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 upload_metadata(directory, create_csv='', review='', max_size='128m', verbose=False, debug=False): """ Draft or review metadata files for uploading files to Open Humans. The target directory should either represent files for a single member (no subdirectories), or contain a subdi...	[ "def", "upload_metadata", "(", "directory", ",", "create_csv", "=", "''", ",", "review", "=", "''", ",", "max_size", "=", "'128m'", ",", "verbose", "=", "False", ",", "debug", "=", "False", ")", ":", "set_log_level", "(", "debug", ",", "verbose", ")", ...	44.40625	0.000689
def find_all_output_in_range(self, ifo, currSeg, useSplitLists=False): """ Return all files that overlap the specified segment. """ if not useSplitLists: # Slower, but simpler method outFiles = [i for i in self if ifo in i.ifo_list] outFiles = [i for i...	[ "def", "find_all_output_in_range", "(", "self", ",", "ifo", ",", "currSeg", ",", "useSplitLists", "=", "False", ")", ":", "if", "not", "useSplitLists", ":", "# Slower, but simpler method", "outFiles", "=", "[", "i", "for", "i", "in", "self", "if", "ifo", "in...	48.147059	0.01018
def decode(self, encoded_packet): """Decode a transmitted package.""" b64 = False if not isinstance(encoded_packet, binary_types): encoded_packet = encoded_packet.encode('utf-8') elif not isinstance(encoded_packet, bytes): encoded_packet = bytes(encoded_packet) ...	[ "def", "decode", "(", "self", ",", "encoded_packet", ")", ":", "b64", "=", "False", "if", "not", "isinstance", "(", "encoded_packet", ",", "binary_types", ")", ":", "encoded_packet", "=", "encoded_packet", ".", "encode", "(", "'utf-8'", ")", "elif", "not", ...	42.216216	0.001252
def attempt_advance(self, blocksize, timeout=10): """ Attempt to advance the frame buffer. Retry upon failure, except if the frame file is beyond the timeout limit. Parameters ---------- blocksize: int The number of seconds to attempt to read from the channel ...	[ "def", "attempt_advance", "(", "self", ",", "blocksize", ",", "timeout", "=", "10", ")", ":", "if", "self", ".", "force_update_cache", ":", "self", ".", "update_cache", "(", ")", "try", ":", "if", "self", ".", "increment_update_cache", ":", "self", ".", ...	36.114286	0.002311
def mutating_join(args, *kwargs): """ generic function for mutating dplyr-style joins """ # candidate for improvement left = args[0] right = args[1] if 'by' in kwargs: left_cols, right_cols = get_join_cols(kwargs['by']) else: left_cols, right_cols = None, None if 'suffixes' in kwargs: dsuf...	[ "def", "mutating_join", "(", "", "args", ",", "", "*", "kwargs", ")", ":", "# candidate for improvement", "left", "=", "args", "[", "0", "]", "right", "=", "args", "[", "1", "]", "if", "'by'", "in", "kwargs", ":", "left_cols", ",", "right_cols", "=",...	34.478261	0.017178
def _MarkerFactory(marker_code, stream, offset): """ Return \|_Marker\| or subclass instance appropriate for marker at offset in stream having marker_code. """ if marker_code == JPEG_MARKER_CODE.APP0: marker_cls = _App0Marker elif marker_code == JPEG_MARKER_CODE.APP1: marker_...	[ "def", "_MarkerFactory", "(", "marker_code", ",", "stream", ",", "offset", ")", ":", "if", "marker_code", "==", "JPEG_MARKER_CODE", ".", "APP0", ":", "marker_cls", "=", "_App0Marker", "elif", "marker_code", "==", "JPEG_MARKER_CODE", ".", "APP1", ":", "marker_cls...	36.928571	0.001887
def size_of_varint_2(value): """ Number of bytes needed to encode an integer in variable-length format. """ value = (value << 1) ^ (value >> 63) if value <= 0x7f: return 1 if value <= 0x3fff: return 2 if value <= 0x1fffff: return 3 if value <= 0xfffffff: retur...	[ "def", "size_of_varint_2", "(", "value", ")", ":", "value", "=", "(", "value", "<<", "1", ")", "^", "(", "value", ">>", "63", ")", "if", "value", "<=", "0x7f", ":", "return", "1", "if", "value", "<=", "0x3fff", ":", "return", "2", "if", "value", ...	24.478261	0.001709
def set_path(self, path, val): """ Set the given value at the supplied path where path is either a tuple of strings or a string in A.B.C format. """ path = tuple(path.split('.')) if isinstance(path , str) else tuple(path) disallowed = [p for p in path if not type(self)._...	[ "def", "set_path", "(", "self", ",", "path", ",", "val", ")", ":", "path", "=", "tuple", "(", "path", ".", "split", "(", "'.'", ")", ")", "if", "isinstance", "(", "path", ",", "str", ")", "else", "tuple", "(", "path", ")", "disallowed", "=", "[",...	44.0625	0.008333
def full_name(self): """ str: func_name(type1,type2) Return the function signature without the return values """ name, parameters, _ = self.signature return name+'('+','.join(parameters)+')'	[ "def", "full_name", "(", "self", ")", ":", "name", ",", "parameters", ",", "_", "=", "self", ".", "signature", "return", "name", "+", "'('", "+", "','", ".", "join", "(", "parameters", ")", "+", "')'" ]	34.285714	0.00813
def get(self, block=True, timeout=None): """Get item from underlying queue.""" return self._queue.get(block, timeout)	[ "def", "get", "(", "self", ",", "block", "=", "True", ",", "timeout", "=", "None", ")", ":", "return", "self", ".", "_queue", ".", "get", "(", "block", ",", "timeout", ")" ]	43.666667	0.015038
def argument_count(self): """ Uses the command line arguments to fill the count function and call it. """ arguments, _ = self.argparser.parse_known_args() return self.count(**vars(arguments))	[ "def", "argument_count", "(", "self", ")", ":", "arguments", ",", "_", "=", "self", ".", "argparser", ".", "parse_known_args", "(", ")", "return", "self", ".", "count", "(", "", "", "vars", "(", "arguments", ")", ")" ]	38.333333	0.012766
def save_function(self, obj, name=None): """ Registered with the dispatch to handle all function types. Determines what kind of function obj is (e.g. lambda, defined at interactive prompt, etc) and handles the pickling appropriately. """ try: should_special_case = ob...	[ "def", "save_function", "(", "self", ",", "obj", ",", "name", "=", "None", ")", ":", "try", ":", "should_special_case", "=", "obj", "in", "_BUILTIN_TYPE_CONSTRUCTORS", "except", "TypeError", ":", "# Methods of builtin types aren't hashable in python 2.", "should_special...	41.393617	0.001004
def represent_as_string(iterable): """ Represent a number in the form of a string. (8, 6, 8, '.', 0, 15) -> "868.0F" Args: iterable - Number represented as an iterable container of digits. Returns: Number represented as a string of digits. >>> represent_as_string((8, ...	[ "def", "represent_as_string", "(", "iterable", ")", ":", "keep", "=", "(", "\".\"", ",", "\"[\"", ",", "\"]\"", ")", "return", "\"\"", ".", "join", "(", "tuple", "(", "int_to_str_digit", "(", "i", ")", "if", "i", "not", "in", "keep", "else", "i", "fo...	30.25	0.002004
def _set_initial(self, C_in, scale_in): r"""Set the initial values for parameters and Wilson coefficients at the scale `scale_in`.""" self.C_in = C_in self.scale_in = scale_in	[ "def", "_set_initial", "(", "self", ",", "C_in", ",", "scale_in", ")", ":", "self", ".", "C_in", "=", "C_in", "self", ".", "scale_in", "=", "scale_in" ]	40.6	0.009662
def distance(line, point): """ infinite line to point or line to line distance is point is given as line - use middle point of that liune """ x0, y0, x1, y1 = line try: p1, p2 = point except ValueError: # line is given instead of point p1, p2 = middle(point) n1 = ...	[ "def", "distance", "(", "line", ",", "point", ")", ":", "x0", ",", "y0", ",", "x1", ",", "y1", "=", "line", "try", ":", "p1", ",", "p2", "=", "point", "except", "ValueError", ":", "# line is given instead of point", "p1", ",", "p2", "=", "middle", "(...	28	0.002304
def htseq_counts_chart (self): """ Make the HTSeq Count assignment rates plot """ cats = OrderedDict() cats['assigned'] = { 'name': 'Assigned' } cats['ambiguous'] = { 'name': 'Ambiguous' } cats['alignment_not_unique'] = { 'name': 'Alignment Not Unique' } cats['no...	[ "def", "htseq_counts_chart", "(", "self", ")", ":", "cats", "=", "OrderedDict", "(", ")", "cats", "[", "'assigned'", "]", "=", "{", "'name'", ":", "'Assigned'", "}", "cats", "[", "'ambiguous'", "]", "=", "{", "'name'", ":", "'Ambiguous'", "}", "cats", ...	45.058824	0.024297
def sorted_bfs_edges(G, source=None): """Produce edges in a breadth-first-search starting at source. Neighbors appear in the order a linguist would expect in a syntax tree. The result will only contain edges that express a dominance or spanning relation, i.e. edges expressing pointing or precedence rel...	[ "def", "sorted_bfs_edges", "(", "G", ",", "source", "=", "None", ")", ":", "if", "source", "is", "None", ":", "source", "=", "G", ".", "root", "xpos", "=", "horizontal_positions", "(", "G", ",", "source", ")", "visited", "=", "set", "(", "[", "source...	33.487805	0.000708
def compute_vest_stat(vest_dict, ref_aa, somatic_aa, codon_pos, stat_func=np.mean, default_val=0.0): """Compute missense VEST score statistic. Note: non-missense mutations are intentially not filtered out and will take a default value of zero. Parameters ...	[ "def", "compute_vest_stat", "(", "vest_dict", ",", "ref_aa", ",", "somatic_aa", ",", "codon_pos", ",", "stat_func", "=", "np", ".", "mean", ",", "default_val", "=", "0.0", ")", ":", "# return default value if VEST scores are missing", "if", "vest_dict", "is", "Non...	28.761905	0.000801
def estimate_cpd(self, node): """ Method to estimate the CPD for a given variable. Parameters ---------- node: int, string (any hashable python object) The name of the variable for which the CPD is to be estimated. Returns ------- CPD: Tabula...	[ "def", "estimate_cpd", "(", "self", ",", "node", ")", ":", "state_counts", "=", "self", ".", "state_counts", "(", "node", ")", "# if a column contains only `0`s (no states observed for some configuration", "# of parents' states) fill that column uniformly instead", "state_counts"...	37.410714	0.002326
def update(self,dt): """ Should be called regularly to move the actor. This method does nothing if the :py:attr:`enabled` property is set to False. This method is called automatically and should not be called manually. """ if not self.enabled: ...	[ "def", "update", "(", "self", ",", "dt", ")", ":", "if", "not", "self", ".", "enabled", ":", "return", "dy", "=", "self", ".", "speed", "", "dt", "", "self", ".", "move", "x", ",", "y", ",", "z", "=", "self", ".", "actor", ".", "_pos", "new...	31.857143	0.021786
