kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def querymany(self, sql_query, columns, seq_of_parameters): """ Same as .query() but eventually call the .executemany() method of the underlying DBAPI2.0 cursor instead of .execute() """ tmp_query = self.__preparequery(sql_query, columns) if self.__methods[METHOD_MODULE]...	[ "def", "querymany", "(", "self", ",", "sql_query", ",", "columns", ",", "seq_of_parameters", ")", ":", "tmp_query", "=", "self", ".", "__preparequery", "(", "sql_query", ",", "columns", ")", "if", "self", ".", "__methods", "[", "METHOD_MODULE", "]", ".", "...	43.176471	25.411765
def new(self, br, ino, sector_count, load_seg, media_name, system_type, platform_id, bootable): # type: (headervd.BootRecord, inode.Inode, int, int, str, int, int, bool) -> None ''' A method to create a new El Torito Boot Catalog. Parameters: br - The boot record th...	[ "def", "new", "(", "self", ",", "br", ",", "ino", ",", "sector_count", ",", "load_seg", ",", "media_name", ",", "system_type", ",", "platform_id", ",", "bootable", ")", ":", "# type: (headervd.BootRecord, inode.Inode, int, int, str, int, int, bool) -> None", "if", "se...	42.6875	25.8125
def get_path(self, repo): """ Return the path for the repo """ if repo.endswith('.git'): repo = repo.split('.git')[0] org, name = repo.split('/')[-2:] path = self.plugins_dir path = join(path, org, name) return path, org, name	[ "def", "get_path", "(", "self", ",", "repo", ")", ":", "if", "repo", ".", "endswith", "(", "'.git'", ")", ":", "repo", "=", "repo", ".", "split", "(", "'.git'", ")", "[", "0", "]", "org", ",", "name", "=", "repo", ".", "split", "(", "'/'", ")",...	34.875	5.625
def http_request(self, path="/", method="GET", host=None, port=None, json=False, data=None): """ perform a HTTP request :param path: str, path within the request, e.g. "/api/version" :param method: str, HTTP method :param host: str, if None, set to 127.0.0.1 :param port:...	[ "def", "http_request", "(", "self", ",", "path", "=", "\"/\"", ",", "method", "=", "\"GET\"", ",", "host", "=", "None", ",", "port", "=", "None", ",", "json", "=", "False", ",", "data", "=", "None", ")", ":", "host", "=", "host", "or", "'127.0.0.1'...	37.5	19.5
def get_composition(self, composition_id): """Gets the ``Composition`` specified by its ``Id``. arg: composition_id (osid.id.Id): ``Id`` of the ``Composiiton`` return: (osid.repository.Composition) - the composition raise: NotFound - ``composition_id`` not found ...	[ "def", "get_composition", "(", "self", ",", "composition_id", ")", ":", "# Implemented from template for", "# osid.resource.ResourceLookupSession.get_resource", "# NOTE: This implementation currently ignores plenary view", "collection", "=", "JSONClientValidated", "(", "'repository'", ...	51.565217	20.043478
def _get_method_full_name(func): """ Return fully qualified function name. This method will attempt to find "full name" of the given function object. This full name is either of the form "<class name>.<method name>" if the function is a class method, or "<module name>.<func name>" if it's a regular...	[ "def", "_get_method_full_name", "(", "func", ")", ":", "# Python 3.3 already has this information available...", "if", "hasattr", "(", "func", ",", "\"__qualname__\"", ")", ":", "return", "func", ".", "__qualname__", "module", "=", "inspect", ".", "getmodule", "(", ...	40.75	20.178571
def _get_block_result(chars_a, chars_b): """Get the first block from two character lists and compare If character list ``a`` begins with a digit, the :any:`_pop_digit` function is called on both lists to get blocks of all consecutive digits at the start of each list. If the length of the block retu...	[ "def", "_get_block_result", "(", "chars_a", ",", "chars_b", ")", ":", "logger", ".", "debug", "(", "'_get_block_result(%s, %s)'", ",", "chars_a", ",", "chars_b", ")", "first_is_digit", "=", "chars_a", "[", "0", "]", ".", "isdigit", "(", ")", "pop_func", "=",...	45.885714	20.228571
def amalgamate(colcount, snode, snptr, snpar, snpost, merge_function): """ Supernodal amalgamation. colcount, snode, snptr, snpar, snpost = ... amalgamate(colcount, snode, snptr, snpar, snpost, merge_function) PURPOSE Iterates over the clique tree in topological order and greedily ...	[ "def", "amalgamate", "(", "colcount", ",", "snode", ",", "snptr", ",", "snpar", ",", "snpost", ",", "merge_function", ")", ":", "N", "=", "len", "(", "snpost", ")", "ch", "=", "{", "}", "for", "j", "in", "snpost", ":", "if", "snpar", "[", "j", "]...	28.987654	20.444444
def error_of_type(handler: astroid.ExceptHandler, error_type) -> bool: """ Check if the given exception handler catches the given error_type. The handler parameter is a node, representing an ExceptHandler node. The error_type can be an exception, such as AttributeError, the name of an excep...	[ "def", "error_of_type", "(", "handler", ":", "astroid", ".", "ExceptHandler", ",", "error_type", ")", "->", "bool", ":", "def", "stringify_error", "(", "error", ")", ":", "if", "not", "isinstance", "(", "error", ",", "str", ")", ":", "return", "error", "...	35.826087	18.956522
def Brkic_2011_1(Re, eD): r'''Calculates Darcy friction factor using the method in Brkic (2011) [2]_ as shown in [1]_. .. math:: f_d = [-2\log(10^{-0.4343\beta} + \frac{\epsilon}{3.71D})]^{-2} .. math:: \beta = \ln \frac{Re}{1.816\ln\left(\frac{1.1Re}{\ln(1+1.1Re)}\right)} Paramet...	[ "def", "Brkic_2011_1", "(", "Re", ",", "eD", ")", ":", "beta", "=", "log", "(", "Re", "/", "(", "1.816", "", "log", "(", "1.1", "", "Re", "/", "log", "(", "1", "+", "1.1", "", "Re", ")", ")", ")", ")", "return", "(", "-", "2", "", "lo...	28.409091	25
def from_apps(cls, apps): "Takes in an Apps and returns a VersionedProjectState matching it" app_models = {} for model in apps.get_models(include_swapped=True): model_state = VersionedModelState.from_model(model) app_models[(model_state.app_label, model_state.name.lower()...	[ "def", "from_apps", "(", "cls", ",", "apps", ")", ":", "app_models", "=", "{", "}", "for", "model", "in", "apps", ".", "get_models", "(", "include_swapped", "=", "True", ")", ":", "model_state", "=", "VersionedModelState", ".", "from_model", "(", "model", ...	51.571429	23.571429
def render(self, text, add_header=False): """Render the HTML. Parameters ---------- add_header: boolean (default: False) If True, add HTML5 header and footer. Returns ------- str The rendered HTML. """ html = mark_text(te...	[ "def", "render", "(", "self", ",", "text", ",", "add_header", "=", "False", ")", ":", "html", "=", "mark_text", "(", "text", ",", "self", ".", "aesthetics", ",", "self", ".", "rules", ")", "html", "=", "html", ".", "replace", "(", "'\\n'", ",", "'<...	27.9	19.2
def defer(self, args, *kwargs): """Call the function and immediately return an asynchronous object. The calling code will need to check for the result at a later time using: In Python 2/3 using ThreadPools - an AsyncResult (https://docs.python.org/2/library/multiprocessing.html#m...	[ "def", "defer", "(", "self", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "LOG", ".", "debug", "(", "'%s on %s (awaitable %s async %s provider %s)'", ",", "'deferring'", ",", "self", ".", "_func", ",", "self", ".", "_is_awaitable", ",", "self", "."...	37.7	19.7
def forward_for_single_feature_map(self, anchors, objectness, box_regression): """ Arguments: anchors: list[BoxList] objectness: tensor of size N, A, H, W box_regression: tensor of size N, A * 4, H, W """ device = objectness.device N, A, H, W =...	[ "def", "forward_for_single_feature_map", "(", "self", ",", "anchors", ",", "objectness", ",", "box_regression", ")", ":", "device", "=", "objectness", ".", "device", "N", ",", "A", ",", "H", ",", "W", "=", "objectness", ".", "shape", "# put in the same format ...	37.625	21.333333
def loads(xml, force_list=None): """Cria um dicionário com os dados do XML. O dicionário terá como chave o nome do nó root e como valor o conteúdo do nó root. Quando o conteúdo de um nó é uma lista de nós então o valor do nó será um dicionário com uma chave para cada nó. Entretanto, se existir nós,...	[ "def", "loads", "(", "xml", ",", "force_list", "=", "None", ")", ":", "if", "force_list", "is", "None", ":", "force_list", "=", "[", "]", "try", ":", "xml", "=", "remove_illegal_characters", "(", "xml", ")", "doc", "=", "parseString", "(", "xml", ")", ...	34.642857	26.457143
def iofunctions(self): """Input/output functions of the model class.""" lines = Lines() for func in ('open_files', 'close_files', 'load_data', 'save_data'): if ((func == 'load_data') and (getattr(self.model.sequences, 'inputs', None) is None)): con...	[ "def", "iofunctions", "(", "self", ")", ":", "lines", "=", "Lines", "(", ")", "for", "func", "in", "(", "'open_files'", ",", "'close_files'", ",", "'load_data'", ",", "'save_data'", ")", ":", "if", "(", "(", "func", "==", "'load_data'", ")", "and", "("...	47.516129	14.935484
def load_texture(self, file_path): """Generate our sprite's surface by loading the specified image from disk. Note that this automatically centers the origin.""" self.image = pygame.image.load(file_path) self.apply_texture(self.image)	[ "def", "load_texture", "(", "self", ",", "file_path", ")", ":", "self", ".", "image", "=", "pygame", ".", "image", ".", "load", "(", "file_path", ")", "self", ".", "apply_texture", "(", "self", ".", "image", ")" ]	52.6	3.4
def plotstuff(self, T=[0, 1000]): """ Create a scatter plot of the contents of the database, with entries on the interval T. Parameters ---------- T : list Time interval. Returns ------- None ...	[ "def", "plotstuff", "(", "self", ",", "T", "=", "[", "0", ",", "1000", "]", ")", ":", "fig", "=", "plt", ".", "figure", "(", "figsize", "=", "(", "10", ",", "10", ")", ")", "ax", "=", "fig", ".", "add_subplot", "(", "111", ")", "neurons", "="...	25.184211	20.552632
def visit_For(self, node): """ OUT = (node,) + last body statements RAISES = body's that are not break or continue """ currs = (node,) break_currs = tuple() raises = () # handle body for n in node.body: self.result.add_node(n) ...	[ "def", "visit_For", "(", "self", ",", "node", ")", ":", "currs", "=", "(", "node", ",", ")", "break_currs", "=", "tuple", "(", ")", "raises", "=", "(", ")", "# handle body", "for", "n", "in", "node", ".", "body", ":", "self", ".", "result", ".", ...	34.472222	10.194444
def status(self): """ In most cases, reading status will return the same value as `mode`. In cases where there is an `auto` mode additional values may be returned, such as `no-device` or `error`. See individual port driver documentation for the full list of possible values. ...	[ "def", "status", "(", "self", ")", ":", "self", ".", "_status", ",", "value", "=", "self", ".", "get_attr_string", "(", "self", ".", "_status", ",", "'status'", ")", "return", "value" ]	46	22
