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

text stringlengths 75 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 0.18
def frompsl(args): """ %prog frompsl old.new.psl old.fasta new.fasta Generate chain file from psl file. The pipeline is describe in: <http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver> """ from jcvi.formats.sizes import Sizes p = OptionParser(frompsl.__doc__) opts, args =...	[ "def", "frompsl", "(", "args", ")", ":", "from", "jcvi", ".", "formats", ".", "sizes", "import", "Sizes", "p", "=", "OptionParser", "(", "frompsl", ".", "__doc__", ")", "opts", ",", "args", "=", "p", ".", "parse_args", "(", "args", ")", "if", "len", ...	32.557692	0.000573
def getInstitutions(self, tags = None, seperator = ";", _getTag = False): """Returns a list of the names of institutions. This is done by looking (in order) for any of fields in _tags_ and splitting the strings on _seperator_ (in case of multiple institutions). If no strings are found an empty list will be retu...	[ "def", "getInstitutions", "(", "self", ",", "tags", "=", "None", ",", "seperator", "=", "\";\"", ",", "_getTag", "=", "False", ")", ":", "return", "self", ".", "getInvestigators", "(", "tags", "=", "tags", ",", "seperator", "=", "seperator", ",", "_getTa...	39.954545	0.018889
def create_birthday(min_age=18, max_age=80): """ Create a random birthday fomr someone between the ages of min_age and max_age """ age = random.randint(min_age, max_age) start = datetime.date.today() - datetime.timedelta(days=random.randint(0, 365)) return start - datetime.timedelta(days=age * 3...	[ "def", "create_birthday", "(", "min_age", "=", "18", ",", "max_age", "=", "80", ")", ":", "age", "=", "random", ".", "randint", "(", "min_age", ",", "max_age", ")", "start", "=", "datetime", ".", "date", ".", "today", "(", ")", "-", "datetime", ".", ...	45.285714	0.009288
def register(self, object_tool_class, model_class=None): """ Registers the given model(s) with the given object tool class. The model(s) should be Model classes, not instances. If a model class isn't given the object tool class will be registered for all models. If a m...	[ "def", "register", "(", "self", ",", "object_tool_class", ",", "model_class", "=", "None", ")", ":", "if", "not", "object_tool_class", ":", "return", "None", "# Don't validate unless required.", "if", "object_tool_class", "and", "settings", ".", "DEBUG", ":", "fro...	35.947368	0.001426
def from_string(url, default_protocol='telnet'): """ Parses the given URL and returns an URL object. There are some differences to Python's built-in URL parser: - It is less strict, many more inputs are accepted. This is necessary to allow for passing a simple hostname as a UR...	[ "def", "from_string", "(", "url", ",", "default_protocol", "=", "'telnet'", ")", ":", "if", "url", "is", "None", ":", "raise", "TypeError", "(", "'Expected string but got'", "+", "type", "(", "url", ")", ")", "# Extract the protocol name from the URL.", "result", ...	34.441176	0.00083
def line(surf, start, end, color=BLACK, width=1, style=FLAT): """Draws an antialiased line on the surface.""" width = round(width, 1) if width == 1: # return pygame.draw.aaline(surf, color, start, end) return gfxdraw.line(surf, start, end, color) start = V2(start) end = V2(end)...	[ "def", "line", "(", "surf", ",", "start", ",", "end", ",", "color", "=", "BLACK", ",", "width", "=", "1", ",", "style", "=", "FLAT", ")", ":", "width", "=", "round", "(", "width", ",", "1", ")", "if", "width", "==", "1", ":", "# return pygame.dra...	25.638889	0.001044
def dumps_tabledata(value, format_name="rst_grid_table", **kwargs): """ :param tabledata.TableData value: Tabular data to dump. :param str format_name: Dumped format name of tabular data. Available formats are described in :py:meth:`~pytablewriter.TableWriterFactory.create_from_forma...	[ "def", "dumps_tabledata", "(", "value", ",", "format_name", "=", "\"rst_grid_table\"", ",", "", "", "kwargs", ")", ":", "from", ".", "_factory", "import", "TableWriterFactory", "if", "not", "value", ":", "raise", "TypeError", "(", "\"value must be a tabledata.Ta...	28.944444	0.000929
def save_schedule(self): ''' Save the current schedule ''' self.persist() # Fire the complete event back along with the list of schedule evt = salt.utils.event.get_event('minion', opts=self.opts, listen=False) evt.fire_event({'complete': True}, ...	[ "def", "save_schedule", "(", "self", ")", ":", "self", ".", "persist", "(", ")", "# Fire the complete event back along with the list of schedule", "evt", "=", "salt", ".", "utils", ".", "event", ".", "get_event", "(", "'minion'", ",", "opts", "=", "self", ".", ...	35.7	0.008197
def start(): ''' Start simple_server() ''' from wsgiref.simple_server import make_server # When started outside of salt-api __opts__ will not be injected if '__opts__' not in globals(): globals()['__opts__'] = get_opts() if __virtual__() is False: raise SystemExit(1...	[ "def", "start", "(", ")", ":", "from", "wsgiref", ".", "simple_server", "import", "make_server", "# When started outside of salt-api __opts__ will not be injected", "if", "'__opts__'", "not", "in", "globals", "(", ")", ":", "globals", "(", ")", "[", "'__opts__'", "]...	24.772727	0.001767
def Disc( pos=(0, 0, 0), normal=(0, 0, 1), r1=0.5, r2=1, c="coral", bc="darkgreen", lw=1, alpha=1, res=12, resphi=None, ): """ Build a 2D disc of internal radius `r1` and outer radius `r2`, oriented perpendicular to `normal`. \|Disk\| """ ps = vtk.vtkDi...	[ "def", "Disc", "(", "pos", "=", "(", "0", ",", "0", ",", "0", ")", ",", "normal", "=", "(", "0", ",", "0", ",", "1", ")", ",", "r1", "=", "0.5", ",", "r2", "=", "1", ",", "c", "=", "\"coral\"", ",", "bc", "=", "\"darkgreen\"", ",", "lw", ...	25.666667	0.001317
def lock(self): # type: () -> Installer """ Prepare the installer for locking only. """ self.update() self.execute_operations(False) self._lock = True return self	[ "def", "lock", "(", "self", ")", ":", "# type: () -> Installer", "self", ".", "update", "(", ")", "self", ".", "execute_operations", "(", "False", ")", "self", ".", "_lock", "=", "True", "return", "self" ]	23.555556	0.009091
def is_connected(self): """Return connection status""" self._connected = self._connected and self._conn.is_connected() return self._connected	[ "def", "is_connected", "(", "self", ")", ":", "self", ".", "_connected", "=", "self", ".", "_connected", "and", "self", ".", "_conn", ".", "is_connected", "(", ")", "return", "self", ".", "_connected" ]	40.5	0.012121
def __isValidZIP(self, suffix): """Determine if the suffix is `.zip` format""" if suffix and isinstance(suffix, string_types): if suffix.endswith(".zip"): return True return False	[ "def", "__isValidZIP", "(", "self", ",", "suffix", ")", ":", "if", "suffix", "and", "isinstance", "(", "suffix", ",", "string_types", ")", ":", "if", "suffix", ".", "endswith", "(", "\".zip\"", ")", ":", "return", "True", "return", "False" ]	38.5	0.008475
def read_json(directory, data_files='data/js/tweets/*.js'): ''' Scrape a twitter archive file. Inspiration from https://github.com/mshea/Parse-Twitter-Archive ''' files = path.join(directory, data_files) for fname in iglob(files): with open(fname, 'r') as f: # Twitter's JSON...	[ "def", "read_json", "(", "directory", ",", "data_files", "=", "'data/js/tweets/*.js'", ")", ":", "files", "=", "path", ".", "join", "(", "directory", ",", "data_files", ")", "for", "fname", "in", "iglob", "(", "files", ")", ":", "with", "open", "(", "fna...	30.8125	0.001969
def get_entry_point(key, value): """Check if registered entry point is available for a given name and load it. Otherwise, return None. key (unicode): Entry point name. value (unicode): Name of entry point to load. RETURNS: The loaded entry point or None. """ for entry_point in pkg_resources...	[ "def", "get_entry_point", "(", "key", ",", "value", ")", ":", "for", "entry_point", "in", "pkg_resources", ".", "iter_entry_points", "(", "key", ")", ":", "if", "entry_point", ".", "name", "==", "value", ":", "return", "entry_point", ".", "load", "(", ")" ...	37.272727	0.002381
def write_pp_file(filename,pp_df): """write a pilot points dataframe to a pilot points file Parameters ---------- filename : str pilot points file to write pp_df : pandas.DataFrame a dataframe that has columns "x","y","zone", and "value" """ with open(filename,'w') as f: ...	[ "def", "write_pp_file", "(", "filename", ",", "pp_df", ")", ":", "with", "open", "(", "filename", ",", "'w'", ")", "as", "f", ":", "f", ".", "write", "(", "pp_df", ".", "to_string", "(", "col_space", "=", "0", ",", "columns", "=", "PP_NAMES", ",", ...	32.944444	0.014754
def cdx_sort_closest(closest, cdx_iter, limit=10): """ sort CDXCaptureResult by closest to timestamp. """ closest_cdx = [] closest_keys = [] closest_sec = timestamp_to_sec(closest) for cdx in cdx_iter: sec = timestamp_to_sec(cdx[TIMESTAMP]) key = abs(closest_sec - sec) ...	[ "def", "cdx_sort_closest", "(", "closest", ",", "cdx_iter", ",", "limit", "=", "10", ")", ":", "closest_cdx", "=", "[", "]", "closest_keys", "=", "[", "]", "closest_sec", "=", "timestamp_to_sec", "(", "closest", ")", "for", "cdx", "in", "cdx_iter", ":", ...	27.241379	0.002445
def _parse_file(cls, path, pickle=False): """parse a .chain file into a list of the type [(L{Chain}, arr, arr, arr) ...] :param fname: name of the file""" fname = path if fname.endswith(".gz"): fname = path[:-3] if fname.endswith('.pkl'): #you asked for...	[ "def", "_parse_file", "(", "cls", ",", "path", ",", "pickle", "=", "False", ")", ":", "fname", "=", "path", "if", "fname", ".", "endswith", "(", "\".gz\"", ")", ":", "fname", "=", "path", "[", ":", "-", "3", "]", "if", "fname", ".", "endswith", "...	43.038462	0.008741
def import_field(field_classpath): """ Imports a field by its dotted class path, prepending "django.db.models" to raw class names and raising an exception if the import fails. """ if '.' in field_classpath: fully_qualified = field_classpath else: fully_qualified = "django.db.mode...	[ "def", "import_field", "(", "field_classpath", ")", ":", "if", "'.'", "in", "field_classpath", ":", "fully_qualified", "=", "field_classpath", "else", ":", "fully_qualified", "=", "\"django.db.models.%s\"", "%", "field_classpath", "try", ":", "return", "import_dotted_...	42	0.001553
def merge(self, evaluation_context: 'EvaluationContext') -> None: """ Merges the provided evaluation context to the current evaluation context. :param evaluation_context: Evaluation context to merge. """ self.global_context.merge(evaluation_context.global_context) self.lo...	[ "def", "merge", "(", "self", ",", "evaluation_context", ":", "'EvaluationContext'", ")", "->", "None", ":", "self", ".", "global_context", ".", "merge", "(", "evaluation_context", ".", "global_context", ")", "self", ".", "local_context", ".", "merge", "(", "ev...	52.142857	0.008086