def create_entry(i): """ Input: { path - path where to create an entry (data_uoa) - data UOA (data_uid) - if uoa is an alias, we can force data UID (force) - if 'yes', force creation even if directory already exists } Output: { ...	[ "def", "create_entry", "(", "i", ")", ":", "p0", "=", "i", ".", "get", "(", "'path'", ",", "''", ")", "d", "=", "i", ".", "get", "(", "'data_uoa'", ",", "''", ")", "di", "=", "i", ".", "get", "(", "'data_uid'", ",", "''", ")", "xforce", "=", ...	27.389313	0.04411
def CDQ(cpu): """ EDX:EAX = sign-extend of EAX """ cpu.EDX = Operators.EXTRACT(Operators.SEXTEND(cpu.EAX, 32, 64), 32, 32)	[ "def", "CDQ", "(", "cpu", ")", ":", "cpu", ".", "EDX", "=", "Operators", ".", "EXTRACT", "(", "Operators", ".", "SEXTEND", "(", "cpu", ".", "EAX", ",", "32", ",", "64", ")", ",", "32", ",", "32", ")" ]	30	0.012987
def do_init_cached_fields(self): """ Initialize each fields of the fields_desc dict, or use the cached fields information """ cls_name = self.__class__ # Build the fields information if Packet.class_default_fields.get(cls_name, None) is None: self.pr...	[ "def", "do_init_cached_fields", "(", "self", ")", ":", "cls_name", "=", "self", ".", "__class__", "# Build the fields information", "if", "Packet", ".", "class_default_fields", ".", "get", "(", "cls_name", ",", "None", ")", "is", "None", ":", "self", ".", "pre...	39.818182	0.00223
def ext_import(soname, module_subpath=""): """ Loads a turicreate toolkit module (a shared library) into the tc.extensions namespace. Toolkit module created via SDK can either be directly imported, e.g. ``import example`` or via this function, e.g. ``turicreate.ext_import("example.so")``. Use `...	[ "def", "ext_import", "(", "soname", ",", "module_subpath", "=", "\"\"", ")", ":", "unity", "=", "_get_unity", "(", ")", "import", "os", "if", "os", ".", "path", ".", "exists", "(", "soname", ")", ":", "soname", "=", "os", ".", "path", ".", "abspath",...	34.071429	0.001019
def fft_convolve(in1, in2, conv_device="cpu", conv_mode="linear", store_on_gpu=False): """ This function determines the convolution of two inputs using the FFT. Contains an implementation for both CPU and GPU. INPUTS: in1 (no default): Array containing one set of data, possibl...	[ "def", "fft_convolve", "(", "in1", ",", "in2", ",", "conv_device", "=", "\"cpu\"", ",", "conv_mode", "=", "\"linear\"", ",", "store_on_gpu", "=", "False", ")", ":", "# NOTE: Circular convolution assumes a periodic repetition of the input. This can cause edge effects. Linear",...	37.464286	0.00836
def http_auth_required(realm): """Decorator that protects endpoints using Basic HTTP authentication. :param realm: optional realm name""" def decorator(fn): @wraps(fn) def wrapper(args, kwargs): if _check_http_auth(): return fn(args, **kwargs) if...	[ "def", "http_auth_required", "(", "realm", ")", ":", "def", "decorator", "(", "fn", ")", ":", "@", "wraps", "(", "fn", ")", "def", "wrapper", "(", "", "args", ",", "", "*", "kwargs", ")", ":", "if", "_check_http_auth", "(", ")", ":", "return", "f...	33.727273	0.001311
def build_access_required(function_or_param_name): """Decorator ensures user has access to the build ID in the request. May be used in two ways: @build_access_required def my_func(build): ... @build_access_required('custom_build_id_param') def my_func(build): ...	[ "def", "build_access_required", "(", "function_or_param_name", ")", ":", "def", "get_wrapper", "(", "param_name", ",", "f", ")", ":", "@", "functools", ".", "wraps", "(", "f", ")", "def", "wrapped", "(", "", "args", ",", "", "*", "kwargs", ")", ":", ...	32.166667	0.001006
def render(self, compress=False): """Return a rendered representation of the color. If `compress` is true, the shortest possible representation is used; otherwise, named colors are rendered as names and all others are rendered as hex (or with the rgba function). """ if ...	[ "def", "render", "(", "self", ",", "compress", "=", "False", ")", ":", "if", "not", "compress", "and", "self", ".", "original_literal", ":", "return", "self", ".", "original_literal", "candidates", "=", "[", "]", "# TODO this assumes CSS resolution is 8-bit per ch...	34.522727	0.001921
def file_exists(self, filename, directory=False, note=None, loglevel=logging.DEBUG): """Return True if file exists on the target host, else False @param filename: Filename to determine the existence of. @param directory: Indicate that the fil...	[ "def", "file_exists", "(", "self", ",", "filename", ",", "directory", "=", "False", ",", "note", "=", "None", ",", "loglevel", "=", "logging", ".", "DEBUG", ")", ":", "shutit", "=", "self", ".", "shutit", "shutit", ".", "handle_note", "(", "note", ",",...	39.297297	0.034899
def separable_conv_block(inputs, filters, dilation_rates_and_kernel_sizes, kwargs): """A block of separable convolutions.""" return conv_block_internal(separable_conv, inputs, filters, dilation_rates_and_kernel_sizes, kwargs)	[ "def", "separable_conv_block", "(", "inputs", ",", "filters", ",", "dilation_rates_and_kernel_sizes", ",", "", "", "kwargs", ")", ":", "return", "conv_block_internal", "(", "separable_conv", ",", "inputs", ",", "filters", ",", "dilation_rates_and_kernel_sizes", ",",...	56.6	0.010453
def tuple_to_qfont(tup): """ Create a QFont from tuple: (family [string], size [int], italic [bool], bold [bool]) """ if not isinstance(tup, tuple) or len(tup) != 4 \ or not is_text_string(tup[0]) \ or not isinstance(tup[1], int) \ or not isinstance(tup[2], bool) \ or...	[ "def", "tuple_to_qfont", "(", "tup", ")", ":", "if", "not", "isinstance", "(", "tup", ",", "tuple", ")", "or", "len", "(", "tup", ")", "!=", "4", "or", "not", "is_text_string", "(", "tup", "[", "0", "]", ")", "or", "not", "isinstance", "(", "tup", ...	29.444444	0.001828
def get(self, session, **kwargs): '''taobao.fenxiao.cooperation.get 获取供应商的合作关系信息获取供应商的合作关系信息''' request = TOPRequest('taobao.fenxiao.cooperation.get') for k, v in kwargs.iteritems(): if k not in ('status', 'start_date', 'end_date', 'trade_type', 'page_no', 'page_siz...	[ "def", "get", "(", "self", ",", "session", ",", "", "", "kwargs", ")", ":", "request", "=", "TOPRequest", "(", "'taobao.fenxiao.cooperation.get'", ")", "for", "k", ",", "v", "in", "kwargs", ".", "iteritems", "(", ")", ":", "if", "k", "not", "in", "...	52.6	0.018692
def page(self, course, errors=None, saved=False): """ Get all data and display the page """ return self.template_helper.get_renderer().course_admin.settings(course, errors, saved)	[ "def", "page", "(", "self", ",", "course", ",", "errors", "=", "None", ",", "saved", "=", "False", ")", ":", "return", "self", ".", "template_helper", ".", "get_renderer", "(", ")", ".", "course_admin", ".", "settings", "(", "course", ",", "errors", ",...	64.333333	0.015385
def open(self): """initialize visit variables""" self.stats = self.linter.add_stats() self._returns = [] self._branches = defaultdict(int) self._stmts = []	[ "def", "open", "(", "self", ")", ":", "self", ".", "stats", "=", "self", ".", "linter", ".", "add_stats", "(", ")", "self", ".", "_returns", "=", "[", "]", "self", ".", "_branches", "=", "defaultdict", "(", "int", ")", "self", ".", "_stmts", "=", ...	31.666667	0.010256
def check_ns_run_threads(run): """Check thread labels and thread_min_max have expected properties. Parameters ---------- run: dict Nested sampling run to check. Raises ------ AssertionError If run does not have expected properties. """ assert run['thread_labels'].dt...	[ "def", "check_ns_run_threads", "(", "run", ")", ":", "assert", "run", "[", "'thread_labels'", "]", ".", "dtype", "==", "int", "uniq_th", "=", "np", ".", "unique", "(", "run", "[", "'thread_labels'", "]", ")", "assert", "np", ".", "array_equal", "(", "np"...	41.03125	0.000744
def update(gandi, address, dest_add, dest_del): """Update a domain mail forward.""" source, domain = address if not dest_add and not dest_del: gandi.echo('Nothing to update: you must provide destinations to ' 'update, use --dest-add/-a or -dest-del/-d parameters.') return...	[ "def", "update", "(", "gandi", ",", "address", ",", "dest_add", ",", "dest_del", ")", ":", "source", ",", "domain", "=", "address", "if", "not", "dest_add", "and", "not", "dest_del", ":", "gandi", ".", "echo", "(", "'Nothing to update: you must provide destina...	33.25	0.002439
def _augment_book(self, uuid, event): """ Checks if the newly created object is a book and only has an ISBN. If so, tries to fetch the book data off the internet. :param uuid: uuid of book to augment :param client: requesting client """ try: if not is...	[ "def", "_augment_book", "(", "self", ",", "uuid", ",", "event", ")", ":", "try", ":", "if", "not", "isbnmeta", ":", "self", ".", "log", "(", "\"No isbntools found! Install it to get full \"", "\"functionality!\"", ",", "lvl", "=", "warn", ")", "return", "new_b...	40.506667	0.000964
def Unlock(fd, path): """Release the lock on the file. Args: fd: int, the file descriptor of the file to unlock. path: string, the name of the file to lock. Raises: IOError, raised from flock while attempting to release a file lock. """ try: fcntl.flock(fd, fcntl.LOCK_UN \| fcntl.LOCK_NB) e...	[ "def", "Unlock", "(", "fd", ",", "path", ")", ":", "try", ":", "fcntl", ".", "flock", "(", "fd", ",", "fcntl", ".", "LOCK_UN", "\|", "fcntl", ".", "LOCK_NB", ")", "except", "IOError", "as", "e", ":", "if", "e", ".", "errno", "==", "errno", ".", ...	30.529412	0.013084
def get_arg_parse(): """Parses the Command Line Arguments using argparse.""" # Create parser object: objParser = argparse.ArgumentParser() # Add argument to namespace -config file path: objParser.add_argument('-config', required=True, metavar='/path/to/config.csv', ...	[ "def", "get_arg_parse", "(", ")", ":", "# Create parser object:", "objParser", "=", "argparse", ".", "ArgumentParser", "(", ")", "# Add argument to namespace -config file path:", "objParser", ".", "add_argument", "(", "'-config'", ",", "required", "=", "True", ",", "m...	44.035714	0.000397
def pidfile(self): """Get the absolute path of the pidfile.""" return os.path.abspath( os.path.expandvars( os.path.expanduser( self._pidfile, ), ), )	[ "def", "pidfile", "(", "self", ")", ":", "return", "os", ".", "path", ".", "abspath", "(", "os", ".", "path", ".", "expandvars", "(", "os", ".", "path", ".", "expanduser", "(", "self", ".", "_pidfile", ",", ")", ",", ")", ",", ")" ]	26.777778	0.008032