def _callable_contents(obj): """Return the signature contents of a callable Python object. """ try: # Test if obj is a method. return _function_contents(obj.__func__) except AttributeError: try: # Test if obj is a callable object. return _function_content...	[ "def", "_callable_contents", "(", "obj", ")", ":", "try", ":", "# Test if obj is a method.", "return", "_function_contents", "(", "obj", ".", "__func__", ")", "except", "AttributeError", ":", "try", ":", "# Test if obj is a callable object.", "return", "_function_conten...	30	15.6
def get_text_path(self): """ Returns the path of the directory containing text if they exist in this dataset. """ for res in self.dsDoc['dataResources']: resPath = res['resPath'] resType = res['resType'] isCollection = res['isCollection'] i...	[ "def", "get_text_path", "(", "self", ")", ":", "for", "res", "in", "self", ".", "dsDoc", "[", "'dataResources'", "]", ":", "resPath", "=", "res", "[", "'resPath'", "]", "resType", "=", "res", "[", "'resType'", "]", "isCollection", "=", "res", "[", "'is...	43.307692	17.615385
def selection_index_to_idx(self, key, selection_index): '''return a mission idx from a selection_index''' a = key.split(' ') if a[0] != 'mission' or len(a) != 2: print("Bad mission object %s" % key) return None midx = int(a[1]) if midx < 0 or midx >= len(s...	[ "def", "selection_index_to_idx", "(", "self", ",", "key", ",", "selection_index", ")", ":", "a", "=", "key", ".", "split", "(", "' '", ")", "if", "a", "[", "0", "]", "!=", "'mission'", "or", "len", "(", "a", ")", "!=", "2", ":", "print", "(", "\"...	40.125	13.625
def init_opdata(l, from_mod, version=None, is_pypy=False): """Sets up a number of the structures found in Python's opcode.py. Python opcode.py routines assign attributes to modules. In order to do this in a modular way here, the local dictionary for the module is passed. """ if version: ...	[ "def", "init_opdata", "(", "l", ",", "from_mod", ",", "version", "=", "None", ",", "is_pypy", "=", "False", ")", ":", "if", "version", ":", "l", "[", "'python_version'", "]", "=", "version", "l", "[", "'is_pypy'", "]", "=", "is_pypy", "l", "[", "'cmp...	37.035714	15.464286
def to_name(self) -> str: """ Convert to ANSI color name :return: ANSI color name """ return { self.BLACK: 'black', self.RED: 'red', self.GREEN: 'green', self.YELLOW: 'yellow', self.BLUE: 'blue', self.MAGENTA...	[ "def", "to_name", "(", "self", ")", "->", "str", ":", "return", "{", "self", ".", "BLACK", ":", "'black'", ",", "self", ".", "RED", ":", "'red'", ",", "self", ".", "GREEN", ":", "'green'", ",", "self", ".", "YELLOW", ":", "'yellow'", ",", "self", ...	26.866667	9.266667
def clear_all(self): """Delete all Mentions from given split the database.""" logger.info("Clearing ALL Mentions.") self.session.query(Mention).delete(synchronize_session="fetch") # With no Mentions, there should be no Candidates also self.session.query(Candidate).delete(synchro...	[ "def", "clear_all", "(", "self", ")", ":", "logger", ".", "info", "(", "\"Clearing ALL Mentions.\"", ")", "self", ".", "session", ".", "query", "(", "Mention", ")", ".", "delete", "(", "synchronize_session", "=", "\"fetch\"", ")", "# With no Mentions, there shou...	49.5	21.5
def init_ui(self): """Setup control widget UI.""" self.control_layout = QHBoxLayout() self.setLayout(self.control_layout) self.reset_button = QPushButton() self.reset_button.setFixedSize(40, 40) self.reset_button.setIcon(QtGui.QIcon(WIN_PATH)) self.game_timer = QL...	[ "def", "init_ui", "(", "self", ")", ":", "self", ".", "control_layout", "=", "QHBoxLayout", "(", ")", "self", ".", "setLayout", "(", "self", ".", "control_layout", ")", "self", ".", "reset_button", "=", "QPushButton", "(", ")", "self", ".", "reset_button",...	43.941176	11.588235
def register_actions(self, shortcut_manager): """Register callback methods for triggered actions :param rafcon.gui.shortcut_manager.ShortcutManager shortcut_manager: Shortcut Manager Object holding mappings between shortcuts and actions. """ super(DescriptionEditorController...	[ "def", "register_actions", "(", "self", ",", "shortcut_manager", ")", ":", "super", "(", "DescriptionEditorController", ",", "self", ")", ".", "register_actions", "(", "shortcut_manager", ")", "shortcut_manager", ".", "add_callback_for_action", "(", "\"abort\"", ",", ...	53.25	24.625
def cluster_assignments(self): """ Return an array of cluster assignments corresponding to the most recent set of instances clustered. :return: the cluster assignments :rtype: ndarray """ array = javabridge.call(self.jobject, "getClusterAssignments", "()[D") if a...	[ "def", "cluster_assignments", "(", "self", ")", ":", "array", "=", "javabridge", ".", "call", "(", "self", ".", "jobject", ",", "\"getClusterAssignments\"", ",", "\"()[D\"", ")", "if", "array", "is", "None", ":", "return", "None", "else", ":", "return", "j...	36.083333	21.916667
def eventFilter(self, watchedObject, event): """ Calls commitAndClose when the tab and back-tab are pressed. This is necessary because, normally the event filter of QStyledItemDelegate does this for us. However, that event filter works on this object, not on the sub editor. """ ...	[ "def", "eventFilter", "(", "self", ",", "watchedObject", ",", "event", ")", ":", "if", "event", ".", "type", "(", ")", "==", "QtCore", ".", "QEvent", ".", "KeyPress", ":", "key", "=", "event", ".", "key", "(", ")", "if", "key", "in", "(", "Qt", "...	45.142857	19.571429
def run(self): """ Kill any open Redshift sessions for the given database. """ connection = self.output().connect() # kill any sessions other than ours and # internal Redshift sessions (rdsdb) query = ("select pg_terminate_backend(process) " "from...	[ "def", "run", "(", "self", ")", ":", "connection", "=", "self", ".", "output", "(", ")", ".", "connect", "(", ")", "# kill any sessions other than ours and", "# internal Redshift sessions (rdsdb)", "query", "=", "(", "\"select pg_terminate_backend(process) \"", "\"from ...	41.5	18.131579
def submit_job(manager, job_config): """ Launch new job from specified config. May have been previously 'setup' if 'setup_params' in job_config is empty. """ # job_config is raw dictionary from JSON (from MQ or HTTP endpoint). job_id = job_config.get('job_id') try: command_line = job_con...	[ "def", "submit_job", "(", "manager", ",", "job_config", ")", ":", "# job_config is raw dictionary from JSON (from MQ or HTTP endpoint).", "job_id", "=", "job_config", ".", "get", "(", "'job_id'", ")", "try", ":", "command_line", "=", "job_config", ".", "get", "(", "...	42.285714	18.020408
def delete_dataset( self, name, retry=google.api_core.gapic_v1.method.DEFAULT, timeout=google.api_core.gapic_v1.method.DEFAULT, metadata=None, ): """ Deletes a dataset and all of its contents. Returns empty response in the ``response`` field when it co...	[ "def", "delete_dataset", "(", "self", ",", "name", ",", "retry", "=", "google", ".", "api_core", ".", "gapic_v1", ".", "method", ".", "DEFAULT", ",", "timeout", "=", "google", ".", "api_core", ".", "gapic_v1", ".", "method", ".", "DEFAULT", ",", "metadat...	39.423529	22.364706
def download(url, fname=None): """ Downloads a file. Args: url (str): The URL to download. fname (Optional[str]): The filename to store the downloaded file in. If `None`, take the filename from the URL. Defaults to `None`. Returns: The filename the URL was downloa...	[ "def", "download", "(", "url", ",", "fname", "=", "None", ")", ":", "# Determine the filename", "if", "fname", "is", "None", ":", "fname", "=", "url", ".", "split", "(", "'/'", ")", "[", "-", "1", "]", "# Stream the URL as a file, copying to local disk", "wi...	28.121212	21.333333
def swipe_bottom(self, steps=10, args, selectors): """ Swipe the UI object with selectors* from center to bottom See `Swipe Left` for more details. """ self.device(**selectors).swipe.down(steps=steps)	[ "def", "swipe_bottom", "(", "self", ",", "steps", "=", "10", ",", "", "args", ",", "", "", "selectors", ")", ":", "self", ".", "device", "(", "", "*", "selectors", ")", ".", "swipe", ".", "down", "(", "steps", "=", "steps", ")" ]	34.142857	13.857143
def _dictlist_to_lists(dl, *keys): ''' convert a list of dictionaries to a dictionary of lists >>> dl = [{'a': 'test', 'b': 3}, {'a': 'zaz', 'b': 444}, {'a': 'wow', 'b': 300}] >>> _dictlist_to_lists(dl) (['test', 'zaz', 'wow'], [3, 444, 300]) ''' lists = [] for k in keys: ...	[ "def", "_dictlist_to_lists", "(", "dl", ",", "*", "keys", ")", ":", "lists", "=", "[", "]", "for", "k", "in", "keys", ":", "lists", ".", "append", "(", "[", "]", ")", "for", "item", "in", "dl", ":", "for", "i", ",", "key", "in", "enumerate", "(...	29	16.111111
def get_cloud_service(self, cloud_service_id): ''' The Get Cloud Service operation gets all the resources (job collections) in the cloud service. cloud_service_id: The cloud service id ''' _validate_not_none('cloud_service_id', cloud_service_id) path ...	[ "def", "get_cloud_service", "(", "self", ",", "cloud_service_id", ")", ":", "_validate_not_none", "(", "'cloud_service_id'", ",", "cloud_service_id", ")", "path", "=", "self", ".", "_get_cloud_services_path", "(", "cloud_service_id", ")", "return", "self", ".", "_pe...	37.454545	21.454545
def create_table(table, connection, schema=None): """Create a single table, primarily used din migrations""" orig_schemas = {} # These schema shenanigans are almost certainly wrong. # But they are expedient. For Postgres, it puts the library # tables in the Library schema. We n...	[ "def", "create_table", "(", "table", ",", "connection", ",", "schema", "=", "None", ")", ":", "orig_schemas", "=", "{", "}", "# These schema shenanigans are almost certainly wrong.", "# But they are expedient. For Postgres, it puts the library", "# tables in the Library schema. W...	42.916667	24.333333
def list_results(self, number, username): """ [deprecated] 建議使用方法 `get_question_results()` """ # 取得新 API 的結果 data = self.get_question_results(number, username) # 實作相容的結構 result = [] for number in data: # 儲存題目資訊 result += [(number, d...	[ "def", "list_results", "(", "self", ",", "number", ",", "username", ")", ":", "# 取得新 API 的結果", "data", "=", "self", ".", "get_question_results", "(", "number", ",", "username", ")", "# 實作相容的結構", "result", "=", "[", "]", "for", "number", "in", "data", ":", ...	27.538462	13.692308
def load(self, format=None, , kwargs={}): ''' deserialize object from the file. auto detect format by file extension name if `format` is None. for example, `.json` will detect as `json`. raise `FormatNotFoundError` on unknown format. * raise `SerializeError` on any s...	[ "def", "load", "(", "self", ",", "format", "=", "None", ",", "*", ",", "kwargs", "=", "{", "}", ")", ":", "return", "load", "(", "self", ",", "format", "=", "format", ",", "kwargs", "=", "kwargs", ")" ]	36.181818	21.272727
