kejian/codesearchnet-python-pep8-full · Datasets at Hugging Face

text stringlengths 75 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 0.18
def disttar(target, source, env): """tar archive builder""" import tarfile env_dict = env.Dictionary() if env_dict.get("DISTTAR_FORMAT") in ["gz", "bz2"]: tar_format = env_dict["DISTTAR_FORMAT"] else: tar_format = "" # split the target ...	[ "def", "disttar", "(", "target", ",", "source", ",", "env", ")", ":", "import", "tarfile", "env_dict", "=", "env", ".", "Dictionary", "(", ")", "if", "env_dict", ".", "get", "(", "\"DISTTAR_FORMAT\"", ")", "in", "[", "\"gz\"", ",", "\"bz2\"", "]", ":",...	34.257143	0.008921
def discard_config(self): """Discard changes (rollback 0).""" self.device.cu.rollback(rb_id=0) if not self.config_lock: self._unlock()	[ "def", "discard_config", "(", "self", ")", ":", "self", ".", "device", ".", "cu", ".", "rollback", "(", "rb_id", "=", "0", ")", "if", "not", "self", ".", "config_lock", ":", "self", ".", "_unlock", "(", ")" ]	33.2	0.011765
def start(self, max_value=None, init=True): '''Starts measuring time, and prints the bar at 0%. It returns self so you can use it like this: Args: max_value (int): The maximum value of the progressbar reinit (bool): Initialize the progressbar, this is useful if you ...	[ "def", "start", "(", "self", ",", "max_value", "=", "None", ",", "init", "=", "True", ")", ":", "if", "init", ":", "self", ".", "init", "(", ")", "# Prevent multiple starts", "if", "self", ".", "start_time", "is", "not", "None", ":", "# pragma: no cover"...	32.753846	0.000912
def append(self, data): """Append data to a file.""" data_length = len(data) if self._size + data_length > self._flush_size: self.flush() if not self._exclusive and data_length > _FILE_POOL_MAX_SIZE: raise errors.Error( "Too big input %s (%s)." % (data_length, _FILE_POOL_MAX_SIZE...	[ "def", "append", "(", "self", ",", "data", ")", ":", "data_length", "=", "len", "(", "data", ")", "if", "self", ".", "_size", "+", "data_length", ">", "self", ".", "_flush_size", ":", "self", ".", "flush", "(", ")", "if", "not", "self", ".", "_excl...	29.333333	0.015419
def time_average(rho, t): r"""Return a time-averaged density matrix (using trapezium rule). We test a basic two-level system. >>> import numpy as np >>> from scipy.constants import physical_constants >>> from sympy import Matrix, symbols >>> from fast.electric_field import electric_field_ampli...	[ "def", "time_average", "(", "rho", ",", "t", ")", ":", "T", "=", "t", "[", "-", "1", "]", "-", "t", "[", "0", "]", "dt", "=", "t", "[", "1", "]", "-", "t", "[", "0", "]", "rhoav", "=", "np", ".", "sum", "(", "rho", "[", "1", ":", "-",...	33.54386	0.000508
def _recv_loop(self): """Sits in tight loop collecting data received from peer and processing it. """ required_len = BGP_MIN_MSG_LEN conn_lost_reason = "Connection lost as protocol is no longer active" try: while True: next_bytes = self._socket...	[ "def", "_recv_loop", "(", "self", ")", ":", "required_len", "=", "BGP_MIN_MSG_LEN", "conn_lost_reason", "=", "\"Connection lost as protocol is no longer active\"", "try", ":", "while", "True", ":", "next_bytes", "=", "self", ".", "_socket", ".", "recv", "(", "requir...	40.5	0.002193
def list(self, **params): """ Retrieve all lead unqualified reasons Returns all lead unqualified reasons available to the user according to the parameters provided :calls: ``get /lead_unqualified_reasons`` :param dict params: (optional) Search options. :return: List of ...	[ "def", "list", "(", "self", ",", "", "", "params", ")", ":", "_", ",", "_", ",", "lead_unqualified_reasons", "=", "self", ".", "http_client", ".", "get", "(", "\"/lead_unqualified_reasons\"", ",", "params", "=", "params", ")", "return", "lead_unqualified_r...	42.142857	0.008292