def plot(self, ax, scatter=True, grid=True, progress_colors=True, progress_max=1., depth=10, plot_dims=[0,1]): """ Plot a projection on 2D of the Tree. Parameters ---------- ax : plt axis scatter : bool If the points are ploted grid : bool ...	[ "def", "plot", "(", "self", ",", "ax", ",", "scatter", "=", "True", ",", "grid", "=", "True", ",", "progress_colors", "=", "True", ",", "progress_max", "=", "1.", ",", "depth", "=", "10", ",", "plot_dims", "=", "[", "0", ",", "1", "]", ")", ":", ...	33.62963	0.009636
def wrap(text, width=70, **kwargs): """Wrap a single paragraph of text, returning a list of wrapped lines. Reformat the single paragraph in 'text' so it fits in lines of no more than 'width' columns, and return a list of wrapped lines. By default, tabs in 'text' are expanded with string.expandtabs(), ...	[ "def", "wrap", "(", "text", ",", "width", "=", "70", ",", "", "", "kwargs", ")", ":", "w", "=", "TextWrapper", "(", "width", "=", "width", ",", "", "", "kwargs", ")", "return", "w", ".", "wrap", "(", "text", ")" ]	46.5	0.001757
def contains(self, url: str): '''Return whether the URL is in the table.''' try: self.get_one(url) except NotFound: return False else: return True	[ "def", "contains", "(", "self", ",", "url", ":", "str", ")", ":", "try", ":", "self", ".", "get_one", "(", "url", ")", "except", "NotFound", ":", "return", "False", "else", ":", "return", "True" ]	23	0.009302
def __setkey(key): """ Set up the key schedule from the encryption key. """ global C, D, KS, E shifts = (1, 1, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 1) # First, generate C and D by permuting the key. The lower order bit of each # 8-bit char is not used, so C and D are only 28 bits apiece....	[ "def", "__setkey", "(", "key", ")", ":", "global", "C", ",", "D", ",", "KS", ",", "E", "shifts", "=", "(", "1", ",", "1", ",", "2", ",", "2", ",", "2", ",", "2", ",", "2", ",", "2", ",", "1", ",", "2", ",", "2", ",", "2", ",", "2", ...	25.351351	0.001027
def _expand_if_needed(self, dims, write_dims, start, offset): """ expand the on-disk image if the indended write will extend beyond the existing dimensions """ from operator import mul if numpy.isscalar(start): start_is_scalar = True else: ...	[ "def", "_expand_if_needed", "(", "self", ",", "dims", ",", "write_dims", ",", "start", ",", "offset", ")", ":", "from", "operator", "import", "mul", "if", "numpy", ".", "isscalar", "(", "start", ")", ":", "start_is_scalar", "=", "True", "else", ":", "sta...	34.759259	0.001036
def mean(arrays, masks=None, dtype=None, out=None, zeros=None, scales=None, weights=None): """Combine arrays using the mean, with masks and offsets. Arrays and masks are a list of array objects. All input arrays have the same shape. If present, the masks have the same shape also. ...	[ "def", "mean", "(", "arrays", ",", "masks", "=", "None", ",", "dtype", "=", "None", ",", "out", "=", "None", ",", "zeros", "=", "None", ",", "scales", "=", "None", ",", "weights", "=", "None", ")", ":", "return", "generic_combine", "(", "intl_combine...	36.131579	0.000709
def timelag_filter(function, pad=True, index=0): '''Filtering in the time-lag domain. This is primarily useful for adapting image filters to operate on `recurrence_to_lag` output. Using `timelag_filter` is equivalent to the following sequence of operations: >>> data_tl = librosa.segment.recur...	[ "def", "timelag_filter", "(", "function", ",", "pad", "=", "True", ",", "index", "=", "0", ")", ":", "def", "__my_filter", "(", "wrapped_f", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "'''Decorator to wrap the filter'''", "# Map the input data into t...	32.542169	0.000359
def select_ignore_interrupts(iwtd, owtd, ewtd, timeout=None): '''This is a wrapper around select.select() that ignores signals. If select.select raises a select.error exception and errno is an EINTR error then it is ignored. Mainly this is used to ignore sigwinch (terminal resize). ''' # if select...	[ "def", "select_ignore_interrupts", "(", "iwtd", ",", "owtd", ",", "ewtd", ",", "timeout", "=", "None", ")", ":", "# if select() is interrupted by a signal (errno==EINTR) then", "# we loop back and enter the select() again.", "if", "timeout", "is", "not", "None", ":", "end...	40.518519	0.000893
def trunk_mode(self, **kwargs): """Set trunk mode (trunk, trunk-no-default-vlan). Args: int_type (str): Type of interface. (gigabitethernet, tengigabitethernet, etc) name (str): Name of interface. (1/0/5, 1/0/10, etc) mode (str): Trunk port mode (trun...	[ "def", "trunk_mode", "(", "self", ",", "", "", "kwargs", ")", ":", "int_type", "=", "kwargs", ".", "pop", "(", "'int_type'", ")", ".", "lower", "(", ")", "name", "=", "kwargs", ".", "pop", "(", "'name'", ")", "mode", "=", "kwargs", ".", "pop", ...	42.885246	0.000747
def addConcept(self, conceptUri, weight, label = None, conceptType = None): """ add a relevant concept to the topic page @param conceptUri: uri of the concept to be added @param weight: importance of the provided concept (typically in range 1 - 50) """ assert isinstance(w...	[ "def", "addConcept", "(", "self", ",", "conceptUri", ",", "weight", ",", "label", "=", "None", ",", "conceptType", "=", "None", ")", ":", "assert", "isinstance", "(", "weight", ",", "(", "float", ",", "int", ")", ")", ",", "\"weight value has to be a posit...	54.909091	0.019544
def baseline_or_audit(self, allow_deletion=False, audit_only=False): """Baseline synchonization or audit. Both functions implemented in this routine because audit is a prerequisite for a baseline sync. In the case of baseline sync the last timestamp seen is recorded as client state. ...	[ "def", "baseline_or_audit", "(", "self", ",", "allow_deletion", "=", "False", ",", "audit_only", "=", "False", ")", ":", "action", "=", "(", "'audit'", "if", "(", "audit_only", ")", "else", "'baseline sync'", ")", "self", ".", "logger", ".", "debug", "(", ...	50.313953	0.00204
def recall(self): """Calculates recall :return: Recall """ true_pos = self.matrix[0][0] false_neg = self.matrix[0][1] return divide(1.0 * true_pos, true_pos + false_neg)	[ "def", "recall", "(", "self", ")", ":", "true_pos", "=", "self", ".", "matrix", "[", "0", "]", "[", "0", "]", "false_neg", "=", "self", ".", "matrix", "[", "0", "]", "[", "1", "]", "return", "divide", "(", "1.0", "*", "true_pos", ",", "true_pos",...	26.375	0.009174
def run(addr, commands, kwargs): """ Non-threaded batch command runner returning output results """ results = [] handler = VarnishHandler(addr, *kwargs) for cmd in commands: if isinstance(cmd, tuple) and len(cmd)>1: results.extend([getattr(handler, c[0].replace('.','_'))(...	[ "def", "run", "(", "addr", ",", "", "commands", ",", "", "", "kwargs", ")", ":", "results", "=", "[", "]", "handler", "=", "VarnishHandler", "(", "addr", ",", "", "*", "kwargs", ")", "for", "cmd", "in", "commands", ":", "if", "isinstance", "(",...	34.428571	0.012121
def rio_save(self, filename, fformat=None, fill_value=None, dtype=np.uint8, compute=True, tags=None, keep_palette=False, cmap=None, **format_kwargs): """Save the image using rasterio. Overviews can be added to the file using the `overviews` kwarg, eg::...	[ "def", "rio_save", "(", "self", ",", "filename", ",", "fformat", "=", "None", ",", "fill_value", "=", "None", ",", "dtype", "=", "np", ".", "uint8", ",", "compute", "=", "True", ",", "tags", "=", "None", ",", "keep_palette", "=", "False", ",", "cmap"...	39.656863	0.001206
def cube2map(data_cube, layout): r"""Cube to Map This method transforms the input data from a 3D cube to a 2D map with a specified layout Parameters ---------- data_cube : np.ndarray Input data cube, 3D array of 2D images Layout : tuple 2D layout of 2D images Returns ...	[ "def", "cube2map", "(", "data_cube", ",", "layout", ")", ":", "if", "data_cube", ".", "ndim", "!=", "3", ":", "raise", "ValueError", "(", "'The input data must have 3 dimensions.'", ")", "if", "data_cube", ".", "shape", "[", "0", "]", "!=", "np", ".", "pro...	24.444444	0.000874
def regularization(variables, regtype, regcoef, name="regularization"): """Compute the regularization tensor. Parameters ---------- variables : list of tf.Variable List of model variables. regtype : str Type of regularization. Can be ["none", "l1", "l2"...	[ "def", "regularization", "(", "variables", ",", "regtype", ",", "regcoef", ",", "name", "=", "\"regularization\"", ")", ":", "with", "tf", ".", "name_scope", "(", "name", ")", ":", "if", "regtype", "!=", "'none'", ":", "regs", "=", "tf", ".", "constant",...	28.571429	0.001934
def dumps(data, **kwargs): """Convert a PPMP entity to JSON. Additional arguments are the same as accepted by `json.dumps`.""" def _encoder(value): if isinstance(value, datetime.datetime): return value.isoformat() if hasattr(value, "_data"): return value._data ...	[ "def", "dumps", "(", "data", ",", "", "", "kwargs", ")", ":", "def", "_encoder", "(", "value", ")", ":", "if", "isinstance", "(", "value", ",", "datetime", ".", "datetime", ")", ":", "return", "value", ".", "isoformat", "(", ")", "if", "hasattr", ...	29.571429	0.002342
def run_from_cli(): """ Perform an update instigated from a CLI. """ arg_parser = argparse.ArgumentParser( description='Read and write properties in a wp-config.php file. ' 'Include a --value argument to set the value, omit it to ' 'read the value of the ...	[ "def", "run_from_cli", "(", ")", ":", "arg_parser", "=", "argparse", ".", "ArgumentParser", "(", "description", "=", "'Read and write properties in a wp-config.php file. '", "'Include a --value argument to set the value, omit it to '", "'read the value of the specified key.'", ",", ...	30.261538	0.000492
def as_yaml(self): """ as_yaml """ self.set_reprdict_from_attributes() return "---\n" + yaml.dump(self.m_reprdict, default_flow_style=False)	[ "def", "as_yaml", "(", "self", ")", ":", "self", ".", "set_reprdict_from_attributes", "(", ")", "return", "\"---\\n\"", "+", "yaml", ".", "dump", "(", "self", ".", "m_reprdict", ",", "default_flow_style", "=", "False", ")" ]	29.166667	0.011111
def fromxml(node): """Static method return an OutputTemplate instance from the given XML description. Node can be a string or an etree._Element.""" if not isinstance(node,ElementTree._Element): #pylint: disable=protected-access node = parsexmlstring(node) assert node.tag.lower() == '...	[ "def", "fromxml", "(", "node", ")", ":", "if", "not", "isinstance", "(", "node", ",", "ElementTree", ".", "_Element", ")", ":", "#pylint: disable=protected-access", "node", "=", "parsexmlstring", "(", "node", ")", "assert", "node", ".", "tag", ".", "lower", ...	47.162791	0.010145