def reasonable_desired_version(self, desired_version, allow_equal=False, allow_patch_skip=False): """ Determine whether the desired version is a reasonable next version. Parameters ---------- desired_version: str the proposed next ve...	[ "def", "reasonable_desired_version", "(", "self", ",", "desired_version", ",", "allow_equal", "=", "False", ",", "allow_patch_skip", "=", "False", ")", ":", "try", ":", "desired_version", "=", "desired_version", ".", "base_version", "except", ":", "pass", "(", "...	33.425532	20.957447
def _serialize_input_list(input_value): """Recursively serialize task input list""" input_list = [] for item in input_value: if isinstance(item, list): input_list.append(Task._serialize_input_list(item)) else: if isinstance(item, File): ...	[ "def", "_serialize_input_list", "(", "input_value", ")", ":", "input_list", "=", "[", "]", "for", "item", "in", "input_value", ":", "if", "isinstance", "(", "item", ",", "list", ")", ":", "input_list", ".", "append", "(", "Task", ".", "_serialize_input_list"...	39.090909	10.272727
def modified_lines(self, r, file_name): """Returns the line numbers of a file which have been changed.""" cmd = self.file_diff_cmd(r, file_name) diff = shell_out_ignore_exitcode(cmd, cwd=self.root) return list(self.modified_lines_from_diff(diff))	[ "def", "modified_lines", "(", "self", ",", "r", ",", "file_name", ")", ":", "cmd", "=", "self", ".", "file_diff_cmd", "(", "r", ",", "file_name", ")", "diff", "=", "shell_out_ignore_exitcode", "(", "cmd", ",", "cwd", "=", "self", ".", "root", ")", "ret...	54.8	8.6
def skew_matrix(w): '''Return the skew matrix of a direction w.''' return np.array([[0, -w[2], w[1]], [w[2], 0, -w[0]], [-w[1], w[0], 0]])	[ "def", "skew_matrix", "(", "w", ")", ":", "return", "np", ".", "array", "(", "[", "[", "0", ",", "-", "w", "[", "2", "]", ",", "w", "[", "1", "]", "]", ",", "[", "w", "[", "2", "]", ",", "0", ",", "-", "w", "[", "0", "]", "]", ",", ...	36.8	7.2
def bezout(a, b): '''Compute the bezout algorithm of a and b, i.e. it returns u, v, p such as: p = GCD(a,b) a * u + b * v = p Copied from http://www.labri.fr/perso/betrema/deug/poly/euclide.html. ''' u = 1 v = 0 s = 0 t = 1 while b > 0: q = a // b ...	[ "def", "bezout", "(", "a", ",", "b", ")", ":", "u", "=", "1", "v", "=", "0", "s", "=", "0", "t", "=", "1", "while", "b", ">", "0", ":", "q", "=", "a", "//", "b", "r", "=", "a", "%", "b", "a", "=", "b", "b", "=", "r", "tmp", "=", "...	19.25	27.083333
def untar_file(filename, location): """Untar the file (tar file located at filename) to the destination location""" if not os.path.exists(location): os.makedirs(location) if filename.lower().endswith('.gz') or filename.lower().endswith('.tgz'): mode = 'r:gz' elif filename.lower().endswit...	[ "def", "untar_file", "(", "filename", ",", "location", ")", ":", "if", "not", "os", ".", "path", ".", "exists", "(", "location", ")", ":", "os", ".", "makedirs", "(", "location", ")", "if", "filename", ".", "lower", "(", ")", ".", "endswith", "(", ...	39.156863	15.019608
def get_all_cpv_use(cp): ''' .. versionadded:: 2015.8.0 Uses portage to determine final USE flags and settings for an emerge. @type cp: string @param cp: eg cat/pkg @rtype: lists @return use, use_expand_hidden, usemask, useforce ''' cpv = _get_cpv(cp) portage = _get_portage() ...	[ "def", "get_all_cpv_use", "(", "cp", ")", ":", "cpv", "=", "_get_cpv", "(", "cp", ")", "portage", "=", "_get_portage", "(", ")", "use", "=", "None", "_porttree", "(", ")", ".", "dbapi", ".", "settings", ".", "unlock", "(", ")", "try", ":", "_porttree...	33.103448	18.827586
def AddIndex(self, path_segment_index): """Adds a path segment index and sets its weight to 0. Args: path_segment_index: an integer containing the path segment index. Raises: ValueError: if the path segment weights already contains the path segment index. """ if path_...	[ "def", "AddIndex", "(", "self", ",", "path_segment_index", ")", ":", "if", "path_segment_index", "in", "self", ".", "_weight_per_index", ":", "raise", "ValueError", "(", "'Path segment index already set.'", ")", "self", ".", "_weight_per_index", "[", "path_segment_ind...	32.642857	19.571429
def _work_path_to_rel_final_path(path, upload_path_mapping, upload_base_dir): """ Check if `path` is a work-rooted path, and convert to a relative final-rooted path """ if not path or not isinstance(path, str): return path upload_path = None # First, check in the mapping: if it's there is a...	[ "def", "_work_path_to_rel_final_path", "(", "path", ",", "upload_path_mapping", ",", "upload_base_dir", ")", ":", "if", "not", "path", "or", "not", "isinstance", "(", "path", ",", "str", ")", ":", "return", "path", "upload_path", "=", "None", "# First, check in ...	39.785714	21.178571
def _default_bridge(self): """ Get an instance of the ENBridge object using ctypes. """ objc = self.objc ENBridge = objc.objc_getClass('ENBridge') return objc.objc_msgSend(ENBridge, objc.sel_registerName('instance'))	[ "def", "_default_bridge", "(", "self", ")", ":", "objc", "=", "self", ".", "objc", "ENBridge", "=", "objc", ".", "objc_getClass", "(", "'ENBridge'", ")", "return", "objc", ".", "objc_msgSend", "(", "ENBridge", ",", "objc", ".", "sel_registerName", "(", "'i...	48.8	15.2
def _try_switches(self, lines, index): """ For each switch in the Collector object, pass a list of string, representing lines of text in a file, and an index to the current line to try to flip the switch. A switch will only flip on if the line passes its 'test_on' method, and wil...	[ "def", "_try_switches", "(", "self", ",", "lines", ",", "index", ")", ":", "for", "s", "in", "self", ".", "_switches", ":", "s", ".", "switch", "(", "lines", ",", "index", ")" ]	45.384615	18.923077
def write_object_to_file(self, query_results, filename, fmt="csv", coerce_to_timestamp=False, record_time_added=False): """ Write query results to file. ...	[ "def", "write_object_to_file", "(", "self", ",", "query_results", ",", "filename", ",", "fmt", "=", "\"csv\"", ",", "coerce_to_timestamp", "=", "False", ",", "record_time_added", "=", "False", ")", ":", "fmt", "=", "fmt", ".", "lower", "(", ")", "if", "fmt...	49.231481	25.305556
def plot_monthly_ic_heatmap(mean_monthly_ic, ax=None): """ Plots a heatmap of the information coefficient or returns by month. Parameters ---------- mean_monthly_ic : pd.DataFrame The mean monthly IC for N periods forward. Returns ------- ax : matplotlib.Axes The axes t...	[ "def", "plot_monthly_ic_heatmap", "(", "mean_monthly_ic", ",", "ax", "=", "None", ")", ":", "mean_monthly_ic", "=", "mean_monthly_ic", ".", "copy", "(", ")", "num_plots", "=", "len", "(", "mean_monthly_ic", ".", "columns", ")", "v_spaces", "=", "(", "(", "nu...	24.857143	19.964286
def recv_file_from_remote(dev, src_filename, dst_file, filesize): """Intended to be passed to the `remote` function as the xfer_func argument. Matches up with send_file_to_host. """ bytes_remaining = filesize if not HAS_BUFFER: bytes_remaining *= 2 # hexlify makes each byte into 2 bu...	[ "def", "recv_file_from_remote", "(", "dev", ",", "src_filename", ",", "dst_file", ",", "filesize", ")", ":", "bytes_remaining", "=", "filesize", "if", "not", "HAS_BUFFER", ":", "bytes_remaining", "*=", "2", "# hexlify makes each byte into 2", "buf_size", "=", "BUFFE...	40.666667	12.037037
def inverse(x): """ Transform to Timedelta from numerical format """ try: x = [pd.Timedelta(int(i)) for i in x] except TypeError: x = pd.Timedelta(int(x)) return x	[ "def", "inverse", "(", "x", ")", ":", "try", ":", "x", "=", "[", "pd", ".", "Timedelta", "(", "int", "(", "i", ")", ")", "for", "i", "in", "x", "]", "except", "TypeError", ":", "x", "=", "pd", ".", "Timedelta", "(", "int", "(", "x", ")", ")...	25.222222	13
def get_file(self, commit, path, offset_bytes=0, size_bytes=0, extract_value=True): """ Returns an iterator of the contents contents of a file at a specific Commit. Params: * commit: A tuple, string, or Commit object representing the commit. * path: The path of the file. ...	[ "def", "get_file", "(", "self", ",", "commit", ",", "path", ",", "offset_bytes", "=", "0", ",", "size_bytes", "=", "0", ",", "extract_value", "=", "True", ")", ":", "req", "=", "proto", ".", "GetFileRequest", "(", "file", "=", "proto", ".", "File", "...	46.615385	22.153846
def create_comment(self, body): """Create a comment on this issue. :param str body: (required), comment body :returns: :class:`IssueComment <github3.issues.comment.IssueComment>` """ json = None if body: url = self._build_url('comments', base_url=self._api) ...	[ "def", "create_comment", "(", "self", ",", "body", ")", ":", "json", "=", "None", "if", "body", ":", "url", "=", "self", ".", "_build_url", "(", "'comments'", ",", "base_url", "=", "self", ".", "_api", ")", "json", "=", "self", ".", "_json", "(", "...	39	17.916667
def unique(s): """Return a list of the elements in s, but without duplicates. For example, unique([1,2,3,1,2,3]) is some permutation of [1,2,3], unique("abcabc") some permutation of ["a", "b", "c"], and unique(([1, 2], [2, 3], [1, 2])) some permutation of [[2, 3], [1, 2]]. For best speed, all ...	[ "def", "unique", "(", "s", ")", ":", "n", "=", "len", "(", "s", ")", "if", "n", "==", "0", ":", "return", "[", "]", "# Try using a dict first, as that's the fastest and will usually", "# work. If it doesn't work, it will usually fail quickly, so it", "# usually doesn't c...	31.823529	23.014706
def from_path_by_size(dir_path, min_size=0, max_size=1 << 40): """Create a new FileCollection, and select all files that size in a range:: dir_path = "your/path" # select by file size larger than 100MB fc = FileCollection.from_path_by_size( ...	[ "def", "from_path_by_size", "(", "dir_path", ",", "min_size", "=", "0", ",", "max_size", "=", "1", "<<", "40", ")", ":", "def", "filter", "(", "winfile", ")", ":", "if", "(", "winfile", ".", "size_on_disk", ">=", "min_size", ")", "and", "(", "winfile",...	37.925926	15.333333
def _schema_options(p): """ Add options specific to schema subcommand. """ p.add_argument( 'resource', metavar='selector', nargs='?', default=None).completer = _schema_tab_completer p.add_argument( '--summary', action="store_true", help="Summarize counts of available resourc...	[ "def", "_schema_options", "(", "p", ")", ":", "p", ".", "add_argument", "(", "'resource'", ",", "metavar", "=", "'selector'", ",", "nargs", "=", "'?'", ",", "default", "=", "None", ")", ".", "completer", "=", "_schema_tab_completer", "p", ".", "add_argumen...	48.461538	22.615385