def xrify_tuples(self, tup): """Make xarray.DataArray from tuple.""" return xr.DataArray(tup, dims=['bands'], coords={'bands': self.data['bands']})	[ "def", "xrify_tuples", "(", "self", ",", "tup", ")", ":", "return", "xr", ".", "DataArray", "(", "tup", ",", "dims", "=", "[", "'bands'", "]", ",", "coords", "=", "{", "'bands'", ":", "self", ".", "data", "[", "'bands'", "]", "}", ")" ]	43	0.009132
def winddir_text(pts): "Convert wind direction from 0..15 to compass point text" global _winddir_text_array if pts is None: return None if not isinstance(pts, int): pts = int(pts + 0.5) % 16 if not _winddir_text_array: _ = pywws.localisation.translation.ugettext _wind...	[ "def", "winddir_text", "(", "pts", ")", ":", "global", "_winddir_text_array", "if", "pts", "is", "None", ":", "return", "None", "if", "not", "isinstance", "(", "pts", ",", "int", ")", ":", "pts", "=", "int", "(", "pts", "+", "0.5", ")", "%", "16", ...	36.5625	0.001667
def comments(self, limit=None): """GETs user's comments. Calls :meth:`narwal.Reddit.user_comments`. :param limit: max number of comments to get """ return self._reddit.user_comments(self.name, limit=limit)	[ "def", "comments", "(", "self", ",", "limit", "=", "None", ")", ":", "return", "self", ".", "_reddit", ".", "user_comments", "(", "self", ".", "name", ",", "limit", "=", "limit", ")" ]	40.333333	0.012146
def api_url(self): '''return the api url of this request''' return pathjoin(Request.path, self.id, url=self.bin.api_url)	[ "def", "api_url", "(", "self", ")", ":", "return", "pathjoin", "(", "Request", ".", "path", ",", "self", ".", "id", ",", "url", "=", "self", ".", "bin", ".", "api_url", ")" ]	44.666667	0.014706
def visit_addresses(frame, return_addresses): """ Visits all of the addresses, returns a new dict which contains just the addressed elements Parameters ---------- frame return_addresses: a dictionary, keys will be column names of the resulting dataframe, and are what the us...	[ "def", "visit_addresses", "(", "frame", ",", "return_addresses", ")", ":", "outdict", "=", "dict", "(", ")", "for", "real_name", ",", "(", "pyname", ",", "address", ")", "in", "return_addresses", ".", "items", "(", ")", ":", "if", "address", ":", "xrval"...	28.6875	0.002107
def _get_section_name(cls, parser): """Parse options from relevant section.""" for section_name in cls.POSSIBLE_SECTION_NAMES: if parser.has_section(section_name): return section_name return None	[ "def", "_get_section_name", "(", "cls", ",", "parser", ")", ":", "for", "section_name", "in", "cls", ".", "POSSIBLE_SECTION_NAMES", ":", "if", "parser", ".", "has_section", "(", "section_name", ")", ":", "return", "section_name", "return", "None" ]	34.571429	0.008065
def show_driver(devname): ''' Queries the specified network device for associated driver information CLI Example: .. code-block:: bash salt '*' ethtool.show_driver <devname> ''' try: module = ethtool.get_module(devname) except IOError: log.error('Driver informatio...	[ "def", "show_driver", "(", "devname", ")", ":", "try", ":", "module", "=", "ethtool", ".", "get_module", "(", "devname", ")", "except", "IOError", ":", "log", ".", "error", "(", "'Driver information not implemented on %s'", ",", "devname", ")", "return", "'Not...	21.448276	0.001538
def create_application_configuration(self, name, properties, description=None): """Create an application configuration. Args: name (str, optional): Only return application configurations containing property name that matches `name`. `name` can be a .. versionadded 1.12 "...	[ "def", "create_application_configuration", "(", "self", ",", "name", ",", "properties", ",", "description", "=", "None", ")", ":", "if", "not", "hasattr", "(", "self", ",", "'applicationConfigurations'", ")", ":", "raise", "NotImplementedError", "(", ")", "cv", ...	43.411765	0.009284
def cache_id(service, name, sub_resource=None, resource_id=None, invalidate=False, region=None, key=None, keyid=None, profile=None): ''' Cache, invalidate, or retrieve an AWS resource id keyed by name. .. code-block:: python __utils__['boto.cache_id']('ec2', 'myinstance',...	[ "def", "cache_id", "(", "service", ",", "name", ",", "sub_resource", "=", "None", ",", "resource_id", "=", "None", ",", "invalidate", "=", "False", ",", "region", "=", "None", ",", "key", "=", "None", ",", "keyid", "=", "None", ",", "profile", "=", "...	31.861111	0.001692
def register(cls, use_admin=True): """Register with the API a :class:`sandman.model.Model` class and associated endpoint. :param cls: User-defined class derived from :class:`sandman.model.Model` to be registered with the endpoint returned by :func:`endpoint()` :type cls: :class:`sandman...	[ "def", "register", "(", "cls", ",", "use_admin", "=", "True", ")", ":", "with", "app", ".", "app_context", "(", ")", ":", "if", "getattr", "(", "current_app", ",", "'class_references'", ",", "None", ")", "is", "None", ":", "current_app", ".", "class_refe...	38.368421	0.001339
def _Triple(S): """Procedure to calculate the triple point pressure and temperature for seawater Parameters ---------- S : float Salinity, [kg/kg] Returns ------- prop : dict Dictionary with the triple point properties: * Tt: Triple point temperature, [K] ...	[ "def", "_Triple", "(", "S", ")", ":", "def", "f", "(", "parr", ")", ":", "T", ",", "P", "=", "parr", "pw", "=", "_Region1", "(", "T", ",", "P", ")", "gw", "=", "pw", "[", "\"h\"", "]", "-", "T", "*", "pw", "[", "\"s\"", "]", "pv", "=", ...	22.487805	0.00104
def gradient_angle(self): """Angle in float degrees of line of a linear gradient. Read/Write. May be \|None\|, indicating the angle is inherited from the style hierarchy. An angle of 0.0 corresponds to a left-to-right gradient. Increasing angles represent clockwise rotation of the line, ...	[ "def", "gradient_angle", "(", "self", ")", ":", "# ---case 1: gradient path is explicit, but not linear---", "path", "=", "self", ".", "_gradFill", ".", "path", "if", "path", "is", "not", "None", ":", "raise", "ValueError", "(", "'not a linear gradient'", ")", "# --...	44.225806	0.001428
def _activate(self): """ShuffledMux's activate is similar to StochasticMux, but there is no 'n_active', since all the streams are always available. """ self.streams_ = [None] * self.n_streams # Weights of the active streams. # Once a stream is exhausted, it is set to 0. ...	[ "def", "_activate", "(", "self", ")", ":", "self", ".", "streams_", "=", "[", "None", "]", "*", "self", ".", "n_streams", "# Weights of the active streams.", "# Once a stream is exhausted, it is set to 0.", "# Upon activation, this is just a copy of self.weights.", "self", ...	41.789474	0.002463
def _clean(self): """Run by housekeeper thread""" now = time.time() for jwt in self.jwts.keys(): if (now - self.jwts[jwt]) > (self.age * 2): del self.jwts[jwt]	[ "def", "_clean", "(", "self", ")", ":", "now", "=", "time", ".", "time", "(", ")", "for", "jwt", "in", "self", ".", "jwts", ".", "keys", "(", ")", ":", "if", "(", "now", "-", "self", ".", "jwts", "[", "jwt", "]", ")", ">", "(", "self", ".",...	34.333333	0.009479
def disconnect_handler(remote, args, *kwargs): """Handle unlinking of remote account. This default handler will just delete the remote account link. You may wish to extend this module to perform clean-up in the remote service before removing the link (e.g. removing install webhooks). :param remo...	[ "def", "disconnect_handler", "(", "remote", ",", "", "args", ",", "", "*", "kwargs", ")", ":", "if", "not", "current_user", ".", "is_authenticated", ":", "return", "current_app", ".", "login_manager", ".", "unauthorized", "(", ")", "with", "db", ".", "se...	33.652174	0.001256
def _set_error_handler_callbacks(self, app): """ Sets the error handler callbacks used by this extension """ @app.errorhandler(NoAuthorizationError) def handle_auth_error(e): return self._unauthorized_callback(str(e)) @app.errorhandler(CSRFError) def ...	[ "def", "_set_error_handler_callbacks", "(", "self", ",", "app", ")", ":", "@", "app", ".", "errorhandler", "(", "NoAuthorizationError", ")", "def", "handle_auth_error", "(", "e", ")", ":", "return", "self", ".", "_unauthorized_callback", "(", "str", "(", "e", ...	38.390625	0.001587
def main(): """Define the CLI inteface/commands.""" arguments = docopt(__doc__) cfg_filename = pkg_resources.resource_filename( 'knowledge_base', 'config/virtuoso.ini' ) kb = KnowledgeBase(cfg_filename) # the user has issued a `find` command if arguments["find"]: sea...	[ "def", "main", "(", ")", ":", "arguments", "=", "docopt", "(", "__doc__", ")", "cfg_filename", "=", "pkg_resources", ".", "resource_filename", "(", "'knowledge_base'", ",", "'config/virtuoso.ini'", ")", "kb", "=", "KnowledgeBase", "(", "cfg_filename", ")", "# th...	29.736842	0.001713
def _assign_clusters(self): """Assign the samples to the closest centroids to create clusters """ self.clusters = np.array([self._closest_centroid(x) for x in self._X])	[ "def", "_assign_clusters", "(", "self", ")", ":", "self", ".", "clusters", "=", "np", ".", "array", "(", "[", "self", ".", "_closest_centroid", "(", "x", ")", "for", "x", "in", "self", ".", "_X", "]", ")" ]	47.25	0.010417
def fromJSON(value): """loads the GP object from a JSON string """ j = json.loads(value) v = GPDate() if "defaultValue" in j: v.value = j['defaultValue'] else: v.value = j['value'] if 'paramName' in j: v.paramName = j['paramName'] ...	[ "def", "fromJSON", "(", "value", ")", ":", "j", "=", "json", ".", "loads", "(", "value", ")", "v", "=", "GPDate", "(", ")", "if", "\"defaultValue\"", "in", "j", ":", "v", ".", "value", "=", "j", "[", "'defaultValue'", "]", "else", ":", "v", ".", ...	30.947368	0.013201
def popall(self, key, default=_marker): """Remove all occurrences of key and return the list of corresponding values. If key is not found, default is returned if given, otherwise KeyError is raised. """ found = False identity = self._title(key) ret = [] ...	[ "def", "popall", "(", "self", ",", "key", ",", "default", "=", "_marker", ")", ":", "found", "=", "False", "identity", "=", "self", ".", "_title", "(", "key", ")", "ret", "=", "[", "]", "for", "i", "in", "range", "(", "len", "(", "self", ".", "...	30.038462	0.002481
def min(self): """ Returns the minimum value of the domain. :rtype: `float` or `np.inf` """ return int(self._min) if not np.isinf(self._min) else self._min	[ "def", "min", "(", "self", ")", ":", "return", "int", "(", "self", ".", "_min", ")", "if", "not", "np", ".", "isinf", "(", "self", ".", "_min", ")", "else", "self", ".", "_min" ]	27.142857	0.010204
