checking is ...	[ "def", "set_minimum_level", "(", "self", ",", "level", "=", "0", ",", "stdoutFlag", "=", "True", ",", "fileFlag", "=", "True", ")", ":", "# check flags", "assert", "isinstance", "(", "stdoutFlag", ",", "bool", ")", ",", "\"stdoutFlag must be boolean\"", "asser...	51.459459	25.837838
def _handle_eio_message(self, sid, data): """Dispatch Engine.IO messages.""" if sid in self._binary_packet: pkt = self._binary_packet[sid] if pkt.add_attachment(data): del self._binary_packet[sid] if pkt.packet_type == packet.BINARY_EVENT: ...	[ "def", "_handle_eio_message", "(", "self", ",", "sid", ",", "data", ")", ":", "if", "sid", "in", "self", ".", "_binary_packet", ":", "pkt", "=", "self", ".", "_binary_packet", "[", "sid", "]", "if", "pkt", ".", "add_attachment", "(", "data", ")", ":", ...	49.703704	14.888889
def _customer_lifetime_value( transaction_prediction_model, frequency, recency, T, monetary_value, time=12, discount_rate=0.01, freq="D" ): """ Compute the average lifetime value for a group of one or more customers. This method computes the average lifetime value for a group of one or more customers. ...	[ "def", "_customer_lifetime_value", "(", "transaction_prediction_model", ",", "frequency", ",", "recency", ",", "T", ",", "monetary_value", ",", "time", "=", "12", ",", "discount_rate", "=", "0.01", ",", "freq", "=", "\"D\"", ")", ":", "df", "=", "pd", ".", ...	40.478261	28
def update_time_reset_passwd(user_name, the_time): ''' Update the time when user reset passwd. ''' entry = TabMember.update( time_reset_passwd=the_time, ).where(TabMember.user_name == user_name) try: entry.execute() return True ...	[ "def", "update_time_reset_passwd", "(", "user_name", ",", "the_time", ")", ":", "entry", "=", "TabMember", ".", "update", "(", "time_reset_passwd", "=", "the_time", ",", ")", ".", "where", "(", "TabMember", ".", "user_name", "==", "user_name", ")", "try", ":...	28.416667	15.916667
def events(self): '''check for events a list of events''' ret = [] while self.out_queue.qsize(): ret.append(self.out_queue.get()) return ret	[ "def", "events", "(", "self", ")", ":", "ret", "=", "[", "]", "while", "self", ".", "out_queue", ".", "qsize", "(", ")", ":", "ret", ".", "append", "(", "self", ".", "out_queue", ".", "get", "(", ")", ")", "return", "ret" ]	29.833333	13.833333
def total_proper_motion(pmra, pmdecl, decl): '''This calculates the total proper motion of an object. Parameters ---------- pmra : float or array-like The proper motion(s) in right ascension, measured in mas/yr. pmdecl : float or array-like The proper motion(s) in declination, me...	[ "def", "total_proper_motion", "(", "pmra", ",", "pmdecl", ",", "decl", ")", ":", "pm", "=", "np", ".", "sqrt", "(", "pmdecl", "", "pmdecl", "+", "pmra", "", "pmra", "", "np", ".", "cos", "(", "np", ".", "radians", "(", "decl", ")", ")", "", ...	24.333333	26.925926
def find_blocked_reactions(model, reaction_list=None, zero_cutoff=None, open_exchanges=False, processes=None): """ Find reactions that cannot carry any flux. The question whether or not a reaction is...	[ "def", "find_blocked_reactions", "(", "model", ",", "reaction_list", "=", "None", ",", "zero_cutoff", "=", "None", ",", "open_exchanges", "=", "False", ",", "processes", "=", "None", ")", ":", "zero_cutoff", "=", "normalize_cutoff", "(", "model", ",", "zero_cu...	38.380952	20.095238
def get(self, attr: FetchAttribute) -> MaybeBytes: """Return the bytes representation of the given message attribue. Args: attr: The fetch attribute. Raises: :class:`NotFetchable` """ attr_name = attr.value.decode('ascii') method = getattr(self,...	[ "def", "get", "(", "self", ",", "attr", ":", "FetchAttribute", ")", "->", "MaybeBytes", ":", "attr_name", "=", "attr", ".", "value", ".", "decode", "(", "'ascii'", ")", "method", "=", "getattr", "(", "self", ",", "'_get_'", "+", "attr_name", ".", "repl...	28.846154	18.384615
def read_many(self, start_sequence, min_count, max_count): """ Reads a batch of items from the Ringbuffer. If the number of available items after the first read item is smaller than the max_count, these items are returned. So it could be the number of items read is smaller than the max_c...	[ "def", "read_many", "(", "self", ",", "start_sequence", ",", "min_count", ",", "max_count", ")", ":", "check_not_negative", "(", "start_sequence", ",", "\"sequence can't be smaller than 0\"", ")", "check_true", "(", "max_count", ">=", "min_count", ",", "\"max count sh...	71.25	42.15
def _species_subdir( ensembl_release, species="homo_sapiens", filetype="gtf", server=ENSEMBL_FTP_SERVER): """ Assume ensembl_release has already been normalize by calling function but species might be either a common name or latin name. """ return SPECIES_SUBDIR_TEMPL...	[ "def", "_species_subdir", "(", "ensembl_release", ",", "species", "=", "\"homo_sapiens\"", ",", "filetype", "=", "\"gtf\"", ",", "server", "=", "ENSEMBL_FTP_SERVER", ")", ":", "return", "SPECIES_SUBDIR_TEMPLATE", "%", "{", "\"release\"", ":", "ensembl_release", ",",...	29.571429	13.285714
def elbv2_load_balancer_arn_suffix(self, lookup, default=None): """ Args: lookup: the friendly name of the v2 elb to look up default: value to return in case of no match Returns: The shorthand fragment of the ALB's ARN, of the form `app//` """ try: elb = self._elbv2_load_ba...	[ "def", "elbv2_load_balancer_arn_suffix", "(", "self", ",", "lookup", ",", "default", "=", "None", ")", ":", "try", ":", "elb", "=", "self", ".", "_elbv2_load_balancer", "(", "lookup", ")", "m", "=", "re", ".", "search", "(", "r'.+?(app\\/[^\\/]+\\/[^\\/]+)$'",...	33.142857	18.571429
def integers(num, minimum, maximum, base=10): # TODO: Ensure numbers within bounds """Random integers within specified interval. The integer generator generates truly random integers in the specified interval. Parameters ---------- num : int, bounds=[1, 1E4] Total number of integ...	[ "def", "integers", "(", "num", ",", "minimum", ",", "maximum", ",", "base", "=", "10", ")", ":", "# TODO: Ensure numbers within bounds", "function", "=", "'integers'", "num", ",", "minimum", ",", "maximum", "=", "list", "(", "map", "(", "int", ",", "[", ...	29.197183	20.267606
def GetFileSystemReferenceCount(self, path_spec): """Retrieves the reference count of a cached file system object. Args: path_spec (PathSpec): path specification. Returns: int: reference count or None if there is no file system object for the corresponding path specification cached. ...	[ "def", "GetFileSystemReferenceCount", "(", "self", ",", "path_spec", ")", ":", "identifier", "=", "self", ".", "_GetFileSystemCacheIdentifier", "(", "path_spec", ")", "cache_value", "=", "self", ".", "_file_system_cache", ".", "GetCacheValue", "(", "identifier", ")"...	32.8125	20.75
def add_wf(self,wf_obj): """ Adds a token to the text layer @type wf_obj: L{Cwf} @param wf_obj: the token object """ if self.text_layer is None: self.text_layer = Ctext(type=self.type) self.root.append(self.text_layer.get_node()) self.text_...	[ "def", "add_wf", "(", "self", ",", "wf_obj", ")", ":", "if", "self", ".", "text_layer", "is", "None", ":", "self", ".", "text_layer", "=", "Ctext", "(", "type", "=", "self", ".", "type", ")", "self", ".", "root", ".", "append", "(", "self", ".", ...	33.1	6.5