def parse(self, fail_callback=None): """ Parse text fields and file fields for values and files """ # get text fields for field in self.field_arguments: self.values[field['name']] = self.__get_value(field['name']) if self.values[field['name']] is None and field['requ...	[ "def", "parse", "(", "self", ",", "fail_callback", "=", "None", ")", ":", "# get text fields\r", "for", "field", "in", "self", ".", "field_arguments", ":", "self", ".", "values", "[", "field", "[", "'name'", "]", "]", "=", "self", ".", "__get_value", "("...	49.5625	12.5
def _get_client(self): """ S3 Boto3 client Returns: boto3.session.Session.client: client """ client_kwargs = self._storage_parameters.get('client', dict()) # Handles unsecure mode if self._unsecure: client_kwargs = client_kwargs.copy() ...	[ "def", "_get_client", "(", "self", ")", ":", "client_kwargs", "=", "self", ".", "_storage_parameters", ".", "get", "(", "'client'", ",", "dict", "(", ")", ")", "# Handles unsecure mode", "if", "self", ".", "_unsecure", ":", "client_kwargs", "=", "client_kwargs...	27.6	18.4
def text(files): '''Returns the whole transcribed text''' sentences = convert_timestamps(files) out = [] for s in sentences: out.append(' '.join([w[0] for w in s['words']])) return '\n'.join(out)	[ "def", "text", "(", "files", ")", ":", "sentences", "=", "convert_timestamps", "(", "files", ")", "out", "=", "[", "]", "for", "s", "in", "sentences", ":", "out", ".", "append", "(", "' '", ".", "join", "(", "[", "w", "[", "0", "]", "for", "w", ...	31	15
def find_range(self, interval): """wrapper for find""" return self.find(self.tree, interval, self.start, self.end)	[ "def", "find_range", "(", "self", ",", "interval", ")", ":", "return", "self", ".", "find", "(", "self", ".", "tree", ",", "interval", ",", "self", ".", "start", ",", "self", ".", "end", ")" ]	42.666667	12
def ystep(self): r"""Minimise Augmented Lagrangian with respect to :math:`\mathbf{y}`. """ self.Y = np.asarray(sp.prox_l2( self.AX + self.U, (self.lmbda/self.rho)*self.Wtvna, axis=self.saxes), dtype=self.dtype)	[ "def", "ystep", "(", "self", ")", ":", "self", ".", "Y", "=", "np", ".", "asarray", "(", "sp", ".", "prox_l2", "(", "self", ".", "AX", "+", "self", ".", "U", ",", "(", "self", ".", "lmbda", "/", "self", ".", "rho", ")", "*", "self", ".", "W...	32.5	13.5
def _find_files(dirpath: str) -> 'Iterable[str]': """Find files recursively. Returns a generator that yields paths in no particular order. """ for dirpath, dirnames, filenames in os.walk(dirpath, topdown=True, followlinks=True): if os.path.basenam...	[ "def", "_find_files", "(", "dirpath", ":", "str", ")", "->", "'Iterable[str]'", ":", "for", "dirpath", ",", "dirnames", ",", "filenames", "in", "os", ".", "walk", "(", "dirpath", ",", "topdown", "=", "True", ",", "followlinks", "=", "True", ")", ":", "...	40.909091	15.545455
def install_twisted(): """ If twisted is available, make `emit' return a DeferredList This has been successfully tested with Twisted 14.0 and later. """ global emit, _call_partial try: from twisted.internet import defer emit = _emit_twisted _call_partial = defer.maybeDef...	[ "def", "install_twisted", "(", ")", ":", "global", "emit", ",", "_call_partial", "try", ":", "from", "twisted", ".", "internet", "import", "defer", "emit", "=", "_emit_twisted", "_call_partial", "=", "defer", ".", "maybeDeferred", "return", "True", "except", "...	28.933333	16
def draw(self, **kwargs): """ Called from the fit method, this method creates the canvas and draws the distribution plot on it. Parameters ---------- kwargs: generic keyword arguments. """ # Prepare the data bins = np.arange(self.N) word...	[ "def", "draw", "(", "self", ",", "", "", "kwargs", ")", ":", "# Prepare the data", "bins", "=", "np", ".", "arange", "(", "self", ".", "N", ")", "words", "=", "[", "self", ".", "features", "[", "i", "]", "for", "i", "in", "self", ".", "sorted_"...	32.064516	18.064516
def create_all(self, progress_callback: Optional[callable] = None) -> Dict[str, object]: """ Creates all the models discovered from fixture files in :attr:`fixtures_dir`. :param progress_callback: An optional function to track progress. It must take three paramete...	[ "def", "create_all", "(", "self", ",", "progress_callback", ":", "Optional", "[", "callable", "]", "=", "None", ")", "->", "Dict", "[", "str", ",", "object", "]", ":", "if", "not", "self", ".", "_loaded", ":", "self", ".", "_load_data", "(", ")", "# ...	46.953488	25.697674
def concat(cls, variables, dim='concat_dim', positions=None, shortcut=False): """Specialized version of Variable.concat for IndexVariable objects. This exists because we want to avoid converting Index objects to NumPy arrays, if possible. """ if not isinstance(dim...	[ "def", "concat", "(", "cls", ",", "variables", ",", "dim", "=", "'concat_dim'", ",", "positions", "=", "None", ",", "shortcut", "=", "False", ")", ":", "if", "not", "isinstance", "(", "dim", ",", "str", ")", ":", "dim", ",", "=", "dim", ".", "dims"...	34.324324	19
def make_xeditable(instance=None, extra_attrs=[], args, *kwargs): """ Converts the contents of the column into an ``<a>`` tag with the required DOM attributes to power the X-Editable UI. The following keyword arguments are all optional, but may be provided when pre-calling the helper, to customiz...	[ "def", "make_xeditable", "(", "instance", "=", "None", ",", "extra_attrs", "=", "[", "]", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "if", "instance", "is", "None", ":", "# Preloading kwargs into the helper for deferred execution", "helper", "=", "pa...	45.315315	26.297297
def _exec_config_str(self, lhs, rhs): """execute self.config.<lhs> = <rhs> * expands ~ with expanduser * tries to assign with raw eval, otherwise assigns with just the string, allowing `--C.a=foobar` and `--C.a="foobar"` to be equivalent. Not equivalent are `--C.a...	[ "def", "_exec_config_str", "(", "self", ",", "lhs", ",", "rhs", ")", ":", "rhs", "=", "os", ".", "path", ".", "expanduser", "(", "rhs", ")", "try", ":", "# Try to see if regular Python syntax will work. This", "# won't handle strings as the quote marks are removed", "...	39.421053	16
def current_time(self) -> datetime: """Extract current time.""" _date = datetime.strptime(self.obj.SBRes.SBReq.StartT.get("date"), "%Y%m%d") _time = datetime.strptime(self.obj.SBRes.SBReq.StartT.get("time"), "%H:%M") return datetime.combine(_date.date(), _time.time())	[ "def", "current_time", "(", "self", ")", "->", "datetime", ":", "_date", "=", "datetime", ".", "strptime", "(", "self", ".", "obj", ".", "SBRes", ".", "SBReq", ".", "StartT", ".", "get", "(", "\"date\"", ")", ",", "\"%Y%m%d\"", ")", "_time", "=", "da...	59.2	22.2
def make_url(contents, domain=DEFAULT_DOMAIN, force_gist=False, size_for_gist=MAX_URL_LEN): """ Returns the URL to open given the domain and contents. If the file contents are large, an anonymous gist will be created. Parameters ---------- contents * string - assumed to be...	[ "def", "make_url", "(", "contents", ",", "domain", "=", "DEFAULT_DOMAIN", ",", "force_gist", "=", "False", ",", "size_for_gist", "=", "MAX_URL_LEN", ")", ":", "contents", "=", "make_geojson", "(", "contents", ")", "if", "len", "(", "contents", ")", "<=", "...	33.176471	19.588235
def get_choices(module_name): """ Retrieve members from ``module_name``'s ``__all__`` list. :rtype: list """ try: module = importlib.import_module(module_name) if hasattr(module, '__all__'): return module.__all__ else: return [name for name, _ in insp...	[ "def", "get_choices", "(", "module_name", ")", ":", "try", ":", "module", "=", "importlib", ".", "import_module", "(", "module_name", ")", "if", "hasattr", "(", "module", ",", "'__all__'", ")", ":", "return", "module", ".", "__all__", "else", ":", "return"...	28.533333	17.333333
def get_repo_data(saltenv='base'): ''' Returns the existing package metadata db. Will create it, if it does not exist, however will not refresh it. Args: saltenv (str): Salt environment. Default ``base`` Returns: dict: A dict containing contents of metadata db. CLI Example: ...	[ "def", "get_repo_data", "(", "saltenv", "=", "'base'", ")", ":", "# we only call refresh_db if it does not exist, as we want to return", "# the existing data even if its old, other parts of the code call this,", "# but they will call refresh if they need too.", "repo_details", "=", "_get_r...	32.446809	22.021277
def _error_repr(error): """A compact unique representation of an error.""" error_repr = repr(error) if len(error_repr) > 200: error_repr = hash(type(error)) return error_repr	[ "def", "_error_repr", "(", "error", ")", ":", "error_repr", "=", "repr", "(", "error", ")", "if", "len", "(", "error_repr", ")", ">", "200", ":", "error_repr", "=", "hash", "(", "type", "(", "error", ")", ")", "return", "error_repr" ]	32.166667	10.166667
def _mitogen_reset(self, mode): """ Forget everything we know about the connected context. This function cannot be called _reset() since that name is used as a public API by Ansible 2.4 wait_for_connection plug-in. :param str mode: Name of ContextService method to us...	[ "def", "_mitogen_reset", "(", "self", ",", "mode", ")", ":", "if", "not", "self", ".", "context", ":", "return", "self", ".", "chain", ".", "reset", "(", ")", "self", ".", "parent", ".", "call_service", "(", "service_name", "=", "'ansible_mitogen.services....	31.208333	18.541667
def _next_pattern(self): """Parses the next pattern by matching each in turn.""" current_state = self.state_stack[-1] position = self._position for pattern in self.patterns: if current_state not in pattern.states: continue m = pattern.regex.match(...	[ "def", "_next_pattern", "(", "self", ")", ":", "current_state", "=", "self", ".", "state_stack", "[", "-", "1", "]", "position", "=", "self", ".", "_position", "for", "pattern", "in", "self", ".", "patterns", ":", "if", "current_state", "not", "in", "pat...	32.868421	17.789474
def notebook_system_output(): """Get a context manager that attempts to use `wurlitzer <https://github.com/minrk/wurlitzer>`__ to capture system-level stdout/stderr within a Jupyter Notebook shell, without affecting normal operation when run as a Python script. For example: >>> sys_pipes = sporco.u...	[ "def", "notebook_system_output", "(", ")", ":", "from", "contextlib", "import", "contextmanager", "@", "contextmanager", "def", "null_context_manager", "(", ")", ":", "yield", "if", "in_notebook", "(", ")", ":", "try", ":", "from", "wurlitzer", "import", "sys_pi...	28	20.46875