def init_from_fcnxs(ctx, fcnxs_symbol, fcnxs_args_from, fcnxs_auxs_from): """ use zero initialization for better convergence, because it tends to oputut 0, and the label 0 stands for background, which may occupy most size of one image. """ fcnxs_args = fcnxs_args_from.copy() fcnxs_auxs = fcnxs_auxs_...	[ "def", "init_from_fcnxs", "(", "ctx", ",", "fcnxs_symbol", ",", "fcnxs_args_from", ",", "fcnxs_auxs_from", ")", ":", "fcnxs_args", "=", "fcnxs_args_from", ".", "copy", "(", ")", "fcnxs_auxs", "=", "fcnxs_auxs_from", ".", "copy", "(", ")", "for", "k", ",", "v...	47.952381	0.010219
def determine_name(func): """ Given a function, returns the name of the function. Ex:: from random import choice determine_name(choice) # Returns 'choice' :param func: The callable :type func: function :returns: Name string """ if hasattr(func, '__name__'): re...	[ "def", "determine_name", "(", "func", ")", ":", "if", "hasattr", "(", "func", ",", "'__name__'", ")", ":", "return", "func", ".", "__name__", "elif", "hasattr", "(", "func", ",", "'__class__'", ")", ":", "return", "func", ".", "__class__", ".", "__name__...	23.347826	0.001789
def generate_keywords(additional_keywords=None): """Generates gettext keywords list :arg additional_keywords: dict of keyword -> value :returns: dict of keyword -> values for Babel extraction Here's what Babel has for DEFAULT_KEYWORDS:: DEFAULT_KEYWORDS = { '_': None, ...	[ "def", "generate_keywords", "(", "additional_keywords", "=", "None", ")", ":", "# Shallow copy", "keywords", "=", "dict", "(", "BABEL_KEYWORDS", ")", "keywords", ".", "update", "(", "{", "'_lazy'", ":", "None", ",", "'gettext_lazy'", ":", "None", ",", "'ugette...	25.490909	0.000687
def create_snapshots(self, volumes, *kwargs): """Create snapshots of the listed volumes. :param volumes: List of names of the volumes to snapshot. :type volumes: list of str :param \\*kwargs: See the REST API Guide on your array for the documentation on the ...	[ "def", "create_snapshots", "(", "self", ",", "volumes", ",", "", "", "kwargs", ")", ":", "data", "=", "{", "\"source\"", ":", "volumes", ",", "\"snap\"", ":", "True", "}", "data", ".", "update", "(", "kwargs", ")", "return", "self", ".", "_request", ...	37.294118	0.009231
def addr(self): """ Get the concrete address of the instruction pointer, without triggering SimInspect breakpoints or generating SimActions. An integer is returned, or an exception is raised if the instruction pointer is symbolic. :return: an int """ ip = self.regs._ip ...	[ "def", "addr", "(", "self", ")", ":", "ip", "=", "self", ".", "regs", ".", "_ip", "if", "isinstance", "(", "ip", ",", "SootAddressDescriptor", ")", ":", "return", "ip", "return", "self", ".", "solver", ".", "eval_one", "(", "self", ".", "regs", ".", ...	35.916667	0.00905
def flush(self, safe=None): ''' Perform all database operations currently in the queue''' result = None for index, op in enumerate(self.queue): try: result = op.execute() except: self.clear_queue() self.clear_cache() raise self.clear_queue() return result	[ "def", "flush", "(", "self", ",", "safe", "=", "None", ")", ":", "result", "=", "None", "for", "index", ",", "op", "in", "enumerate", "(", "self", ".", "queue", ")", ":", "try", ":", "result", "=", "op", ".", "execute", "(", ")", "except", ":", ...	23	0.04878
def get_package_hashes( package, version=None, algorithm=DEFAULT_ALGORITHM, python_versions=(), verbose=False, include_prereleases=False, lookup_memory=None, index_url=DEFAULT_INDEX_URL, ): """ Gets the hashes for the given package. >>> get_package_hashes('hashin') { ...	[ "def", "get_package_hashes", "(", "package", ",", "version", "=", "None", ",", "algorithm", "=", "DEFAULT_ALGORITHM", ",", "python_versions", "=", "(", ")", ",", "verbose", "=", "False", ",", "include_prereleases", "=", "False", ",", "lookup_memory", "=", "Non...	30.352941	0.001877
def launch(self, argv=None, showusageonnoargs=False, width=0, helphint="Use with --help for more information.\n", debug_parser=False): """Do the usual stuff to initiallize the program. Read config files and parse argumen...	[ "def", "launch", "(", "self", ",", "argv", "=", "None", ",", "showusageonnoargs", "=", "False", ",", "width", "=", "0", ",", "helphint", "=", "\"Use with --help for more information.\\n\"", ",", "debug_parser", "=", "False", ")", ":", "if", "showusageonnoargs", ...	40.9	0.009074
def ellipse(data, channels, center, a, b, theta=0, log=False, full_output=False): """ Gate that preserves events inside an ellipse-shaped region. Events are kept if they satisfy the following relationship:: (x/a)2 + (y/b)2 <= 1 where `x` and `y` are the coordinates...	[ "def", "ellipse", "(", "data", ",", "channels", ",", "center", ",", "a", ",", "b", ",", "theta", "=", "0", ",", "log", "=", "False", ",", "full_output", "=", "False", ")", ":", "# Extract channels in which to gate", "if", "len", "(", "channels", ")", "...	32.033708	0.002382
def is_allowed(self, user_agent, url, syntax=GYM2008): """True if the user agent is permitted to visit the URL. The syntax parameter can be GYM2008 (the default) or MK1996 for strict adherence to the traditional standard. """ if PY_MAJOR_VERSION < 3: # The r...	[ "def", "is_allowed", "(", "self", ",", "user_agent", ",", "url", ",", "syntax", "=", "GYM2008", ")", ":", "if", "PY_MAJOR_VERSION", "<", "3", ":", "# The robot rules are stored internally as Unicode. The two lines ", "# below ensure that the parameters passed to this function...	53.451613	0.008892
def what_if_I_upgrade(conn, pkg_name='openquake.server.db.schema.upgrades', extract_scripts='extract_upgrade_scripts'): """ :param conn: a DB API 2 connection :param str pkg_name: the name of the package with the upgrade scripts :param extract_scripts: name ...	[ "def", "what_if_I_upgrade", "(", "conn", ",", "pkg_name", "=", "'openquake.server.db.schema.upgrades'", ",", "extract_scripts", "=", "'extract_upgrade_scripts'", ")", ":", "msg_safe_", "=", "'\\nThe following scripts can be applied safely:\\n%s'", "msg_slow_", "=", "'\\nPlease ...	43.089286	0.000405
def decompress(input_dir, dcm_pattern='.dcm'): """ Decompress all .dcm files recursively found in DICOM_DIR. This uses 'gdcmconv --raw'. It works when 'dcm2nii' shows the `Unsupported Transfer Syntax` error. This error is usually caused by lack of JPEG2000 support in dcm2nii compilation. Read mor...	[ "def", "decompress", "(", "input_dir", ",", "dcm_pattern", "=", "'*.dcm'", ")", ":", "dcmfiles", "=", "sorted", "(", "recursive_glob", "(", "input_dir", ",", "dcm_pattern", ")", ")", "for", "dcm", "in", "dcmfiles", ":", "cmd", "=", "'gdcmconv --raw -i \"{0}\" ...	33.807692	0.002212
def signature(self): """Get data signature""" self._data.sort() str_to_sign = self._delimiter.join(self._data) return hashlib.sha1(str_to_sign).hexdigest()	[ "def", "signature", "(", "self", ")", ":", "self", ".", "_data", ".", "sort", "(", ")", "str_to_sign", "=", "self", ".", "_delimiter", ".", "join", "(", "self", ".", "_data", ")", "return", "hashlib", ".", "sha1", "(", "str_to_sign", ")", ".", "hexdi...	36.6	0.010695
def load_market_data(trading_day=None, trading_days=None, bm_symbol='SPY', environ=None): """ Load benchmark returns and treasury yield curves for the given calendar and benchmark symbol. Benchmarks are downloaded as a Series from IEX Trading. Treasury curves are US Treasury B...	[ "def", "load_market_data", "(", "trading_day", "=", "None", ",", "trading_days", "=", "None", ",", "bm_symbol", "=", "'SPY'", ",", "environ", "=", "None", ")", ":", "if", "trading_day", "is", "None", ":", "trading_day", "=", "get_calendar", "(", "'XNYS'", ...	35.74026	0.000354
def host_events(self, host): ''' Given a host name, this will return all task events executed on that host ''' all_host_events = filter(lambda x: 'event_data' in x and 'host' in x['event_data'] and x['event_data']['host'] == host, self.events) ret...	[ "def", "host_events", "(", "self", ",", "host", ")", ":", "all_host_events", "=", "filter", "(", "lambda", "x", ":", "'event_data'", "in", "x", "and", "'host'", "in", "x", "[", "'event_data'", "]", "and", "x", "[", "'event_data'", "]", "[", "'host'", "...	47.571429	0.011799
def generate_certificates(base_dir, *peer_names, pubKeyDir=None, secKeyDir=None, sigKeyDir=None, verkeyDir=None, clean=True): ''' Generate client and server CURVE certificate files''' pubKeyDir = pubKeyDir or 'public_keys' secKeyDir = secKeyDir or 'private...	[ "def", "generate_certificates", "(", "base_dir", ",", "*", "peer_names", ",", "pubKeyDir", "=", "None", ",", "secKeyDir", "=", "None", ",", "sigKeyDir", "=", "None", ",", "verkeyDir", "=", "None", ",", "clean", "=", "True", ")", ":", "pubKeyDir", "=", "p...	39.976744	0.000568
def _lookup_abs(self, p, klass, create=1): """ Fast (?) lookup of a normalized absolute path. This method is intended for use by internal lookups with already-normalized path data. For general-purpose lookups, use the FS.Entry(), FS.Dir() or FS.File() methods. The ca...	[ "def", "_lookup_abs", "(", "self", ",", "p", ",", "klass", ",", "create", "=", "1", ")", ":", "k", "=", "_my_normcase", "(", "p", ")", "try", ":", "result", "=", "self", ".", "_lookupDict", "[", "k", "]", "except", "KeyError", ":", "if", "not", "...	43.219512	0.002208
def create_csv(filename, csv_data, mode="w"): """ Create a CSV file with the given data and store it in the file with the given name. :param filename: name of the file to store the data in :pram csv_data: the data to be stored in the file :param mode: the mode in which we have to open the file....	[ "def", "create_csv", "(", "filename", ",", "csv_data", ",", "mode", "=", "\"w\"", ")", ":", "with", "open", "(", "filename", ",", "mode", ")", "as", "f", ":", "csv_data", ".", "replace", "(", "\"_\"", ",", "r\"\\_\"", ")", "f", ".", "write", "(", "...	33.714286	0.002062
def experiment(self): """The identifier or the experiment that is currently processed""" if self._experiment is None: self._experiment = list(self.config.experiments.keys())[-1] return self._experiment	[ "def", "experiment", "(", "self", ")", ":", "if", "self", ".", "_experiment", "is", "None", ":", "self", ".", "_experiment", "=", "list", "(", "self", ".", "config", ".", "experiments", ".", "keys", "(", ")", ")", "[", "-", "1", "]", "return", "sel...	46.6	0.008439
