kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def check_for_upload_create(self, relative_path=None): """Traverse the relative_path tree and check for files that need to be uploaded/created. Relativity here refers to the shared directory tree.""" for f in os.listdir( path_join( self.local_path, relative_path) if ...	[ "def", "check_for_upload_create", "(", "self", ",", "relative_path", "=", "None", ")", ":", "for", "f", "in", "os", ".", "listdir", "(", "path_join", "(", "self", ".", "local_path", ",", "relative_path", ")", "if", "relative_path", "else", "self", ".", "lo...	46.777778	20.222222
def delete_checkpoint(self, checkpoint_dir): """Removes subdirectory within checkpoint_folder Parameters ---------- checkpoint_dir : path to checkpoint """ if os.path.isfile(checkpoint_dir): shutil.rmtree(os.path.dirname(checkpoint_dir)) else: ...	[ "def", "delete_checkpoint", "(", "self", ",", "checkpoint_dir", ")", ":", "if", "os", ".", "path", ".", "isfile", "(", "checkpoint_dir", ")", ":", "shutil", ".", "rmtree", "(", "os", ".", "path", ".", "dirname", "(", "checkpoint_dir", ")", ")", "else", ...	34.8	10.3
def init_bounds(self): """ Process bounds this process is currently initialized with. This gets triggered by using the ``init_bounds`` kwarg. If not set, it will be equal to self.bounds. """ if self._raw["init_bounds"] is None: return self.bounds else...	[ "def", "init_bounds", "(", "self", ")", ":", "if", "self", ".", "_raw", "[", "\"init_bounds\"", "]", "is", "None", ":", "return", "self", ".", "bounds", "else", ":", "return", "Bounds", "(", "*", "_validate_bounds", "(", "self", ".", "_raw", "[", "\"in...	34.727273	18.727273
def is_dictlist(data): ''' Returns True if data is a list of one-element dicts (as found in many SLS schemas), otherwise returns False ''' if isinstance(data, list): for element in data: if isinstance(element, dict): if len(element) != 1: retur...	[ "def", "is_dictlist", "(", "data", ")", ":", "if", "isinstance", "(", "data", ",", "list", ")", ":", "for", "element", "in", "data", ":", "if", "isinstance", "(", "element", ",", "dict", ")", ":", "if", "len", "(", "element", ")", "!=", "1", ":", ...	28.428571	17
def validate_additional_properties(self, valid_response, response): """Validates additional properties. In additional properties, we only need to compare the values of the dict, not the keys Args: valid_response: An example response (for example generated in ...	[ "def", "validate_additional_properties", "(", "self", ",", "valid_response", ",", "response", ")", ":", "assert", "isinstance", "(", "valid_response", ",", "dict", ")", "assert", "isinstance", "(", "response", ",", "dict", ")", "# the type of the value of the first ke...	42.3125	21.895833
def _read_file(self, filename): """ Read contents of given file. """ try: with open(filename, "r") as fhandle: stats = float(fhandle.readline().rstrip("\n")) except Exception: stats = None return stats	[ "def", "_read_file", "(", "self", ",", "filename", ")", ":", "try", ":", "with", "open", "(", "filename", ",", "\"r\"", ")", "as", "fhandle", ":", "stats", "=", "float", "(", "fhandle", ".", "readline", "(", ")", ".", "rstrip", "(", "\"\\n\"", ")", ...	25.454545	14.727273
def _ssid_inventory(self, inventory, ssid): """ Filters an inventory to only return servers matching ssid """ matching_hosts = {} for host in inventory: if inventory[host]['comment'] == ssid: matching_hosts[host] = inventory[host] return match...	[ "def", "_ssid_inventory", "(", "self", ",", "inventory", ",", "ssid", ")", ":", "matching_hosts", "=", "{", "}", "for", "host", "in", "inventory", ":", "if", "inventory", "[", "host", "]", "[", "'comment'", "]", "==", "ssid", ":", "matching_hosts", "[", ...	32	12.6
def _extract_germline(in_file, data): """Extract germline calls non-somatic, non-filtered calls. """ out_file = "%s-germline.vcf" % utils.splitext_plus(in_file)[0] if not utils.file_uptodate(out_file, in_file) and not utils.file_uptodate(out_file + ".gz", in_file): with file_transaction(data, ou...	[ "def", "_extract_germline", "(", "in_file", ",", "data", ")", ":", "out_file", "=", "\"%s-germline.vcf\"", "%", "utils", ".", "splitext_plus", "(", "in_file", ")", "[", "0", "]", "if", "not", "utils", ".", "file_uptodate", "(", "out_file", ",", "in_file", ...	54.5	18.9375
def angleDiff(angle1, angle2, take_smaller=True): """ smallest difference between 2 angles code from http://stackoverflow.com/questions/1878907/the-smallest-difference-between-2-angles """ a = np.arctan2(np.sin(angle1 - angle2), np.cos(angle1 - angle2)) if isinstance(a, np.ndarray) and take_smal...	[ "def", "angleDiff", "(", "angle1", ",", "angle2", ",", "take_smaller", "=", "True", ")", ":", "a", "=", "np", ".", "arctan2", "(", "np", ".", "sin", "(", "angle1", "-", "angle2", ")", ",", "np", ".", "cos", "(", "angle1", "-", "angle2", ")", ")",...	36.642857	14.928571
def _map_segmentation_mask_to_stft_domain(mask, times, frequencies, stft_times, stft_frequencies): """ Maps the given `mask`, which is in domain (`frequencies`, `times`) to the new domain (`stft_frequencies`, `stft_times`) and returns the result. """ assert mask.shape == (frequencies.shape[0], times...	[ "def", "_map_segmentation_mask_to_stft_domain", "(", "mask", ",", "times", ",", "frequencies", ",", "stft_times", ",", "stft_frequencies", ")", ":", "assert", "mask", ".", "shape", "==", "(", "frequencies", ".", "shape", "[", "0", "]", ",", "times", ".", "sh...	45.956522	29
def estimate_rate_matrix(C, dt=1.0, method='KL', sparsity=None, t_agg=None, pi=None, tol=1.0E7, K0=None, maxiter=100000, on_error='raise'): r"""Estimate a reversible rate matrix from a count matrix. Parameters ---------- C : (N,N) ndarray count ...	[ "def", "estimate_rate_matrix", "(", "C", ",", "dt", "=", "1.0", ",", "method", "=", "'KL'", ",", "sparsity", "=", "None", ",", "t_agg", "=", "None", ",", "pi", "=", "None", ",", "tol", "=", "1.0E7", ",", "K0", "=", "None", ",", "maxiter", "=", "1...	43.686131	27.226277
def redirect_display(self, on): ''' on: * True -> set $DISPLAY to virtual screen * False -> set $DISPLAY to original screen :param on: bool ''' d = self.new_display_var if on else self.old_display_var if d is None: log.debug('unset DISPLAY')...	[ "def", "redirect_display", "(", "self", ",", "on", ")", ":", "d", "=", "self", ".", "new_display_var", "if", "on", "else", "self", ".", "old_display_var", "if", "d", "is", "None", ":", "log", ".", "debug", "(", "'unset DISPLAY'", ")", "del", "os", ".",...	29	16.866667
def tasks_from_queue(self, tiger, queue, state, skip=0, limit=1000, load_executions=0): """ Returns a tuple with the following information: * total items in the queue * tasks from the given queue in the given state, latest first. An integer may be passed in th...	[ "def", "tasks_from_queue", "(", "self", ",", "tiger", ",", "queue", ",", "state", ",", "skip", "=", "0", ",", "limit", "=", "1000", ",", "load_executions", "=", "0", ")", ":", "key", "=", "tiger", ".", "_key", "(", "state", ",", "queue", ")", "pipe...	42.711111	24.044444
def parser(self): """ Creates a parser for the method based on the documentation. :return <OptionParser> """ usage = self.usage() if self.__doc__: usage += '\n' + nstr(self.__doc__) parse = PARSER_CLASS(usage=usage) shorts = {v: ...	[ "def", "parser", "(", "self", ")", ":", "usage", "=", "self", ".", "usage", "(", ")", "if", "self", ".", "__doc__", ":", "usage", "+=", "'\\n'", "+", "nstr", "(", "self", ".", "__doc__", ")", "parse", "=", "PARSER_CLASS", "(", "usage", "=", "usage"...	27.205882	17.676471
def load_from_json(data): """ Load a :class:`Item` from a dictionary ot string (that will be parsed as json) """ if isinstance(data, str): data = json.loads(data) return Item(data['title'], data['uri'])	[ "def", "load_from_json", "(", "data", ")", ":", "if", "isinstance", "(", "data", ",", "str", ")", ":", "data", "=", "json", ".", "loads", "(", "data", ")", "return", "Item", "(", "data", "[", "'title'", "]", ",", "data", "[", "'uri'", "]", ")" ]	31.875	11.875
def p_statement_switch(p): 'statement : SWITCH LPAREN expr RPAREN switch_case_list' p[0] = ast.Switch(p[3], p[5], lineno=p.lineno(1))	[ "def", "p_statement_switch", "(", "p", ")", ":", "p", "[", "0", "]", "=", "ast", ".", "Switch", "(", "p", "[", "3", "]", ",", "p", "[", "5", "]", ",", "lineno", "=", "p", ".", "lineno", "(", "1", ")", ")" ]	46.333333	15.666667
def cardinality(self): """ This is an over-approximation of the cardinality of this DSIS. :return: """ cardinality = 0 for si in self._si_set: cardinality += si.cardinality return cardinality	[ "def", "cardinality", "(", "self", ")", ":", "cardinality", "=", "0", "for", "si", "in", "self", ".", "_si_set", ":", "cardinality", "+=", "si", ".", "cardinality", "return", "cardinality" ]	25.1	15.3
def import_admins(self): """ save admins to local DB """ self.message('saving admins into local DB') saved_admins = [] for olduser in OldUser.objects.all(): try: user = User.objects.get(Q(username=olduser.username) \| Q(email=olduser.email)) excep...	[ "def", "import_admins", "(", "self", ")", ":", "self", ".", "message", "(", "'saving admins into local DB'", ")", "saved_admins", "=", "[", "]", "for", "olduser", "in", "OldUser", ".", "objects", ".", "all", "(", ")", ":", "try", ":", "user", "=", "User"...	42.179487	19.025641
def _is_valid_token(self, auth_token): ''' Check if this is a valid salt-api token or valid Salt token salt-api tokens are regular session tokens that tie back to a real Salt token. Salt tokens are tokens generated by Salt's eauth system. :return bool: True if valid, False if n...	[ "def", "_is_valid_token", "(", "self", ",", "auth_token", ")", ":", "# Make sure that auth token is hex. If it's None, or something other", "# than hex, this will raise a ValueError.", "try", ":", "int", "(", "auth_token", ",", "16", ")", "except", "(", "TypeError", ",", ...	41.448276	26.758621
def sun_rise_set_transit_spa(times, latitude, longitude, how='numpy', delta_t=67.0, numthreads=4): """ Calculate the sunrise, sunset, and sun transit times using the NREL SPA algorithm described in [1]. If numba is installed, the functions can be compiled to machine cod...	[ "def", "sun_rise_set_transit_spa", "(", "times", ",", "latitude", ",", "longitude", ",", "how", "=", "'numpy'", ",", "delta_t", "=", "67.0", ",", "numthreads", "=", "4", ")", ":", "# Added by Tony Lorenzo (@alorenzo175), University of Arizona, 2015", "lat", "=", "la...	38.227848	22.379747