def hardware_info(self, mask=0xFFFFFFFF): """Returns a list of 32 integer values corresponding to the bitfields specifying the power consumption of the target. The values returned by this function only have significance if the J-Link is powering the target. The words, indexed, ...	[ "def", "hardware_info", "(", "self", ",", "mask", "=", "0xFFFFFFFF", ")", ":", "buf", "=", "(", "ctypes", ".", "c_uint32", "*", "32", ")", "(", ")", "res", "=", "self", ".", "_dll", ".", "JLINKARM_GetHWInfo", "(", "mask", ",", "ctypes", ".", "byref",...	39.142857	17.828571
def diff_iter(base, other, options=None, *kwargs): """Compare a Record with another object (usually a record of the same type), and yield differences as :py:class:`DiffInfo` instances. args: ``base=``\ Record* The 'base' object to compare against. The enumeration in :py:c...	[ "def", "diff_iter", "(", "base", ",", "other", ",", "options", "=", "None", ",", "", "", "kwargs", ")", ":", "if", "options", "is", "None", ":", "options", "=", "DiffOptions", "(", "", "", "kwargs", ")", "elif", "len", "(", "kwargs", ")", ":", ...	39.275862	21.896552
def upload_file(body): """accepts file uploads""" # <body> is a simple dictionary of {filename: b'content'} print('body: ', body) return {'filename': list(body.keys()).pop(), 'filesize': len(list(body.values()).pop())}	[ "def", "upload_file", "(", "body", ")", ":", "# <body> is a simple dictionary of {filename: b'content'}", "print", "(", "'body: '", ",", "body", ")", "return", "{", "'filename'", ":", "list", "(", "body", ".", "keys", "(", ")", ")", ".", "pop", "(", ")", ","...	46	21.2
def save_file_data(self, path): """ Implements the abstract method of the ExternalEditor class. """ try: # just create file with empty text first; this command also creates the whole path to the file filesystem.write_file(os.path.join(path, storage.SCRIPT_FILE), "", creat...	[ "def", "save_file_data", "(", "self", ",", "path", ")", ":", "try", ":", "# just create file with empty text first; this command also creates the whole path to the file", "filesystem", ".", "write_file", "(", "os", ".", "path", ".", "join", "(", "path", ",", "storage", ...	65.181818	33.909091
def paginate(self, url, key, params=None): """ Fetch a sequence of paginated resources from the API endpoint. The initial request to ``url`` and all subsequent requests must respond with a JSON object; the field specified by ``key`` must be a list, whose elements will be yielded...	[ "def", "paginate", "(", "self", ",", "url", ",", "key", ",", "params", "=", "None", ")", ":", "if", "params", "is", "None", ":", "params", "=", "{", "}", "if", "self", ".", "per_page", "is", "not", "None", "and", "\"per_page\"", "not", "in", "param...	46.425	19.975
def _add_observation(self, x_to_add, y_to_add): """Add observation to window, updating means/variance efficiently.""" self._add_observation_to_means(x_to_add, y_to_add) self._add_observation_to_variances(x_to_add, y_to_add) self.window_size += 1	[ "def", "_add_observation", "(", "self", ",", "x_to_add", ",", "y_to_add", ")", ":", "self", ".", "_add_observation_to_means", "(", "x_to_add", ",", "y_to_add", ")", "self", ".", "_add_observation_to_variances", "(", "x_to_add", ",", "y_to_add", ")", "self", ".",...	54.6	11.6
def get_first_unanswered_question(self, assessment_section_id): """Gets the first unanswered question in this assesment section. arg: assessment_section_id (osid.id.Id): ``Id`` of the ``AssessmentSection`` return: (osid.assessment.Question) - the first unanswered ...	[ "def", "get_first_unanswered_question", "(", "self", ",", "assessment_section_id", ")", ":", "questions", "=", "self", ".", "get_unanswered_questions", "(", "assessment_section_id", ")", "if", "not", "questions", ".", "available", "(", ")", ":", "raise", "errors", ...	49	21.45
def is_compatible_assembly_level(self, ncbi_assembly_level): """Check if a given ncbi assembly level string matches the configured assembly levels.""" configured_ncbi_strings = [self._LEVELS[level] for level in self.assembly_level] return ncbi_assembly_level in configured_ncbi_strings	[ "def", "is_compatible_assembly_level", "(", "self", ",", "ncbi_assembly_level", ")", ":", "configured_ncbi_strings", "=", "[", "self", ".", "_LEVELS", "[", "level", "]", "for", "level", "in", "self", ".", "assembly_level", "]", "return", "ncbi_assembly_level", "in...	76.5	22.25
def code_to_session(self, js_code): """ 登录凭证校验。通过 wx.login() 接口获得临时登录凭证 code 后传到开发者服务器调用此接口完成登录流程。更多使用方法详见小程序登录详情请参考 https://developers.weixin.qq.com/miniprogram/dev/api/code2Session.html :param js_code: :return: """ return self._get( 'sns/j...	[ "def", "code_to_session", "(", "self", ",", "js_code", ")", ":", "return", "self", ".", "_get", "(", "'sns/jscode2session'", ",", "params", "=", "{", "'appid'", ":", "self", ".", "appid", ",", "'secret'", ":", "self", ".", "secret", ",", "'js_code'", ":"...	29.222222	17.333333
def moral_graph(model, format='raw', prog='dot', path=None, name=None): """ moral_graph(model,format='raw', prog='dot', path=None) Draws the moral graph for this model and writes it to path with filename name. Returns the pydot 'dot' object for further user manipulation. GraphViz and PyDot must be...	[ "def", "moral_graph", "(", "model", ",", "format", "=", "'raw'", ",", "prog", "=", "'dot'", ",", "path", "=", "None", ",", "name", "=", "None", ")", ":", "if", "not", "pydot_imported", ":", "raise", "ImportError", "(", "'PyDot must be installed to use the mo...	32.647887	19.915493
def getNumberOfRequiredVerifications(self): """Returns the number of required verifications a test for this analysis requires before being transitioned to 'verified' state :returns: number of required verifications """ num = self.getField('NumberOfRequiredVerifications').get(self...	[ "def", "getNumberOfRequiredVerifications", "(", "self", ")", ":", "num", "=", "self", ".", "getField", "(", "'NumberOfRequiredVerifications'", ")", ".", "get", "(", "self", ")", "if", "num", "<", "1", ":", "return", "self", ".", "bika_setup", ".", "getNumber...	46.888889	16.222222
def submit_tasks(self, wait=False): """ Submits the task in self and wait. TODO: change name. """ for task in self: task.start() if wait: for task in self: task.wait()	[ "def", "submit_tasks", "(", "self", ",", "wait", "=", "False", ")", ":", "for", "task", "in", "self", ":", "task", ".", "start", "(", ")", "if", "wait", ":", "for", "task", "in", "self", ":", "task", ".", "wait", "(", ")" ]	23.1	11.7
def assert_transform_exists(cli, transform_path): """ Asserts that the transform exists. :param cli: :param transform_path: :return: """ result = commands.query_transform_exists(cli, transform_path) assert result is True return result	[ "def", "assert_transform_exists", "(", "cli", ",", "transform_path", ")", ":", "result", "=", "commands", ".", "query_transform_exists", "(", "cli", ",", "transform_path", ")", "assert", "result", "is", "True", "return", "result" ]	26.1	14.1
def update_snapshots(self, snapshots_data: List[Tuple[str, int]]): """Given a list of snapshot data, update them in the DB The snapshots_data should be a list of tuples of snapshots data and identifiers in that order. """ cursor = self.conn.cursor() cursor.executemany( ...	[ "def", "update_snapshots", "(", "self", ",", "snapshots_data", ":", "List", "[", "Tuple", "[", "str", ",", "int", "]", "]", ")", ":", "cursor", "=", "self", ".", "conn", ".", "cursor", "(", ")", "cursor", ".", "executemany", "(", "'UPDATE state_snapshot ...	36.666667	16.666667