def get_validation_col_names(df): """ Input: validated pandas DataFrame (using validate_df) Output: names of all value validation columns, names of all presence validation columns, names of all type validation columns, names of all missing group columns, names...	[ "def", "get_validation_col_names", "(", "df", ")", ":", "value_cols", "=", "df", ".", "columns", ".", "str", ".", "match", "(", "\"^value_pass_\"", ")", "present_cols", "=", "df", ".", "columns", ".", "str", ".", "match", "(", "\"^presence_pass\"", ")", "t...	46.208333	0.001767
def spawn_watcher(self, label, target=None, eternal=False): """Spawns a config watcher in a separate daemon thread. If a particular config value changes, and the item has a ``watch_target`` defined, then that method will be called. If a ``target`` is passed in, then it will call the ``...	[ "def", "spawn_watcher", "(", "self", ",", "label", ",", "target", "=", "None", ",", "eternal", "=", "False", ")", ":", "if", "label", "not", "in", "self", ".", "_sources", ":", "raise", "YapconfSourceError", "(", "'Cannot watch %s no source named %s'", "%", ...	37.37931	0.001799
def rows(self, *args) -> List[List[Well]]: """ Accessor function used to navigate through a labware by row. With indexing one can treat it as a typical python nested list. To access row A for example, simply write: labware.rows()[0]. This will output ['A1', 'A2', 'A3', 'A4'...] ...	[ "def", "rows", "(", "self", ",", "*", "args", ")", "->", "List", "[", "List", "[", "Well", "]", "]", ":", "row_dict", "=", "self", ".", "_create_indexed_dictionary", "(", "group", "=", "1", ")", "keys", "=", "sorted", "(", "row_dict", ")", "if", "n...	38.714286	0.0018
def cluster_and_update(records, group_dist=50, eps=100): """ Update records, by clustering their positions using the DBSCAN algorithm. Returns a dictionnary associating new antenna identifiers to (lat, lon) location tuples. .. note:: Use this function to cluster fine-grained GPS records. Param...	[ "def", "cluster_and_update", "(", "records", ",", "group_dist", "=", "50", ",", "eps", "=", "100", ")", ":", "# Run the DBSCAN algorithm with all stop locations and 1 minimal point.", "stops", "=", "get_stops", "(", "records", ",", "group_dist", ")", "labels", "=", ...	36.027778	0.000751
def _get_callable(self, func, *targets): """ If func is already a callable, it is returned directly. If it's a string, it is assumed to be a method on one of the objects supplied in targets and that is returned. If no method with the specified name is found, an AttributeError is raised. ...	[ "def", "_get_callable", "(", "self", ",", "func", ",", "*", "targets", ")", ":", "if", "not", "callable", "(", "func", ")", ":", "func_name", "=", "func", "func", "=", "next", "(", "(", "getattr", "(", "obj", ",", "func", ",", "None", ")", "for", ...	45.190476	0.008256
def _datetime_view( request, template, dt, timeslot_factory=None, items=None, params=None ): ''' Build a time slot grid representation for the given datetime ``dt``. See utils.create_timeslot_table documentation for items and params. Context parameters: ``day`` the ...	[ "def", "_datetime_view", "(", "request", ",", "template", ",", "dt", ",", "timeslot_factory", "=", "None", ",", "items", "=", "None", ",", "params", "=", "None", ")", ":", "timeslot_factory", "=", "timeslot_factory", "or", "utils", ".", "create_timeslot_table"...	21.75	0.001222
def create(source, requirement_files=None, force=False, keep_wheels=False, archive_destination_dir='.', python_versions=None, validate_archive=False, wheel_args='', archive_format='zip', build_tag=''): """Create a Wag...	[ "def", "create", "(", "source", ",", "requirement_files", "=", "None", ",", "force", "=", "False", ",", "keep_wheels", "=", "False", ",", "archive_destination_dir", "=", "'.'", ",", "python_versions", "=", "None", ",", "validate_archive", "=", "False", ",", ...	33.554217	0.000349
def create_package_file(root, master_package, subroot, py_files, opts, subs): """Build the text of the file and write the file.""" text = format_heading(1, '%s' % makename(master_package, subroot)) if opts.modulefirst: text += format_directive(subroot, master_package) text += '\n' # bu...	[ "def", "create_package_file", "(", "root", ",", "master_package", ",", "subroot", ",", "py_files", ",", "opts", ",", "subs", ")", ":", "text", "=", "format_heading", "(", "1", ",", "'%s'", "%", "makename", "(", "master_package", ",", "subroot", ")", ")", ...	42.134615	0.000892
def compute_pointwise_distances(self, other, default=None): """ Compute the minimal distance between each point on self and other. Parameters ---------- other : tuple of number \ or imgaug.augmentables.kps.Keypoint \ or imgaug.augmentables.LineStr...	[ "def", "compute_pointwise_distances", "(", "self", ",", "other", ",", "default", "=", "None", ")", ":", "import", "shapely", ".", "geometry", "from", ".", "kps", "import", "Keypoint", "if", "isinstance", "(", "other", ",", "Keypoint", ")", ":", "other", "=...	34.214286	0.00203
def get_uuid_like_indexes_on_table(model): """ Gets a list of database index names for the given model for the uuid-containing fields that have had a like-index created on them. :param model: Django model :return: list of database rows; the first field of each row is an index name """ ...	[ "def", "get_uuid_like_indexes_on_table", "(", "model", ")", ":", "with", "default_connection", ".", "cursor", "(", ")", "as", "c", ":", "indexes", "=", "select_uuid_like_indexes_on_table", "(", "model", ",", "c", ")", "return", "indexes" ]	35.916667	0.002262
def get_main_filename_attr(self): '''Returns the main filename attribute of the entry. As an entry can have multiple FILENAME attributes, this function allows to return the main one, i.e., the one with the lowest attribute id and the "biggest" namespace. ''' fn_attrs = s...	[ "def", "get_main_filename_attr", "(", "self", ")", ":", "fn_attrs", "=", "self", ".", "get_attributes", "(", "AttrTypes", ".", "FILE_NAME", ")", "high_attr_id", "=", "0xFFFFFFFF", "main_fn", "=", "None", "if", "fn_attrs", "is", "not", "None", ":", "#search for...	45.814815	0.008709
def _refresh_state(self): """ Get the state of a job. If the job is complete this does nothing; otherwise it gets a refreshed copy of the job resource. """ # TODO(gram): should we put a choke on refreshes? E.g. if the last call was less than # a second ago should we return the cached value? ...	[ "def", "_refresh_state", "(", "self", ")", ":", "# TODO(gram): should we put a choke on refreshes? E.g. if the last call was less than", "# a second ago should we return the cached value?", "if", "self", ".", "_is_complete", ":", "return", "try", ":", "response", "=", "self", "...	38.857143	0.011659
def t_LABELDECL(self, token): ur'-\s<label>\s\[(?P<label>.+?)\]\s(?P<text>.+?)\n' label = token.lexer.lexmatch.group("label").decode("utf8") text = token.lexer.lexmatch.group("text").decode("utf8") token.value = (label, text) token.lexer.lineno += 1 return token	[ "def", "t_LABELDECL", "(", "self", ",", "token", ")", ":", "label", "=", "token", ".", "lexer", ".", "lexmatch", ".", "group", "(", "\"label\"", ")", ".", "decode", "(", "\"utf8\"", ")", "text", "=", "token", ".", "lexer", ".", "lexmatch", ".", "grou...	43.714286	0.022436
def cmap_from_color(color, dark=False): ''' Generates a matplotlib colormap from a single color. Colormap will be built, by default, from white to ``color``. Args: color: Can be one of several things: 1. Hex code 2. HTML color name 3. RGB tuple da...	[ "def", "cmap_from_color", "(", "color", ",", "dark", "=", "False", ")", ":", "if", "dark", ":", "return", "sns", ".", "dark_palette", "(", "color", ",", "as_cmap", "=", "True", ")", "else", ":", "return", "sns", ".", "light_palette", "(", "color", ",",...	24.222222	0.001471
def __Logout(si): """ Disconnect (logout) service instance @param si: Service instance (returned from Connect) """ try: if si: content = si.RetrieveContent() content.sessionManager.Logout() except Exception as e: pass	[ "def", "__Logout", "(", "si", ")", ":", "try", ":", "if", "si", ":", "content", "=", "si", ".", "RetrieveContent", "(", ")", "content", ".", "sessionManager", ".", "Logout", "(", ")", "except", "Exception", "as", "e", ":", "pass" ]	23.181818	0.030189
def get_angles(self, angle_id): """Get sun-satellite viewing angles""" tic = datetime.now() sunz40km = self._data["ang"][:, :, 0] * 1e-2 satz40km = self._data["ang"][:, :, 1] * 1e-2 azidiff40km = self._data["ang"][:, :, 2] * 1e-2 try: from geotiepoints.inte...	[ "def", "get_angles", "(", "self", ",", "angle_id", ")", ":", "tic", "=", "datetime", ".", "now", "(", ")", "sunz40km", "=", "self", ".", "_data", "[", "\"ang\"", "]", "[", ":", ",", ":", ",", "0", "]", "*", "1e-2", "satz40km", "=", "self", ".", ...	37.323529	0.002304
def profile(): """View for editing a profile.""" # Create forms verification_form = VerificationForm(formdata=None, prefix="verification") profile_form = profile_form_factory() # Process forms form = request.form.get('submit', None) if form == 'profile': handle_profile_form(profile_...	[ "def", "profile", "(", ")", ":", "# Create forms", "verification_form", "=", "VerificationForm", "(", "formdata", "=", "None", ",", "prefix", "=", "\"verification\"", ")", "profile_form", "=", "profile_form_factory", "(", ")", "# Process forms", "form", "=", "requ...	33.235294	0.001721
def _load_output_data_port_models(self): """Reloads the output data port models directly from the the state """ self.output_data_ports = [] for output_data_port in self.state.output_data_ports.values(): self._add_model(self.output_data_ports, output_data_port, DataPortModel)	[ "def", "_load_output_data_port_models", "(", "self", ")", ":", "self", ".", "output_data_ports", "=", "[", "]", "for", "output_data_port", "in", "self", ".", "state", ".", "output_data_ports", ".", "values", "(", ")", ":", "self", ".", "_add_model", "(", "se...	52.333333	0.009404
def _cacheSequenceInfoType(self): """Figure out whether reset, sequenceId, both or neither are present in the data. Compute once instead of every time. Taken from filesource.py""" hasReset = self.resetFieldName is not None hasSequenceId = self.sequenceIdFieldName is not None if hasReset a...	[ "def", "_cacheSequenceInfoType", "(", "self", ")", ":", "hasReset", "=", "self", ".", "resetFieldName", "is", "not", "None", "hasSequenceId", "=", "self", ".", "sequenceIdFieldName", "is", "not", "None", "if", "hasReset", "and", "not", "hasSequenceId", ":", "s...	35.4	0.009629
def run_jar(jar_name, more_args=None, properties=None, hadoop_conf_dir=None, keep_streams=True): """ Run a jar on Hadoop (``hadoop jar`` command). All arguments are passed to :func:`run_cmd` (``args = [jar_name] + more_args``) . """ if hu.is_readable(jar_name): args = [jar_n...	[ "def", "run_jar", "(", "jar_name", ",", "more_args", "=", "None", ",", "properties", "=", "None", ",", "hadoop_conf_dir", "=", "None", ",", "keep_streams", "=", "True", ")", ":", "if", "hu", ".", "is_readable", "(", "jar_name", ")", ":", "args", "=", "...	32.777778	0.001647