def print_last_values(): """Print the last 10 values.""" iterable = archive.list_parameter_values('/YSS/SIMULATOR/BatteryVoltage1', descending=True) for pval in islice(iterable, 0, 10): print(pval)	[ "def", "print_last_values", "(", ")", ":", "iterable", "=", "archive", ".", "list_parameter_values", "(", "'/YSS/SIMULATOR/BatteryVoltage1'", ",", "descending", "=", "True", ")", "for", "pval", "in", "islice", "(", "iterable", ",", "0", ",", "10", ")", ":", ...	42.833333	16
def add_client(self, client_identifier): """Add a client.""" if client_identifier in self.clients: _LOGGER.error('%s already in group %s', client_identifier, self.identifier) return new_clients = self.clients new_clients.append(client_identifier) yield fro...	[ "def", "add_client", "(", "self", ",", "client_identifier", ")", ":", "if", "client_identifier", "in", "self", ".", "clients", ":", "_LOGGER", ".", "error", "(", "'%s already in group %s'", ",", "client_identifier", ",", "self", ".", "identifier", ")", "return",...	47.727273	17.090909
def buildable(self, values: Optional[dict]=None, method: Optional[str]=None) -> bool: """Return True if this rule can build with the values and method.""" if method is not None and method not in self.methods: return False defaults_match = all( values[key] == self.defaults...	[ "def", "buildable", "(", "self", ",", "values", ":", "Optional", "[", "dict", "]", "=", "None", ",", "method", ":", "Optional", "[", "str", "]", "=", "None", ")", "->", "bool", ":", "if", "method", "is", "not", "None", "and", "method", "not", "in",...	59.375	29.375
def flush(self): """Flush GL commands This is a wrapper for glFlush(). This also flushes the GLIR command queue. """ if hasattr(self, 'flush_commands'): context = self else: context = get_current_canvas().context context.glir.command('...	[ "def", "flush", "(", "self", ")", ":", "if", "hasattr", "(", "self", ",", "'flush_commands'", ")", ":", "context", "=", "self", "else", ":", "context", "=", "get_current_canvas", "(", ")", ".", "context", "context", ".", "glir", ".", "command", "(", "'...	29.916667	14.5
def validate_order_params(self, asset, amount, limit_price, stop_price, style): """ Helper method for validating parameters to the order API function. ...	[ "def", "validate_order_params", "(", "self", ",", "asset", ",", "amount", ",", "limit_price", ",", "stop_price", ",", "style", ")", ":", "if", "not", "self", ".", "initialized", ":", "raise", "OrderDuringInitialize", "(", "msg", "=", "\"order() can only be calle...	34.794118	17.617647
def write_file(self, path, name, data, content_type=None, archive=False, raw=False): """Write a file to the file data store at the given path :param str path: The path (directory) into which the file should be written. :param str name: The name of the file to be written. ...	[ "def", "write_file", "(", "self", ",", "path", ",", "name", ",", "data", ",", "content_type", "=", "None", ",", "archive", "=", "False", ",", "raw", "=", "False", ")", ":", "path", "=", "validate_type", "(", "path", ",", "*", "six", ".", "string_type...	41.584906	21.943396
def getNodeByNameChain(node, chain_list): """ Walk down a chain of node names and get the nodes they represent e.g. [ "entry", "content", "bag", "fileCount" ] """ working_list = chain_list[:] working_list.reverse() current_node = node while len(working_list): current_name = work...	[ "def", "getNodeByNameChain", "(", "node", ",", "chain_list", ")", ":", "working_list", "=", "chain_list", "[", ":", "]", "working_list", ".", "reverse", "(", ")", "current_node", "=", "node", "while", "len", "(", "working_list", ")", ":", "current_name", "="...	34.125	13.875
def random_ipv4(cidr='10.0.0.0/8'): """ Return a random IPv4 address from the given CIDR block. :key str cidr: CIDR block :returns: An IPv4 address from the given CIDR block :rtype: ipaddress.IPv4Address """ try: u_cidr = unicode(cidr) except NameError: u_cidr = cidr ...	[ "def", "random_ipv4", "(", "cidr", "=", "'10.0.0.0/8'", ")", ":", "try", ":", "u_cidr", "=", "unicode", "(", "cidr", ")", "except", "NameError", ":", "u_cidr", "=", "cidr", "network", "=", "ipaddress", ".", "ip_network", "(", "u_cidr", ")", "start", "=",...	30.176471	10.882353
def update_subtotals(self, current, sub_key): """ updates sub_total counts for the class instance based on the current dictionary counts args: ----- current: current dictionary counts sub_key: the key/value to use for the subtotals """ ...	[ "def", "update_subtotals", "(", "self", ",", "current", ",", "sub_key", ")", ":", "if", "not", "self", ".", "sub_counts", ".", "get", "(", "sub_key", ")", ":", "self", ".", "sub_counts", "[", "sub_key", "]", "=", "{", "}", "for", "item", "in", "curre...	31.166667	14.944444
def import_obj(clsname, default_module=None): """ Import the object given by clsname. If default_module is specified, import from this module. """ if default_module is not None: if not clsname.startswith(default_module + '.'): clsname = '{0}.{1}'.format(default_module, clsname) ...	[ "def", "import_obj", "(", "clsname", ",", "default_module", "=", "None", ")", ":", "if", "default_module", "is", "not", "None", ":", "if", "not", "clsname", ".", "startswith", "(", "default_module", "+", "'.'", ")", ":", "clsname", "=", "'{0}.{1}'", ".", ...	36.6	12.466667
def sbo_list(): """Return all SBo packages """ sbo_packages = [] for pkg in os.listdir(_meta_.pkg_path): if pkg.endswith("_SBo"): sbo_packages.append(pkg) return sbo_packages	[ "def", "sbo_list", "(", ")", ":", "sbo_packages", "=", "[", "]", "for", "pkg", "in", "os", ".", "listdir", "(", "_meta_", ".", "pkg_path", ")", ":", "if", "pkg", ".", "endswith", "(", "\"_SBo\"", ")", ":", "sbo_packages", ".", "append", "(", "pkg", ...	25.875	9.5
def ask_list(question: str, default: list = None) -> list: """Asks for a comma seperated list of strings""" default_q = " [default: {0}]: ".format( ",".join(default)) if default is not None else "" answer = input("{0} [{1}]: ".format(question, default_q)) if answer == "": return default...	[ "def", "ask_list", "(", "question", ":", "str", ",", "default", ":", "list", "=", "None", ")", "->", "list", ":", "default_q", "=", "\" [default: {0}]: \"", ".", "format", "(", "\",\"", ".", "join", "(", "default", ")", ")", "if", "default", "is", "not...	40.666667	16.666667
def processEnded(self, reason): """ Connected process shut down """ log_debug("{name} process exited", name=self.name) if self.deferred: if reason.type == ProcessDone: self.deferred.callback(reason.value.exitCode) elif reason.type == Proces...	[ "def", "processEnded", "(", "self", ",", "reason", ")", ":", "log_debug", "(", "\"{name} process exited\"", ",", "name", "=", "self", ".", "name", ")", "if", "self", ".", "deferred", ":", "if", "reason", ".", "type", "==", "ProcessDone", ":", "self", "."...	36.090909	8.818182
def box_model_domain(num_points=2, **kwargs): """Creates a box model domain (a single abstract axis). :param int num_points: number of boxes [default: 2] :returns: Domain with single axis of type ``'abstract'`` and ``self.domain_type = 'box'`` :rty...	[ "def", "box_model_domain", "(", "num_points", "=", "2", ",", "", "", "kwargs", ")", ":", "ax", "=", "Axis", "(", "axis_type", "=", "'abstract'", ",", "num_points", "=", "num_points", ")", "boxes", "=", "_Domain", "(", "axes", "=", "ax", ",", "*", "...	31.304348	22.26087
def adaptive_gaussian_prior_builder( getter, name, args, *kwargs): """A pre-canned builder for adaptive scalar gaussian prior distributions. Given a true `getter` function and arguments forwarded from `tf.get_variable`, return a distribution object for a scalar-valued adaptive gaussian prior which will b...	[ "def", "adaptive_gaussian_prior_builder", "(", "getter", ",", "name", ",", "", "args", ",", "", "", "kwargs", ")", ":", "kwargs", "[", "\"shape\"", "]", "=", "(", ")", "loc_var", "=", "getter", "(", "name", "+", "\"_prior_loc\"", ",", "", "args", "...	44.833333	20.9
def remove_vcf_info(keyword, variant_line=None, variant_dict=None): """Remove the information of a info field of a vcf variant line or a variant dict. Arguments: variant_line (str): A vcf formatted variant line variant_dict (dict): A variant dictionary keyword (str): The in...	[ "def", "remove_vcf_info", "(", "keyword", ",", "variant_line", "=", "None", ",", "variant_dict", "=", "None", ")", ":", "logger", ".", "debug", "(", "\"Removing variant information {0}\"", ".", "format", "(", "keyword", ")", ")", "fixed_variant", "=", "None", ...	31.982456	18.701754
def get_pattern(self, field_name): """ Get a regular expression to match a formatting directive that references the given field name. :param field_name: The name of the field to match (a string). :returns: A compiled regular expression object. """ return re.compile(self....	[ "def", "get_pattern", "(", "self", ",", "field_name", ")", ":", "return", "re", ".", "compile", "(", "self", ".", "raw_pattern", ".", "replace", "(", "r'\\w+'", ",", "field_name", ")", ",", "re", ".", "VERBOSE", ")" ]	45.625	24.375
async def move_rel(self, mount: top_types.Mount, delta: top_types.Point, speed: float = None): """ Move the critical point of the specified mount by a specified displacement in a specified direction, at the specified speed. 'speed' sets the speed of all axes to the given v...	[ "async", "def", "move_rel", "(", "self", ",", "mount", ":", "top_types", ".", "Mount", ",", "delta", ":", "top_types", ".", "Point", ",", "speed", ":", "float", "=", "None", ")", ":", "if", "not", "self", ".", "_current_position", ":", "raise", "MustHo...	40.32	17.36
def add_surface(self, name, surface): """Adds a top-level attribute with the given name to the module.""" assert surface is not None if hasattr(self.module, name): raise ThriftCompilerError( 'Cannot define "%s". The name has already been used.' % name ) ...	[ "def", "add_surface", "(", "self", ",", "name", ",", "surface", ")", ":", "assert", "surface", "is", "not", "None", "if", "hasattr", "(", "self", ".", "module", ",", "name", ")", ":", "raise", "ThriftCompilerError", "(", "'Cannot define \"%s\". The name has al...	35.4	15.9
def not_next(e): """ Create a PEG function for negative lookahead. """ def match_not_next(s, grm=None, pos=0): try: e(s, grm, pos) except PegreError as ex: return PegreResult(s, Ignore, (pos, pos)) else: raise PegreError('Negative lookahead fai...	[ "def", "not_next", "(", "e", ")", ":", "def", "match_not_next", "(", "s", ",", "grm", "=", "None", ",", "pos", "=", "0", ")", ":", "try", ":", "e", "(", "s", ",", "grm", ",", "pos", ")", "except", "PegreError", "as", "ex", ":", "return", "Pegre...	28.75	13.583333