def shrink_pool(arg, opts, shell_opts): """ Shrink a pool by removing the ranges in opts from it """ if not pool: print("No pool with name '%s' found." % arg, file=sys.stderr) sys.exit(1) if 'remove' in opts: res = Prefix.list({'prefix': opts['remove'], 'pool_id': pool.id}) ...	[ "def", "shrink_pool", "(", "arg", ",", "opts", ",", "shell_opts", ")", ":", "if", "not", "pool", ":", "print", "(", "\"No pool with name '%s' found.\"", "%", "arg", ",", "file", "=", "sys", ".", "stderr", ")", "sys", ".", "exit", "(", "1", ")", "if", ...	34.956522	19.782609
def create_entry(self, json): """Create :class:`.resources.Entry` from JSON. :param json: JSON dict. :return: Entry instance. """ sys = json['sys'] ct = sys['contentType']['sys']['id'] fields = json['fields'] raw_fields = copy.deepcopy(fields) # ...	[ "def", "create_entry", "(", "self", ",", "json", ")", ":", "sys", "=", "json", "[", "'sys'", "]", "ct", "=", "sys", "[", "'contentType'", "]", "[", "'sys'", "]", "[", "'id'", "]", "fields", "=", "json", "[", "'fields'", "]", "raw_fields", "=", "cop...	32.578947	15.026316
def file_hash(load, fnd): ''' Return an MD5 file hash ''' if 'env' in load: # "env" is not supported; Use "saltenv". load.pop('env') ret = {} if 'saltenv' not in load: return ret if 'path' not in fnd or 'bucket' not in fnd or not fnd['path']: return ret ...	[ "def", "file_hash", "(", "load", ",", "fnd", ")", ":", "if", "'env'", "in", "load", ":", "# \"env\" is not supported; Use \"saltenv\".", "load", ".", "pop", "(", "'env'", ")", "ret", "=", "{", "}", "if", "'saltenv'", "not", "in", "load", ":", "return", "...	22.307692	23
def sendcommand(self, name, kwargs): """ send a named parametrized command to the other side. """ self.log("sending command %s(%s)" % (name, kwargs)) self.channel.send((name, kwargs))	[ "def", "sendcommand", "(", "self", ",", "name", ",", "", "", "kwargs", ")", ":", "self", ".", "log", "(", "\"sending command %s(**%s)\"", "%", "(", "name", ",", "kwargs", ")", ")", "self", ".", "channel", ".", "send", "(", "(", "name", ",", "kwargs...	52	6
def u128(self, name, value=None, align=None): """Add an unsigned 16 byte integer field to template. This is an convenience method that simply calls `Uint` keyword with predefined length.""" self.uint(16, name, value, align)	[ "def", "u128", "(", "self", ",", "name", ",", "value", "=", "None", ",", "align", "=", "None", ")", ":", "self", ".", "uint", "(", "16", ",", "name", ",", "value", ",", "align", ")" ]	48.8	9.2
def encode_grib2_percentile(self): """ Encodes member percentile data to GRIB2 format. Returns: Series of GRIB2 messages """ lscale = 1e6 grib_id_start = [7, 0, 14, 14, 2] gdsinfo = np.array([0, np.product(self.data.shape[-2:]), 0, 0, 30], dtype=np.in...	[ "def", "encode_grib2_percentile", "(", "self", ")", ":", "lscale", "=", "1e6", "grib_id_start", "=", "[", "7", ",", "0", ",", "14", ",", "14", ",", "2", "]", "gdsinfo", "=", "np", ".", "array", "(", "[", "0", ",", "np", ".", "product", "(", "self...	60.396825	27.920635
def _run_program(self, bin, fastafile, params=None): """ Run XXmotif and predict motifs from a FASTA file. Parameters ---------- bin : str Command used to run the tool. fastafile : str Name of the FASTA input file. params : dict,...	[ "def", "_run_program", "(", "self", ",", "bin", ",", "fastafile", ",", "params", "=", "None", ")", ":", "params", "=", "self", ".", "_parse_params", "(", "params", ")", "outfile", "=", "os", ".", "path", ".", "join", "(", "self", ".", "tmpdir", ",", ...	27.833333	18.833333
def get(self, request, enterprise_uuid, program_uuid): """ Show Program Landing page for the Enterprise's Program. Render the Enterprise's Program Enrollment page for a specific program. The Enterprise and Program are both selected by their respective UUIDs. Unauthenticated lea...	[ "def", "get", "(", "self", ",", "request", ",", "enterprise_uuid", ",", "program_uuid", ")", ":", "verify_edx_resources", "(", ")", "enterprise_customer", "=", "get_enterprise_customer_or_404", "(", "enterprise_uuid", ")", "context_data", "=", "get_global_context", "(...	49.952381	29.380952
def avg(self, key=None): """ Get the average value of a given key. :param key: The key to get the average for :type key: mixed :rtype: float or int """ count = self.count() if count: return self.sum(key) / count	[ "def", "avg", "(", "self", ",", "key", "=", "None", ")", ":", "count", "=", "self", ".", "count", "(", ")", "if", "count", ":", "return", "self", ".", "sum", "(", "key", ")", "/", "count" ]	21.384615	16.461538
def cnst_A1(self, X, Xf=None): r"""Compute :math:`A_1 \mathbf{x}` component of ADMM problem constraint. In this case :math:`A_1 \mathbf{x} = (\Gamma_0^T \;\; \Gamma_1^T \;\; \ldots )^T \mathbf{x}`. """ if Xf is None: Xf = sl.rfftn(X, axes=self.cri.axisN) retu...	[ "def", "cnst_A1", "(", "self", ",", "X", ",", "Xf", "=", "None", ")", ":", "if", "Xf", "is", "None", ":", "Xf", "=", "sl", ".", "rfftn", "(", "X", ",", "axes", "=", "self", ".", "cri", ".", "axisN", ")", "return", "sl", ".", "irfftn", "(", ...	41	14.545455
def collection(self, *collection_path): """Get a reference to a collection. For a top-level collection: .. code-block:: python >>> client.collection('top') For a sub-collection: .. code-block:: python >>> client.collection('mydocs/doc/subcol') ...	[ "def", "collection", "(", "self", ",", "*", "collection_path", ")", ":", "if", "len", "(", "collection_path", ")", "==", "1", ":", "path", "=", "collection_path", "[", "0", "]", ".", "split", "(", "_helpers", ".", "DOCUMENT_PATH_DELIMITER", ")", "else", ...	29.085714	22.514286
def add_omim_info(genes, alias_genes, genemap_lines, mim2gene_lines): """Add omim information We collect information on what phenotypes that are associated with a gene, what inheritance models that are associated and the correct omim id. Args: genes(dict): Dictionary with all genes ...	[ "def", "add_omim_info", "(", "genes", ",", "alias_genes", ",", "genemap_lines", ",", "mim2gene_lines", ")", ":", "LOG", ".", "info", "(", "\"Add omim info\"", ")", "omim_genes", "=", "get_mim_genes", "(", "genemap_lines", ",", "mim2gene_lines", ")", "for", "hgnc...	38.464286	22.25
def _limit_is_valid_or_none(self, params): """ Validates that a given limit is not present or is well-formed. :param params: Query params. :return: Returns True if a limit is present or is well-formed. """ if not "limit" in params or not params["limit"]: retu...	[ "def", "_limit_is_valid_or_none", "(", "self", ",", "params", ")", ":", "if", "not", "\"limit\"", "in", "params", "or", "not", "params", "[", "\"limit\"", "]", ":", "return", "True", "if", "not", "isinstance", "(", "params", "[", "\"limit\"", "]", ",", "...	35.214286	16.214286
def add_resource(self, resource): """Add a resource to the list of interesting resources""" if resource.exists(): self.resources[resource] = self.timekeeper.get_indicator(resource) else: self.resources[resource] = None	[ "def", "add_resource", "(", "self", ",", "resource", ")", ":", "if", "resource", ".", "exists", "(", ")", ":", "self", ".", "resources", "[", "resource", "]", "=", "self", ".", "timekeeper", ".", "get_indicator", "(", "resource", ")", "else", ":", "sel...	43.5	14.333333