def status(name, maximum=None, minimum=None, absolute=False, free=False): ''' Return the current disk usage stats for the named mount point name Disk mount or directory for which to check used space maximum The maximum disk utilization minimum The minimum disk utilization ...	[ "def", "status", "(", "name", ",", "maximum", "=", "None", ",", "minimum", "=", "None", ",", "absolute", "=", "False", ",", "free", "=", "False", ")", ":", "# Monitoring state, no changes will be made so no test interface needed", "ret", "=", "{", "'name'", ":",...	32.614035	0.000522
def _lookup_nexus_bindings(query_type, session=None, **bfilter): """Look up 'query_type' Nexus bindings matching the filter. :param query_type: 'all', 'one' or 'first' :param session: db session :param bfilter: filter for bindings query :returns: bindings if query gave a result, else r...	[ "def", "_lookup_nexus_bindings", "(", "query_type", ",", "session", "=", "None", ",", "", "", "bfilter", ")", ":", "if", "session", "is", "None", ":", "session", "=", "bc", ".", "get_reader_session", "(", ")", "query_method", "=", "getattr", "(", "sessio...	35.65	0.001366
def guess_rank(M_E): '''Guess the rank of the incomplete matrix ''' n, m = M_E.shape epsilon = np.count_nonzero(M_E) / np.sqrt(m * n) _, S0, _ = svds_descending(M_E, min(100, max(M_E.shape) - 1)) S0 = np.diag(S0) S1 = S0[:-1] - S0[1:] S1_ = S1 / np.mean(S1[-10:]) r1 = 0 la...	[ "def", "guess_rank", "(", "M_E", ")", ":", "n", ",", "m", "=", "M_E", ".", "shape", "epsilon", "=", "np", ".", "count_nonzero", "(", "M_E", ")", "/", "np", ".", "sqrt", "(", "m", "*", "n", ")", "_", ",", "S0", ",", "_", "=", "svds_descending", ...	28.178571	0.001225
def rsem_mapped_reads_plot(self): """ Make the rsem assignment rates plot """ # Plot categories keys = OrderedDict() keys['Unique'] = { 'color': '#437bb1', 'name': 'Aligned uniquely to a gene' } keys['Multi'] = { 'color': '#e63491', 'name': 'Aligned to multiple genes'...	[ "def", "rsem_mapped_reads_plot", "(", "self", ")", ":", "# Plot categories", "keys", "=", "OrderedDict", "(", ")", "keys", "[", "'Unique'", "]", "=", "{", "'color'", ":", "'#437bb1'", ",", "'name'", ":", "'Aligned uniquely to a gene'", "}", "keys", "[", "'Mult...	40.8	0.024904
def chunk_count(self): """Return a count of the chunks in this world folder.""" c = 0 for r in self.iter_regions(): c += r.chunk_count() return c	[ "def", "chunk_count", "(", "self", ")", ":", "c", "=", "0", "for", "r", "in", "self", ".", "iter_regions", "(", ")", ":", "c", "+=", "r", ".", "chunk_count", "(", ")", "return", "c" ]	30.666667	0.010582
def randomize(self, force = 0): """ Initialize node biases to random values in the range [-max, max]. """ if force or not self.frozen: self.weight = randomArray(self.size, self._maxRandom)	[ "def", "randomize", "(", "self", ",", "force", "=", "0", ")", ":", "if", "force", "or", "not", "self", ".", "frozen", ":", "self", ".", "weight", "=", "randomArray", "(", "self", ".", "size", ",", "self", ".", "_maxRandom", ")" ]	37.833333	0.017241
def add_model(self, propname, model, regen_mode='normal', **kwargs): r""" Adds a new model to the models dictionary (``object.models``) Parameters ---------- propname : string The name of the property to be calculated by the model. model : function ...	[ "def", "add_model", "(", "self", ",", "propname", ",", "model", ",", "regen_mode", "=", "'normal'", ",", "", "", "kwargs", ")", ":", "if", "propname", "in", "kwargs", ".", "values", "(", ")", ":", "# Prevent infinite loops of look-ups", "raise", "Exception...	44.255814	0.001028
def gru(name, input, state, kernel_r, kernel_u, kernel_c, bias_r, bias_u, bias_c, new_state, number_of_gates = 2): ''' - zt = f(XtWz + Ht_1Rz + Wbz + Rbz) - rt = f(XtWr + Ht_1Rr + Wbr + Rbr) - ht = g(XtWh + (rt . Ht_1)Rh + Rbh + Wbh) - Ht = (1-zt).ht + zt.Ht_1 ''' ...	[ "def", "gru", "(", "name", ",", "input", ",", "state", ",", "kernel_r", ",", "kernel_u", ",", "kernel_c", ",", "bias_r", ",", "bias_u", ",", "bias_c", ",", "new_state", ",", "number_of_gates", "=", "2", ")", ":", "nn", "=", "Build", "(", "name", ")",...	31.115385	0.008393
def header(self): """Generates HTTP header for this cookie.""" if self._send_cookie: morsel = Morsel() cookie_value = Session.encode_sid(self._config.secret, self._sid) if self._config.encrypt_key: cipher = AESCipher(self._config.encrypt_key) ...	[ "def", "header", "(", "self", ")", ":", "if", "self", ".", "_send_cookie", ":", "morsel", "=", "Morsel", "(", ")", "cookie_value", "=", "Session", ".", "encode_sid", "(", "self", ".", "_config", ".", "secret", ",", "self", ".", "_sid", ")", "if", "se...	32.820513	0.002276
def replace_row(self, line, ndx): """ replace a grids row at index 'ndx' with 'line' """ for col in range(len(line)): self.set_tile(ndx, col, line[col])	[ "def", "replace_row", "(", "self", ",", "line", ",", "ndx", ")", ":", "for", "col", "in", "range", "(", "len", "(", "line", ")", ")", ":", "self", ".", "set_tile", "(", "ndx", ",", "col", ",", "line", "[", "col", "]", ")" ]	32.166667	0.020202
def write_to_influxdb(received_data): ''' Convert data into RuuviCollecor naming schme and scale ''' dataFormat = received_data[1]["data_format"] if ('data_format' in received_data[1]) else None fields = {} fields["temperature"] = received_data[1]["temperature"] if ('temperature' i...	[ "def", "write_to_influxdb", "(", "received_data", ")", ":", "dataFormat", "=", "received_data", "[", "1", "]", "[", "\"data_format\"", "]", "if", "(", "'data_format'", "in", "received_data", "[", "1", "]", ")", "else", "None", "fields", "=", "{", "}", "fie...	67.758621	0.012544
def __do_query_into_hash(conn, sql_str): ''' Perform the query that is passed to it (sql_str). Returns: results in a dict. ''' mod = sys._getframe().f_code.co_name log.debug('%s<--(%s)', mod, sql_str) rtn_results = [] try: cursor = conn.cursor() except MySQLdb.MySQ...	[ "def", "__do_query_into_hash", "(", "conn", ",", "sql_str", ")", ":", "mod", "=", "sys", ".", "_getframe", "(", ")", ".", "f_code", ".", "co_name", "log", ".", "debug", "(", "'%s<--(%s)'", ",", "mod", ",", "sql_str", ")", "rtn_results", "=", "[", "]", ...	22.772727	0.000957
def map_as_completed(func, iterables, kwargs): """map_as_completed(func, iterables) Equivalent to map, but the results are returned as soon as they are made available. :param func: Any picklable callable object (function or class object with __call__ method); this object will be called to...	[ "def", "map_as_completed", "(", "func", ",", "", "iterables", ",", "", "", "kwargs", ")", ":", "# TODO: Handle timeout", "for", "future", "in", "as_completed", "(", "_mapFuture", "(", "func", ",", "", "iterables", ")", ")", ":", "yield", "future", ".",...	46.315789	0.001114
def _num_required_args(func): """ Number of args for func >>> def foo(a, b, c=None): ... return a + b + c >>> _num_required_args(foo) 2 >>> def bar(*args): ... return sum(args) >>> print(_num_required_args(bar)) None borrowed from: https:/...	[ "def", "_num_required_args", "(", "func", ")", ":", "try", ":", "spec", "=", "inspect", ".", "getargspec", "(", "func", ")", "if", "spec", ".", "varargs", ":", "return", "None", "num_defaults", "=", "len", "(", "spec", ".", "defaults", ")", "if", "spec...	23.2	0.001656
def _osquery(sql, format='json'): ''' Helper function to run raw osquery queries ''' ret = { 'result': True, } cmd = ['osqueryi'] + ['--json'] + [sql] res = __salt__['cmd.run_all'](cmd) if res['stderr']: ret['result'] = False ret['error'] = res['stderr'] else...	[ "def", "_osquery", "(", "sql", ",", "format", "=", "'json'", ")", ":", "ret", "=", "{", "'result'", ":", "True", ",", "}", "cmd", "=", "[", "'osqueryi'", "]", "+", "[", "'--json'", "]", "+", "[", "sql", "]", "res", "=", "__salt__", "[", "'cmd.run...	24.117647	0.002347
def strict_parse(cls, query_str, *specs, extra_parameters=True): """ Parse query and return :class:`.WStrictURIQuery` object :param query_str: query component of URI to parse :param specs: list of parameters specifications :param extra_parameters: whether parameters that was not specified in "specs" are allowe...	[ "def", "strict_parse", "(", "cls", ",", "query_str", ",", "", "specs", ",", "extra_parameters", "=", "True", ")", ":", "plain_result", "=", "cls", ".", "parse", "(", "query_str", ")", "return", "WStrictURIQuery", "(", "plain_result", ",", "", "specs", ",...	46.5	0.025316
def upgrade_account(self, account=None, **kwargs): """ Upgrade an account to Lifetime membership :param str account: (optional) the account to allow access to (defaults to ``default_account``) """ if not account: if "default_account" in self.config: ...	[ "def", "upgrade_account", "(", "self", ",", "account", "=", "None", ",", "", "", "kwargs", ")", ":", "if", "not", "account", ":", "if", "\"default_account\"", "in", "self", ".", "config", ":", "account", "=", "self", ".", "config", "[", "\"default_acco...	40.714286	0.002286
def implied_vol(self, value, precision=1.0e-5, iters=100): """Get implied vol at the specified price using an iterative approach. There is no closed-form inverse of BSM-value as a function of sigma, so start at an anchoring volatility level from Brenner & Subrahmanyam (1988) and wo...	[ "def", "implied_vol", "(", "self", ",", "value", ",", "precision", "=", "1.0e-5", ",", "iters", "=", "100", ")", ":", "vol", "=", "np", ".", "sqrt", "(", "2.0", "", "np", ".", "pi", "/", "self", ".", "T", ")", "", "(", "value", "/", "self", ...	35.75	0.001946
def query(self, dataset='hsapiens_gene_ensembl', attributes=[], filters={}, filename=None): """mapping ids using BioMart. :param dataset: str, default: 'hsapiens_gene_ensembl' :param attributes: str, list, tuple :param filters: dict, {'filter name': list(filter value)} ...	[ "def", "query", "(", "self", ",", "dataset", "=", "'hsapiens_gene_ensembl'", ",", "attributes", "=", "[", "]", ",", "filters", "=", "{", "}", ",", "filename", "=", "None", ")", ":", "if", "not", "attributes", ":", "attributes", "=", "[", "'ensembl_gene_i...	45.559322	0.009104
def com_adobe_fonts_check_cff2_call_depth(ttFont): """Is the CFF2 subr/gsubr call depth > 10?""" any_failures = False cff = ttFont['CFF2'].cff for top_dict in cff.topDictIndex: for fd_index, font_dict in enumerate(top_dict.FDArray): if hasattr(font_dict, 'Private'): ...	[ "def", "com_adobe_fonts_check_cff2_call_depth", "(", "ttFont", ")", ":", "any_failures", "=", "False", "cff", "=", "ttFont", "[", "'CFF2'", "]", ".", "cff", "for", "top_dict", "in", "cff", ".", "topDictIndex", ":", "for", "fd_index", ",", "font_dict", "in", ...	36.647059	0.001565