def spy(iterable, n=1): """Return a 2-tuple with a list containing the first n elements of iterable, and an iterator with the same items as iterable. This allows you to "look ahead" at the items in the iterable without advancing it. There is one item in the list by default: >>> itera...	[ "def", "spy", "(", "iterable", ",", "n", "=", "1", ")", ":", "it", "=", "iter", "(", "iterable", ")", "head", "=", "take", "(", "n", ",", "it", ")", "return", "head", ",", "chain", "(", "head", ",", "it", ")" ]	25.926829	21.512195
def adaptive(u_kn, N_k, f_k, tol = 1.0e-12, options = None): """ Determine dimensionless free energies by a combination of Newton-Raphson iteration and self-consistent iteration. Picks whichever method gives the lowest gradient. Is slower than NR since it calculates the log norms twice each iteration. ...	[ "def", "adaptive", "(", "u_kn", ",", "N_k", ",", "f_k", ",", "tol", "=", "1.0e-12", ",", "options", "=", "None", ")", ":", "# put the defaults here in case we get passed an 'options' dictionary that is only partial", "options", ".", "setdefault", "(", "'verbose'", ","...	45.938053	29.230088
def slice_shape(self, tensor_shape): """Shape of each slice of the Tensor. Args: tensor_shape: Shape. Returns: list of integers with length tensor_shape.ndims. Raises: ValueError: If a Tensor dimension is not divisible by the corresponding Mesh dimension. """ tensor_...	[ "def", "slice_shape", "(", "self", ",", "tensor_shape", ")", ":", "tensor_layout", "=", "self", ".", "tensor_layout", "(", "tensor_shape", ")", "ret", "=", "[", "]", "for", "tensor_dim", ",", "mesh_axis", "in", "zip", "(", "tensor_shape", ",", "tensor_layout...	31.535714	18.392857
def index(): """ This is not served anywhere in the web application. It is used explicitly in the context of generating static files since flask-frozen requires url_for's to crawl content. url_for's are not used with host.show_host directly and are instead dynamically generated through javascrip...	[ "def", "index", "(", ")", ":", "if", "current_app", ".", "config", "[", "'ARA_PLAYBOOK_OVERRIDE'", "]", "is", "not", "None", ":", "override", "=", "current_app", ".", "config", "[", "'ARA_PLAYBOOK_OVERRIDE'", "]", "hosts", "=", "(", "models", ".", "Host", ...	42.3125	19.6875
def acquire_read(self, timeout=None): """ Acquire a read lock for the current thread, waiting at most timeout seconds or doing a non-blocking check in case timeout is <= 0. In case timeout is None, the call to acquire_read blocks until the lock request can be serviced. ...	[ "def", "acquire_read", "(", "self", ",", "timeout", "=", "None", ")", ":", "if", "timeout", "is", "not", "None", ":", "endtime", "=", "time", ".", "time", "(", ")", "+", "timeout", "me", "=", "threading", ".", "currentThread", "(", ")", "self", ".", ...	40.5	13.681818
def create_index(self, collection, index_name, kwargs): """Safely attempt to create index.""" try: self.connection[collection].create_index(index_name, kwargs) except Exception as exc: LOG.warn("Error tuning mongodb database: %s", exc)	[ "def", "create_index", "(", "self", ",", "collection", ",", "index_name", ",", "", "", "kwargs", ")", ":", "try", ":", "self", ".", "connection", "[", "collection", "]", ".", "create_index", "(", "index_name", ",", "", "", "kwargs", ")", "except", ...	47	18.166667
def getTransformForOverlayCoordinates(self, ulOverlayHandle, eTrackingOrigin, coordinatesInOverlay): """Get the transform in 3d space associated with a specific 2d point in the overlay's coordinate space (where 0,0 is the lower left). -Z points out of the overlay""" fn = self.function_table.getTransfor...	[ "def", "getTransformForOverlayCoordinates", "(", "self", ",", "ulOverlayHandle", ",", "eTrackingOrigin", ",", "coordinatesInOverlay", ")", ":", "fn", "=", "self", ".", "function_table", ".", "getTransformForOverlayCoordinates", "pmatTransform", "=", "HmdMatrix34_t", "(", ...	73	26.857143
def writelines(self, lines): ''' Write a list of lines to the stream. Line separators are not added, so it is usual for each of the lines provided to have a line separator at the end. :param lines: ''' if self.__closed: raise OSError() for line in lines: ...	[ "def", "writelines", "(", "self", ",", "lines", ")", ":", "if", "self", ".", "__closed", ":", "raise", "OSError", "(", ")", "for", "line", "in", "lines", ":", "self", ".", "write", "(", "line", ")" ]	37.666667	29.444444
def _traverse_relationship_rev_objs(self, rel2dst2srcs, goobj_parent, goids_seen): """Traverse from source GO down children.""" parent_id = goobj_parent.id goids_seen.add(parent_id) ##A self.go2obj[parent_id] = goobj_parent # Update goids_seen and go2obj with parent alt_ids ...	[ "def", "_traverse_relationship_rev_objs", "(", "self", ",", "rel2dst2srcs", ",", "goobj_parent", ",", "goids_seen", ")", ":", "parent_id", "=", "goobj_parent", ".", "id", "goids_seen", ".", "add", "(", "parent_id", ")", "##A self.go2obj[parent_id] = goobj_parent", "# ...	54.526316	16.421053
def add_member(self, user_lookup_attribute_value): """ Attempts to add a member to the AD group. :param user_lookup_attribute_value: The value for the LDAP_GROUPS_USER_LOOKUP_ATTRIBUTE. :type user_lookup_attribute_value: str :raises: AccountDoesNotExist if the provided accoun...	[ "def", "add_member", "(", "self", ",", "user_lookup_attribute_value", ")", ":", "add_member", "=", "{", "'member'", ":", "(", "MODIFY_ADD", ",", "[", "self", ".", "_get_user_dn", "(", "user_lookup_attribute_value", ")", "]", ")", "}", "self", ".", "_attempt_mo...	60.823529	40
def _to_tuple(self, _list): """ Recursively converts lists to tuples """ result = list() for l in _list: if isinstance(l, list): result.append(tuple(self._to_tuple(l))) else: result.append(l) return tuple(result)	[ "def", "_to_tuple", "(", "self", ",", "_list", ")", ":", "result", "=", "list", "(", ")", "for", "l", "in", "_list", ":", "if", "isinstance", "(", "l", ",", "list", ")", ":", "result", ".", "append", "(", "tuple", "(", "self", ".", "_to_tuple", "...	32.444444	12.222222
def do_GET(self): """ Handle the retrieval of the code """ parsed_url = urlparse(self.path) if parsed_url[2] == "/" + SERVER_REDIRECT_PATH: # 2 = Path parsed_query = parse_qs(parsed_url[4]) # 4 = Query if "code" not in parsed_query: self.send_response(200) self.send_header("Content-Type", "t...	[ "def", "do_GET", "(", "self", ")", ":", "parsed_url", "=", "urlparse", "(", "self", ".", "path", ")", "if", "parsed_url", "[", "2", "]", "==", "\"/\"", "+", "SERVER_REDIRECT_PATH", ":", "# 2 = Path", "parsed_query", "=", "parse_qs", "(", "parsed_url", "[",...	31.289474	21.289474
def _fill_empty_sessions(self, fill_subjects, fill_visits): """ Fill in tree with additional empty subjects and/or visits to allow the study to pull its inputs from external repositories """ if fill_subjects is None: fill_subjects = [s.id for s in self.subjects] ...	[ "def", "_fill_empty_sessions", "(", "self", ",", "fill_subjects", ",", "fill_visits", ")", ":", "if", "fill_subjects", "is", "None", ":", "fill_subjects", "=", "[", "s", ".", "id", "for", "s", "in", "self", ".", "subjects", "]", "if", "fill_visits", "is", ...	44.592593	12.814815
def create_intent(project_id, display_name, training_phrases_parts, message_texts): """Create an intent of the given intent type.""" import dialogflow_v2 as dialogflow intents_client = dialogflow.IntentsClient() parent = intents_client.project_agent_path(project_id) training_phras...	[ "def", "create_intent", "(", "project_id", ",", "display_name", ",", "training_phrases_parts", ",", "message_texts", ")", ":", "import", "dialogflow_v2", "as", "dialogflow", "intents_client", "=", "dialogflow", ".", "IntentsClient", "(", ")", "parent", "=", "intents...	40	18.538462
def _cram_to_fastq_region(cram_file, work_dir, base_name, region, data): """Convert CRAM to fastq in a specified region. """ ref_file = tz.get_in(["reference", "fasta", "base"], data) resources = config_utils.get_resources("bamtofastq", data["config"]) cores = tz.get_in(["config", "algorithm", "num_...	[ "def", "_cram_to_fastq_region", "(", "cram_file", ",", "work_dir", ",", "base_name", ",", "region", ",", "data", ")", ":", "ref_file", "=", "tz", ".", "get_in", "(", "[", "\"reference\"", ",", "\"fasta\"", ",", "\"base\"", "]", ",", "data", ")", "resources...	64.75	27.75
def unique_iter(src, key=None): """Yield unique elements from the iterable, src, based on key, in the order in which they first appeared in src. >>> repetitious = [1, 2, 3] * 10 >>> list(unique_iter(repetitious)) [1, 2, 3] By default, key is the object itself, but key can either be a...	[ "def", "unique_iter", "(", "src", ",", "key", "=", "None", ")", ":", "if", "not", "is_iterable", "(", "src", ")", ":", "raise", "TypeError", "(", "'expected an iterable, not %r'", "%", "type", "(", "src", ")", ")", "if", "key", "is", "None", ":", "key_...	32.823529	19.147059
def get_api_client(cls): """Get an API client (with configuration).""" config = cloudsmith_api.Configuration() client = cls() client.config = config client.api_client.rest_client = RestClient() user_agent = getattr(config, "user_agent", None) if user_agent: client.api_client.user_ag...	[ "def", "get_api_client", "(", "cls", ")", ":", "config", "=", "cloudsmith_api", ".", "Configuration", "(", ")", "client", "=", "cls", "(", ")", "client", ".", "config", "=", "config", "client", ".", "api_client", ".", "rest_client", "=", "RestClient", "(",...	29.529412	17.470588
def run(self): """Run git add and commit with message if provided.""" if os.system('git add .'): sys.exit(1) if self.message is not None: os.system('git commit -a -m "' + self.message + '"') else: os.system('git commit -a')	[ "def", "run", "(", "self", ")", ":", "if", "os", ".", "system", "(", "'git add .'", ")", ":", "sys", ".", "exit", "(", "1", ")", "if", "self", ".", "message", "is", "not", "None", ":", "os", ".", "system", "(", "'git commit -a -m \"'", "+", "self",...	35.5	13.25
def _find_links(self): processed = {} links = [] body = re.search('<[^>]body[^>]>(.+?)</body>', self.text, re.S).group(1) """ The link follow by the span.t-mark-rev will contained c++xx information. Consider the below case <a href="LinkA">LinkA</a> <...	[ "def", "_find_links", "(", "self", ")", ":", "processed", "=", "{", "}", "links", "=", "[", "]", "body", "=", "re", ".", "search", "(", "'<[^>]body[^>]>(.+?)</body>'", ",", "self", ".", "text", ",", "re", ".", "S", ")", ".", "group", "(", "1", ")...	35.6	17.771429
def serve(content): """Write content to a temp file and serve it in browser""" temp_folder = tempfile.gettempdir() temp_file_name = tempfile.gettempprefix() + str(uuid.uuid4()) + ".html" # Generate a file path with a random name in temporary dir temp_file_path = os.path.join(temp_folder, temp_file_n...	[ "def", "serve", "(", "content", ")", ":", "temp_folder", "=", "tempfile", ".", "gettempdir", "(", ")", "temp_file_name", "=", "tempfile", ".", "gettempprefix", "(", ")", "+", "str", "(", "uuid", ".", "uuid4", "(", ")", ")", "+", "\".html\"", "# Generate ...	33.1	18