def get(self): """Return the file content as a string.""" r = self._session.get(self.content, headers={'Accept': '/'}) return r.content	[ "def", "get", "(", "self", ")", ":", "r", "=", "self", ".", "_session", ".", "get", "(", "self", ".", "content", ",", "headers", "=", "{", "'Accept'", ":", "'/'", "}", ")", "return", "r", ".", "content" ]	39.5	18
def resolve_zone_file_to_profile(zone_file, address_or_public_key): """ Resolves a zone file to a profile and checks to makes sure the tokens are signed with a key that corresponds to the address or public key provided. """ if is_profile_in_legacy_format(zone_file): return zone_file ...	[ "def", "resolve_zone_file_to_profile", "(", "zone_file", ",", "address_or_public_key", ")", ":", "if", "is_profile_in_legacy_format", "(", "zone_file", ")", ":", "return", "zone_file", "try", ":", "token_file_url", "=", "get_token_file_url_from_zone_file", "(", "zone_file...	35.266667	25.066667
def set_default_locators_and_formatters(self, axis): """ Set up the locators and formatters for the scale. Parameters ---------- axis: matplotlib.axis Axis for which to set locators and formatters. """ axis.set_major_locator(_LogicleLocator(self._tra...	[ "def", "set_default_locators_and_formatters", "(", "self", ",", "axis", ")", ":", "axis", ".", "set_major_locator", "(", "_LogicleLocator", "(", "self", ".", "_transform", ")", ")", "axis", ".", "set_minor_locator", "(", "_LogicleLocator", "(", "self", ".", "_tr...	37.4	20.333333
def cee_map_remap_fabric_priority_fabric_remapped_priority(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") cee_map = ET.SubElement(config, "cee-map", xmlns="urn:brocade.com:mgmt:brocade-cee-map") name_key = ET.SubElement(cee_map, "name") name_key...	[ "def", "cee_map_remap_fabric_priority_fabric_remapped_priority", "(", "self", ",", "", "", "kwargs", ")", ":", "config", "=", "ET", ".", "Element", "(", "\"config\"", ")", "cee_map", "=", "ET", ".", "SubElement", "(", "config", ",", "\"cee-map\"", ",", "xmln...	50.785714	21
async def websocket_disconnect(self, message): """ Handle the disconnect message. This is propagated to all upstream applications. """ # set this flag so as to ensure we don't send a downstream `websocket.close` message due to all # child applications closing. se...	[ "async", "def", "websocket_disconnect", "(", "self", ",", "message", ")", ":", "# set this flag so as to ensure we don't send a downstream `websocket.close` message due to all", "# child applications closing.", "self", ".", "closing", "=", "True", "# inform all children", "await", ...	37.5	13.833333
def dict(self): '''Returns a dictionary representing this query.''' d = dict() d['key'] = str(self.key) if self.limit is not None: d['limit'] = self.limit if self.offset > 0: d['offset'] = self.offset if self.offset_key: d['offset_key'] = str(self.offset_key) if len(self.f...	[ "def", "dict", "(", "self", ")", ":", "d", "=", "dict", "(", ")", "d", "[", "'key'", "]", "=", "str", "(", "self", ".", "key", ")", "if", "self", ".", "limit", "is", "not", "None", ":", "d", "[", "'limit'", "]", "=", "self", ".", "limit", "...	28.058824	18.411765
def check_credentials(self): """ Check that ``username`` and ``password`` have been set, and raise an exception if not. """ if self.username is None or self.password is None: raise DistlibException('username and password must be set') pm = HTTPPasswordMgr() ...	[ "def", "check_credentials", "(", "self", ")", ":", "if", "self", ".", "username", "is", "None", "or", "self", ".", "password", "is", "None", ":", "raise", "DistlibException", "(", "'username and password must be set'", ")", "pm", "=", "HTTPPasswordMgr", "(", "...	44.454545	16.454545
def highlightSubsequence(sequence, x1, x2, start=' [', stop = '] ') : """returns a sequence where the subsequence in [x1, x2[ is placed in bewteen 'start' and 'stop'""" seq = list(sequence) print x1, x2-1, len(seq) seq[x1] = start + seq[x1] seq[x2-1] = seq[x2-1] + stop return ''.join(seq)	[ "def", "highlightSubsequence", "(", "sequence", ",", "x1", ",", "x2", ",", "start", "=", "' ['", ",", "stop", "=", "'] '", ")", ":", "seq", "=", "list", "(", "sequence", ")", "print", "x1", ",", "x2", "-", "1", ",", "len", "(", "seq", ")", "seq",...	32.222222	16.444444
def retrieve_outputs(self): """ Declare the outputs of the algorithms as attributes: x_final, y_final, metrics. """ metrics = {} for obs in self._observers['cv_metrics']: metrics[obs.name] = obs.retrieve_metrics() self.metrics = metrics	[ "def", "retrieve_outputs", "(", "self", ")", ":", "metrics", "=", "{", "}", "for", "obs", "in", "self", ".", "_observers", "[", "'cv_metrics'", "]", ":", "metrics", "[", "obs", ".", "name", "]", "=", "obs", ".", "retrieve_metrics", "(", ")", "self", ...	32.111111	13.444444
def portfolio_performance( expected_returns, cov_matrix, weights, verbose=False, risk_free_rate=0.02 ): """ After optimising, calculate (and optionally print) the performance of the optimal portfolio. Currently calculates expected return, volatility, and the Sharpe ratio. :param expected_returns: e...	[ "def", "portfolio_performance", "(", "expected_returns", ",", "cov_matrix", ",", "weights", ",", "verbose", "=", "False", ",", "risk_free_rate", "=", "0.02", ")", ":", "if", "isinstance", "(", "weights", ",", "dict", ")", ":", "if", "isinstance", "(", "expec...	44.3	18.3
def crossover(self, chromosome, point1, point2=None): """ Exchange DNA with another chromosome of equal length at one or two common points. For example, consider chromosomes: 1. 11110000 2. 00001111 If the crossover point is 4, the exchange results...	[ "def", "crossover", "(", "self", ",", "chromosome", ",", "point1", ",", "point2", "=", "None", ")", ":", "assert", "self", ".", "length", "==", "chromosome", ".", "length", "if", "point2", "is", "None", ":", "new_dna", "=", "self", ".", "dna", "[", "...	37.75	25.083333
def _key(self, username, frozen=False): """Translate a username into a key for Redis.""" if frozen: return self.frozen + username return self.prefix + username	[ "def", "_key", "(", "self", ",", "username", ",", "frozen", "=", "False", ")", ":", "if", "frozen", ":", "return", "self", ".", "frozen", "+", "username", "return", "self", ".", "prefix", "+", "username" ]	38.2	5.4
def _collapse_transcripts(in_file, window, data, out_dir, include_gene_names=True): """Collapse transcripts into min/max coordinates and optionally add windows. """ if out_dir is None: out_dir = os.path.dirname(in_file) out_file = os.path.join(out_dir, "%s-transcripts...	[ "def", "_collapse_transcripts", "(", "in_file", ",", "window", ",", "data", ",", "out_dir", ",", "include_gene_names", "=", "True", ")", ":", "if", "out_dir", "is", "None", ":", "out_dir", "=", "os", ".", "path", ".", "dirname", "(", "in_file", ")", "out...	57.194444	22.444444
def nic_list(self, bridge): """ List nics attached to bridge :param bridge: bridge name """ args = { 'name': bridge, } self._bridge_chk.check(args) return self._client.json('bridge.nic-list', args)	[ "def", "nic_list", "(", "self", ",", "bridge", ")", ":", "args", "=", "{", "'name'", ":", "bridge", ",", "}", "self", ".", "_bridge_chk", ".", "check", "(", "args", ")", "return", "self", ".", "_client", ".", "json", "(", "'bridge.nic-list'", ",", "a...	18.857143	19.428571