def unsign_url_safe(token, secret_key, salt=None, **kw): """ To sign url safe data. If expires_in is provided it will Time the signature :param token: :param secret_key: :param salt: (string) a namespace key :param kw: :return: """ if len(token.split(".")) == 3: s = URLSa...	[ "def", "unsign_url_safe", "(", "token", ",", "secret_key", ",", "salt", "=", "None", ",", "", "", "kw", ")", ":", "if", "len", "(", "token", ".", "split", "(", "\".\"", ")", ")", "==", "3", ":", "s", "=", "URLSafeTimedSerializer2", "(", "secret_key...	35.208333	0.002304
def encrypt(self, data, recipients, *kwargs): """Encrypt the message contained in ``data`` to ``recipients``. :param str data: The file or bytestream to encrypt. :param str recipients: The recipients to encrypt to. Recipients must be specified keyID/fingerprint. Care should be ta...	[ "def", "encrypt", "(", "self", ",", "data", ",", "", "recipients", ",", "", "*", "kwargs", ")", ":", "if", "_is_stream", "(", "data", ")", ":", "stream", "=", "data", "else", ":", "stream", "=", "_make_binary_stream", "(", "data", ",", "self", ".",...	46.771739	0.000455
def stack_encoders(self, layers): """ Stack encoding layers, this must be done before stacking decoding layers. """ self.stack(layers) self.encoding_layes.extend(layers)	[ "def", "stack_encoders", "(", "self", ",", "", "layers", ")", ":", "self", ".", "stack", "(", "", "layers", ")", "self", ".", "encoding_layes", ".", "extend", "(", "layers", ")" ]	34.333333	0.014218
def pull_requests(self): ''' Looks for any of the following pull request formats in the description field: pr12345, pr 2345, PR2345, PR 2345 ''' pr_numbers = re.findall(r"[pP][rR]\s?[0-9]+", self.description) pr_numbers += re.findall(re.compile("pull\s?request\s?[0-9...	[ "def", "pull_requests", "(", "self", ")", ":", "pr_numbers", "=", "re", ".", "findall", "(", "r\"[pP][rR]\\s?[0-9]+\"", ",", "self", ".", "description", ")", "pr_numbers", "+=", "re", ".", "findall", "(", "re", ".", "compile", "(", "\"pull\\s?request\\s?[0-9]+...	39	0.014614
def next_formatted_pair(self): """\ Returns a :class:`FormattedPair <shorten.store.FormattedPair>` containing attributes `key`, `token`, `formatted_key` and `formatted_token`. Calling this method will always consume a key and token. """ key = self.key_gen.next() token = self...	[ "def", "next_formatted_pair", "(", "self", ")", ":", "key", "=", "self", ".", "key_gen", ".", "next", "(", ")", "token", "=", "self", ".", "token_gen", ".", "create_token", "(", "key", ")", "fkey", "=", "self", ".", "formatter", ".", "format_key", "(",...	37.230769	0.020161
def render(self, at): # draw bg surf = self.surf surf.fill(BASE3) bg = pygame.Surface((self.size[0], self.bar_height)) bg.fill(BASE2) surf.blit(bg, (0, 0)) # draw bar ratio = self.gauge.get(at) / float(self.gauge.max(at)) if ratio > 1: ...	[ "def", "render", "(", "self", ",", "at", ")", ":", "# draw bg", "surf", "=", "self", ".", "surf", "surf", ".", "fill", "(", "BASE3", ")", "bg", "=", "pygame", ".", "Surface", "(", "(", "self", ".", "size", "[", "0", "]", ",", "self", ".", "bar_...	36.346939	0.00164
def _get_newsfeeds(self, uri, detail_level = None): '''General purpose function to get newsfeeds Args: uri uri for the feed base detail_level arguments for req str ['ALL', 'CONDENSED'] return list of feed dicts parse at your convenience ''' if detail_level: if detail_level not in ['ALL', 'CON...	[ "def", "_get_newsfeeds", "(", "self", ",", "uri", ",", "detail_level", "=", "None", ")", ":", "if", "detail_level", ":", "if", "detail_level", "not", "in", "[", "'ALL'", ",", "'CONDENSED'", "]", ":", "return", "requests", ".", "codes", ".", "bad_request", ...	43.846154	0.036082
def write_raster_window( in_tile=None, in_data=None, out_profile=None, out_tile=None, out_path=None, tags=None, bucket_resource=None ): """ Write a window from a numpy array to an output file. Parameters ---------- in_tile : ``BufferedTile`` ``BufferedTile`` with a data attribute ho...	[ "def", "write_raster_window", "(", "in_tile", "=", "None", ",", "in_data", "=", "None", ",", "out_profile", "=", "None", ",", "out_tile", "=", "None", ",", "out_path", "=", "None", ",", "tags", "=", "None", ",", "bucket_resource", "=", "None", ")", ":", ...	36.885714	0.000754
def build_articles_from_article_xmls(article_xmls, detail="full", build_parts=None, remove_tags=None): """ Given a list of article XML filenames, convert to article objects """ poa_articles = [] for article_xml in article_xmls: print("working on ", arti...	[ "def", "build_articles_from_article_xmls", "(", "article_xmls", ",", "detail", "=", "\"full\"", ",", "build_parts", "=", "None", ",", "remove_tags", "=", "None", ")", ":", "poa_articles", "=", "[", "]", "for", "article_xml", "in", "article_xmls", ":", "print", ...	35.1875	0.00173
def _write2(self, data, multithread=True, *kwargs): ''' :param data: Data to be written :type data: str or mmap object :param multithread: If True, sends multiple write requests asynchronously :type multithread: boolean Writes the data data* to the file. .. no...	[ "def", "_write2", "(", "self", ",", "data", ",", "multithread", "=", "True", ",", "", "", "kwargs", ")", ":", "if", "not", "USING_PYTHON2", ":", "assert", "(", "isinstance", "(", "data", ",", "bytes", ")", ")", "self", ".", "_ensure_write_bufsize", "...	38.192982	0.001791
def voronoi(script, target_layer=0, source_layer=1, backward=True): """ Given a Mesh 'M' and a Pointset 'P', the filter projects each vertex of P over M and color M according to the geodesic distance from these projected points. Projection and coloring are done on a per vertex basis. Ar...	[ "def", "voronoi", "(", "script", ",", "target_layer", "=", "0", ",", "source_layer", "=", "1", ",", "backward", "=", "True", ")", ":", "filter_xml", "=", "''", ".", "join", "(", "[", "' <filter name=\"Voronoi Vertex Coloring\">\\n'", ",", "' <Param name=\"Co...	37.26087	0.000569
def _set_load_action(self, mem_addr, rec_count, retries, read_complete=False): """Calculate the next record to read. If the last record was successful and one record was being read then look for the next record until we get to the high water mark. If the last r...	[ "def", "_set_load_action", "(", "self", ",", "mem_addr", ",", "rec_count", ",", "retries", ",", "read_complete", "=", "False", ")", ":", "if", "self", ".", "_have_all_records", "(", ")", ":", "mem_addr", "=", "None", "rec_count", "=", "0", "retries", "=", ...	39.06383	0.001594
def findNextItem(self, item): """ Returns the next item in the tree. :param item \| <QtGui.QTreeWidgetItem> :return <QtGui.QTreeWidgetItem> """ if not item: return None if item.childCount(): re...	[ "def", "findNextItem", "(", "self", ",", "item", ")", ":", "if", "not", "item", ":", "return", "None", "if", "item", ".", "childCount", "(", ")", ":", "return", "item", ".", "child", "(", "0", ")", "while", "item", ".", "parent", "(", ")", ":", "...	27.541667	0.011696
def t_offset(self, s): r'[+]\d+' pos = self.pos self.add_token('OFFSET', s) self.pos = pos + len(s)	[ "def", "t_offset", "(", "self", ",", "s", ")", ":", "pos", "=", "self", ".", "pos", "self", ".", "add_token", "(", "'OFFSET'", ",", "s", ")", "self", ".", "pos", "=", "pos", "+", "len", "(", "s", ")" ]	25.4	0.015267
def _parse_prefix_as_idd(idd_pattern, number): """Strips the IDD from the start of the number if present. Helper function used by _maybe_strip_i18n_prefix_and_normalize(). Returns a 2-tuple: - Boolean indicating if IDD was stripped - Number with IDD stripped """ match = idd_pattern.mat...	[ "def", "_parse_prefix_as_idd", "(", "idd_pattern", ",", "number", ")", ":", "match", "=", "idd_pattern", ".", "match", "(", "number", ")", "if", "match", ":", "match_end", "=", "match", ".", "end", "(", ")", "# Only strip this if the first digit after the match is...	38.666667	0.001202
def process_non_raw_string_token(self, prefix, string_body, start_row): """check for bad escapes in a non-raw string. prefix: lowercase string of eg 'ur' string prefix markers. string_body: the un-parsed body of the string, not including the quote marks. start_row: integer line ...	[ "def", "process_non_raw_string_token", "(", "self", ",", "prefix", ",", "string_body", ",", "start_row", ")", ":", "# Walk through the string; if we see a backslash then escape the next", "# character, and skip over it. If we see a non-escaped character,", "# alert, and continue.", "#...	45.571429	0.001754
def is_b_connected(H, source_node, target_node): """Checks if a target node is B-connected to a source node. A node t is B-connected to a node s iff: - t is s, or - there exists an edge in the backward star of t such that all nodes in the tail of that edge are B-connected to s ...	[ "def", "is_b_connected", "(", "H", ",", "source_node", ",", "target_node", ")", ":", "b_visited_nodes", ",", "Pv", ",", "Pe", ",", "v", "=", "b_visit", "(", "H", ",", "source_node", ")", "return", "target_node", "in", "b_visited_nodes" ]	43.05	0.001136
def getargs(obj): """Get the names and default values of a function's arguments""" if inspect.isfunction(obj) or inspect.isbuiltin(obj): func_obj = obj elif inspect.ismethod(obj): func_obj = get_meth_func(obj) elif inspect.isclass(obj) and hasattr(obj, '__init__'): func_obj = get...	[ "def", "getargs", "(", "obj", ")", ":", "if", "inspect", ".", "isfunction", "(", "obj", ")", "or", "inspect", ".", "isbuiltin", "(", "obj", ")", ":", "func_obj", "=", "obj", "elif", "inspect", ".", "ismethod", "(", "obj", ")", ":", "func_obj", "=", ...	34.27027	0.002301
def strace_set_buffer_size(self, size): """Sets the STRACE buffer size. Args: self (JLink): the ``JLink`` instance. Returns: ``None`` Raises: JLinkException: on error. """ size = ctypes.c_uint32(size) res = self._dll.JLINK_STRACE_C...	[ "def", "strace_set_buffer_size", "(", "self", ",", "size", ")", ":", "size", "=", "ctypes", ".", "c_uint32", "(", "size", ")", "res", "=", "self", ".", "_dll", ".", "JLINK_STRACE_Control", "(", "enums", ".", "JLinkStraceCommand", ".", "SET_BUFFER_SIZE", ",",...	26.611111	0.008065
def setup_components_and_tf_funcs(self, custom_getter=None): """ Constructs the extra Replay memory. """ custom_getter = super(QDemoModel, self).setup_components_and_tf_funcs(custom_getter) self.demo_memory = Replay( states=self.states_spec, internals=sel...	[ "def", "setup_components_and_tf_funcs", "(", "self", ",", "custom_getter", "=", "None", ")", ":", "custom_getter", "=", "super", "(", "QDemoModel", ",", "self", ")", ".", "setup_components_and_tf_funcs", "(", "custom_getter", ")", "self", ".", "demo_memory", "=", ...	31.444444	0.002056