def parents(self) -> List[str]: """ Return the list of parents SHAs. :return: List[str] parents """ parents = [] for p in self._c_object.parents: parents.append(p.hexsha) return parents	[ "def", "parents", "(", "self", ")", "->", "List", "[", "str", "]", ":", "parents", "=", "[", "]", "for", "p", "in", "self", ".", "_c_object", ".", "parents", ":", "parents", ".", "append", "(", "p", ".", "hexsha", ")", "return", "parents" ]	24.5	9.7
def _solve_k_from_mu(data, k_array, nll, *args): """ For given args, return k_agg from searching some k_range. Parameters ---------- data : array k_range : array nll : function args : Returns -------- :float Minimum k_agg """ # TODO: See if a root finder l...	[ "def", "_solve_k_from_mu", "(", "data", ",", "k_array", ",", "nll", ",", "*", "args", ")", ":", "# TODO: See if a root finder like fminbound would work with Decimal used in", "# logpmf method (will this work with arrays?)", "nll_array", "=", "np", ".", "zeros", "(", "len", ...	20.241379	23.551724
def strip_flags(self, idx): """strip(1 byte) radiotap.flags :idx: int :return: int idx :return: collections.namedtuple """ flags = collections.namedtuple( 'flags', ['cfp', 'preamble', 'wep', 'fragmentation', 'fcs', 'datapad', ...	[ "def", "strip_flags", "(", "self", ",", "idx", ")", ":", "flags", "=", "collections", ".", "namedtuple", "(", "'flags'", ",", "[", "'cfp'", ",", "'preamble'", ",", "'wep'", ",", "'fragmentation'", ",", "'fcs'", ",", "'datapad'", ",", "'badfcs'", ",", "'s...	35.142857	9.428571
def reload(module, exclude=['sys', 'os.path', '__builtin__', '__main__']): """Recursively reload all modules used in the given module. Optionally takes a list of modules to exclude from reloading. The default exclude list contains sys, __main__, and __builtin__, to prevent, e.g., resetting display, ex...	[ "def", "reload", "(", "module", ",", "exclude", "=", "[", "'sys'", ",", "'os.path'", ",", "'__builtin__'", ",", "'__main__'", "]", ")", ":", "global", "found_now", "for", "i", "in", "exclude", ":", "found_now", "[", "i", "]", "=", "1", "try", ":", "w...	37.266667	18.733333
def delete(self): """Delete the instance.""" if lib.EnvDeleteInstance(self._env, self._ist) != 1: raise CLIPSError(self._env)	[ "def", "delete", "(", "self", ")", ":", "if", "lib", ".", "EnvDeleteInstance", "(", "self", ".", "_env", ",", "self", ".", "_ist", ")", "!=", "1", ":", "raise", "CLIPSError", "(", "self", ".", "_env", ")" ]	37.5	11
def get(self, wheel=False): """Downloads the package from PyPI. Returns: Full path of the downloaded file. Raises: PermissionError if the save_dir is not writable. """ try: url = get_url(self.client, self.name, self.version, ...	[ "def", "get", "(", "self", ",", "wheel", "=", "False", ")", ":", "try", ":", "url", "=", "get_url", "(", "self", ".", "client", ",", "self", ".", "name", ",", "self", ".", "version", ",", "wheel", ",", "hashed_format", "=", "True", ")", "[", "0",...	35.681818	16.227273
def format(args): """ %prog format infasta outfasta Reformat FASTA file and also clean up names. """ sequential_choices = ("replace", "prefix", "suffix") p = OptionParser(format.__doc__) p.add_option("--pairs", default=False, action="store_true", help="Add trailing /1 and /2 for...	[ "def", "format", "(", "args", ")", ":", "sequential_choices", "=", "(", "\"replace\"", ",", "\"prefix\"", ",", "\"suffix\"", ")", "p", "=", "OptionParser", "(", "format", ".", "__doc__", ")", "p", ".", "add_option", "(", "\"--pairs\"", ",", "default", "=",...	40.537815	19.159664
def load_molecule_in_rdkit_smiles(self, molSize,kekulize=True,bonds=[],bond_color=None,atom_color = {}, size= {} ): """ Loads mol file in rdkit without the hydrogens - they do not have to appear in the final figure. Once loaded, the molecule is converted to SMILES format which RDKit appears to ...	[ "def", "load_molecule_in_rdkit_smiles", "(", "self", ",", "molSize", ",", "kekulize", "=", "True", ",", "bonds", "=", "[", "]", ",", "bond_color", "=", "None", ",", "atom_color", "=", "{", "}", ",", "size", "=", "{", "}", ")", ":", "mol_in_rdkit", "=",...	52.021277	28.06383
def send(self, obj_id): """ Send email to the assigned lists :param obj_id: int :return: dict\|str """ response = self._client.session.post( '{url}/{id}/send'.format( url=self.endpoint_url, id=obj_id ) ) return self....	[ "def", "send", "(", "self", ",", "obj_id", ")", ":", "response", "=", "self", ".", "_client", ".", "session", ".", "post", "(", "'{url}/{id}/send'", ".", "format", "(", "url", "=", "self", ".", "endpoint_url", ",", "id", "=", "obj_id", ")", ")", "ret...	25.692308	12.769231
def distance(self, physical_qubit1, physical_qubit2): """Returns the undirected distance between physical_qubit1 and physical_qubit2. Args: physical_qubit1 (int): A physical qubit physical_qubit2 (int): Another physical qubit Returns: int: The undirected dis...	[ "def", "distance", "(", "self", ",", "physical_qubit1", ",", "physical_qubit2", ")", ":", "if", "physical_qubit1", "not", "in", "self", ".", "physical_qubits", ":", "raise", "CouplingError", "(", "\"%s not in coupling graph\"", "%", "(", "physical_qubit1", ",", ")...	41.55	20.55
def induce(self, b, filestem='default', examples=None, pos=None, neg=None, cn2sd=True, printOutput=False): """ Generate features and find subgroups. :param filestem: The base name of this experiment. ...	[ "def", "induce", "(", "self", ",", "b", ",", "filestem", "=", "'default'", ",", "examples", "=", "None", ",", "pos", "=", "None", ",", "neg", "=", "None", ",", "cn2sd", "=", "True", ",", "printOutput", "=", "False", ")", ":", "# Write the inputs", "s...	41.396552	20.258621
def precipitable_water(self, value=999.0): """Corresponds to IDD Field `precipitable_water` Args: value (float): value for IDD Field `precipitable_water` Unit: mm Missing value: 999.0 if `value` is None it will not be checked against the ...	[ "def", "precipitable_water", "(", "self", ",", "value", "=", "999.0", ")", ":", "if", "value", "is", "not", "None", ":", "try", ":", "value", "=", "float", "(", "value", ")", "except", "ValueError", ":", "raise", "ValueError", "(", "'value {} need to be of...	33.086957	18.695652
def xmlFile(path, mode='r'): """lxml cannot parse XML files starting with a BOM (see http://www.w3.org/TR/2000/REC-xml-20001006 in F.1.) In case such XML file is used, we must skip these characters So we open all XML files for read with 'xmlFile'. TODO: File this issue to lxml ML or tracker (feature...	[ "def", "xmlFile", "(", "path", ",", "mode", "=", "'r'", ")", ":", "fh", "=", "file", "(", "path", ",", "mode", ")", "while", "fh", ".", "read", "(", "1", ")", "!=", "'<'", ":", "# Ignoring everything before '<?xml...'", "pass", "fh", ".", "seek", "("...	36.466667	17.333333
def showMessageOverlay(self, pchText, pchCaption, pchButton0Text, pchButton1Text, pchButton2Text, pchButton3Text): """Show the message overlay. This will block and return you a result.""" fn = self.function_table.showMessageOverlay result = fn(pchText, pchCaption, pchButton0Text, pchButton1Text...	[ "def", "showMessageOverlay", "(", "self", ",", "pchText", ",", "pchCaption", ",", "pchButton0Text", ",", "pchButton1Text", ",", "pchButton2Text", ",", "pchButton3Text", ")", ":", "fn", "=", "self", ".", "function_table", ".", "showMessageOverlay", "result", "=", ...	61.666667	34.666667
def _match_iter_generic(self, path_elements, start_at): """Implementation of match_iter for >1 self.elements""" length = len(path_elements) # If bound to start, we stop searching at the first element if self.bound_start: end = 1 else: end = length - self....	[ "def", "_match_iter_generic", "(", "self", ",", "path_elements", ",", "start_at", ")", ":", "length", "=", "len", "(", "path_elements", ")", "# If bound to start, we stop searching at the first element", "if", "self", ".", "bound_start", ":", "end", "=", "1", "else"...	37.194444	18.166667
def user_has_permission(self, user, name): """ verify user has permission """ targetRecord = AuthMembership.objects(creator=self.client, user=user).first() if not targetRecord: return False for group in targetRecord.groups: if self.has_permission(group.role, name)...	[ "def", "user_has_permission", "(", "self", ",", "user", ",", "name", ")", ":", "targetRecord", "=", "AuthMembership", ".", "objects", "(", "creator", "=", "self", ".", "client", ",", "user", "=", "user", ")", ".", "first", "(", ")", "if", "not", "targe...	40.222222	13.555556
def getPointsForInterpolation(self,EndOfPrdvP,aNrmNow): ''' Finds interpolation points (c,m) for the consumption function. Parameters ---------- EndOfPrdvP : np.array Array of end-of-period marginal values. aNrmNow : np.array Array of end-of-perio...	[ "def", "getPointsForInterpolation", "(", "self", ",", "EndOfPrdvP", ",", "aNrmNow", ")", ":", "cNrmNow", "=", "self", ".", "uPinv", "(", "EndOfPrdvP", ")", "mNrmNow", "=", "cNrmNow", "+", "aNrmNow", "# Limiting consumption is zero as m approaches mNrmMin", "c_for_inte...	33.451613	20.870968
def get_ethernet_settings(self): """ Gets the Ethernet interconnect settings for the Logical Interconnect. Returns: dict: Ethernet Interconnect Settings """ uri = "{}/ethernetSettings".format(self.data["uri"]) return self._helper.do_get(uri)	[ "def", "get_ethernet_settings", "(", "self", ")", ":", "uri", "=", "\"{}/ethernetSettings\"", ".", "format", "(", "self", ".", "data", "[", "\"uri\"", "]", ")", "return", "self", ".", "_helper", ".", "do_get", "(", "uri", ")" ]	32.666667	15.333333
def _temporal_distance_pdf(self): """ Temporal distance probability density function. Returns ------- non_delta_peak_split_points: numpy.array non_delta_peak_densities: numpy.array len(density) == len(temporal_distance_split_points_ordered) -1 delta_p...	[ "def", "_temporal_distance_pdf", "(", "self", ")", ":", "temporal_distance_split_points_ordered", ",", "norm_cdf", "=", "self", ".", "_temporal_distance_cdf", "(", ")", "delta_peak_loc_to_probability_mass", "=", "{", "}", "non_delta_peak_split_points", "=", "[", "temporal...	47.206897	21.827586
def _JzStaeckelIntegrandSquared(v,E,Lz,I3V,delta,u0,cosh2u0,sinh2u0, potu0pi2,pot): #potu0pi2= potentialStaeckel(u0,nu.pi/2.,pot,delta) """The J_z integrand: p_v(v)/2/delta^2""" sin2v= nu.sin(v)*2. dV= cosh2u0potu0pi2\ -(sinh2u0+sin2v)*potentialStaeckel(u0,v,pot...	[ "def", "_JzStaeckelIntegrandSquared", "(", "v", ",", "E", ",", "Lz", ",", "I3V", ",", "delta", ",", "u0", ",", "cosh2u0", ",", "sinh2u0", ",", "potu0pi2", ",", "pot", ")", ":", "#potu0pi2= potentialStaeckel(u0,nu.pi/2.,pot,delta)", "sin2v", "=", "nu", ".", "...	46.5	13.625