def set_local(self, key=None, value=None, data=None, **kwdata): """ Locally store some data associated with this conversation. Data can be passed in either as a single dict, or as key-word args. For example, if you need to store the previous value of a remote field to determine...	[ "def", "set_local", "(", "self", ",", "key", "=", "None", ",", "value", "=", "None", ",", "data", "=", "None", ",", "", "", "kwdata", ")", ":", "if", "data", "is", "None", ":", "data", "=", "{", "}", "if", "key", "is", "not", "None", ":", "...	39.870968	0.00158
def reset_params(self): """(Re)set all parameters.""" units = [self.input_units] units += [self.hidden_units] * self.num_hidden units += [self.output_units] sequence = [] for u0, u1 in zip(units, units[1:]): sequence.append(nn.Linear(u0, u1)) sequ...	[ "def", "reset_params", "(", "self", ")", ":", "units", "=", "[", "self", ".", "input_units", "]", "units", "+=", "[", "self", ".", "hidden_units", "]", "*", "self", ".", "num_hidden", "units", "+=", "[", "self", ".", "output_units", "]", "sequence", "=...	32.176471	0.003552
def find_page_of_state_m(self, state_m): """Return the identifier and page of a given state model :param state_m: The state model to be searched :return: page containing the state and the state_identifier """ for state_identifier, page_info in list(self.tabs.items()): ...	[ "def", "find_page_of_state_m", "(", "self", ",", "state_m", ")", ":", "for", "state_identifier", ",", "page_info", "in", "list", "(", "self", ".", "tabs", ".", "items", "(", ")", ")", ":", "if", "page_info", "[", "'state_m'", "]", "is", "state_m", ":", ...	43.3	0.004525
def get_model(self, model_name): """ TODO: Need to validate model name has 2x '.' chars """ klass = None try: module_name, class_name = model_name.rsplit('.', 1) mod = __import__(module_name, fromlist=[class_name]) klass = getattr(mod, class_na...	[ "def", "get_model", "(", "self", ",", "model_name", ")", ":", "klass", "=", "None", "try", ":", "module_name", ",", "class_name", "=", "model_name", ".", "rsplit", "(", "'.'", ",", "1", ")", "mod", "=", "__import__", "(", "module_name", ",", "fromlist", ...	33.076923	0.004525
def to_bytes(s): """ 将字符串转换成字节数组 :param s: 要转换成字节数组的字符串 :return: 转换成字节数组的字符串 """ if bytes != str: if type(s) == str: return s.encode('utf-8') return s	[ "def", "to_bytes", "(", "s", ")", ":", "if", "bytes", "!=", "str", ":", "if", "type", "(", "s", ")", "==", "str", ":", "return", "s", ".", "encode", "(", "'utf-8'", ")", "return", "s" ]	18.9	0.005051
def _init(self): """Read the line number.""" self._line_number = next_line( self._communication.last_requested_line_number, self._file.read(1)[0])	[ "def", "_init", "(", "self", ")", ":", "self", ".", "_line_number", "=", "next_line", "(", "self", ".", "_communication", ".", "last_requested_line_number", ",", "self", ".", "_file", ".", "read", "(", "1", ")", "[", "0", "]", ")" ]	36.4	0.010753
def log_the_survey_settings( log, pathToYamlFile): """ Create a MD log of the survey settings Key Arguments: - ``log`` -- logger - ``pathToYamlFile`` -- yaml results file Return: - None """ ################ > IMPORTS ################ ## STA...	[ "def", "log_the_survey_settings", "(", "log", ",", "pathToYamlFile", ")", ":", "################ > IMPORTS ################", "## STANDARD LIB ##", "## THIRD PARTY ##", "import", "yaml", "## LOCAL APPLICATION ##", "from", "datetime", "import", "datetime", ",", "date", ",", ...	42.777108	0.003441