def output_after_run(self, run): """ The method output_after_run() prints filename, result, time and status of a run to terminal and stores all data in XML """ # format times, type is changed from float to string! cputime_str = util.format_number(run.cputime, TIME_PRECIS...	[ "def", "output_after_run", "(", "self", ",", "run", ")", ":", "# format times, type is changed from float to string!", "cputime_str", "=", "util", ".", "format_number", "(", "run", ".", "cputime", ",", "TIME_PRECISION", ")", "walltime_str", "=", "util", ".", "format...	44.119403	26.268657
def variant_support(variants, allele_support_df, ignore_missing=False): ''' Collect the read evidence support for the given variants. Parameters ---------- variants : iterable of varcode.Variant allele_support_df : dataframe Allele support dataframe, as output by the varlens-allele-su...	[ "def", "variant_support", "(", "variants", ",", "allele_support_df", ",", "ignore_missing", "=", "False", ")", ":", "missing", "=", "[", "c", "for", "c", "in", "EXPECTED_COLUMNS", "if", "c", "not", "in", "allele_support_df", ".", "columns", "]", "if", "missi...	35.14433	22.587629
def get_template(template_file='', **kwargs): """Get the Jinja2 template and renders with dict _kwargs_. Args: template_file (str): name of the template file kwargs: Keywords to use for rendering the Jinja2 template. Returns: String of rendered JSON template. """ template ...	[ "def", "get_template", "(", "template_file", "=", "''", ",", "", "", "kwargs", ")", ":", "template", "=", "get_template_object", "(", "template_file", ")", "LOG", ".", "info", "(", "'Rendering template %s'", ",", "template", ".", "filename", ")", "for", "k...	28.47619	19.285714
def commutes( m1: np.ndarray, m2: np.ndarray, *, rtol: float = 1e-5, atol: float = 1e-8) -> bool: """Determines if two matrices approximately commute. Two matrices A and B commute if they are square and have the same size and AB = BA. Args: m1: One of th...	[ "def", "commutes", "(", "m1", ":", "np", ".", "ndarray", ",", "m2", ":", "np", ".", "ndarray", ",", "*", ",", "rtol", ":", "float", "=", "1e-5", ",", "atol", ":", "float", "=", "1e-8", ")", "->", "bool", ":", "return", "(", "m1", ".", "shape", ...	31.458333	21
def create_new_csv(samples, args): """create csv file that can be use with bcbio -w template""" out_fn = os.path.splitext(args.csv)[0] + "-merged.csv" logger.info("Preparing new csv: %s" % out_fn) with file_transaction(out_fn) as tx_out: with open(tx_out, 'w') as handle: handle.write...	[ "def", "create_new_csv", "(", "samples", ",", "args", ")", ":", "out_fn", "=", "os", ".", "path", ".", "splitext", "(", "args", ".", "csv", ")", "[", "0", "]", "+", "\"-merged.csv\"", "logger", ".", "info", "(", "\"Preparing new csv: %s\"", "%", "out_fn"...	56.3	17.3
def store_hash_configuration(self, lshash): """ Stores hash configuration """ self.redis_object.set(lshash.hash_name+'_conf', pickle.dumps(lshash.get_config()))	[ "def", "store_hash_configuration", "(", "self", ",", "lshash", ")", ":", "self", ".", "redis_object", ".", "set", "(", "lshash", ".", "hash_name", "+", "'_conf'", ",", "pickle", ".", "dumps", "(", "lshash", ".", "get_config", "(", ")", ")", ")" ]	37.6	12
def args(self) -> str: """Provides arguments for the command.""" return '{}{}{}{}{}{}{}{}{}{}{}'.format( to_ascii_hex(self._index, 2), to_ascii_hex(self._group_number, 2), to_ascii_hex(self._unit_number, 2), to_ascii_hex(int(self._enable_status), 4), ...	[ "def", "args", "(", "self", ")", "->", "str", ":", "return", "'{}{}{}{}{}{}{}{}{}{}{}'", ".", "format", "(", "to_ascii_hex", "(", "self", ".", "_index", ",", "2", ")", ",", "to_ascii_hex", "(", "self", ".", "_group_number", ",", "2", ")", ",", "to_ascii_...	56.714286	18.642857
def clinvar_submission_lines(submission_objs, submission_header): """Create the lines to include in a Clinvar submission csv file from a list of submission objects and a custom document header Args: submission_objs(list): a list of objects (variants or casedata) to include in a csv file ...	[ "def", "clinvar_submission_lines", "(", "submission_objs", ",", "submission_header", ")", ":", "submission_lines", "=", "[", "]", "for", "submission_obj", "in", "submission_objs", ":", "# Loop over the submission objects. Each of these is a line", "csv_line", "=", "[", "]",...	54.5	35.636364
def main(argv: Optional[Sequence[str]] = None) -> None: """Parse arguments and process the exam assignment.""" parser = ArgumentParser(description="Convert Jupyter Notebook exams to PDFs") parser.add_argument( "--exam", type=int, required=True, help="Exam number to convert", ...	[ "def", "main", "(", "argv", ":", "Optional", "[", "Sequence", "[", "str", "]", "]", "=", "None", ")", "->", "None", ":", "parser", "=", "ArgumentParser", "(", "description", "=", "\"Convert Jupyter Notebook exams to PDFs\"", ")", "parser", ".", "add_argument",...	35.388889	21.166667
def create_waf(self, name, waf_type): """ Creates a WAF with the given type. :param name: Name of the WAF. :param waf_type: WAF type. ('mod_security', 'Snort', 'Imperva SecureSphere', 'F5 BigIP ASM', 'DenyAll rWeb') """ params = { 'name': name, 'ty...	[ "def", "create_waf", "(", "self", ",", "name", ",", "waf_type", ")", ":", "params", "=", "{", "'name'", ":", "name", ",", "'type'", ":", "waf_type", "}", "return", "self", ".", "_request", "(", "'POST'", ",", "'rest/wafs/new'", ",", "params", ")" ]	35.909091	16.818182
def hms(self, msg, tic=None, prt=sys.stdout): """Print elapsed time and message.""" if tic is None: tic = self.tic now = timeit.default_timer() hms = str(datetime.timedelta(seconds=(now-tic))) prt.write('{HMS}: {MSG}\n'.format(HMS=hms, MSG=msg)) return now	[ "def", "hms", "(", "self", ",", "msg", ",", "tic", "=", "None", ",", "prt", "=", "sys", ".", "stdout", ")", ":", "if", "tic", "is", "None", ":", "tic", "=", "self", ".", "tic", "now", "=", "timeit", ".", "default_timer", "(", ")", "hms", "=", ...	38.625	12.25
def tree_token_generator(el, indentation_level=0): """ Internal generator that yields tokens for the given HTML element as follows: - A tuple (LXML element, BEGIN, indentation_level) - Text right after the start of the tag, or None. - Recursively calls the token generator for all child objects ...	[ "def", "tree_token_generator", "(", "el", ",", "indentation_level", "=", "0", ")", ":", "if", "not", "isinstance", "(", "el", ".", "tag", ",", "string_class", ")", ":", "return", "tag_name", "=", "el", ".", "tag", ".", "lower", "(", ")", "is_indentation"...	24.944444	21.833333
def south_field_triple(self): "Returns a suitable description of this field for South." from south.modelsinspector import introspector field_class = "django.db.models.fields.CharField" args, kwargs = introspector(self) return (field_class, args, kwargs)	[ "def", "south_field_triple", "(", "self", ")", ":", "from", "south", ".", "modelsinspector", "import", "introspector", "field_class", "=", "\"django.db.models.fields.CharField\"", "args", ",", "kwargs", "=", "introspector", "(", "self", ")", "return", "(", "field_cl...	48	11.666667
def allByAge(self, cascadeFetch=False): ''' allByAge - Get the underlying objects which match the filter criteria, ordered oldest -> newest If you are doing a queue or just need the head/tail, consider .first() and .last() instead. @param cascadeFetch <bool> Default False, If True, all Foreign objects ass...	[ "def", "allByAge", "(", "self", ",", "cascadeFetch", "=", "False", ")", ":", "matchedKeys", "=", "self", ".", "getPrimaryKeys", "(", "sortByAge", "=", "True", ")", "if", "matchedKeys", ":", "return", "self", ".", "getMultiple", "(", "matchedKeys", ",", "ca...	43.5625	35.3125
def getPrinted(self): """ returns "0", "1" or "2" to indicate Printed state. 0 -> Never printed. 1 -> Printed after last publish 2 -> Printed but republished afterwards. """ workflow = getToolByName(self, 'portal_workflow') review_state = workflow.getI...	[ "def", "getPrinted", "(", "self", ")", ":", "workflow", "=", "getToolByName", "(", "self", ",", "'portal_workflow'", ")", "review_state", "=", "workflow", ".", "getInfoFor", "(", "self", ",", "'review_state'", ",", "''", ")", "if", "review_state", "not", "in...	37.954545	12.727273
def do_build(self, argv): """\ build [TARGETS] Build the specified TARGETS and their dependencies. 'b' is a synonym. """ import SCons.Node import SCons.SConsign import SCons.Script.Main options = copy.deepcopy(self.options...	[ "def", "do_build", "(", "self", ",", "argv", ")", ":", "import", "SCons", ".", "Node", "import", "SCons", ".", "SConsign", "import", "SCons", ".", "Script", ".", "Main", "options", "=", "copy", ".", "deepcopy", "(", "self", ".", "options", ")", "option...	39.927928	22.333333
def _define_jco_args(cmd_parser): """ Define job configuration arguments. Returns groups defined, currently one. """ jo_group = cmd_parser.add_argument_group('Job options', 'Job configuration options') jo_group.add_argument('--job-name', help='Job name') jo_group.add_argument('--preload', a...	[ "def", "_define_jco_args", "(", "cmd_parser", ")", ":", "jo_group", "=", "cmd_parser", ".", "add_argument_group", "(", "'Job options'", ",", "'Job configuration options'", ")", "jo_group", ".", "add_argument", "(", "'--job-name'", ",", "help", "=", "'Job name'", ")"...	53.625	41.25
def build_dependencies(self): """ Build the dependencies for this module. Parse the code with ast, find all the import statements, convert them into Dependency objects. """ highest = self.dsm or self.root if self is highest: highest = LeafNode() ...	[ "def", "build_dependencies", "(", "self", ")", ":", "highest", "=", "self", ".", "dsm", "or", "self", ".", "root", "if", "self", "is", "highest", ":", "highest", "=", "LeafNode", "(", ")", "for", "_import", "in", "self", ".", "parse_code", "(", ")", ...	37.555556	11.333333
def get_fixed_argv(self): # pragma: no cover """Get proper arguments for re-running the command. This is primarily for fixing some issues under Windows. First, there was a bug in Windows when running an executable located at a path with a space in it. This has become a non-iss...	[ "def", "get_fixed_argv", "(", "self", ")", ":", "# pragma: no cover", "argv", "=", "sys", ".", "argv", "[", ":", "]", "if", "sys", ".", "platform", "==", "'win32'", "and", "argv", "[", "0", "]", ".", "endswith", "(", "'.py'", ")", ":", "argv", ".", ...	44.142857	23.190476
def copy_package(owner, repo, identifier, destination): """Copy a package to another repository.""" client = get_packages_api() with catch_raise_api_exception(): data, _, headers = client.packages_copy_with_http_info( owner=owner, repo=repo, identifier=identifier...	[ "def", "copy_package", "(", "owner", ",", "repo", ",", "identifier", ",", "destination", ")", ":", "client", "=", "get_packages_api", "(", ")", "with", "catch_raise_api_exception", "(", ")", ":", "data", ",", "_", ",", "headers", "=", "client", ".", "packa...	32.285714	15.642857