def train(epoch): """ train model on each epoch in trainset """ global trainloader global testloader global net global criterion global optimizer logger.debug("Epoch: %d", epoch) net.train() train_loss = 0 correct = 0 total = 0 for batch_idx, (inputs, targets) in e...	[ "def", "train", "(", "epoch", ")", ":", "global", "trainloader", "global", "testloader", "global", "net", "global", "criterion", "global", "optimizer", "logger", ".", "debug", "(", "\"Epoch: %d\"", ",", "epoch", ")", "net", ".", "train", "(", ")", "train_los...	23.35	0.001028
def _gen_dimension_table(self): """ 2D array describing each registered dimension together with headers - for use in __str__ """ headers = ['Dimension Name', 'Description', 'Global Size', 'Extents'] table = [] for dimval in sorted(self.dimensions(copy...	[ "def", "_gen_dimension_table", "(", "self", ")", ":", "headers", "=", "[", "'Dimension Name'", ",", "'Description'", ",", "'Global Size'", ",", "'Extents'", "]", "table", "=", "[", "]", "for", "dimval", "in", "sorted", "(", "self", ".", "dimensions", "(", ...	33	0.00982
def shouldSkipUrl(self, url, data): """Skip pages without images.""" return url in ( self.stripUrl % '130217', # video self.stripUrl % '130218', # video self.stripUrl % '130226', # video self.stripUrl % '130424', # video )	[ "def", "shouldSkipUrl", "(", "self", ",", "url", ",", "data", ")", ":", "return", "url", "in", "(", "self", ".", "stripUrl", "%", "'130217'", ",", "# video", "self", ".", "stripUrl", "%", "'130218'", ",", "# video", "self", ".", "stripUrl", "%", "'1302...	35.875	0.020408
def fromfits(infilename, hdu = 0, verbose = True): """ Reads a FITS file and returns a 2D numpy array of the data. Use hdu to specify which HDU you want (default = primary = 0) """ pixelarray, hdr = pyfits.getdata(infilename, hdu, header=True) pixelarray = np.asarray(pixelarray).transpose()...	[ "def", "fromfits", "(", "infilename", ",", "hdu", "=", "0", ",", "verbose", "=", "True", ")", ":", "pixelarray", ",", "hdr", "=", "pyfits", ".", "getdata", "(", "infilename", ",", "hdu", ",", "header", "=", "True", ")", "pixelarray", "=", "np", ".", ...	37.6875	0.016181
def _extract_multi_indexer_columns(self, header, index_names, col_names, passed_names=False): """ extract and return the names, index_names, col_names header is a list-of-lists returned from the parsers """ if len(header) < 2: return header[...	[ "def", "_extract_multi_indexer_columns", "(", "self", ",", "header", ",", "index_names", ",", "col_names", ",", "passed_names", "=", "False", ")", ":", "if", "len", "(", "header", ")", "<", "2", ":", "return", "header", "[", "0", "]", ",", "index_names", ...	38.203704	0.001418
def update_environment_variables(self, filename): """Updating OS environment variables and current script path and filename.""" self.env.update(os.environ.copy()) self.env.update({'PIPELINE_BASH_FILE': filename})	[ "def", "update_environment_variables", "(", "self", ",", "filename", ")", ":", "self", ".", "env", ".", "update", "(", "os", ".", "environ", ".", "copy", "(", ")", ")", "self", ".", "env", ".", "update", "(", "{", "'PIPELINE_BASH_FILE'", ":", "filename",...	58.25	0.012712
def cdk_module_matches_env(env_name, env_config, env_vars): """Return bool on whether cdk command should continue in current env.""" if env_config.get(env_name): current_env_config = env_config[env_name] if isinstance(current_env_config, type(True)) and current_env_config: return Tru...	[ "def", "cdk_module_matches_env", "(", "env_name", ",", "env_config", ",", "env_vars", ")", ":", "if", "env_config", ".", "get", "(", "env_name", ")", ":", "current_env_config", "=", "env_config", "[", "env_name", "]", "if", "isinstance", "(", "current_env_config...	46.7	0.001049
def make_sparse(arr, kind='block', fill_value=None, dtype=None, copy=False): """ Convert ndarray to sparse format Parameters ---------- arr : ndarray kind : {'block', 'integer'} fill_value : NaN or another value dtype : np.dtype, optional copy : bool, default False Returns ...	[ "def", "make_sparse", "(", "arr", ",", "kind", "=", "'block'", ",", "fill_value", "=", "None", ",", "dtype", "=", "None", ",", "copy", "=", "False", ")", ":", "arr", "=", "_sanitize_values", "(", "arr", ")", "if", "arr", ".", "ndim", ">", "1", ":",...	28.924528	0.000631
def handle_friday(next_date: Datum, period: str, mult: int, start_date: Datum): """ Extracted the calculation for when the next_day is Friday """ assert isinstance(next_date, Datum) assert isinstance(start_date, Datum) # Starting from line 220. tmp_sat = next_date.clone() tmp_sat.add_days(1) ...	[ "def", "handle_friday", "(", "next_date", ":", "Datum", ",", "period", ":", "str", ",", "mult", ":", "int", ",", "start_date", ":", "Datum", ")", ":", "assert", "isinstance", "(", "next_date", ",", "Datum", ")", "assert", "isinstance", "(", "start_date", ...	36.15	0.000673
def http_exception_error_handler( exception): """ Handle HTTP exception :param werkzeug.exceptions.HTTPException exception: Raised exception A response is returned, as formatted by the :py:func:`response` function. """ assert issubclass(type(exception), HTTPException), type(exception)...	[ "def", "http_exception_error_handler", "(", "exception", ")", ":", "assert", "issubclass", "(", "type", "(", "exception", ")", ",", "HTTPException", ")", ",", "type", "(", "exception", ")", "assert", "hasattr", "(", "exception", ",", "\"code\"", ")", "assert",...	29.933333	0.00216
def optimize_png_file(f, o=None): """ Use pngquant for optimize PNG-image. f - path to input image file or file-object. o - path to output image file or file-object for save result. NOTICE: f and o can not be of different type """ if isinstance(f, basestring): if o is None: ...	[ "def", "optimize_png_file", "(", "f", ",", "o", "=", "None", ")", ":", "if", "isinstance", "(", "f", ",", "basestring", ")", ":", "if", "o", "is", "None", ":", "o", "=", "f", "else", ":", "assert", "isinstance", "(", "o", ",", "basestring", ")", ...	28.171429	0.001961
def baseline(self, rf='', v0='0..', v1='', v2='', off=None): """Defines a baselin measure. It has to specify a reference code, uvw quantity values (see introduction for the action on a scalar quantity with either a vector or scalar value, and when a vector of quantities is given), and op...	[ "def", "baseline", "(", "self", ",", "rf", "=", "''", ",", "v0", "=", "'0..'", ",", "v1", "=", "''", ",", "v2", "=", "''", ",", "off", "=", "None", ")", ":", "loc", "=", "{", "'type'", ":", "\"baseline\"", ",", "'refer'", ":", "rf", "}", "loc...	44.142857	0.001584
def merge_files(context): """ Given a context containing path to template, env, and service: merge config into template and output the result to stdout Args: context: a populated context object """ resolver = EFTemplateResolver( profile=context.profile, region=context.region, env=conte...	[ "def", "merge_files", "(", "context", ")", ":", "resolver", "=", "EFTemplateResolver", "(", "profile", "=", "context", ".", "profile", ",", "region", "=", "context", ".", "region", ",", "env", "=", "context", ".", "env", ",", "service", "=", "context", "...	37.309524	0.013988
def load_mplstyle(): """Try to load conf.plot.mplstyle matplotlib style.""" plt = importlib.import_module('matplotlib.pyplot') if conf.plot.mplstyle: for style in conf.plot.mplstyle.split(): stfile = config.CONFIG_DIR / (style + '.mplstyle') if stfile.is_file(): ...	[ "def", "load_mplstyle", "(", ")", ":", "plt", "=", "importlib", ".", "import_module", "(", "'matplotlib.pyplot'", ")", "if", "conf", ".", "plot", ".", "mplstyle", ":", "for", "style", "in", "conf", ".", "plot", ".", "mplstyle", ".", "split", "(", ")", ...	37.0625	0.001645
def count_cycles(series, ndigits=None, left=False, right=False): """Count cycles in the series. Parameters ---------- series : iterable sequence of numbers ndigits : int, optional Round cycle magnitudes to the given number of digits before counting. left: bool, optional If True,...	[ "def", "count_cycles", "(", "series", ",", "ndigits", "=", "None", ",", "left", "=", "False", ",", "right", "=", "False", ")", ":", "counts", "=", "defaultdict", "(", "float", ")", "round_", "=", "_get_round_function", "(", "ndigits", ")", "for", "low", ...	34	0.0011
def genes_by_alias(hgnc_genes): """Return a dictionary with hgnc symbols as keys Value of the dictionaries are information about the hgnc ids for a symbol. If the symbol is primary for a gene then 'true_id' will exist. A list of hgnc ids that the symbol points to is in ids. Args: hgnc_gene...	[ "def", "genes_by_alias", "(", "hgnc_genes", ")", ":", "alias_genes", "=", "{", "}", "for", "hgnc_id", "in", "hgnc_genes", ":", "gene", "=", "hgnc_genes", "[", "hgnc_id", "]", "# This is the primary symbol:", "hgnc_symbol", "=", "gene", "[", "'hgnc_symbol'", "]",...	31.1	0.001559
def _map_or_starmap_async(function, iterable, args, kwargs, map_or_starmap): """ Shared function between parmap.map_async and parmap.starmap_async. Refer to those functions for details. """ arg_newarg = (("parallel", "pm_parallel"), ("chunksize", "pm_chunksize"), ("pool", "pm_pool"...	[ "def", "_map_or_starmap_async", "(", "function", ",", "iterable", ",", "args", ",", "kwargs", ",", "map_or_starmap", ")", ":", "arg_newarg", "=", "(", "(", "\"parallel\"", ",", "\"pm_parallel\"", ")", ",", "(", "\"chunksize\"", ",", "\"pm_chunksize\"", ")", ",...	46.72093	0.000488
def PushEvent(self, timestamp, event_data): """Pushes a serialized event onto the heap. Args: timestamp (int): event timestamp, which contains the number of micro seconds since January 1, 1970, 00:00:00 UTC. event_data (bytes): serialized event. """ heap_values = (timestamp, event...	[ "def", "PushEvent", "(", "self", ",", "timestamp", ",", "event_data", ")", ":", "heap_values", "=", "(", "timestamp", ",", "event_data", ")", "heapq", ".", "heappush", "(", "self", ".", "_heap", ",", "heap_values", ")", "self", ".", "data_size", "+=", "l...	36.181818	0.002451
def key_slice(self, start_key, end_key, reverse=False): """T.key_slice(start_key, end_key) -> key iterator: start_key <= key < end_key. Yields keys in ascending order if reverse is False else in descending order. """ return (k for k, v in self.iter_items(start_key, end_key, reve...	[ "def", "key_slice", "(", "self", ",", "start_key", ",", "end_key", ",", "reverse", "=", "False", ")", ":", "return", "(", "k", "for", "k", ",", "v", "in", "self", ".", "iter_items", "(", "start_key", ",", "end_key", ",", "reverse", "=", "reverse", ")...	46.714286	0.012012
def custom_add_user_view(request): ''' The page to add a new user. ''' page_name = "Admin - Add User" add_user_form = AddUserForm(request.POST or None, initial={ 'status': UserProfile.RESIDENT, }) if add_user_form.is_valid(): add_user_form.save() message = MESSAGES['USER_...	[ "def", "custom_add_user_view", "(", "request", ")", ":", "page_name", "=", "\"Admin - Add User\"", "add_user_form", "=", "AddUserForm", "(", "request", ".", "POST", "or", "None", ",", "initial", "=", "{", "'status'", ":", "UserProfile", ".", "RESIDENT", ",", "...	45.058824	0.001279