def upload_metadata(directory, create_csv='', review='', max_size='128m', verbose=False, debug=False): """ Draft or review metadata files for uploading files to Open Humans. The target directory should either represent files for a single member (no subdirectories), or contain a subdi...

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def find_all_output_in_range(self, ifo, currSeg, useSplitLists=False): """ Return all files that overlap the specified segment. """ if not useSplitLists: # Slower, but simpler method outFiles = [i for i in self if ifo in i.ifo_list] outFiles = [i for i...

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def decode(self, encoded_packet): """Decode a transmitted package.""" b64 = False if not isinstance(encoded_packet, binary_types): encoded_packet = encoded_packet.encode('utf-8') elif not isinstance(encoded_packet, bytes): encoded_packet = bytes(encoded_packet) ...

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def attempt_advance(self, blocksize, timeout=10): """ Attempt to advance the frame buffer. Retry upon failure, except if the frame file is beyond the timeout limit. Parameters ---------- blocksize: int The number of seconds to attempt to read from the channel ...

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def mutating_join(*args, **kwargs): """ generic function for mutating dplyr-style joins """ # candidate for improvement left = args[0] right = args[1] if 'by' in kwargs: left_cols, right_cols = get_join_cols(kwargs['by']) else: left_cols, right_cols = None, None if 'suffixes' in kwargs: dsuf...

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def _MarkerFactory(marker_code, stream, offset): """ Return |_Marker| or subclass instance appropriate for marker at *offset* in *stream* having *marker_code*. """ if marker_code == JPEG_MARKER_CODE.APP0: marker_cls = _App0Marker elif marker_code == JPEG_MARKER_CODE.APP1: marker_...

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def size_of_varint_2(value): """ Number of bytes needed to encode an integer in variable-length format. """ value = (value << 1) ^ (value >> 63) if value <= 0x7f: return 1 if value <= 0x3fff: return 2 if value <= 0x1fffff: return 3 if value <= 0xfffffff: retur...

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def set_path(self, path, val): """ Set the given value at the supplied path where path is either a tuple of strings or a string in A.B.C format. """ path = tuple(path.split('.')) if isinstance(path , str) else tuple(path) disallowed = [p for p in path if not type(self)._...

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def full_name(self): """ str: func_name(type1,type2) Return the function signature without the return values """ name, parameters, _ = self.signature return name+'('+','.join(parameters)+')'

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def get(self, block=True, timeout=None): """Get item from underlying queue.""" return self._queue.get(block, timeout)

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def argument_count(self): """ Uses the command line arguments to fill the count function and call it. """ arguments, _ = self.argparser.parse_known_args() return self.count(**vars(arguments))

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def save_function(self, obj, name=None): """ Registered with the dispatch to handle all function types. Determines what kind of function obj is (e.g. lambda, defined at interactive prompt, etc) and handles the pickling appropriately. """ try: should_special_case = ob...

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def represent_as_string(iterable): """ Represent a number in the form of a string. (8, 6, 8, '.', 0, 15) -> "868.0F" Args: iterable - Number represented as an iterable container of digits. Returns: Number represented as a string of digits. >>> represent_as_string((8, ...

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def _set_initial(self, C_in, scale_in): r"""Set the initial values for parameters and Wilson coefficients at the scale `scale_in`.""" self.C_in = C_in self.scale_in = scale_in

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def distance(line, point): """ infinite line to point or line to line distance is point is given as line - use middle point of that liune """ x0, y0, x1, y1 = line try: p1, p2 = point except ValueError: # line is given instead of point p1, p2 = middle(point) n1 = ...

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def htseq_counts_chart (self): """ Make the HTSeq Count assignment rates plot """ cats = OrderedDict() cats['assigned'] = { 'name': 'Assigned' } cats['ambiguous'] = { 'name': 'Ambiguous' } cats['alignment_not_unique'] = { 'name': 'Alignment Not Unique' } cats['no...