def querymany(self, sql_query, columns, seq_of_parameters): """ Same as .query() but eventually call the .executemany() method of the underlying DBAPI2.0 cursor instead of .execute() """ tmp_query = self.__preparequery(sql_query, columns) if self.__methods[METHOD_MODULE]...

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def new(self, br, ino, sector_count, load_seg, media_name, system_type, platform_id, bootable): # type: (headervd.BootRecord, inode.Inode, int, int, str, int, int, bool) -> None ''' A method to create a new El Torito Boot Catalog. Parameters: br - The boot record th...

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42.6875

25.8125

def get_path(self, repo): """ Return the path for the repo """ if repo.endswith('.git'): repo = repo.split('.git')[0] org, name = repo.split('/')[-2:] path = self.plugins_dir path = join(path, org, name) return path, org, name

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def http_request(self, path="/", method="GET", host=None, port=None, json=False, data=None): """ perform a HTTP request :param path: str, path within the request, e.g. "/api/version" :param method: str, HTTP method :param host: str, if None, set to 127.0.0.1 :param port:...

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37.5

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def get_composition(self, composition_id): """Gets the ``Composition`` specified by its ``Id``. arg: composition_id (osid.id.Id): ``Id`` of the ``Composiiton`` return: (osid.repository.Composition) - the composition raise: NotFound - ``composition_id`` not found ...

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51.565217

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def _get_method_full_name(func): """ Return fully qualified function name. This method will attempt to find "full name" of the given function object. This full name is either of the form "<class name>.<method name>" if the function is a class method, or "<module name>.<func name>" if it's a regular...

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40.75

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def _get_block_result(chars_a, chars_b): """Get the first block from two character lists and compare If character list ``a`` begins with a digit, the :any:`_pop_digit` function is called on both lists to get blocks of all consecutive digits at the start of each list. If the length of the block retu...

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45.885714

20.228571

def amalgamate(colcount, snode, snptr, snpar, snpost, merge_function): """ Supernodal amalgamation. colcount, snode, snptr, snpar, snpost = ... amalgamate(colcount, snode, snptr, snpar, snpost, merge_function) PURPOSE Iterates over the clique tree in topological order and greedily ...

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28.987654

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def error_of_type(handler: astroid.ExceptHandler, error_type) -> bool: """ Check if the given exception handler catches the given error_type. The *handler* parameter is a node, representing an ExceptHandler node. The *error_type* can be an exception, such as AttributeError, the name of an excep...

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35.826087

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def Brkic_2011_1(Re, eD): r'''Calculates Darcy friction factor using the method in Brkic (2011) [2]_ as shown in [1]_. .. math:: f_d = [-2\log(10^{-0.4343\beta} + \frac{\epsilon}{3.71D})]^{-2} .. math:: \beta = \ln \frac{Re}{1.816\ln\left(\frac{1.1Re}{\ln(1+1.1Re)}\right)} Paramet...

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28.409091

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def from_apps(cls, apps): "Takes in an Apps and returns a VersionedProjectState matching it" app_models = {} for model in apps.get_models(include_swapped=True): model_state = VersionedModelState.from_model(model) app_models[(model_state.app_label, model_state.name.lower()...

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51.571429

23.571429

def render(self, text, add_header=False): """Render the HTML. Parameters ---------- add_header: boolean (default: False) If True, add HTML5 header and footer. Returns ------- str The rendered HTML. """ html = mark_text(te...

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27.9

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def defer(self, *args, **kwargs): """Call the function and immediately return an asynchronous object. The calling code will need to check for the result at a later time using: In Python 2/3 using ThreadPools - an AsyncResult (https://docs.python.org/2/library/multiprocessing.html#m...

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37.7

19.7

def forward_for_single_feature_map(self, anchors, objectness, box_regression): """ Arguments: anchors: list[BoxList] objectness: tensor of size N, A, H, W box_regression: tensor of size N, A * 4, H, W """ device = objectness.device N, A, H, W =...

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37.625

21.333333

def loads(xml, force_list=None): """Cria um dicionário com os dados do XML. O dicionário terá como chave o nome do nó root e como valor o conteúdo do nó root. Quando o conteúdo de um nó é uma lista de nós então o valor do nó será um dicionário com uma chave para cada nó. Entretanto, se existir nós,...

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34.642857

26.457143

def iofunctions(self): """Input/output functions of the model class.""" lines = Lines() for func in ('open_files', 'close_files', 'load_data', 'save_data'): if ((func == 'load_data') and (getattr(self.model.sequences, 'inputs', None) is None)): con...

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47.516129

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def load_texture(self, file_path): """Generate our sprite's surface by loading the specified image from disk. Note that this automatically centers the origin.""" self.image = pygame.image.load(file_path) self.apply_texture(self.image)

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52.6

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def plotstuff(self, T=[0, 1000]): """ Create a scatter plot of the contents of the database, with entries on the interval T. Parameters ---------- T : list Time interval. Returns ------- None ...