def frompsl(args): """ %prog frompsl old.new.psl old.fasta new.fasta Generate chain file from psl file. The pipeline is describe in: <http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver> """ from jcvi.formats.sizes import Sizes p = OptionParser(frompsl.__doc__) opts, args =...

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def getInstitutions(self, tags = None, seperator = ";", _getTag = False): """Returns a list of the names of institutions. This is done by looking (in order) for any of fields in _tags_ and splitting the strings on _seperator_ (in case of multiple institutions). If no strings are found an empty list will be retu...

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def create_birthday(min_age=18, max_age=80): """ Create a random birthday fomr someone between the ages of min_age and max_age """ age = random.randint(min_age, max_age) start = datetime.date.today() - datetime.timedelta(days=random.randint(0, 365)) return start - datetime.timedelta(days=age * 3...

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def register(self, object_tool_class, model_class=None): """ Registers the given model(s) with the given object tool class. The model(s) should be Model classes, not instances. If a model class isn't given the object tool class will be registered for all models. If a m...

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def from_string(url, default_protocol='telnet'): """ Parses the given URL and returns an URL object. There are some differences to Python's built-in URL parser: - It is less strict, many more inputs are accepted. This is necessary to allow for passing a simple hostname as a UR...

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def line(surf, start, end, color=BLACK, width=1, style=FLAT): """Draws an antialiased line on the surface.""" width = round(width, 1) if width == 1: # return pygame.draw.aaline(surf, color, start, end) return gfxdraw.line(surf, *start, *end, color) start = V2(*start) end = V2(*end)...

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def dumps_tabledata(value, format_name="rst_grid_table", **kwargs): """ :param tabledata.TableData value: Tabular data to dump. :param str format_name: Dumped format name of tabular data. Available formats are described in :py:meth:`~pytablewriter.TableWriterFactory.create_from_forma...

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def save_schedule(self): ''' Save the current schedule ''' self.persist() # Fire the complete event back along with the list of schedule evt = salt.utils.event.get_event('minion', opts=self.opts, listen=False) evt.fire_event({'complete': True}, ...

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def start(): ''' Start simple_server() ''' from wsgiref.simple_server import make_server # When started outside of salt-api __opts__ will not be injected if '__opts__' not in globals(): globals()['__opts__'] = get_opts() if __virtual__() is False: raise SystemExit(1...

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def Disc( pos=(0, 0, 0), normal=(0, 0, 1), r1=0.5, r2=1, c="coral", bc="darkgreen", lw=1, alpha=1, res=12, resphi=None, ): """ Build a 2D disc of internal radius `r1` and outer radius `r2`, oriented perpendicular to `normal`. |Disk| """ ps = vtk.vtkDi...

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def lock(self): # type: () -> Installer """ Prepare the installer for locking only. """ self.update() self.execute_operations(False) self._lock = True return self

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def is_connected(self): """Return connection status""" self._connected = self._connected and self._conn.is_connected() return self._connected

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def __isValidZIP(self, suffix): """Determine if the suffix is `.zip` format""" if suffix and isinstance(suffix, string_types): if suffix.endswith(".zip"): return True return False

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def read_json(directory, data_files='data/js/tweets/*.js'): ''' Scrape a twitter archive file. Inspiration from https://github.com/mshea/Parse-Twitter-Archive ''' files = path.join(directory, data_files) for fname in iglob(files): with open(fname, 'r') as f: # Twitter's JSON...

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def get_entry_point(key, value): """Check if registered entry point is available for a given name and load it. Otherwise, return None. key (unicode): Entry point name. value (unicode): Name of entry point to load. RETURNS: The loaded entry point or None. """ for entry_point in pkg_resources...

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def write_pp_file(filename,pp_df): """write a pilot points dataframe to a pilot points file Parameters ---------- filename : str pilot points file to write pp_df : pandas.DataFrame a dataframe that has columns "x","y","zone", and "value" """ with open(filename,'w') as f: ...

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def cdx_sort_closest(closest, cdx_iter, limit=10): """ sort CDXCaptureResult by closest to timestamp. """ closest_cdx = [] closest_keys = [] closest_sec = timestamp_to_sec(closest) for cdx in cdx_iter: sec = timestamp_to_sec(cdx[TIMESTAMP]) key = abs(closest_sec - sec) ...

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def _parse_file(cls, path, pickle=False): """parse a .chain file into a list of the type [(L{Chain}, arr, arr, arr) ...] :param fname: name of the file""" fname = path if fname.endswith(".gz"): fname = path[:-3] if fname.endswith('.pkl'): #you asked for...