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def sorted_bfs_edges(G, source=None): """Produce edges in a breadth-first-search starting at source. Neighbors appear in the order a linguist would expect in a syntax tree. The result will only contain edges that express a dominance or spanning relation, i.e. edges expressing pointing or precedence rel...

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def compute_vest_stat(vest_dict, ref_aa, somatic_aa, codon_pos, stat_func=np.mean, default_val=0.0): """Compute missense VEST score statistic. Note: non-missense mutations are intentially not filtered out and will take a default value of zero. Parameters ...

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def estimate_cpd(self, node): """ Method to estimate the CPD for a given variable. Parameters ---------- node: int, string (any hashable python object) The name of the variable for which the CPD is to be estimated. Returns ------- CPD: Tabula...

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def update(self,dt): """ Should be called regularly to move the actor. This method does nothing if the :py:attr:`enabled` property is set to False. This method is called automatically and should not be called manually. """ if not self.enabled: ...

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def create_entry(i): """ Input: { path - path where to create an entry (data_uoa) - data UOA (data_uid) - if uoa is an alias, we can force data UID (force) - if 'yes', force creation even if directory already exists } Output: { ...

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def CDQ(cpu): """ EDX:EAX = sign-extend of EAX """ cpu.EDX = Operators.EXTRACT(Operators.SEXTEND(cpu.EAX, 32, 64), 32, 32)

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def do_init_cached_fields(self): """ Initialize each fields of the fields_desc dict, or use the cached fields information """ cls_name = self.__class__ # Build the fields information if Packet.class_default_fields.get(cls_name, None) is None: self.pr...

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def ext_import(soname, module_subpath=""): """ Loads a turicreate toolkit module (a shared library) into the tc.extensions namespace. Toolkit module created via SDK can either be directly imported, e.g. ``import example`` or via this function, e.g. ``turicreate.ext_import("example.so")``. Use `...

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def fft_convolve(in1, in2, conv_device="cpu", conv_mode="linear", store_on_gpu=False): """ This function determines the convolution of two inputs using the FFT. Contains an implementation for both CPU and GPU. INPUTS: in1 (no default): Array containing one set of data, possibl...

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def http_auth_required(realm): """Decorator that protects endpoints using Basic HTTP authentication. :param realm: optional realm name""" def decorator(fn): @wraps(fn) def wrapper(*args, **kwargs): if _check_http_auth(): return fn(*args, **kwargs) if...

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def build_access_required(function_or_param_name): """Decorator ensures user has access to the build ID in the request. May be used in two ways: @build_access_required def my_func(build): ... @build_access_required('custom_build_id_param') def my_func(build): ...

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def render(self, compress=False): """Return a rendered representation of the color. If `compress` is true, the shortest possible representation is used; otherwise, named colors are rendered as names and all others are rendered as hex (or with the rgba function). """ if ...

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def file_exists(self, filename, directory=False, note=None, loglevel=logging.DEBUG): """Return True if file exists on the target host, else False @param filename: Filename to determine the existence of. @param directory: Indicate that the fil...

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def separable_conv_block(inputs, filters, dilation_rates_and_kernel_sizes, **kwargs): """A block of separable convolutions.""" return conv_block_internal(separable_conv, inputs, filters, dilation_rates_and_kernel_sizes, **kwargs)

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def tuple_to_qfont(tup): """ Create a QFont from tuple: (family [string], size [int], italic [bool], bold [bool]) """ if not isinstance(tup, tuple) or len(tup) != 4 \ or not is_text_string(tup[0]) \ or not isinstance(tup[1], int) \ or not isinstance(tup[2], bool) \ or...

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def get(self, session, **kwargs): '''taobao.fenxiao.cooperation.get 获取供应商的合作关系信息获取供应商的合作关系信息''' request = TOPRequest('taobao.fenxiao.cooperation.get') for k, v in kwargs.iteritems(): if k not in ('status', 'start_date', 'end_date', 'trade_type', 'page_no', 'page_siz...

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def page(self, course, errors=None, saved=False): """ Get all data and display the page """ return self.template_helper.get_renderer().course_admin.settings(course, errors, saved)

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def open(self): """initialize visit variables""" self.stats = self.linter.add_stats() self._returns = [] self._branches = defaultdict(int) self._stmts = []

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def check_ns_run_threads(run): """Check thread labels and thread_min_max have expected properties. Parameters ---------- run: dict Nested sampling run to check. Raises ------ AssertionError If run does not have expected properties. """ assert run['thread_labels'].dt...

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def update(gandi, address, dest_add, dest_del): """Update a domain mail forward.""" source, domain = address if not dest_add and not dest_del: gandi.echo('Nothing to update: you must provide destinations to ' 'update, use --dest-add/-a or -dest-del/-d parameters.') return...

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def _augment_book(self, uuid, event): """ Checks if the newly created object is a book and only has an ISBN. If so, tries to fetch the book data off the internet. :param uuid: uuid of book to augment :param client: requesting client """ try: if not is...

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def Unlock(fd, path): """Release the lock on the file. Args: fd: int, the file descriptor of the file to unlock. path: string, the name of the file to lock. Raises: IOError, raised from flock while attempting to release a file lock. """ try: fcntl.flock(fd, fcntl.LOCK_UN | fcntl.LOCK_NB) e...

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def get_arg_parse(): """Parses the Command Line Arguments using argparse.""" # Create parser object: objParser = argparse.ArgumentParser() # Add argument to namespace -config file path: objParser.add_argument('-config', required=True, metavar='/path/to/config.csv', ...

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def pidfile(self): """Get the absolute path of the pidfile.""" return os.path.abspath( os.path.expandvars( os.path.expanduser( self._pidfile, ), ), )

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def xrify_tuples(self, tup): """Make xarray.DataArray from tuple.""" return xr.DataArray(tup, dims=['bands'], coords={'bands': self.data['bands']})

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def winddir_text(pts): "Convert wind direction from 0..15 to compass point text" global _winddir_text_array if pts is None: return None if not isinstance(pts, int): pts = int(pts + 0.5) % 16 if not _winddir_text_array: _ = pywws.localisation.translation.ugettext _wind...

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def comments(self, limit=None): """GETs user's comments. Calls :meth:`narwal.Reddit.user_comments`. :param limit: max number of comments to get """ return self._reddit.user_comments(self.name, limit=limit)

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def api_url(self): '''return the api url of this request''' return pathjoin(Request.path, self.id, url=self.bin.api_url)

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def visit_addresses(frame, return_addresses): """ Visits all of the addresses, returns a new dict which contains just the addressed elements Parameters ---------- frame return_addresses: a dictionary, keys will be column names of the resulting dataframe, and are what the us...

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def _get_section_name(cls, parser): """Parse options from relevant section.""" for section_name in cls.POSSIBLE_SECTION_NAMES: if parser.has_section(section_name): return section_name return None

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def show_driver(devname): ''' Queries the specified network device for associated driver information CLI Example: .. code-block:: bash salt '*' ethtool.show_driver <devname> ''' try: module = ethtool.get_module(devname) except IOError: log.error('Driver informatio...

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def create_application_configuration(self, name, properties, description=None): """Create an application configuration. Args: name (str, optional): Only return application configurations containing property **name** that matches `name`. `name` can be a .. versionadded 1.12 "...

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def cache_id(service, name, sub_resource=None, resource_id=None, invalidate=False, region=None, key=None, keyid=None, profile=None): ''' Cache, invalidate, or retrieve an AWS resource id keyed by name. .. code-block:: python __utils__['boto.cache_id']('ec2', 'myinstance',...

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def register(cls, use_admin=True): """Register with the API a :class:`sandman.model.Model` class and associated endpoint. :param cls: User-defined class derived from :class:`sandman.model.Model` to be registered with the endpoint returned by :func:`endpoint()` :type cls: :class:`sandman...

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def _Triple(S): """Procedure to calculate the triple point pressure and temperature for seawater Parameters ---------- S : float Salinity, [kg/kg] Returns ------- prop : dict Dictionary with the triple point properties: * Tt: Triple point temperature, [K] ...

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def gradient_angle(self): """Angle in float degrees of line of a linear gradient. Read/Write. May be |None|, indicating the angle is inherited from the style hierarchy. An angle of 0.0 corresponds to a left-to-right gradient. Increasing angles represent clockwise rotation of the line, ...

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def _activate(self): """ShuffledMux's activate is similar to StochasticMux, but there is no 'n_active', since all the streams are always available. """ self.streams_ = [None] * self.n_streams # Weights of the active streams. # Once a stream is exhausted, it is set to 0. ...

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def _clean(self): """Run by housekeeper thread""" now = time.time() for jwt in self.jwts.keys(): if (now - self.jwts[jwt]) > (self.age * 2): del self.jwts[jwt]

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def disconnect_handler(remote, *args, **kwargs): """Handle unlinking of remote account. This default handler will just delete the remote account link. You may wish to extend this module to perform clean-up in the remote service before removing the link (e.g. removing install webhooks). :param remo...

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def _set_error_handler_callbacks(self, app): """ Sets the error handler callbacks used by this extension """ @app.errorhandler(NoAuthorizationError) def handle_auth_error(e): return self._unauthorized_callback(str(e)) @app.errorhandler(CSRFError) def ...

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def main(): """Define the CLI inteface/commands.""" arguments = docopt(__doc__) cfg_filename = pkg_resources.resource_filename( 'knowledge_base', 'config/virtuoso.ini' ) kb = KnowledgeBase(cfg_filename) # the user has issued a `find` command if arguments["find"]: sea...

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def _assign_clusters(self): """Assign the samples to the closest centroids to create clusters """ self.clusters = np.array([self._closest_centroid(x) for x in self._X])

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def fromJSON(value): """loads the GP object from a JSON string """ j = json.loads(value) v = GPDate() if "defaultValue" in j: v.value = j['defaultValue'] else: v.value = j['value'] if 'paramName' in j: v.paramName = j['paramName'] ...

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def popall(self, key, default=_marker): """Remove all occurrences of key and return the list of corresponding values. If key is not found, default is returned if given, otherwise KeyError is raised. """ found = False identity = self._title(key) ret = [] ...