def run_one(self, set_title=False): '''Get exactly one job, run it, and return. Does nothing (but returns :const:`False`) if there is no work to do. Ignores the global mode; this will do work even if :func:`rejester.TaskMaster.get_mode` returns :attr:`~rejester.TaskMaster.TERMI...	[ "def", "run_one", "(", "self", ",", "set_title", "=", "False", ")", ":", "available_gb", "=", "MultiWorker", ".", "available_gb", "(", ")", "unit", "=", "self", ".", "task_master", ".", "get_work", "(", "self", ".", "worker_id", ",", "available_gb", ",", ...	42.545455	21.939394
def sigmaT2(self,R,z,nsigma=None,mc=False,nmc=10000, gl=True,ngl=_DEFAULTNGL,**kwargs): """ NAME: sigmaT2 PURPOSE: calculate sigma_T^2 by marginalizing over velocity INPUT: R - radius at which to calculate this (can be Quantity) ...	[ "def", "sigmaT2", "(", "self", ",", "R", ",", "z", ",", "nsigma", "=", "None", ",", "mc", "=", "False", ",", "nmc", "=", "10000", ",", "gl", "=", "True", ",", "ngl", "=", "_DEFAULTNGL", ",", "", "", "kwargs", ")", ":", "if", "mc", ":", "sur...	41.025974	27.675325
def humanize(self): """ Humanize relative to now: .. testsetup:: from datetime import timedelta from delorean import Delorean .. doctest:: >>> past = Delorean.utcnow() - timedelta(hours=1) >>> past.humanize() 'an hour ago' ...	[ "def", "humanize", "(", "self", ")", ":", "now", "=", "self", ".", "now", "(", "self", ".", "timezone", ")", "return", "humanize", ".", "naturaltime", "(", "now", "-", "self", ")" ]	21.052632	19.157895
def draw_text(self, video_name, out, start, end, x, y, text, color='0xFFFFFF', show_background=0, background_color='0x000000', size=16): """ Draws text over a video @param video_name : name of video input file @param out : name of video output file ...	[ "def", "draw_text", "(", "self", ",", "video_name", ",", "out", ",", "start", ",", "end", ",", "x", ",", "y", ",", "text", ",", "color", "=", "'0xFFFFFF'", ",", "show_background", "=", "0", ",", "background_color", "=", "'0x000000'", ",", "size", "=", ...	42.55814	15.255814
def get_binom(base1, base2, estE, estH): """ return probability of base call """ prior_homo = (1. - estH) / 2. prior_hete = estH ## calculate probs bsum = base1 + base2 hetprob = scipy.misc.comb(bsum, base1)/(2. **(bsum)) homoa = scipy.stats.binom.pmf(base2, bsum, estE)...	[ "def", "get_binom", "(", "base1", ",", "base2", ",", "estE", ",", "estH", ")", ":", "prior_homo", "=", "(", "1.", "-", "estH", ")", "/", "2.", "prior_hete", "=", "estH", "## calculate probs", "bsum", "=", "base1", "+", "base2", "hetprob", "=", "scipy",...	24.321429	17.75
def update_extent(self, extent): # type: (int) -> None ''' Update the extent for this CE record. Parameters: extent - The new extent for this CE record. Returns: Nothing. ''' if not self._initialized: raise pycdlibexception.PyCdlibIn...	[ "def", "update_extent", "(", "self", ",", "extent", ")", ":", "# type: (int) -> None", "if", "not", "self", ".", "_initialized", ":", "raise", "pycdlibexception", ".", "PyCdlibInternalError", "(", "'CE record not yet initialized!'", ")", "self", ".", "bl_cont_area", ...	27.714286	21.714286
def data_dtype(self): """Data type of the data block as determined from `header`. If no header is available (i.e., before it has been initialized), or the header entry ``'mode'`` is missing, the data type gained from the ``dtype`` argument in the initializer is returned. Otherwi...	[ "def", "data_dtype", "(", "self", ")", ":", "if", "not", "self", ".", "header", ":", "return", "self", ".", "_init_data_dtype", "try", ":", "mode", "=", "int", "(", "self", ".", "header", "[", "'mode'", "]", "[", "'value'", "]", ")", "except", "KeyEr...	38.789474	17.736842
def remove_pattern(root, pat, verbose=True): """ Given a directory, and a pattern of files like "garbage.txt" or "*pyc" inside it, remove them. Try not to delete the whole OS while you're at it. """ print("removing pattern", root, pat) combined = root + pat print('combined', combined) ...	[ "def", "remove_pattern", "(", "root", ",", "pat", ",", "verbose", "=", "True", ")", ":", "print", "(", "\"removing pattern\"", ",", "root", ",", "pat", ")", "combined", "=", "root", "+", "pat", "print", "(", "'combined'", ",", "combined", ")", "items", ...	31.555556	13.777778
def find_root_path(absolute_path, relative_path): """ Return the root path of a path relative to an absolute path. Example: @param absolute_path: an absolute path that is ended by the specified relative path. @param relative_path: a relative path that ends the specified absolute p...	[ "def", "find_root_path", "(", "absolute_path", ",", "relative_path", ")", ":", "_absolute_path", "=", "os", ".", "path", ".", "normpath", "(", "absolute_path", ")", "_relative_path", "=", "os", ".", "path", ".", "normpath", "(", "relative_path", ")", "index", ...	32.363636	24.454545
def main(argv=None): '''Command line options.''' program_name = os.path.basename(sys.argv[0]) program_version = "v0.1" program_build_date = "%s" % __updated__ program_version_string = '%%prog %s (%s)' % (program_version, program_build_date) #program_usage = '''usage: spam two eggs''' # op...	[ "def", "main", "(", "argv", "=", "None", ")", ":", "program_name", "=", "os", ".", "path", ".", "basename", "(", "sys", ".", "argv", "[", "0", "]", ")", "program_version", "=", "\"v0.1\"", "program_build_date", "=", "\"%s\"", "%", "__updated__", "program...	38.584416	28.350649
def _param_to_list(self): """ Convert parameters defined in `self._param` to list :return None """ for item in self._params: self.__dict__[item] = list(self.__dict__[item])	[ "def", "_param_to_list", "(", "self", ")", ":", "for", "item", "in", "self", ".", "_params", ":", "self", ".", "__dict__", "[", "item", "]", "=", "list", "(", "self", ".", "__dict__", "[", "item", "]", ")" ]	27.25	15
def confusion(df, labels=['neg', 'pos']): """ Binary classification confusion """ c = pd.DataFrame(np.zeros((2, 2)), dtype=int) a, b = df.columns[:2] # labels[df.columns[:2]] c.columns = sorted(set(df[a]))[:2] c.columns.name = a c.index = list(c.columns) c.index.name = b c1, c2 = c.colu...	[ "def", "confusion", "(", "df", ",", "labels", "=", "[", "'neg'", ",", "'pos'", "]", ")", ":", "c", "=", "pd", ".", "DataFrame", "(", "np", ".", "zeros", "(", "(", "2", ",", "2", ")", ")", ",", "dtype", "=", "int", ")", "a", ",", "b", "=", ...	38.5	12.142857
def connect(self, datas=None): """ Connects ``Pipers`` in the order input -> output. See ``Piper.connect``. According to the pipes (topology). If "datas" is given will connect the input ``Pipers`` to the input data see: ``Dagger.connect_inputs``. Argumensts: ...	[ "def", "connect", "(", "self", ",", "datas", "=", "None", ")", ":", "# if data connect inputs", "if", "datas", ":", "self", ".", "connect_inputs", "(", "datas", ")", "# connect the remaining pipers", "postorder", "=", "self", ".", "postorder", "(", ")", "self"...	44.413793	18.551724
def _add_imports_to_env(self, raw_api): """ Scans raw parser output for import declarations. Checks if the imports are valid, and then creates a reference to the namespace in the environment. Args: raw_api (Tuple[Namespace, List[stone.stone.parser._Element]]): ...	[ "def", "_add_imports_to_env", "(", "self", ",", "raw_api", ")", ":", "for", "namespace", ",", "desc", "in", "raw_api", ":", "for", "item", "in", "desc", ":", "if", "isinstance", "(", "item", ",", "AstImport", ")", ":", "if", "namespace", ".", "name", "...	50.59375	18.65625
def YiqToRgb(y, i, q): '''Convert the color from YIQ coordinates to RGB. Parameters: :y: Tte Y component value [0...1] :i: The I component value [0...1] :q: The Q component value [0...1] Returns: The color as an (r, g, b) tuple in the range: r[0...1], ...	[ "def", "YiqToRgb", "(", "y", ",", "i", ",", "q", ")", ":", "r", "=", "y", "+", "(", "i", "", "0.9562", ")", "+", "(", "q", "", "0.6210", ")", "g", "=", "y", "-", "(", "i", "", "0.2717", ")", "-", "(", "q", "", "0.6485", ")", "b", ...	23	21.4
def update(self, **kwargs): """Updates global configuration settings with given values. First checks if given configuration values differ from current values. If any of the configuration values changed, generates a change event. Currently we generate change event for any configuration c...	[ "def", "update", "(", "self", ",", "", "", "kwargs", ")", ":", "# Update inherited configurations", "super", "(", "CommonConf", ",", "self", ")", ".", "update", "(", "", "", "kwargs", ")", "conf_changed", "=", "False", "# Validate given configurations and ch...	41.827586	20.517241
def UpdateSet(self, dataset): """Updates each hypothesis based on the dataset. This is more efficient than calling Update repeatedly because it waits until the end to Normalize. Modifies the suite directly; if you want to keep the original, make a copy. dataset: a sequ...	[ "def", "UpdateSet", "(", "self", ",", "dataset", ")", ":", "for", "data", "in", "dataset", ":", "for", "hypo", "in", "self", ".", "Values", "(", ")", ":", "like", "=", "self", ".", "Likelihood", "(", "data", ",", "hypo", ")", "self", ".", "Mult", ...	31.055556	17
def is_vertex_coloring(G, coloring): """Determines whether the given coloring is a vertex coloring of graph G. Parameters ---------- G : NetworkX graph The graph on which the vertex coloring is applied. coloring : dict A coloring of the nodes of G. Should be a dict of the form ...	[ "def", "is_vertex_coloring", "(", "G", ",", "coloring", ")", ":", "return", "all", "(", "coloring", "[", "u", "]", "!=", "coloring", "[", "v", "]", "for", "u", ",", "v", "in", "G", ".", "edges", ")" ]	31.571429	23.657143
def delete(self, path='', **params): """ Make a DELETE request to the given path, and return the JSON-decoded result. Keyword parameters will be converted to URL parameters. DELETE requests ask to delete the object represented by this URL. """ params = jsonify_p...	[ "def", "delete", "(", "self", ",", "path", "=", "''", ",", "", "", "params", ")", ":", "params", "=", "jsonify_parameters", "(", "params", ")", "url", "=", "ensure_trailing_slash", "(", "self", ".", "url", "+", "path", ".", "lstrip", "(", "'/'", ")...	37.916667	20.916667
def list_nodes_full(call=None, for_output=True): ''' Return a list of the VMs that are on the provider ''' if call == 'action': raise SaltCloudSystemExit( 'The list_nodes_full function must be called with -f or --function.' ) creds = get_creds() clc.v1.SetCredentials(...	[ "def", "list_nodes_full", "(", "call", "=", "None", ",", "for_output", "=", "True", ")", ":", "if", "call", "==", "'action'", ":", "raise", "SaltCloudSystemExit", "(", "'The list_nodes_full function must be called with -f or --function.'", ")", "creds", "=", "get_cred...	37.285714	19.857143