def init_runner(**kwargs): ''' Initialize the Runner() instance This function will properly initialize both run() and run_async() functions in the same way and return a value instance of Runner. See parameters given to :py:func:`ansible_runner.interface.run` ''' dump_artifacts(kwargs) ...

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def add_view(self, row=None, col=None, row_span=1, col_span=1, **kwargs): """ Create a new ViewBox and add it as a child widget. Parameters ---------- row : int The row in which to add the widget (0 is the topmost row) col : int T...

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def _add_to_cache(key, value): """ Internal method to add a new key-value to the local cache. :param str key: The new url to add to the cache :param str value: The HTTP response for this key. :returns: void """ if key in _CACHE: _CACHE[key].append(value) else: _CACHE[key]...

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def writeMultiByte(self, value, charset): """ Writes a multibyte string to the datastream using the specified character set. @type value: C{str} @param value: The string value to be written. @type charset: C{str} @param charset: The string denoting the character ...

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38.388889

15.944444

def make_query(catalog): """A function to prepare a query """ query = {} request = api.get_request() index = get_search_index_for(catalog) limit = request.form.get("limit") q = request.form.get("q") if len(q) > 0: query[index] = q + "*" else: return None portal_...

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def GetRootFileEntry(self): """Retrieves the root file entry. Returns: TARFileEntry: file entry. """ path_spec = tar_path_spec.TARPathSpec( location=self.LOCATION_ROOT, parent=self._path_spec.parent) return self.GetFileEntryByPathSpec(path_spec)

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def _extract_title(self): """ Extract the title and remove it from the document. If title has already been extracted, this method will do nothing. If removal cannot happen or fails, the document is left untouched. """ if self.title: return for pattern in s...

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def get_bmus(self, activation_map): """Returns Best Matching Units indexes of the activation map. :param activation_map: Activation map computed with self.get_surface_state() :type activation_map: 2D numpy.array :returns: The bmus indexes corresponding to this activation map ...

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def comment_count(self): """ Counts total number of comments on ModelBase object. Comments should always be recorded on ModelBase objects. """ # Get the comment model. comment_model = comments.get_model() modelbase_content_type = ContentType.objects.get(app_label...

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def debug_async(self, conn_id, cmd_name, cmd_args, progress_callback, callback): """Asynchronously complete a named debug command. The command name and arguments are passed to the underlying device adapter and interpreted there. If the command is long running, progress_callback may be ...

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def _replace_auth_key( user, key, enc='ssh-rsa', comment='', options=None, config='.ssh/authorized_keys'): ''' Replace an existing key ''' auth_line = _format_auth_line(key, enc, comment, options or []) lines = [] full = _get_config_file(user, co...

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def poll(self): """Return the run IDs of the finished jobs Returns ------- list(str) The list of the run IDs of the finished jobs """ clusterids = clusterprocids2clusterids(self.clusterprocids_outstanding) clusterprocid_status_list = query_status_fo...

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def tabbar_toggled(self, settings, key, user_data): """If the gconf var use_tabbar be changed, this method will be called and will show/hide the tabbar. """ if settings.get_boolean(key): for n in self.guake.notebook_manager.iter_notebooks(): n.set_property("sh...

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45.8

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def destroy(name): ''' removes a container [stops a container if it's running and] raises ContainerNotExists exception if the specified name is not created ''' if not exists(name): raise ContainerNotExists("The container (%s) does not exist!" % name) cmd = ['lxc-destroy', '-f', '-...

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def _compile_arithmetic_expression(self, expr: Expression, scope: Dict[str, TensorFluent], batch_size: Optional[int] = None, noise: Optional[List[tf.Tensor]] = None...

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def dt_to_struct_time(dt): """ Convert a `datetime.date` or `datetime.datetime` to a `struct_time` representation *with zero values* for data fields that we cannot always rely on for ancient or far-future dates: tm_wday, tm_yday, tm_isdst NOTE: If it wasn't for the requirement that the extra fields...

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async def fetchrow(self, *args, timeout=None): """Execute the statement and return the first row. :param str query: Query text :param args: Query arguments :param float timeout: Optional timeout value in seconds. :return: The first row as a :class:`Record` instance. """...

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33.461538

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def unique(self): """ Return the ``Categorical`` which ``categories`` and ``codes`` are unique. Unused categories are NOT returned. - unordered category: values and categories are sorted by appearance order. - ordered category: values are sorted by appearance order, ca...