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def import_field(field_classpath): """ Imports a field by its dotted class path, prepending "django.db.models" to raw class names and raising an exception if the import fails. """ if '.' in field_classpath: fully_qualified = field_classpath else: fully_qualified = "django.db.mode...

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def merge(self, evaluation_context: 'EvaluationContext') -> None: """ Merges the provided evaluation context to the current evaluation context. :param evaluation_context: Evaluation context to merge. """ self.global_context.merge(evaluation_context.global_context) self.lo...

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def plot(self, ax, scatter=True, grid=True, progress_colors=True, progress_max=1., depth=10, plot_dims=[0,1]): """ Plot a projection on 2D of the Tree. Parameters ---------- ax : plt axis scatter : bool If the points are ploted grid : bool ...

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def wrap(text, width=70, **kwargs): """Wrap a single paragraph of text, returning a list of wrapped lines. Reformat the single paragraph in 'text' so it fits in lines of no more than 'width' columns, and return a list of wrapped lines. By default, tabs in 'text' are expanded with string.expandtabs(), ...

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def contains(self, url: str): '''Return whether the URL is in the table.''' try: self.get_one(url) except NotFound: return False else: return True

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def __setkey(key): """ Set up the key schedule from the encryption key. """ global C, D, KS, E shifts = (1, 1, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 1) # First, generate C and D by permuting the key. The lower order bit of each # 8-bit char is not used, so C and D are only 28 bits apiece....

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def _expand_if_needed(self, dims, write_dims, start, offset): """ expand the on-disk image if the indended write will extend beyond the existing dimensions """ from operator import mul if numpy.isscalar(start): start_is_scalar = True else: ...

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def mean(arrays, masks=None, dtype=None, out=None, zeros=None, scales=None, weights=None): """Combine arrays using the mean, with masks and offsets. Arrays and masks are a list of array objects. All input arrays have the same shape. If present, the masks have the same shape also. ...

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def timelag_filter(function, pad=True, index=0): '''Filtering in the time-lag domain. This is primarily useful for adapting image filters to operate on `recurrence_to_lag` output. Using `timelag_filter` is equivalent to the following sequence of operations: >>> data_tl = librosa.segment.recur...

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def select_ignore_interrupts(iwtd, owtd, ewtd, timeout=None): '''This is a wrapper around select.select() that ignores signals. If select.select raises a select.error exception and errno is an EINTR error then it is ignored. Mainly this is used to ignore sigwinch (terminal resize). ''' # if select...

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def trunk_mode(self, **kwargs): """Set trunk mode (trunk, trunk-no-default-vlan). Args: int_type (str): Type of interface. (gigabitethernet, tengigabitethernet, etc) name (str): Name of interface. (1/0/5, 1/0/10, etc) mode (str): Trunk port mode (trun...

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def addConcept(self, conceptUri, weight, label = None, conceptType = None): """ add a relevant concept to the topic page @param conceptUri: uri of the concept to be added @param weight: importance of the provided concept (typically in range 1 - 50) """ assert isinstance(w...

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def baseline_or_audit(self, allow_deletion=False, audit_only=False): """Baseline synchonization or audit. Both functions implemented in this routine because audit is a prerequisite for a baseline sync. In the case of baseline sync the last timestamp seen is recorded as client state. ...

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def recall(self): """Calculates recall :return: Recall """ true_pos = self.matrix[0][0] false_neg = self.matrix[0][1] return divide(1.0 * true_pos, true_pos + false_neg)

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def run(addr, *commands, **kwargs): """ Non-threaded batch command runner returning output results """ results = [] handler = VarnishHandler(addr, **kwargs) for cmd in commands: if isinstance(cmd, tuple) and len(cmd)>1: results.extend([getattr(handler, c[0].replace('.','_'))(...

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def rio_save(self, filename, fformat=None, fill_value=None, dtype=np.uint8, compute=True, tags=None, keep_palette=False, cmap=None, **format_kwargs): """Save the image using rasterio. Overviews can be added to the file using the `overviews` kwarg, eg::...

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def cube2map(data_cube, layout): r"""Cube to Map This method transforms the input data from a 3D cube to a 2D map with a specified layout Parameters ---------- data_cube : np.ndarray Input data cube, 3D array of 2D images Layout : tuple 2D layout of 2D images Returns ...

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def regularization(variables, regtype, regcoef, name="regularization"): """Compute the regularization tensor. Parameters ---------- variables : list of tf.Variable List of model variables. regtype : str Type of regularization. Can be ["none", "l1", "l2"...

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def dumps(data, **kwargs): """Convert a PPMP entity to JSON. Additional arguments are the same as accepted by `json.dumps`.""" def _encoder(value): if isinstance(value, datetime.datetime): return value.isoformat() if hasattr(value, "_data"): return value._data ...

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def run_from_cli(): """ Perform an update instigated from a CLI. """ arg_parser = argparse.ArgumentParser( description='Read and write properties in a wp-config.php file. ' 'Include a --value argument to set the value, omit it to ' 'read the value of the ...

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def as_yaml(self): """ as_yaml """ self.set_reprdict_from_attributes() return "---\n" + yaml.dump(self.m_reprdict, default_flow_style=False)

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def fromxml(node): """Static method return an OutputTemplate instance from the given XML description. Node can be a string or an etree._Element.""" if not isinstance(node,ElementTree._Element): #pylint: disable=protected-access node = parsexmlstring(node) assert node.tag.lower() == '...

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def get_validation_col_names(df): """ Input: validated pandas DataFrame (using validate_df) Output: names of all value validation columns, names of all presence validation columns, names of all type validation columns, names of all missing group columns, names...

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def spawn_watcher(self, label, target=None, eternal=False): """Spawns a config watcher in a separate daemon thread. If a particular config value changes, and the item has a ``watch_target`` defined, then that method will be called. If a ``target`` is passed in, then it will call the ``...

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def rows(self, *args) -> List[List[Well]]: """ Accessor function used to navigate through a labware by row. With indexing one can treat it as a typical python nested list. To access row A for example, simply write: labware.rows()[0]. This will output ['A1', 'A2', 'A3', 'A4'...] ...

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def cluster_and_update(records, group_dist=50, eps=100): """ Update records, by clustering their positions using the DBSCAN algorithm. Returns a dictionnary associating new antenna identifiers to (lat, lon) location tuples. .. note:: Use this function to cluster fine-grained GPS records. Param...

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def _get_callable(self, func, *targets): """ If func is already a callable, it is returned directly. If it's a string, it is assumed to be a method on one of the objects supplied in targets and that is returned. If no method with the specified name is found, an AttributeError is raised. ...

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def _datetime_view( request, template, dt, timeslot_factory=None, items=None, params=None ): ''' Build a time slot grid representation for the given datetime ``dt``. See utils.create_timeslot_table documentation for items and params. Context parameters: ``day`` the ...

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def create(source, requirement_files=None, force=False, keep_wheels=False, archive_destination_dir='.', python_versions=None, validate_archive=False, wheel_args='', archive_format='zip', build_tag=''): """Create a Wag...

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def create_package_file(root, master_package, subroot, py_files, opts, subs): """Build the text of the file and write the file.""" text = format_heading(1, '%s' % makename(master_package, subroot)) if opts.modulefirst: text += format_directive(subroot, master_package) text += '\n' # bu...

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def compute_pointwise_distances(self, other, default=None): """ Compute the minimal distance between each point on self and other. Parameters ---------- other : tuple of number \ or imgaug.augmentables.kps.Keypoint \ or imgaug.augmentables.LineStr...

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def get_uuid_like_indexes_on_table(model): """ Gets a list of database index names for the given model for the uuid-containing fields that have had a like-index created on them. :param model: Django model :return: list of database rows; the first field of each row is an index name """ ...

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def get_main_filename_attr(self): '''Returns the main filename attribute of the entry. As an entry can have multiple FILENAME attributes, this function allows to return the main one, i.e., the one with the lowest attribute id and the "biggest" namespace. ''' fn_attrs = s...

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def _refresh_state(self): """ Get the state of a job. If the job is complete this does nothing; otherwise it gets a refreshed copy of the job resource. """ # TODO(gram): should we put a choke on refreshes? E.g. if the last call was less than # a second ago should we return the cached value? ...

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def t_LABELDECL(self, token): ur'-\s<label>\s*\[(?P<label>.+?)\]\s*(?P<text>.+?)\n' label = token.lexer.lexmatch.group("label").decode("utf8") text = token.lexer.lexmatch.group("text").decode("utf8") token.value = (label, text) token.lexer.lineno += 1 return token

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def cmap_from_color(color, dark=False): ''' Generates a matplotlib colormap from a single color. Colormap will be built, by default, from white to ``color``. Args: color: Can be one of several things: 1. Hex code 2. HTML color name 3. RGB tuple da...

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def __Logout(si): """ Disconnect (logout) service instance @param si: Service instance (returned from Connect) """ try: if si: content = si.RetrieveContent() content.sessionManager.Logout() except Exception as e: pass

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def get_angles(self, angle_id): """Get sun-satellite viewing angles""" tic = datetime.now() sunz40km = self._data["ang"][:, :, 0] * 1e-2 satz40km = self._data["ang"][:, :, 1] * 1e-2 azidiff40km = self._data["ang"][:, :, 2] * 1e-2 try: from geotiepoints.inte...

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def profile(): """View for editing a profile.""" # Create forms verification_form = VerificationForm(formdata=None, prefix="verification") profile_form = profile_form_factory() # Process forms form = request.form.get('submit', None) if form == 'profile': handle_profile_form(profile_...

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def _load_output_data_port_models(self): """Reloads the output data port models directly from the the state """ self.output_data_ports = [] for output_data_port in self.state.output_data_ports.values(): self._add_model(self.output_data_ports, output_data_port, DataPortModel)

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def _cacheSequenceInfoType(self): """Figure out whether reset, sequenceId, both or neither are present in the data. Compute once instead of every time. Taken from filesource.py""" hasReset = self.resetFieldName is not None hasSequenceId = self.sequenceIdFieldName is not None if hasReset a...

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def run_jar(jar_name, more_args=None, properties=None, hadoop_conf_dir=None, keep_streams=True): """ Run a jar on Hadoop (``hadoop jar`` command). All arguments are passed to :func:`run_cmd` (``args = [jar_name] + more_args``) . """ if hu.is_readable(jar_name): args = [jar_n...