def check_for_upload_create(self, relative_path=None): """Traverse the relative_path tree and check for files that need to be uploaded/created. Relativity here refers to the shared directory tree.""" for f in os.listdir( path_join( self.local_path, relative_path) if ...

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46.777778

20.222222

def delete_checkpoint(self, checkpoint_dir): """Removes subdirectory within checkpoint_folder Parameters ---------- checkpoint_dir : path to checkpoint """ if os.path.isfile(checkpoint_dir): shutil.rmtree(os.path.dirname(checkpoint_dir)) else: ...

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34.8

10.3

def init_bounds(self): """ Process bounds this process is currently initialized with. This gets triggered by using the ``init_bounds`` kwarg. If not set, it will be equal to self.bounds. """ if self._raw["init_bounds"] is None: return self.bounds else...

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34.727273

18.727273

def is_dictlist(data): ''' Returns True if data is a list of one-element dicts (as found in many SLS schemas), otherwise returns False ''' if isinstance(data, list): for element in data: if isinstance(element, dict): if len(element) != 1: retur...

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28.428571

17

def validate_additional_properties(self, valid_response, response): """Validates additional properties. In additional properties, we only need to compare the values of the dict, not the keys Args: valid_response: An example response (for example generated in ...

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42.3125

21.895833

def _read_file(self, filename): """ Read contents of given file. """ try: with open(filename, "r") as fhandle: stats = float(fhandle.readline().rstrip("\n")) except Exception: stats = None return stats

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25.454545

14.727273

def _ssid_inventory(self, inventory, ssid): """ Filters an inventory to only return servers matching ssid """ matching_hosts = {} for host in inventory: if inventory[host]['comment'] == ssid: matching_hosts[host] = inventory[host] return match...

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32

12.6

def _extract_germline(in_file, data): """Extract germline calls non-somatic, non-filtered calls. """ out_file = "%s-germline.vcf" % utils.splitext_plus(in_file)[0] if not utils.file_uptodate(out_file, in_file) and not utils.file_uptodate(out_file + ".gz", in_file): with file_transaction(data, ou...

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54.5

18.9375

def angleDiff(angle1, angle2, take_smaller=True): """ smallest difference between 2 angles code from http://stackoverflow.com/questions/1878907/the-smallest-difference-between-2-angles """ a = np.arctan2(np.sin(angle1 - angle2), np.cos(angle1 - angle2)) if isinstance(a, np.ndarray) and take_smal...

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36.642857

14.928571

def _map_segmentation_mask_to_stft_domain(mask, times, frequencies, stft_times, stft_frequencies): """ Maps the given `mask`, which is in domain (`frequencies`, `times`) to the new domain (`stft_frequencies`, `stft_times`) and returns the result. """ assert mask.shape == (frequencies.shape[0], times...

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45.956522

29

def estimate_rate_matrix(C, dt=1.0, method='KL', sparsity=None, t_agg=None, pi=None, tol=1.0E7, K0=None, maxiter=100000, on_error='raise'): r"""Estimate a reversible rate matrix from a count matrix. Parameters ---------- C : (N,N) ndarray count ...

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43.686131

27.226277

def redirect_display(self, on): ''' on: * True -> set $DISPLAY to virtual screen * False -> set $DISPLAY to original screen :param on: bool ''' d = self.new_display_var if on else self.old_display_var if d is None: log.debug('unset DISPLAY')...

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29

16.866667

def tasks_from_queue(self, tiger, queue, state, skip=0, limit=1000, load_executions=0): """ Returns a tuple with the following information: * total items in the queue * tasks from the given queue in the given state, latest first. An integer may be passed in th...

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42.711111

24.044444

def parser(self): """ Creates a parser for the method based on the documentation. :return <OptionParser> """ usage = self.usage() if self.__doc__: usage += '\n' + nstr(self.__doc__) parse = PARSER_CLASS(usage=usage) shorts = {v: ...

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27.205882

17.676471

def load_from_json(data): """ Load a :class:`Item` from a dictionary ot string (that will be parsed as json) """ if isinstance(data, str): data = json.loads(data) return Item(data['title'], data['uri'])

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31.875

11.875

def p_statement_switch(p): 'statement : SWITCH LPAREN expr RPAREN switch_case_list' p[0] = ast.Switch(p[3], p[5], lineno=p.lineno(1))

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46.333333

15.666667

def cardinality(self): """ This is an over-approximation of the cardinality of this DSIS. :return: """ cardinality = 0 for si in self._si_set: cardinality += si.cardinality return cardinality

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25.1

15.3

def import_admins(self): """ save admins to local DB """ self.message('saving admins into local DB') saved_admins = [] for olduser in OldUser.objects.all(): try: user = User.objects.get(Q(username=olduser.username) | Q(email=olduser.email)) excep...

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42.179487

19.025641

def _is_valid_token(self, auth_token): ''' Check if this is a valid salt-api token or valid Salt token salt-api tokens are regular session tokens that tie back to a real Salt token. Salt tokens are tokens generated by Salt's eauth system. :return bool: True if valid, False if n...