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def cos(duration: int, amp: complex, freq: float = None, phase: float = 0, name: str = None) -> SamplePulse: """Generates cosine wave `SamplePulse`. Applies `left` sampling strategy to generate discrete pulse from continuous function. Args: duration: Duration of pulse. Must be greater than...

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35.882353

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def _verify_same_spaces(self): """Verifies that all the envs have the same observation and action space.""" # Pre-conditions: self._envs is initialized. if self._envs is None: raise ValueError("Environments not initialized.") if not isinstance(self._envs, list): tf.logging.warning("Not ch...

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def sign_transaction(provider: Provider, unsigned: MutableTransaction, key: Kutil) -> Transaction: '''sign transaction with Kutil''' parent_outputs = [find_parent_outputs(provider, i) for i in unsigned.ins] return key.sign_transaction(parent_outputs, unsigned)

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48.166667

22.5

def alleles_to_retrieve(df): """Alleles to retrieve from genome fasta Get a dict of the genome fasta contig title to a list of blastn results of the allele sequences that must be retrieved from the genome contig. Args: df (pandas.DataFrame): blastn results dataframe Returns: {str:...

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37.090909

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def download_current_dataset(self, dest_path=".", dest_filename=None, unzip=True, tournament=1): """Download dataset for the current active round. Args: dest_path (str, optional): destination folder, defaults to `.` dest_filename (str, optional):...

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38.152174

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def conv_cy(self, cy_cl): """Convert cycles (cy/CL) to other units, such as FLOP/s or It/s.""" if not isinstance(cy_cl, PrefixedUnit): cy_cl = PrefixedUnit(cy_cl, '', 'cy/CL') clock = self.machine['clock'] element_size = self.kernel.datatypes_size[self.kernel.datatype] ...

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41.947368

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def compute_disagg(sitecol, sources, cmaker, iml4, trti, bin_edges, oqparam, monitor): # see https://bugs.launchpad.net/oq-engine/+bug/1279247 for an explanation # of the algorithm used """ :param sitecol: a :class:`openquake.hazardlib.site.SiteCollection` instance :param ...

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38.756098

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def create_shortcuts(self): """Create shortcuts for ipyconsole.""" inspect = config_shortcut(self._control.inspect_current_object, context='Console', name='Inspect current object', parent=self) clear_console = config_shortcut(se...

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63.785714

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def get_int_or_uuid(value): """Check if a value is valid as UUID or an integer. This method is mainly used to convert floating IP id to the appropriate type. For floating IP id, integer is used in Nova's original implementation, but UUID is used in Neutron based one. """ try: uuid.UUID(...

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33.583333

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def add_plugin_filepaths(self, filepaths, except_blacklisted=True): """ Adds `filepaths` to the `self.plugin_filepaths`. Recommend passing in absolute filepaths. Method will attempt to convert to absolute paths if they are not already. `filepaths` can be a single object or an it...

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41.117647

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def alter_zero_tip_allowed_states(tree, feature): """ Alters the bottom-up likelihood arrays for zero-distance tips to make sure they do not contradict with other zero-distance tip siblings. :param tree: ete3.Tree, the tree of interest :param feature: str, character for which the likelihood is alte...

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def from_json(self, document): """Create a model database object from a given Json document. Parameters ---------- document : JSON Json representation of the object Returns ModelHandle """ # The timestamp is optional (e.g., in cases where mod...

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31.464286

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def parse_json_feed_file(filename: str) -> JSONFeed: """Parse a JSON feed from a local json file.""" with open(filename) as f: try: root = json.load(f) except json.decoder.JSONDecodeError: raise FeedJSONError('Not a valid JSON document') return parse_json_feed(root)

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def with_dependencies(cls, model_expr, dependency_model, **init_kwargs): """ Initiate a model whose components depend on another model. For example:: >>> x, y, z = variables('x, y, z') >>> dependency_model = Model({y: x**2}) >>> model_dict = {z: y**2} >>>...

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54.795918

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def _clean_text(text): """ Clean up a multiple-line, potentially multiple-paragraph text string. This is used to extract the first paragraph of a string and eliminate line breaks and indentation. Lines will be joined together by a single space. :param text: The text string to clean up. It is...

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26.88

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def add_bonds(self, neighbors, center, color=None, opacity=None, radius=0.1): """ Adds bonds for a site. Args: neighbors: Neighbors of the site. center: The site in the center for all bonds. color: Color of the tubes representing the bonds ...

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33.928571

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def _get_file(src): """ Return content from local or remote file. """ try: if '://' in src or src[0:2] == '//': # Most likely this is remote file response = urllib2.urlopen(src) return response.read() else: with open(src, 'rb') as fh: return f...

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38

16.636364

def _get_pypirc_command(self): """ Get the distutils command for interacting with PyPI configurations. :return: the command. """ from distutils.core import Distribution from distutils.config import PyPIRCCommand d = Distribution() return PyPIRCCommand(d)

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34.444444

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def main(args, prog_name): """ main entry point for the script. :param args: the arguments for this script, as a list of string. Should already have had things like the script name stripped. That is, if there are no args provided, this should be an empty list. """ ...

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31.510638

20.148936

def flush(self): """Flush file contents to 'disk'.""" self._check_open_file() if self.allow_update and not self.is_stream: contents = self._io.getvalue() if self._append: self._sync_io() old_contents = (self.file_object.byte_contents ...

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42.807692

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def show(self, delete_after=20, scale=10, border=None, color='#000', background='#fff'): # pragma: no cover """\ Displays this QR code. This method is mainly intended for debugging purposes. This method saves the output of the :py:meth:`png` method (by default wit...

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34.960784

20.784314

def _log(code, message, level, domain): """Call this to add an entry in the journal""" entry = LogEntry(level, domain, code, message) Logger.journal.append(entry) if Logger.silent: return if level >= Logger._verbosity: _print_entry(entry)

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def acquire_discharge(self, cav, payload): ''' Request a discharge macaroon from the caveat location as an HTTP URL. @param cav Third party {pymacaroons.Caveat} to be discharged. @param payload External caveat data {bytes}. @return The acquired macaroon {macaroonbakery.Macaroon} ...

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46

18.411765

def forward(self, is_train=False, **kwargs): """Calculate the outputs specified by the bound symbol. Parameters ---------- is_train: bool, optional Whether this forward is for evaluation purpose. If True, a backward call is expected to follow. **kwargs ...

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40.95

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def _build_response(data, renderer=None): """ Build a response using the renderer from the data :return: """ if isinstance(data, Response) or isinstance(data, BaseResponse): return data if not renderer: raise AttributeError(" Renderer is required") if isinstance(data, dict) o...

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34.1

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def defaultBuilder(value, nt): """Reasonably sensible default handling of put builder """ if callable(value): def logbuilder(V): try: value(V) except: _log.exception("Error in Builder") raise # will be logged again retu...

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29.68

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def set_minimum_level(self, level=0, stdoutFlag=True, fileFlag=True): """ Set the minimum logging level. All levels below the minimum will be ignored at logging. :Parameters: #. level (None, number, str): The minimum level of logging. If None, minimum level checking is ...