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def min(self): """ Returns the minimum value of the domain. :rtype: `float` or `np.inf` """ return int(self._min) if not np.isinf(self._min) else self._min

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def init_from_fcnxs(ctx, fcnxs_symbol, fcnxs_args_from, fcnxs_auxs_from): """ use zero initialization for better convergence, because it tends to oputut 0, and the label 0 stands for background, which may occupy most size of one image. """ fcnxs_args = fcnxs_args_from.copy() fcnxs_auxs = fcnxs_auxs_...

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def determine_name(func): """ Given a function, returns the name of the function. Ex:: from random import choice determine_name(choice) # Returns 'choice' :param func: The callable :type func: function :returns: Name string """ if hasattr(func, '__name__'): re...

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def generate_keywords(additional_keywords=None): """Generates gettext keywords list :arg additional_keywords: dict of keyword -> value :returns: dict of keyword -> values for Babel extraction Here's what Babel has for DEFAULT_KEYWORDS:: DEFAULT_KEYWORDS = { '_': None, ...

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def create_snapshots(self, volumes, **kwargs): """Create snapshots of the listed volumes. :param volumes: List of names of the volumes to snapshot. :type volumes: list of str :param \*\*kwargs: See the REST API Guide on your array for the documentation on the ...

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def addr(self): """ Get the concrete address of the instruction pointer, without triggering SimInspect breakpoints or generating SimActions. An integer is returned, or an exception is raised if the instruction pointer is symbolic. :return: an int """ ip = self.regs._ip ...

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def flush(self, safe=None): ''' Perform all database operations currently in the queue''' result = None for index, op in enumerate(self.queue): try: result = op.execute() except: self.clear_queue() self.clear_cache() raise self.clear_queue() return result

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def get_package_hashes( package, version=None, algorithm=DEFAULT_ALGORITHM, python_versions=(), verbose=False, include_prereleases=False, lookup_memory=None, index_url=DEFAULT_INDEX_URL, ): """ Gets the hashes for the given package. >>> get_package_hashes('hashin') { ...

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def launch(self, argv=None, showusageonnoargs=False, width=0, helphint="Use with --help for more information.\n", debug_parser=False): """Do the usual stuff to initiallize the program. Read config files and parse argumen...

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def ellipse(data, channels, center, a, b, theta=0, log=False, full_output=False): """ Gate that preserves events inside an ellipse-shaped region. Events are kept if they satisfy the following relationship:: (x/a)**2 + (y/b)**2 <= 1 where `x` and `y` are the coordinates...

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def is_allowed(self, user_agent, url, syntax=GYM2008): """True if the user agent is permitted to visit the URL. The syntax parameter can be GYM2008 (the default) or MK1996 for strict adherence to the traditional standard. """ if PY_MAJOR_VERSION < 3: # The r...

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def what_if_I_upgrade(conn, pkg_name='openquake.server.db.schema.upgrades', extract_scripts='extract_upgrade_scripts'): """ :param conn: a DB API 2 connection :param str pkg_name: the name of the package with the upgrade scripts :param extract_scripts: name ...

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def decompress(input_dir, dcm_pattern='*.dcm'): """ Decompress all *.dcm files recursively found in DICOM_DIR. This uses 'gdcmconv --raw'. It works when 'dcm2nii' shows the `Unsupported Transfer Syntax` error. This error is usually caused by lack of JPEG2000 support in dcm2nii compilation. Read mor...

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def signature(self): """Get data signature""" self._data.sort() str_to_sign = self._delimiter.join(self._data) return hashlib.sha1(str_to_sign).hexdigest()

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def load_market_data(trading_day=None, trading_days=None, bm_symbol='SPY', environ=None): """ Load benchmark returns and treasury yield curves for the given calendar and benchmark symbol. Benchmarks are downloaded as a Series from IEX Trading. Treasury curves are US Treasury B...

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def host_events(self, host): ''' Given a host name, this will return all task events executed on that host ''' all_host_events = filter(lambda x: 'event_data' in x and 'host' in x['event_data'] and x['event_data']['host'] == host, self.events) ret...

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

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def _lookup_abs(self, p, klass, create=1): """ Fast (?) lookup of a *normalized* absolute path. This method is intended for use by internal lookups with already-normalized path data. For general-purpose lookups, use the FS.Entry(), FS.Dir() or FS.File() methods. The ca...

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def create_csv(filename, csv_data, mode="w"): """ Create a CSV file with the given data and store it in the file with the given name. :param filename: name of the file to store the data in :pram csv_data: the data to be stored in the file :param mode: the mode in which we have to open the file....

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def experiment(self): """The identifier or the experiment that is currently processed""" if self._experiment is None: self._experiment = list(self.config.experiments.keys())[-1] return self._experiment

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def status(name, maximum=None, minimum=None, absolute=False, free=False): ''' Return the current disk usage stats for the named mount point name Disk mount or directory for which to check used space maximum The maximum disk utilization minimum The minimum disk utilization ...

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def _lookup_nexus_bindings(query_type, session=None, **bfilter): """Look up 'query_type' Nexus bindings matching the filter. :param query_type: 'all', 'one' or 'first' :param session: db session :param bfilter: filter for bindings query :returns: bindings if query gave a result, else r...

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def guess_rank(M_E): '''Guess the rank of the incomplete matrix ''' n, m = M_E.shape epsilon = np.count_nonzero(M_E) / np.sqrt(m * n) _, S0, _ = svds_descending(M_E, min(100, max(M_E.shape) - 1)) S0 = np.diag(S0) S1 = S0[:-1] - S0[1:] S1_ = S1 / np.mean(S1[-10:]) r1 = 0 la...

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def rsem_mapped_reads_plot(self): """ Make the rsem assignment rates plot """ # Plot categories keys = OrderedDict() keys['Unique'] = { 'color': '#437bb1', 'name': 'Aligned uniquely to a gene' } keys['Multi'] = { 'color': '#e63491', 'name': 'Aligned to multiple genes'...

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def chunk_count(self): """Return a count of the chunks in this world folder.""" c = 0 for r in self.iter_regions(): c += r.chunk_count() return c

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def randomize(self, force = 0): """ Initialize node biases to random values in the range [-max, max]. """ if force or not self.frozen: self.weight = randomArray(self.size, self._maxRandom)

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def add_model(self, propname, model, regen_mode='normal', **kwargs): r""" Adds a new model to the models dictionary (``object.models``) Parameters ---------- propname : string The name of the property to be calculated by the model. model : function ...

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def gru(name, input, state, kernel_r, kernel_u, kernel_c, bias_r, bias_u, bias_c, new_state, number_of_gates = 2): ''' - zt = f(Xt*Wz + Ht_1*Rz + Wbz + Rbz) - rt = f(Xt*Wr + Ht_1*Rr + Wbr + Rbr) - ht = g(Xt*Wh + (rt . Ht_1)*Rh + Rbh + Wbh) - Ht = (1-zt).ht + zt.Ht_1 ''' ...

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def header(self): """Generates HTTP header for this cookie.""" if self._send_cookie: morsel = Morsel() cookie_value = Session.encode_sid(self._config.secret, self._sid) if self._config.encrypt_key: cipher = AESCipher(self._config.encrypt_key) ...

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def replace_row(self, line, ndx): """ replace a grids row at index 'ndx' with 'line' """ for col in range(len(line)): self.set_tile(ndx, col, line[col])

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def write_to_influxdb(received_data): ''' Convert data into RuuviCollecor naming schme and scale ''' dataFormat = received_data[1]["data_format"] if ('data_format' in received_data[1]) else None fields = {} fields["temperature"] = received_data[1]["temperature"] if ('temperature' i...

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def __do_query_into_hash(conn, sql_str): ''' Perform the query that is passed to it (sql_str). Returns: results in a dict. ''' mod = sys._getframe().f_code.co_name log.debug('%s<--(%s)', mod, sql_str) rtn_results = [] try: cursor = conn.cursor() except MySQLdb.MySQ...

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def map_as_completed(func, *iterables, **kwargs): """map_as_completed(func, *iterables) Equivalent to map, but the results are returned as soon as they are made available. :param func: Any picklable callable object (function or class object with *__call__* method); this object will be called to...

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def _num_required_args(func): """ Number of args for func >>> def foo(a, b, c=None): ... return a + b + c >>> _num_required_args(foo) 2 >>> def bar(*args): ... return sum(args) >>> print(_num_required_args(bar)) None borrowed from: https:/...

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def _osquery(sql, format='json'): ''' Helper function to run raw osquery queries ''' ret = { 'result': True, } cmd = ['osqueryi'] + ['--json'] + [sql] res = __salt__['cmd.run_all'](cmd) if res['stderr']: ret['result'] = False ret['error'] = res['stderr'] else...

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def strict_parse(cls, query_str, *specs, extra_parameters=True): """ Parse query and return :class:`.WStrictURIQuery` object :param query_str: query component of URI to parse :param specs: list of parameters specifications :param extra_parameters: whether parameters that was not specified in "specs" are allowe...

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def upgrade_account(self, account=None, **kwargs): """ Upgrade an account to Lifetime membership :param str account: (optional) the account to allow access to (defaults to ``default_account``) """ if not account: if "default_account" in self.config: ...

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def implied_vol(self, value, precision=1.0e-5, iters=100): """Get implied vol at the specified price using an iterative approach. There is no closed-form inverse of BSM-value as a function of sigma, so start at an anchoring volatility level from Brenner & Subrahmanyam (1988) and wo...

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def query(self, dataset='hsapiens_gene_ensembl', attributes=[], filters={}, filename=None): """mapping ids using BioMart. :param dataset: str, default: 'hsapiens_gene_ensembl' :param attributes: str, list, tuple :param filters: dict, {'filter name': list(filter value)} ...

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45.559322

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def com_adobe_fonts_check_cff2_call_depth(ttFont): """Is the CFF2 subr/gsubr call depth > 10?""" any_failures = False cff = ttFont['CFF2'].cff for top_dict in cff.topDictIndex: for fd_index, font_dict in enumerate(top_dict.FDArray): if hasattr(font_dict, 'Private'): ...

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36.647059

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