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41.448276

26.758621

def sun_rise_set_transit_spa(times, latitude, longitude, how='numpy', delta_t=67.0, numthreads=4): """ Calculate the sunrise, sunset, and sun transit times using the NREL SPA algorithm described in [1]. If numba is installed, the functions can be compiled to machine cod...

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38.227848

22.379747

def print_last_values(): """Print the last 10 values.""" iterable = archive.list_parameter_values('/YSS/SIMULATOR/BatteryVoltage1', descending=True) for pval in islice(iterable, 0, 10): print(pval)

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42.833333

16

def add_client(self, client_identifier): """Add a client.""" if client_identifier in self.clients: _LOGGER.error('%s already in group %s', client_identifier, self.identifier) return new_clients = self.clients new_clients.append(client_identifier) yield fro...

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47.727273

17.090909

def buildable(self, values: Optional[dict]=None, method: Optional[str]=None) -> bool: """Return True if this rule can build with the values and method.""" if method is not None and method not in self.methods: return False defaults_match = all( values[key] == self.defaults...

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59.375

29.375

def flush(self): """Flush GL commands This is a wrapper for glFlush(). This also flushes the GLIR command queue. """ if hasattr(self, 'flush_commands'): context = self else: context = get_current_canvas().context context.glir.command('...

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29.916667

14.5

def validate_order_params(self, asset, amount, limit_price, stop_price, style): """ Helper method for validating parameters to the order API function. ...

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34.794118

17.617647

def write_file(self, path, name, data, content_type=None, archive=False, raw=False): """Write a file to the file data store at the given path :param str path: The path (directory) into which the file should be written. :param str name: The name of the file to be written. ...

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41.584906

21.943396

def getNodeByNameChain(node, chain_list): """ Walk down a chain of node names and get the nodes they represent e.g. [ "entry", "content", "bag", "fileCount" ] """ working_list = chain_list[:] working_list.reverse() current_node = node while len(working_list): current_name = work...

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34.125

13.875

def random_ipv4(cidr='10.0.0.0/8'): """ Return a random IPv4 address from the given CIDR block. :key str cidr: CIDR block :returns: An IPv4 address from the given CIDR block :rtype: ipaddress.IPv4Address """ try: u_cidr = unicode(cidr) except NameError: u_cidr = cidr ...

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def update_subtotals(self, current, sub_key): """ updates sub_total counts for the class instance based on the current dictionary counts args: ----- current: current dictionary counts sub_key: the key/value to use for the subtotals """ ...

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def import_obj(clsname, default_module=None): """ Import the object given by clsname. If default_module is specified, import from this module. """ if default_module is not None: if not clsname.startswith(default_module + '.'): clsname = '{0}.{1}'.format(default_module, clsname) ...

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def sbo_list(): """Return all SBo packages """ sbo_packages = [] for pkg in os.listdir(_meta_.pkg_path): if pkg.endswith("_SBo"): sbo_packages.append(pkg) return sbo_packages

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25.875

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def ask_list(question: str, default: list = None) -> list: """Asks for a comma seperated list of strings""" default_q = " [default: {0}]: ".format( ",".join(default)) if default is not None else "" answer = input("{0} [{1}]: ".format(question, default_q)) if answer == "": return default...

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40.666667

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def processEnded(self, reason): """ Connected process shut down """ log_debug("{name} process exited", name=self.name) if self.deferred: if reason.type == ProcessDone: self.deferred.callback(reason.value.exitCode) elif reason.type == Proces...

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def box_model_domain(num_points=2, **kwargs): """Creates a box model domain (a single abstract axis). :param int num_points: number of boxes [default: 2] :returns: Domain with single axis of type ``'abstract'`` and ``self.domain_type = 'box'`` :rty...

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def adaptive_gaussian_prior_builder( getter, name, *args, **kwargs): """A pre-canned builder for adaptive scalar gaussian prior distributions. Given a true `getter` function and arguments forwarded from `tf.get_variable`, return a distribution object for a scalar-valued adaptive gaussian prior which will b...

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def remove_vcf_info(keyword, variant_line=None, variant_dict=None): """Remove the information of a info field of a vcf variant line or a variant dict. Arguments: variant_line (str): A vcf formatted variant line variant_dict (dict): A variant dictionary keyword (str): The in...

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def get_pattern(self, field_name): """ Get a regular expression to match a formatting directive that references the given field name. :param field_name: The name of the field to match (a string). :returns: A compiled regular expression object. """ return re.compile(self....

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async def move_rel(self, mount: top_types.Mount, delta: top_types.Point, speed: float = None): """ Move the critical point of the specified mount by a specified displacement in a specified direction, at the specified speed. 'speed' sets the speed of all axes to the given v...

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40.32

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def add_surface(self, name, surface): """Adds a top-level attribute with the given name to the module.""" assert surface is not None if hasattr(self.module, name): raise ThriftCompilerError( 'Cannot define "%s". The name has already been used.' % name ) ...

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def not_next(e): """ Create a PEG function for negative lookahead. """ def match_not_next(s, grm=None, pos=0): try: e(s, grm, pos) except PegreError as ex: return PegreResult(s, Ignore, (pos, pos)) else: raise PegreError('Negative lookahead fai...

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28.75

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def spy(iterable, n=1): """Return a 2-tuple with a list containing the first *n* elements of *iterable*, and an iterator with the same items as *iterable*. This allows you to "look ahead" at the items in the iterable without advancing it. There is one item in the list by default: >>> itera...

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25.926829

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def adaptive(u_kn, N_k, f_k, tol = 1.0e-12, options = None): """ Determine dimensionless free energies by a combination of Newton-Raphson iteration and self-consistent iteration. Picks whichever method gives the lowest gradient. Is slower than NR since it calculates the log norms twice each iteration. ...

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45.938053

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def slice_shape(self, tensor_shape): """Shape of each slice of the Tensor. Args: tensor_shape: Shape. Returns: list of integers with length tensor_shape.ndims. Raises: ValueError: If a Tensor dimension is not divisible by the corresponding Mesh dimension. """ tensor_...

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def index(): """ This is not served anywhere in the web application. It is used explicitly in the context of generating static files since flask-frozen requires url_for's to crawl content. url_for's are not used with host.show_host directly and are instead dynamically generated through javascrip...

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def acquire_read(self, timeout=None): """ Acquire a read lock for the current thread, waiting at most timeout seconds or doing a non-blocking check in case timeout is <= 0. In case timeout is None, the call to acquire_read blocks until the lock request can be serviced. ...

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40.5

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def create_index(self, collection, index_name, **kwargs): """Safely attempt to create index.""" try: self.connection[collection].create_index(index_name, **kwargs) except Exception as exc: LOG.warn("Error tuning mongodb database: %s", exc)

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def getTransformForOverlayCoordinates(self, ulOverlayHandle, eTrackingOrigin, coordinatesInOverlay): """Get the transform in 3d space associated with a specific 2d point in the overlay's coordinate space (where 0,0 is the lower left). -Z points out of the overlay""" fn = self.function_table.getTransfor...

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73

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def writelines(self, lines): ''' Write a list of lines to the stream. Line separators are not added, so it is usual for each of the lines provided to have a line separator at the end. :param lines: ''' if self.__closed: raise OSError() for line in lines: ...

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37.666667

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def _traverse_relationship_rev_objs(self, rel2dst2srcs, goobj_parent, goids_seen): """Traverse from source GO down children.""" parent_id = goobj_parent.id goids_seen.add(parent_id) ##A self.go2obj[parent_id] = goobj_parent # Update goids_seen and go2obj with parent alt_ids ...

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54.526316

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def add_member(self, user_lookup_attribute_value): """ Attempts to add a member to the AD group. :param user_lookup_attribute_value: The value for the LDAP_GROUPS_USER_LOOKUP_ATTRIBUTE. :type user_lookup_attribute_value: str :raises: **AccountDoesNotExist** if the provided accoun...

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60.823529

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def _to_tuple(self, _list): """ Recursively converts lists to tuples """ result = list() for l in _list: if isinstance(l, list): result.append(tuple(self._to_tuple(l))) else: result.append(l) return tuple(result)

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32.444444

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def do_GET(self): """ Handle the retrieval of the code """ parsed_url = urlparse(self.path) if parsed_url[2] == "/" + SERVER_REDIRECT_PATH: # 2 = Path parsed_query = parse_qs(parsed_url[4]) # 4 = Query if "code" not in parsed_query: self.send_response(200) self.send_header("Content-Type", "t...

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31.289474

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def _fill_empty_sessions(self, fill_subjects, fill_visits): """ Fill in tree with additional empty subjects and/or visits to allow the study to pull its inputs from external repositories """ if fill_subjects is None: fill_subjects = [s.id for s in self.subjects] ...

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44.592593

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def create_intent(project_id, display_name, training_phrases_parts, message_texts): """Create an intent of the given intent type.""" import dialogflow_v2 as dialogflow intents_client = dialogflow.IntentsClient() parent = intents_client.project_agent_path(project_id) training_phras...

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40

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def _cram_to_fastq_region(cram_file, work_dir, base_name, region, data): """Convert CRAM to fastq in a specified region. """ ref_file = tz.get_in(["reference", "fasta", "base"], data) resources = config_utils.get_resources("bamtofastq", data["config"]) cores = tz.get_in(["config", "algorithm", "num_...

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64.75

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def unique_iter(src, key=None): """Yield unique elements from the iterable, *src*, based on *key*, in the order in which they first appeared in *src*. >>> repetitious = [1, 2, 3] * 10 >>> list(unique_iter(repetitious)) [1, 2, 3] By default, *key* is the object itself, but *key* can either be a...

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32.823529

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def get_api_client(cls): """Get an API client (with configuration).""" config = cloudsmith_api.Configuration() client = cls() client.config = config client.api_client.rest_client = RestClient() user_agent = getattr(config, "user_agent", None) if user_agent: client.api_client.user_ag...

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def run(self): """Run git add and commit with message if provided.""" if os.system('git add .'): sys.exit(1) if self.message is not None: os.system('git commit -a -m "' + self.message + '"') else: os.system('git commit -a')

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35.5

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def _find_links(self): processed = {} links = [] body = re.search('<[^>]*body[^>]*>(.+?)</body>', self.text, re.S).group(1) """ The link follow by the span.t-mark-rev will contained c++xx information. Consider the below case <a href="LinkA">LinkA</a> <...