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51.459459

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def _handle_eio_message(self, sid, data): """Dispatch Engine.IO messages.""" if sid in self._binary_packet: pkt = self._binary_packet[sid] if pkt.add_attachment(data): del self._binary_packet[sid] if pkt.packet_type == packet.BINARY_EVENT: ...

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49.703704

14.888889

def _customer_lifetime_value( transaction_prediction_model, frequency, recency, T, monetary_value, time=12, discount_rate=0.01, freq="D" ): """ Compute the average lifetime value for a group of one or more customers. This method computes the average lifetime value for a group of one or more customers. ...

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40.478261

28

def update_time_reset_passwd(user_name, the_time): ''' Update the time when user reset passwd. ''' entry = TabMember.update( time_reset_passwd=the_time, ).where(TabMember.user_name == user_name) try: entry.execute() return True ...

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28.416667

15.916667

def events(self): '''check for events a list of events''' ret = [] while self.out_queue.qsize(): ret.append(self.out_queue.get()) return ret

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29.833333

13.833333

def total_proper_motion(pmra, pmdecl, decl): '''This calculates the total proper motion of an object. Parameters ---------- pmra : float or array-like The proper motion(s) in right ascension, measured in mas/yr. pmdecl : float or array-like The proper motion(s) in declination, me...

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24.333333

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def find_blocked_reactions(model, reaction_list=None, zero_cutoff=None, open_exchanges=False, processes=None): """ Find reactions that cannot carry any flux. The question whether or not a reaction is...

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38.380952

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def get(self, attr: FetchAttribute) -> MaybeBytes: """Return the bytes representation of the given message attribue. Args: attr: The fetch attribute. Raises: :class:`NotFetchable` """ attr_name = attr.value.decode('ascii') method = getattr(self,...

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28.846154

18.384615

def read_many(self, start_sequence, min_count, max_count): """ Reads a batch of items from the Ringbuffer. If the number of available items after the first read item is smaller than the max_count, these items are returned. So it could be the number of items read is smaller than the max_c...

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71.25

42.15

def _species_subdir( ensembl_release, species="homo_sapiens", filetype="gtf", server=ENSEMBL_FTP_SERVER): """ Assume ensembl_release has already been normalize by calling function but species might be either a common name or latin name. """ return SPECIES_SUBDIR_TEMPL...

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29.571429

13.285714

def elbv2_load_balancer_arn_suffix(self, lookup, default=None): """ Args: lookup: the friendly name of the v2 elb to look up default: value to return in case of no match Returns: The shorthand fragment of the ALB's ARN, of the form `app/*/*` """ try: elb = self._elbv2_load_ba...

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33.142857

18.571429

def integers(num, minimum, maximum, base=10): # TODO: Ensure numbers within bounds """Random integers within specified interval. The integer generator generates truly random integers in the specified interval. Parameters ---------- num : int, bounds=[1, 1E4] Total number of integ...

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29.197183

20.267606

def GetFileSystemReferenceCount(self, path_spec): """Retrieves the reference count of a cached file system object. Args: path_spec (PathSpec): path specification. Returns: int: reference count or None if there is no file system object for the corresponding path specification cached. ...

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32.8125

20.75

def add_wf(self,wf_obj): """ Adds a token to the text layer @type wf_obj: L{Cwf} @param wf_obj: the token object """ if self.text_layer is None: self.text_layer = Ctext(type=self.type) self.root.append(self.text_layer.get_node()) self.text_...

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33.1

6.5

def hardware_info(self, mask=0xFFFFFFFF): """Returns a list of 32 integer values corresponding to the bitfields specifying the power consumption of the target. The values returned by this function only have significance if the J-Link is powering the target. The words, indexed, ...

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39.142857

17.828571

def diff_iter(base, other, options=None, **kwargs): """Compare a Record with another object (usually a record of the same type), and yield differences as :py:class:`DiffInfo` instances. args: ``base=``\ *Record* The 'base' object to compare against. The enumeration in :py:c...

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39.275862

21.896552

def upload_file(body): """accepts file uploads""" # <body> is a simple dictionary of {filename: b'content'} print('body: ', body) return {'filename': list(body.keys()).pop(), 'filesize': len(list(body.values()).pop())}

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46

21.2

def save_file_data(self, path): """ Implements the abstract method of the ExternalEditor class. """ try: # just create file with empty text first; this command also creates the whole path to the file filesystem.write_file(os.path.join(path, storage.SCRIPT_FILE), "", creat...

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65.181818

33.909091

def paginate(self, url, key, params=None): """ Fetch a sequence of paginated resources from the API endpoint. The initial request to ``url`` and all subsequent requests must respond with a JSON object; the field specified by ``key`` must be a list, whose elements will be yielded...

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46.425

19.975

def _add_observation(self, x_to_add, y_to_add): """Add observation to window, updating means/variance efficiently.""" self._add_observation_to_means(x_to_add, y_to_add) self._add_observation_to_variances(x_to_add, y_to_add) self.window_size += 1

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54.6

11.6

def get_first_unanswered_question(self, assessment_section_id): """Gets the first unanswered question in this assesment section. arg: assessment_section_id (osid.id.Id): ``Id`` of the ``AssessmentSection`` return: (osid.assessment.Question) - the first unanswered ...

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49

21.45

def is_compatible_assembly_level(self, ncbi_assembly_level): """Check if a given ncbi assembly level string matches the configured assembly levels.""" configured_ncbi_strings = [self._LEVELS[level] for level in self.assembly_level] return ncbi_assembly_level in configured_ncbi_strings

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76.5

22.25

def code_to_session(self, js_code): """ 登录凭证校验。通过 wx.login() 接口获得临时登录凭证 code 后传到开发者服务器调用此接口完成登录流程。更多使用方法详见小程序登录详情请参考 https://developers.weixin.qq.com/miniprogram/dev/api/code2Session.html :param js_code: :return: """ return self._get( 'sns/j...

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29.222222

17.333333

def moral_graph(model, format='raw', prog='dot', path=None, name=None): """ moral_graph(model,format='raw', prog='dot', path=None) Draws the moral graph for this model and writes it to path with filename name. Returns the pydot 'dot' object for further user manipulation. GraphViz and PyDot must be...

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32.647887

19.915493

def getNumberOfRequiredVerifications(self): """Returns the number of required verifications a test for this analysis requires before being transitioned to 'verified' state :returns: number of required verifications """ num = self.getField('NumberOfRequiredVerifications').get(self...

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46.888889

16.222222

def submit_tasks(self, wait=False): """ Submits the task in self and wait. TODO: change name. """ for task in self: task.start() if wait: for task in self: task.wait()

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23.1

11.7

def assert_transform_exists(cli, transform_path): """ Asserts that the transform exists. :param cli: :param transform_path: :return: """ result = commands.query_transform_exists(cli, transform_path) assert result is True return result

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26.1

14.1

def update_snapshots(self, snapshots_data: List[Tuple[str, int]]): """Given a list of snapshot data, update them in the DB The snapshots_data should be a list of tuples of snapshots data and identifiers in that order. """ cursor = self.conn.cursor() cursor.executemany( ...

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36.666667

16.666667

def shrink_pool(arg, opts, shell_opts): """ Shrink a pool by removing the ranges in opts from it """ if not pool: print("No pool with name '%s' found." % arg, file=sys.stderr) sys.exit(1) if 'remove' in opts: res = Prefix.list({'prefix': opts['remove'], 'pool_id': pool.id}) ...