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25.184211

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def visit_For(self, node): """ OUT = (node,) + last body statements RAISES = body's that are not break or continue """ currs = (node,) break_currs = tuple() raises = () # handle body for n in node.body: self.result.add_node(n) ...

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34.472222

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def status(self): """ In most cases, reading status will return the same value as `mode`. In cases where there is an `auto` mode additional values may be returned, such as `no-device` or `error`. See individual port driver documentation for the full list of possible values. ...

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46

22

def _callable_contents(obj): """Return the signature contents of a callable Python object. """ try: # Test if obj is a method. return _function_contents(obj.__func__) except AttributeError: try: # Test if obj is a callable object. return _function_content...

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30

15.6

def get_text_path(self): """ Returns the path of the directory containing text if they exist in this dataset. """ for res in self.dsDoc['dataResources']: resPath = res['resPath'] resType = res['resType'] isCollection = res['isCollection'] i...

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43.307692

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def selection_index_to_idx(self, key, selection_index): '''return a mission idx from a selection_index''' a = key.split(' ') if a[0] != 'mission' or len(a) != 2: print("Bad mission object %s" % key) return None midx = int(a[1]) if midx < 0 or midx >= len(s...

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40.125

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def init_opdata(l, from_mod, version=None, is_pypy=False): """Sets up a number of the structures found in Python's opcode.py. Python opcode.py routines assign attributes to modules. In order to do this in a modular way here, the local dictionary for the module is passed. """ if version: ...

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37.035714

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def to_name(self) -> str: """ Convert to ANSI color name :return: ANSI color name """ return { self.BLACK: 'black', self.RED: 'red', self.GREEN: 'green', self.YELLOW: 'yellow', self.BLUE: 'blue', self.MAGENTA...

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26.866667

9.266667

def clear_all(self): """Delete all Mentions from given split the database.""" logger.info("Clearing ALL Mentions.") self.session.query(Mention).delete(synchronize_session="fetch") # With no Mentions, there should be no Candidates also self.session.query(Candidate).delete(synchro...

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49.5

21.5

def init_ui(self): """Setup control widget UI.""" self.control_layout = QHBoxLayout() self.setLayout(self.control_layout) self.reset_button = QPushButton() self.reset_button.setFixedSize(40, 40) self.reset_button.setIcon(QtGui.QIcon(WIN_PATH)) self.game_timer = QL...

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43.941176

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def register_actions(self, shortcut_manager): """Register callback methods for triggered actions :param rafcon.gui.shortcut_manager.ShortcutManager shortcut_manager: Shortcut Manager Object holding mappings between shortcuts and actions. """ super(DescriptionEditorController...

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def cluster_assignments(self): """ Return an array of cluster assignments corresponding to the most recent set of instances clustered. :return: the cluster assignments :rtype: ndarray """ array = javabridge.call(self.jobject, "getClusterAssignments", "()[D") if a...

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def eventFilter(self, watchedObject, event): """ Calls commitAndClose when the tab and back-tab are pressed. This is necessary because, normally the event filter of QStyledItemDelegate does this for us. However, that event filter works on this object, not on the sub editor. """ ...

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def run(self): """ Kill any open Redshift sessions for the given database. """ connection = self.output().connect() # kill any sessions other than ours and # internal Redshift sessions (rdsdb) query = ("select pg_terminate_backend(process) " "from...

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def submit_job(manager, job_config): """ Launch new job from specified config. May have been previously 'setup' if 'setup_params' in job_config is empty. """ # job_config is raw dictionary from JSON (from MQ or HTTP endpoint). job_id = job_config.get('job_id') try: command_line = job_con...

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def delete_dataset( self, name, retry=google.api_core.gapic_v1.method.DEFAULT, timeout=google.api_core.gapic_v1.method.DEFAULT, metadata=None, ): """ Deletes a dataset and all of its contents. Returns empty response in the ``response`` field when it co...

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def download(url, fname=None): """ Downloads a file. Args: url (str): The URL to download. fname (Optional[str]): The filename to store the downloaded file in. If `None`, take the filename from the URL. Defaults to `None`. Returns: The filename the URL was downloa...

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def swipe_bottom(self, steps=10, *args, **selectors): """ Swipe the UI object with *selectors* from center to bottom See `Swipe Left` for more details. """ self.device(**selectors).swipe.down(steps=steps)

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34.142857

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def _dictlist_to_lists(dl, *keys): ''' convert a list of dictionaries to a dictionary of lists >>> dl = [{'a': 'test', 'b': 3}, {'a': 'zaz', 'b': 444}, {'a': 'wow', 'b': 300}] >>> _dictlist_to_lists(dl) (['test', 'zaz', 'wow'], [3, 444, 300]) ''' lists = [] for k in keys: ...

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29

16.111111

def get_cloud_service(self, cloud_service_id): ''' The Get Cloud Service operation gets all the resources (job collections) in the cloud service. cloud_service_id: The cloud service id ''' _validate_not_none('cloud_service_id', cloud_service_id) path ...

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def create_table(table, connection, schema=None): """Create a single table, primarily used din migrations""" orig_schemas = {} # These schema shenanigans are almost certainly wrong. # But they are expedient. For Postgres, it puts the library # tables in the Library schema. We n...

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42.916667

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def list_results(self, number, username): """ [deprecated] 建議使用方法 `get_question_results()` """ # 取得新 API 的結果 data = self.get_question_results(number, username) # 實作相容的結構 result = [] for number in data: # 儲存題目資訊 result += [(number, d...

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27.538462

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def load(self, format=None, *, kwargs={}): ''' deserialize object from the file. auto detect format by file extension name if `format` is None. for example, `.json` will detect as `json`. * raise `FormatNotFoundError` on unknown format. * raise `SerializeError` on any s...

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def reasonable_desired_version(self, desired_version, allow_equal=False, allow_patch_skip=False): """ Determine whether the desired version is a reasonable next version. Parameters ---------- desired_version: str the proposed next ve...

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def _serialize_input_list(input_value): """Recursively serialize task input list""" input_list = [] for item in input_value: if isinstance(item, list): input_list.append(Task._serialize_input_list(item)) else: if isinstance(item, File): ...

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def modified_lines(self, r, file_name): """Returns the line numbers of a file which have been changed.""" cmd = self.file_diff_cmd(r, file_name) diff = shell_out_ignore_exitcode(cmd, cwd=self.root) return list(self.modified_lines_from_diff(diff))

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54.8

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def skew_matrix(w): '''Return the skew matrix of a direction w.''' return np.array([[0, -w[2], w[1]], [w[2], 0, -w[0]], [-w[1], w[0], 0]])

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36.8

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def bezout(a, b): '''Compute the bezout algorithm of a and b, i.e. it returns u, v, p such as: p = GCD(a,b) a * u + b * v = p Copied from http://www.labri.fr/perso/betrema/deug/poly/euclide.html. ''' u = 1 v = 0 s = 0 t = 1 while b > 0: q = a // b ...

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def untar_file(filename, location): """Untar the file (tar file located at filename) to the destination location""" if not os.path.exists(location): os.makedirs(location) if filename.lower().endswith('.gz') or filename.lower().endswith('.tgz'): mode = 'r:gz' elif filename.lower().endswit...

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39.156863

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def get_all_cpv_use(cp): ''' .. versionadded:: 2015.8.0 Uses portage to determine final USE flags and settings for an emerge. @type cp: string @param cp: eg cat/pkg @rtype: lists @return use, use_expand_hidden, usemask, useforce ''' cpv = _get_cpv(cp) portage = _get_portage() ...

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def AddIndex(self, path_segment_index): """Adds a path segment index and sets its weight to 0. Args: path_segment_index: an integer containing the path segment index. Raises: ValueError: if the path segment weights already contains the path segment index. """ if path_...

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def _work_path_to_rel_final_path(path, upload_path_mapping, upload_base_dir): """ Check if `path` is a work-rooted path, and convert to a relative final-rooted path """ if not path or not isinstance(path, str): return path upload_path = None # First, check in the mapping: if it's there is a...

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def _default_bridge(self): """ Get an instance of the ENBridge object using ctypes. """ objc = self.objc ENBridge = objc.objc_getClass('ENBridge') return objc.objc_msgSend(ENBridge, objc.sel_registerName('instance'))

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48.8

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def _try_switches(self, lines, index): """ For each switch in the Collector object, pass a list of string, representing lines of text in a file, and an index to the current line to try to flip the switch. A switch will only flip on if the line passes its 'test_on' method, and wil...

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def write_object_to_file(self, query_results, filename, fmt="csv", coerce_to_timestamp=False, record_time_added=False): """ Write query results to file. ...

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49.231481

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def plot_monthly_ic_heatmap(mean_monthly_ic, ax=None): """ Plots a heatmap of the information coefficient or returns by month. Parameters ---------- mean_monthly_ic : pd.DataFrame The mean monthly IC for N periods forward. Returns ------- ax : matplotlib.Axes The axes t...

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def recv_file_from_remote(dev, src_filename, dst_file, filesize): """Intended to be passed to the `remote` function as the xfer_func argument. Matches up with send_file_to_host. """ bytes_remaining = filesize if not HAS_BUFFER: bytes_remaining *= 2 # hexlify makes each byte into 2 bu...

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40.666667

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def inverse(x): """ Transform to Timedelta from numerical format """ try: x = [pd.Timedelta(int(i)) for i in x] except TypeError: x = pd.Timedelta(int(x)) return x

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25.222222

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def get_file(self, commit, path, offset_bytes=0, size_bytes=0, extract_value=True): """ Returns an iterator of the contents contents of a file at a specific Commit. Params: * commit: A tuple, string, or Commit object representing the commit. * path: The path of the file. ...

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def create_comment(self, body): """Create a comment on this issue. :param str body: (required), comment body :returns: :class:`IssueComment <github3.issues.comment.IssueComment>` """ json = None if body: url = self._build_url('comments', base_url=self._api) ...

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39

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def unique(s): """Return a list of the elements in s, but without duplicates. For example, unique([1,2,3,1,2,3]) is some permutation of [1,2,3], unique("abcabc") some permutation of ["a", "b", "c"], and unique(([1, 2], [2, 3], [1, 2])) some permutation of [[2, 3], [1, 2]]. For best speed, all ...

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31.823529

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def from_path_by_size(dir_path, min_size=0, max_size=1 << 40): """Create a new FileCollection, and select all files that size in a range:: dir_path = "your/path" # select by file size larger than 100MB fc = FileCollection.from_path_by_size( ...