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35.6

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def serve(content): """Write content to a temp file and serve it in browser""" temp_folder = tempfile.gettempdir() temp_file_name = tempfile.gettempprefix() + str(uuid.uuid4()) + ".html" # Generate a file path with a random name in temporary dir temp_file_path = os.path.join(temp_folder, temp_file_n...

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33.1

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def parents(self) -> List[str]: """ Return the list of parents SHAs. :return: List[str] parents """ parents = [] for p in self._c_object.parents: parents.append(p.hexsha) return parents

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24.5

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def _solve_k_from_mu(data, k_array, nll, *args): """ For given args, return k_agg from searching some k_range. Parameters ---------- data : array k_range : array nll : function args : Returns -------- :float Minimum k_agg """ # TODO: See if a root finder l...

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20.241379

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def strip_flags(self, idx): """strip(1 byte) radiotap.flags :idx: int :return: int idx :return: collections.namedtuple """ flags = collections.namedtuple( 'flags', ['cfp', 'preamble', 'wep', 'fragmentation', 'fcs', 'datapad', ...

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35.142857

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def reload(module, exclude=['sys', 'os.path', '__builtin__', '__main__']): """Recursively reload all modules used in the given module. Optionally takes a list of modules to exclude from reloading. The default exclude list contains sys, __main__, and __builtin__, to prevent, e.g., resetting display, ex...

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37.266667

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def delete(self): """Delete the instance.""" if lib.EnvDeleteInstance(self._env, self._ist) != 1: raise CLIPSError(self._env)

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37.5

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def get(self, wheel=False): """Downloads the package from PyPI. Returns: Full path of the downloaded file. Raises: PermissionError if the save_dir is not writable. """ try: url = get_url(self.client, self.name, self.version, ...

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35.681818

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def format(args): """ %prog format infasta outfasta Reformat FASTA file and also clean up names. """ sequential_choices = ("replace", "prefix", "suffix") p = OptionParser(format.__doc__) p.add_option("--pairs", default=False, action="store_true", help="Add trailing /1 and /2 for...

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40.537815

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def load_molecule_in_rdkit_smiles(self, molSize,kekulize=True,bonds=[],bond_color=None,atom_color = {}, size= {} ): """ Loads mol file in rdkit without the hydrogens - they do not have to appear in the final figure. Once loaded, the molecule is converted to SMILES format which RDKit appears to ...

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52.021277

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def send(self, obj_id): """ Send email to the assigned lists :param obj_id: int :return: dict|str """ response = self._client.session.post( '{url}/{id}/send'.format( url=self.endpoint_url, id=obj_id ) ) return self....

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25.692308

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def distance(self, physical_qubit1, physical_qubit2): """Returns the undirected distance between physical_qubit1 and physical_qubit2. Args: physical_qubit1 (int): A physical qubit physical_qubit2 (int): Another physical qubit Returns: int: The undirected dis...

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41.55

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def induce(self, b, filestem='default', examples=None, pos=None, neg=None, cn2sd=True, printOutput=False): """ Generate features and find subgroups. :param filestem: The base name of this experiment. ...

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def precipitable_water(self, value=999.0): """Corresponds to IDD Field `precipitable_water` Args: value (float): value for IDD Field `precipitable_water` Unit: mm Missing value: 999.0 if `value` is None it will not be checked against the ...

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def xmlFile(path, mode='r'): """lxml cannot parse XML files starting with a BOM (see http://www.w3.org/TR/2000/REC-xml-20001006 in F.1.) In case such XML file is used, we must skip these characters So we open all XML files for read with 'xmlFile'. TODO: File this issue to lxml ML or tracker (feature...

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def showMessageOverlay(self, pchText, pchCaption, pchButton0Text, pchButton1Text, pchButton2Text, pchButton3Text): """Show the message overlay. This will block and return you a result.""" fn = self.function_table.showMessageOverlay result = fn(pchText, pchCaption, pchButton0Text, pchButton1Text...

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def _match_iter_generic(self, path_elements, start_at): """Implementation of match_iter for >1 self.elements""" length = len(path_elements) # If bound to start, we stop searching at the first element if self.bound_start: end = 1 else: end = length - self....

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def user_has_permission(self, user, name): """ verify user has permission """ targetRecord = AuthMembership.objects(creator=self.client, user=user).first() if not targetRecord: return False for group in targetRecord.groups: if self.has_permission(group.role, name)...

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def getPointsForInterpolation(self,EndOfPrdvP,aNrmNow): ''' Finds interpolation points (c,m) for the consumption function. Parameters ---------- EndOfPrdvP : np.array Array of end-of-period marginal values. aNrmNow : np.array Array of end-of-perio...

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def get_ethernet_settings(self): """ Gets the Ethernet interconnect settings for the Logical Interconnect. Returns: dict: Ethernet Interconnect Settings """ uri = "{}/ethernetSettings".format(self.data["uri"]) return self._helper.do_get(uri)

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def _temporal_distance_pdf(self): """ Temporal distance probability density function. Returns ------- non_delta_peak_split_points: numpy.array non_delta_peak_densities: numpy.array len(density) == len(temporal_distance_split_points_ordered) -1 delta_p...

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def _JzStaeckelIntegrandSquared(v,E,Lz,I3V,delta,u0,cosh2u0,sinh2u0, potu0pi2,pot): #potu0pi2= potentialStaeckel(u0,nu.pi/2.,pot,delta) """The J_z integrand: p_v(v)/2/delta^2""" sin2v= nu.sin(v)**2. dV= cosh2u0*potu0pi2\ -(sinh2u0+sin2v)*potentialStaeckel(u0,v,pot...

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def run_one(self, set_title=False): '''Get exactly one job, run it, and return. Does nothing (but returns :const:`False`) if there is no work to do. Ignores the global mode; this will do work even if :func:`rejester.TaskMaster.get_mode` returns :attr:`~rejester.TaskMaster.TERMI...

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def sigmaT2(self,R,z,nsigma=None,mc=False,nmc=10000, gl=True,ngl=_DEFAULTNGL,**kwargs): """ NAME: sigmaT2 PURPOSE: calculate sigma_T^2 by marginalizing over velocity INPUT: R - radius at which to calculate this (can be Quantity) ...

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def humanize(self): """ Humanize relative to now: .. testsetup:: from datetime import timedelta from delorean import Delorean .. doctest:: >>> past = Delorean.utcnow() - timedelta(hours=1) >>> past.humanize() 'an hour ago' ...

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def draw_text(self, video_name, out, start, end, x, y, text, color='0xFFFFFF', show_background=0, background_color='0x000000', size=16): """ Draws text over a video @param video_name : name of video input file @param out : name of video output file ...

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def get_binom(base1, base2, estE, estH): """ return probability of base call """ prior_homo = (1. - estH) / 2. prior_hete = estH ## calculate probs bsum = base1 + base2 hetprob = scipy.misc.comb(bsum, base1)/(2. **(bsum)) homoa = scipy.stats.binom.pmf(base2, bsum, estE)...

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24.321429

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def update_extent(self, extent): # type: (int) -> None ''' Update the extent for this CE record. Parameters: extent - The new extent for this CE record. Returns: Nothing. ''' if not self._initialized: raise pycdlibexception.PyCdlibIn...

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27.714286

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def data_dtype(self): """Data type of the data block as determined from `header`. If no header is available (i.e., before it has been initialized), or the header entry ``'mode'`` is missing, the data type gained from the ``dtype`` argument in the initializer is returned. Otherwi...

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def remove_pattern(root, pat, verbose=True): """ Given a directory, and a pattern of files like "garbage.txt" or "*pyc" inside it, remove them. Try not to delete the whole OS while you're at it. """ print("removing pattern", root, pat) combined = root + pat print('combined', combined) ...

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def find_root_path(absolute_path, relative_path): """ Return the root path of a path relative to an absolute path. Example: @param absolute_path: an absolute path that is ended by the specified relative path. @param relative_path: a relative path that ends the specified absolute p...

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def main(argv=None): '''Command line options.''' program_name = os.path.basename(sys.argv[0]) program_version = "v0.1" program_build_date = "%s" % __updated__ program_version_string = '%%prog %s (%s)' % (program_version, program_build_date) #program_usage = '''usage: spam two eggs''' # op...

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def _param_to_list(self): """ Convert parameters defined in `self._param` to list :return None """ for item in self._params: self.__dict__[item] = list(self.__dict__[item])

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27.25

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def confusion(df, labels=['neg', 'pos']): """ Binary classification confusion """ c = pd.DataFrame(np.zeros((2, 2)), dtype=int) a, b = df.columns[:2] # labels[df.columns[:2]] c.columns = sorted(set(df[a]))[:2] c.columns.name = a c.index = list(c.columns) c.index.name = b c1, c2 = c.colu...

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38.5

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def connect(self, datas=None): """ Connects ``Pipers`` in the order input -> output. See ``Piper.connect``. According to the pipes (topology). If "datas" is given will connect the input ``Pipers`` to the input data see: ``Dagger.connect_inputs``. Argumensts: ...

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def _add_imports_to_env(self, raw_api): """ Scans raw parser output for import declarations. Checks if the imports are valid, and then creates a reference to the namespace in the environment. Args: raw_api (Tuple[Namespace, List[stone.stone.parser._Element]]): ...

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def YiqToRgb(y, i, q): '''Convert the color from YIQ coordinates to RGB. Parameters: :y: Tte Y component value [0...1] :i: The I component value [0...1] :q: The Q component value [0...1] Returns: The color as an (r, g, b) tuple in the range: r[0...1], ...

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def update(self, **kwargs): """Updates global configuration settings with given values. First checks if given configuration values differ from current values. If any of the configuration values changed, generates a change event. Currently we generate change event for any configuration c...

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def UpdateSet(self, dataset): """Updates each hypothesis based on the dataset. This is more efficient than calling Update repeatedly because it waits until the end to Normalize. Modifies the suite directly; if you want to keep the original, make a copy. dataset: a sequ...

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31.055556

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def is_vertex_coloring(G, coloring): """Determines whether the given coloring is a vertex coloring of graph G. Parameters ---------- G : NetworkX graph The graph on which the vertex coloring is applied. coloring : dict A coloring of the nodes of G. Should be a dict of the form ...

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def delete(self, path='', **params): """ Make a DELETE request to the given path, and return the JSON-decoded result. Keyword parameters will be converted to URL parameters. DELETE requests ask to delete the object represented by this URL. """ params = jsonify_p...

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def list_nodes_full(call=None, for_output=True): ''' Return a list of the VMs that are on the provider ''' if call == 'action': raise SaltCloudSystemExit( 'The list_nodes_full function must be called with -f or --function.' ) creds = get_creds() clc.v1.SetCredentials(...

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