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def unsign_url_safe(token, secret_key, salt=None, **kw): """ To sign url safe data. If expires_in is provided it will Time the signature :param token: :param secret_key: :param salt: (string) a namespace key :param kw: :return: """ if len(token.split(".")) == 3: s = URLSa...

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def encrypt(self, data, *recipients, **kwargs): """Encrypt the message contained in ``data`` to ``recipients``. :param str data: The file or bytestream to encrypt. :param str recipients: The recipients to encrypt to. Recipients must be specified keyID/fingerprint. Care should be ta...

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def stack_encoders(self, *layers): """ Stack encoding layers, this must be done before stacking decoding layers. """ self.stack(*layers) self.encoding_layes.extend(layers)

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def pull_requests(self): ''' Looks for any of the following pull request formats in the description field: pr12345, pr 2345, PR2345, PR 2345 ''' pr_numbers = re.findall(r"[pP][rR]\s?[0-9]+", self.description) pr_numbers += re.findall(re.compile("pull\s?request\s?[0-9...

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def next_formatted_pair(self): """\ Returns a :class:`FormattedPair <shorten.store.FormattedPair>` containing attributes `key`, `token`, `formatted_key` and `formatted_token`. Calling this method will always consume a key and token. """ key = self.key_gen.next() token = self...

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def render(self, at): # draw bg surf = self.surf surf.fill(BASE3) bg = pygame.Surface((self.size[0], self.bar_height)) bg.fill(BASE2) surf.blit(bg, (0, 0)) # draw bar ratio = self.gauge.get(at) / float(self.gauge.max(at)) if ratio > 1: ...

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def _get_newsfeeds(self, uri, detail_level = None): '''General purpose function to get newsfeeds Args: uri uri for the feed base detail_level arguments for req str ['ALL', 'CONDENSED'] return list of feed dicts parse at your convenience ''' if detail_level: if detail_level not in ['ALL', 'CON...

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def write_raster_window( in_tile=None, in_data=None, out_profile=None, out_tile=None, out_path=None, tags=None, bucket_resource=None ): """ Write a window from a numpy array to an output file. Parameters ---------- in_tile : ``BufferedTile`` ``BufferedTile`` with a data attribute ho...

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def build_articles_from_article_xmls(article_xmls, detail="full", build_parts=None, remove_tags=None): """ Given a list of article XML filenames, convert to article objects """ poa_articles = [] for article_xml in article_xmls: print("working on ", arti...

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def _write2(self, data, multithread=True, **kwargs): ''' :param data: Data to be written :type data: str or mmap object :param multithread: If True, sends multiple write requests asynchronously :type multithread: boolean Writes the data *data* to the file. .. no...

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def voronoi(script, target_layer=0, source_layer=1, backward=True): """ Given a Mesh 'M' and a Pointset 'P', the filter projects each vertex of P over M and color M according to the geodesic distance from these projected points. Projection and coloring are done on a per vertex basis. Ar...

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def _set_load_action(self, mem_addr, rec_count, retries, read_complete=False): """Calculate the next record to read. If the last record was successful and one record was being read then look for the next record until we get to the high water mark. If the last r...

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def findNextItem(self, item): """ Returns the next item in the tree. :param item | <QtGui.QTreeWidgetItem> :return <QtGui.QTreeWidgetItem> """ if not item: return None if item.childCount(): re...

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def t_offset(self, s): r'[+]\d+' pos = self.pos self.add_token('OFFSET', s) self.pos = pos + len(s)

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def _parse_prefix_as_idd(idd_pattern, number): """Strips the IDD from the start of the number if present. Helper function used by _maybe_strip_i18n_prefix_and_normalize(). Returns a 2-tuple: - Boolean indicating if IDD was stripped - Number with IDD stripped """ match = idd_pattern.mat...

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def process_non_raw_string_token(self, prefix, string_body, start_row): """check for bad escapes in a non-raw string. prefix: lowercase string of eg 'ur' string prefix markers. string_body: the un-parsed body of the string, not including the quote marks. start_row: integer line ...

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def is_b_connected(H, source_node, target_node): """Checks if a target node is B-connected to a source node. A node t is B-connected to a node s iff: - t is s, or - there exists an edge in the backward star of t such that all nodes in the tail of that edge are B-connected to s ...

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def getargs(obj): """Get the names and default values of a function's arguments""" if inspect.isfunction(obj) or inspect.isbuiltin(obj): func_obj = obj elif inspect.ismethod(obj): func_obj = get_meth_func(obj) elif inspect.isclass(obj) and hasattr(obj, '__init__'): func_obj = get...

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def strace_set_buffer_size(self, size): """Sets the STRACE buffer size. Args: self (JLink): the ``JLink`` instance. Returns: ``None`` Raises: JLinkException: on error. """ size = ctypes.c_uint32(size) res = self._dll.JLINK_STRACE_C...

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def setup_components_and_tf_funcs(self, custom_getter=None): """ Constructs the extra Replay memory. """ custom_getter = super(QDemoModel, self).setup_components_and_tf_funcs(custom_getter) self.demo_memory = Replay( states=self.states_spec, internals=sel...

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def train(epoch): """ train model on each epoch in trainset """ global trainloader global testloader global net global criterion global optimizer logger.debug("Epoch: %d", epoch) net.train() train_loss = 0 correct = 0 total = 0 for batch_idx, (inputs, targets) in e...

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def _gen_dimension_table(self): """ 2D array describing each registered dimension together with headers - for use in __str__ """ headers = ['Dimension Name', 'Description', 'Global Size', 'Extents'] table = [] for dimval in sorted(self.dimensions(copy...

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def shouldSkipUrl(self, url, data): """Skip pages without images.""" return url in ( self.stripUrl % '130217', # video self.stripUrl % '130218', # video self.stripUrl % '130226', # video self.stripUrl % '130424', # video )

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def fromfits(infilename, hdu = 0, verbose = True): """ Reads a FITS file and returns a 2D numpy array of the data. Use hdu to specify which HDU you want (default = primary = 0) """ pixelarray, hdr = pyfits.getdata(infilename, hdu, header=True) pixelarray = np.asarray(pixelarray).transpose()...

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def _extract_multi_indexer_columns(self, header, index_names, col_names, passed_names=False): """ extract and return the names, index_names, col_names header is a list-of-lists returned from the parsers """ if len(header) < 2: return header[...

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def update_environment_variables(self, filename): """Updating OS environment variables and current script path and filename.""" self.env.update(os.environ.copy()) self.env.update({'PIPELINE_BASH_FILE': filename})

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58.25

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def cdk_module_matches_env(env_name, env_config, env_vars): """Return bool on whether cdk command should continue in current env.""" if env_config.get(env_name): current_env_config = env_config[env_name] if isinstance(current_env_config, type(True)) and current_env_config: return Tru...

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def make_sparse(arr, kind='block', fill_value=None, dtype=None, copy=False): """ Convert ndarray to sparse format Parameters ---------- arr : ndarray kind : {'block', 'integer'} fill_value : NaN or another value dtype : np.dtype, optional copy : bool, default False Returns ...

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def handle_friday(next_date: Datum, period: str, mult: int, start_date: Datum): """ Extracted the calculation for when the next_day is Friday """ assert isinstance(next_date, Datum) assert isinstance(start_date, Datum) # Starting from line 220. tmp_sat = next_date.clone() tmp_sat.add_days(1) ...

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36.15

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def http_exception_error_handler( exception): """ Handle HTTP exception :param werkzeug.exceptions.HTTPException exception: Raised exception A response is returned, as formatted by the :py:func:`response` function. """ assert issubclass(type(exception), HTTPException), type(exception)...

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def optimize_png_file(f, o=None): """ Use pngquant for optimize PNG-image. f - path to input image file or file-object. o - path to output image file or file-object for save result. NOTICE: f and o can not be of different type """ if isinstance(f, basestring): if o is None: ...

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28.171429

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def baseline(self, rf='', v0='0..', v1='', v2='', off=None): """Defines a baselin measure. It has to specify a reference code, uvw quantity values (see introduction for the action on a scalar quantity with either a vector or scalar value, and when a vector of quantities is given), and op...

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44.142857

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def merge_files(context): """ Given a context containing path to template, env, and service: merge config into template and output the result to stdout Args: context: a populated context object """ resolver = EFTemplateResolver( profile=context.profile, region=context.region, env=conte...

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37.309524

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def load_mplstyle(): """Try to load conf.plot.mplstyle matplotlib style.""" plt = importlib.import_module('matplotlib.pyplot') if conf.plot.mplstyle: for style in conf.plot.mplstyle.split(): stfile = config.CONFIG_DIR / (style + '.mplstyle') if stfile.is_file(): ...

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37.0625

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def count_cycles(series, ndigits=None, left=False, right=False): """Count cycles in the series. Parameters ---------- series : iterable sequence of numbers ndigits : int, optional Round cycle magnitudes to the given number of digits before counting. left: bool, optional If True,...

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34

0.0011

def genes_by_alias(hgnc_genes): """Return a dictionary with hgnc symbols as keys Value of the dictionaries are information about the hgnc ids for a symbol. If the symbol is primary for a gene then 'true_id' will exist. A list of hgnc ids that the symbol points to is in ids. Args: hgnc_gene...

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31.1

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def _map_or_starmap_async(function, iterable, args, kwargs, map_or_starmap): """ Shared function between parmap.map_async and parmap.starmap_async. Refer to those functions for details. """ arg_newarg = (("parallel", "pm_parallel"), ("chunksize", "pm_chunksize"), ("pool", "pm_pool"...

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def PushEvent(self, timestamp, event_data): """Pushes a serialized event onto the heap. Args: timestamp (int): event timestamp, which contains the number of micro seconds since January 1, 1970, 00:00:00 UTC. event_data (bytes): serialized event. """ heap_values = (timestamp, event...

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def key_slice(self, start_key, end_key, reverse=False): """T.key_slice(start_key, end_key) -> key iterator: start_key <= key < end_key. Yields keys in ascending order if reverse is False else in descending order. """ return (k for k, v in self.iter_items(start_key, end_key, reve...

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def custom_add_user_view(request): ''' The page to add a new user. ''' page_name = "Admin - Add User" add_user_form = AddUserForm(request.POST or None, initial={ 'status': UserProfile.RESIDENT, }) if add_user_form.is_valid(): add_user_form.save() message = MESSAGES['USER_...

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45.058824

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