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def _schema_options(p): """ Add options specific to schema subcommand. """ p.add_argument( 'resource', metavar='selector', nargs='?', default=None).completer = _schema_tab_completer p.add_argument( '--summary', action="store_true", help="Summarize counts of available resourc...

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def parse(self, fail_callback=None): """ Parse text fields and file fields for values and files """ # get text fields for field in self.field_arguments: self.values[field['name']] = self.__get_value(field['name']) if self.values[field['name']] is None and field['requ...

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49.5625

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def _get_client(self): """ S3 Boto3 client Returns: boto3.session.Session.client: client """ client_kwargs = self._storage_parameters.get('client', dict()) # Handles unsecure mode if self._unsecure: client_kwargs = client_kwargs.copy() ...

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27.6

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def text(files): '''Returns the whole transcribed text''' sentences = convert_timestamps(files) out = [] for s in sentences: out.append(' '.join([w[0] for w in s['words']])) return '\n'.join(out)

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def find_range(self, interval): """wrapper for find""" return self.find(self.tree, interval, self.start, self.end)

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42.666667

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def ystep(self): r"""Minimise Augmented Lagrangian with respect to :math:`\mathbf{y}`. """ self.Y = np.asarray(sp.prox_l2( self.AX + self.U, (self.lmbda/self.rho)*self.Wtvna, axis=self.saxes), dtype=self.dtype)

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32.5

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def _find_files(dirpath: str) -> 'Iterable[str]': """Find files recursively. Returns a generator that yields paths in no particular order. """ for dirpath, dirnames, filenames in os.walk(dirpath, topdown=True, followlinks=True): if os.path.basenam...

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def install_twisted(): """ If twisted is available, make `emit' return a DeferredList This has been successfully tested with Twisted 14.0 and later. """ global emit, _call_partial try: from twisted.internet import defer emit = _emit_twisted _call_partial = defer.maybeDef...

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28.933333

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def draw(self, **kwargs): """ Called from the fit method, this method creates the canvas and draws the distribution plot on it. Parameters ---------- kwargs: generic keyword arguments. """ # Prepare the data bins = np.arange(self.N) word...

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32.064516

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def create_all(self, progress_callback: Optional[callable] = None) -> Dict[str, object]: """ Creates all the models discovered from fixture files in :attr:`fixtures_dir`. :param progress_callback: An optional function to track progress. It must take three paramete...

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46.953488

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def concat(cls, variables, dim='concat_dim', positions=None, shortcut=False): """Specialized version of Variable.concat for IndexVariable objects. This exists because we want to avoid converting Index objects to NumPy arrays, if possible. """ if not isinstance(dim...

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def make_xeditable(instance=None, extra_attrs=[], *args, **kwargs): """ Converts the contents of the column into an ``<a>`` tag with the required DOM attributes to power the X-Editable UI. The following keyword arguments are all optional, but may be provided when pre-calling the helper, to customiz...

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45.315315

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def _exec_config_str(self, lhs, rhs): """execute self.config.<lhs> = <rhs> * expands ~ with expanduser * tries to assign with raw eval, otherwise assigns with just the string, allowing `--C.a=foobar` and `--C.a="foobar"` to be equivalent. *Not* equivalent are `--C.a...

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39.421053

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def current_time(self) -> datetime: """Extract current time.""" _date = datetime.strptime(self.obj.SBRes.SBReq.StartT.get("date"), "%Y%m%d") _time = datetime.strptime(self.obj.SBRes.SBReq.StartT.get("time"), "%H:%M") return datetime.combine(_date.date(), _time.time())

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def make_url(contents, domain=DEFAULT_DOMAIN, force_gist=False, size_for_gist=MAX_URL_LEN): """ Returns the URL to open given the domain and contents. If the file contents are large, an anonymous gist will be created. Parameters ---------- contents * string - assumed to be...

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def get_choices(module_name): """ Retrieve members from ``module_name``'s ``__all__`` list. :rtype: list """ try: module = importlib.import_module(module_name) if hasattr(module, '__all__'): return module.__all__ else: return [name for name, _ in insp...

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def get_repo_data(saltenv='base'): ''' Returns the existing package metadata db. Will create it, if it does not exist, however will not refresh it. Args: saltenv (str): Salt environment. Default ``base`` Returns: dict: A dict containing contents of metadata db. CLI Example: ...

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32.446809

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def _error_repr(error): """A compact unique representation of an error.""" error_repr = repr(error) if len(error_repr) > 200: error_repr = hash(type(error)) return error_repr

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32.166667

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def _mitogen_reset(self, mode): """ Forget everything we know about the connected context. This function cannot be called _reset() since that name is used as a public API by Ansible 2.4 wait_for_connection plug-in. :param str mode: Name of ContextService method to us...

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def _next_pattern(self): """Parses the next pattern by matching each in turn.""" current_state = self.state_stack[-1] position = self._position for pattern in self.patterns: if current_state not in pattern.states: continue m = pattern.regex.match(...

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def notebook_system_output(): """Get a context manager that attempts to use `wurlitzer <https://github.com/minrk/wurlitzer>`__ to capture system-level stdout/stderr within a Jupyter Notebook shell, without affecting normal operation when run as a Python script. For example: >>> sys_pipes = sporco.u...

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def output_after_run(self, run): """ The method output_after_run() prints filename, result, time and status of a run to terminal and stores all data in XML """ # format times, type is changed from float to string! cputime_str = util.format_number(run.cputime, TIME_PRECIS...

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44.119403

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def variant_support(variants, allele_support_df, ignore_missing=False): ''' Collect the read evidence support for the given variants. Parameters ---------- variants : iterable of varcode.Variant allele_support_df : dataframe Allele support dataframe, as output by the varlens-allele-su...

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def get_template(template_file='', **kwargs): """Get the Jinja2 template and renders with dict _kwargs_. Args: template_file (str): name of the template file kwargs: Keywords to use for rendering the Jinja2 template. Returns: String of rendered JSON template. """ template ...

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28.47619

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def commutes( m1: np.ndarray, m2: np.ndarray, *, rtol: float = 1e-5, atol: float = 1e-8) -> bool: """Determines if two matrices approximately commute. Two matrices A and B commute if they are square and have the same size and AB = BA. Args: m1: One of th...

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31.458333

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def create_new_csv(samples, args): """create csv file that can be use with bcbio -w template""" out_fn = os.path.splitext(args.csv)[0] + "-merged.csv" logger.info("Preparing new csv: %s" % out_fn) with file_transaction(out_fn) as tx_out: with open(tx_out, 'w') as handle: handle.write...

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56.3

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def store_hash_configuration(self, lshash): """ Stores hash configuration """ self.redis_object.set(lshash.hash_name+'_conf', pickle.dumps(lshash.get_config()))

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37.6

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def args(self) -> str: """Provides arguments for the command.""" return '{}{}{}{}{}{}{}{}{}{}{}'.format( to_ascii_hex(self._index, 2), to_ascii_hex(self._group_number, 2), to_ascii_hex(self._unit_number, 2), to_ascii_hex(int(self._enable_status), 4), ...

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56.714286

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def clinvar_submission_lines(submission_objs, submission_header): """Create the lines to include in a Clinvar submission csv file from a list of submission objects and a custom document header Args: submission_objs(list): a list of objects (variants or casedata) to include in a csv file ...

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54.5

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def main(argv: Optional[Sequence[str]] = None) -> None: """Parse arguments and process the exam assignment.""" parser = ArgumentParser(description="Convert Jupyter Notebook exams to PDFs") parser.add_argument( "--exam", type=int, required=True, help="Exam number to convert", ...

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35.388889

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def create_waf(self, name, waf_type): """ Creates a WAF with the given type. :param name: Name of the WAF. :param waf_type: WAF type. ('mod_security', 'Snort', 'Imperva SecureSphere', 'F5 BigIP ASM', 'DenyAll rWeb') """ params = { 'name': name, 'ty...

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35.909091

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def hms(self, msg, tic=None, prt=sys.stdout): """Print elapsed time and message.""" if tic is None: tic = self.tic now = timeit.default_timer() hms = str(datetime.timedelta(seconds=(now-tic))) prt.write('{HMS}: {MSG}\n'.format(HMS=hms, MSG=msg)) return now

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38.625

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def tree_token_generator(el, indentation_level=0): """ Internal generator that yields tokens for the given HTML element as follows: - A tuple (LXML element, BEGIN, indentation_level) - Text right after the start of the tag, or None. - Recursively calls the token generator for all child objects ...

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24.944444

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def south_field_triple(self): "Returns a suitable description of this field for South." from south.modelsinspector import introspector field_class = "django.db.models.fields.CharField" args, kwargs = introspector(self) return (field_class, args, kwargs)

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def allByAge(self, cascadeFetch=False): ''' allByAge - Get the underlying objects which match the filter criteria, ordered oldest -> newest If you are doing a queue or just need the head/tail, consider .first() and .last() instead. @param cascadeFetch <bool> Default False, If True, all Foreign objects ass...

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def getPrinted(self): """ returns "0", "1" or "2" to indicate Printed state. 0 -> Never printed. 1 -> Printed after last publish 2 -> Printed but republished afterwards. """ workflow = getToolByName(self, 'portal_workflow') review_state = workflow.getI...

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def do_build(self, argv): """\ build [TARGETS] Build the specified TARGETS and their dependencies. 'b' is a synonym. """ import SCons.Node import SCons.SConsign import SCons.Script.Main options = copy.deepcopy(self.options...

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def _define_jco_args(cmd_parser): """ Define job configuration arguments. Returns groups defined, currently one. """ jo_group = cmd_parser.add_argument_group('Job options', 'Job configuration options') jo_group.add_argument('--job-name', help='Job name') jo_group.add_argument('--preload', a...

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53.625

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def build_dependencies(self): """ Build the dependencies for this module. Parse the code with ast, find all the import statements, convert them into Dependency objects. """ highest = self.dsm or self.root if self is highest: highest = LeafNode() ...

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def get_fixed_argv(self): # pragma: no cover """Get proper arguments for re-running the command. This is primarily for fixing some issues under Windows. First, there was a bug in Windows when running an executable located at a path with a space in it. This has become a non-iss...

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def copy_package(owner, repo, identifier, destination): """Copy a package to another repository.""" client = get_packages_api() with catch_raise_api_exception(): data, _, headers = client.packages_copy_with_http_info( owner=owner, repo=repo, identifier=identifier...

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