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34.956522

19.782609

def create_entry(self, json): """Create :class:`.resources.Entry` from JSON. :param json: JSON dict. :return: Entry instance. """ sys = json['sys'] ct = sys['contentType']['sys']['id'] fields = json['fields'] raw_fields = copy.deepcopy(fields) # ...

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32.578947

15.026316

def file_hash(load, fnd): ''' Return an MD5 file hash ''' if 'env' in load: # "env" is not supported; Use "saltenv". load.pop('env') ret = {} if 'saltenv' not in load: return ret if 'path' not in fnd or 'bucket' not in fnd or not fnd['path']: return ret ...

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22.307692

23

def sendcommand(self, name, **kwargs): """ send a named parametrized command to the other side. """ self.log("sending command %s(**%s)" % (name, kwargs)) self.channel.send((name, kwargs))

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52

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def u128(self, name, value=None, align=None): """Add an unsigned 16 byte integer field to template. This is an convenience method that simply calls `Uint` keyword with predefined length.""" self.uint(16, name, value, align)

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48.8

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def encode_grib2_percentile(self): """ Encodes member percentile data to GRIB2 format. Returns: Series of GRIB2 messages """ lscale = 1e6 grib_id_start = [7, 0, 14, 14, 2] gdsinfo = np.array([0, np.product(self.data.shape[-2:]), 0, 0, 30], dtype=np.in...

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60.396825

27.920635

def _run_program(self, bin, fastafile, params=None): """ Run XXmotif and predict motifs from a FASTA file. Parameters ---------- bin : str Command used to run the tool. fastafile : str Name of the FASTA input file. params : dict,...

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27.833333

18.833333

def get(self, request, enterprise_uuid, program_uuid): """ Show Program Landing page for the Enterprise's Program. Render the Enterprise's Program Enrollment page for a specific program. The Enterprise and Program are both selected by their respective UUIDs. Unauthenticated lea...

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49.952381

29.380952

def avg(self, key=None): """ Get the average value of a given key. :param key: The key to get the average for :type key: mixed :rtype: float or int """ count = self.count() if count: return self.sum(key) / count

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21.384615

16.461538

def cnst_A1(self, X, Xf=None): r"""Compute :math:`A_1 \mathbf{x}` component of ADMM problem constraint. In this case :math:`A_1 \mathbf{x} = (\Gamma_0^T \;\; \Gamma_1^T \;\; \ldots )^T \mathbf{x}`. """ if Xf is None: Xf = sl.rfftn(X, axes=self.cri.axisN) retu...

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41

14.545455

def collection(self, *collection_path): """Get a reference to a collection. For a top-level collection: .. code-block:: python >>> client.collection('top') For a sub-collection: .. code-block:: python >>> client.collection('mydocs/doc/subcol') ...

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29.085714

22.514286

def add_omim_info(genes, alias_genes, genemap_lines, mim2gene_lines): """Add omim information We collect information on what phenotypes that are associated with a gene, what inheritance models that are associated and the correct omim id. Args: genes(dict): Dictionary with all genes ...

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38.464286

22.25

def _limit_is_valid_or_none(self, params): """ Validates that a given limit is not present or is well-formed. :param params: Query params. :return: Returns True if a limit is present or is well-formed. """ if not "limit" in params or not params["limit"]: retu...

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35.214286

16.214286

def add_resource(self, resource): """Add a resource to the list of interesting resources""" if resource.exists(): self.resources[resource] = self.timekeeper.get_indicator(resource) else: self.resources[resource] = None

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43.5

14.333333

def get(self): """Return the file content as a string.""" r = self._session.get(self.content, headers={'Accept': '*/*'}) return r.content

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39.5

18

def resolve_zone_file_to_profile(zone_file, address_or_public_key): """ Resolves a zone file to a profile and checks to makes sure the tokens are signed with a key that corresponds to the address or public key provided. """ if is_profile_in_legacy_format(zone_file): return zone_file ...

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35.266667

25.066667

def set_default_locators_and_formatters(self, axis): """ Set up the locators and formatters for the scale. Parameters ---------- axis: matplotlib.axis Axis for which to set locators and formatters. """ axis.set_major_locator(_LogicleLocator(self._tra...

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37.4

20.333333

def cee_map_remap_fabric_priority_fabric_remapped_priority(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") cee_map = ET.SubElement(config, "cee-map", xmlns="urn:brocade.com:mgmt:brocade-cee-map") name_key = ET.SubElement(cee_map, "name") name_key...

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50.785714

21

async def websocket_disconnect(self, message): """ Handle the disconnect message. This is propagated to all upstream applications. """ # set this flag so as to ensure we don't send a downstream `websocket.close` message due to all # child applications closing. se...

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37.5

13.833333

def dict(self): '''Returns a dictionary representing this query.''' d = dict() d['key'] = str(self.key) if self.limit is not None: d['limit'] = self.limit if self.offset > 0: d['offset'] = self.offset if self.offset_key: d['offset_key'] = str(self.offset_key) if len(self.f...

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28.058824

18.411765

def check_credentials(self): """ Check that ``username`` and ``password`` have been set, and raise an exception if not. """ if self.username is None or self.password is None: raise DistlibException('username and password must be set') pm = HTTPPasswordMgr() ...

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44.454545

16.454545

def highlightSubsequence(sequence, x1, x2, start=' [', stop = '] ') : """returns a sequence where the subsequence in [x1, x2[ is placed in bewteen 'start' and 'stop'""" seq = list(sequence) print x1, x2-1, len(seq) seq[x1] = start + seq[x1] seq[x2-1] = seq[x2-1] + stop return ''.join(seq)

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32.222222

16.444444

def retrieve_outputs(self): """ Declare the outputs of the algorithms as attributes: x_final, y_final, metrics. """ metrics = {} for obs in self._observers['cv_metrics']: metrics[obs.name] = obs.retrieve_metrics() self.metrics = metrics

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32.111111

13.444444

def portfolio_performance( expected_returns, cov_matrix, weights, verbose=False, risk_free_rate=0.02 ): """ After optimising, calculate (and optionally print) the performance of the optimal portfolio. Currently calculates expected return, volatility, and the Sharpe ratio. :param expected_returns: e...

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44.3

18.3

def crossover(self, chromosome, point1, point2=None): """ Exchange DNA with another chromosome of equal length at one or two common points. For example, consider chromosomes: 1. 11110000 2. 00001111 If the crossover point is 4, the exchange results...

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37.75

25.083333

def _key(self, username, frozen=False): """Translate a username into a key for Redis.""" if frozen: return self.frozen + username return self.prefix + username

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38.2

5.4

def _collapse_transcripts(in_file, window, data, out_dir, include_gene_names=True): """Collapse transcripts into min/max coordinates and optionally add windows. """ if out_dir is None: out_dir = os.path.dirname(in_file) out_file = os.path.join(out_dir, "%s-transcripts...

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57.194444

22.444444

def nic_list(self, bridge): """ List nics attached to bridge :param bridge: bridge name """ args = { 'name': bridge, } self._bridge_chk.check(args) return self._client.json('bridge.nic-list', args)

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18.857143

19.428571