def connection_exists(self, from_obj, to_obj): """ Returns ``True`` if a connection between the given objects exists, else ``False``. """ self._validate_ctypes(from_obj, to_obj) return self.connections.filter(from_pk=from_obj.pk, to_pk=to_obj.pk).exists()	[ "def", "connection_exists", "(", "self", ",", "from_obj", ",", "to_obj", ")", ":", "self", ".", "_validate_ctypes", "(", "from_obj", ",", "to_obj", ")", "return", "self", ".", "connections", ".", "filter", "(", "from_pk", "=", "from_obj", ".", "pk", ",", ...	42.428571	0.009901
def setTerms( self, terms ): """ Sets a simple rule list by accepting a list of strings for terms. \ This is a convenience method for the setRules method. :param rules \| [<str> term, ..] """ return self.setRules([XQueryRule(term = term) for term in terms])	[ "def", "setTerms", "(", "self", ",", "terms", ")", ":", "return", "self", ".", "setRules", "(", "[", "XQueryRule", "(", "term", "=", "term", ")", "for", "term", "in", "terms", "]", ")" ]	39	0.021944
def response_hook(self, r, **kwargs): """The actual hook handler.""" if r.status_code == 401: # Handle server auth. www_authenticate = r.headers.get('www-authenticate', '').lower() auth_type = _auth_type_from_header(www_authenticate) if auth_type is not N...	[ "def", "response_hook", "(", "self", ",", "r", ",", "", "", "kwargs", ")", ":", "if", "r", ".", "status_code", "==", "401", ":", "# Handle server auth.", "www_authenticate", "=", "r", ".", "headers", ".", "get", "(", "'www-authenticate'", ",", "''", ")...	35.322581	0.001778
def _str_extract_noexpand(arr, pat, flags=0): """ Find groups in each string in the Series using passed regular expression. This function is called from str_extract(expand=False), and can return Series, DataFrame, or Index. """ from pandas import DataFrame, Index regex = re.compile(pat...	[ "def", "_str_extract_noexpand", "(", "arr", ",", "pat", ",", "flags", "=", "0", ")", ":", "from", "pandas", "import", "DataFrame", ",", "Index", "regex", "=", "re", ".", "compile", "(", "pat", ",", "flags", "=", "flags", ")", "groups_or_na", "=", "_gro...	35.16129	0.000893
def summary(self): """ A succinct summary of the argument specifier. Unlike the repr, a summary does not have to be complete but must supply the most relevant information about the object to the user. """ print("Items: %s" % len(self)) varying_keys = ', '.join('%r...	[ "def", "summary", "(", "self", ")", ":", "print", "(", "\"Items: %s\"", "%", "len", "(", "self", ")", ")", "varying_keys", "=", "', '", ".", "join", "(", "'%r'", "%", "k", "for", "k", "in", "self", ".", "varying_keys", ")", "print", "(", "\"Varying K...	44.230769	0.006814
def queue(self, blogname, **kwargs): """ Gets posts that are currently in the blog's queue :param limit: an int, the number of posts you want returned :param offset: an int, the post you want to start at, for pagination. :param filter: the post format that you want returned: HTM...	[ "def", "queue", "(", "self", ",", "blogname", ",", "", "", "kwargs", ")", ":", "url", "=", "\"/v2/blog/{}/posts/queue\"", ".", "format", "(", "blogname", ")", "return", "self", ".", "send_api_request", "(", "\"get\"", ",", "url", ",", "kwargs", ",", "[...	44.666667	0.005484
def get_reports(): """ Returns energy data from 1960 to 2014 across various factors. """ if False: # If there was a Test version of this method, it would go here. But alas. pass else: rows = _Constants._DATABASE.execute("SELECT data FROM energy".format( hardw...	[ "def", "get_reports", "(", ")", ":", "if", "False", ":", "# If there was a Test version of this method, it would go here. But alas.", "pass", "else", ":", "rows", "=", "_Constants", ".", "_DATABASE", ".", "execute", "(", "\"SELECT data FROM energy\"", ".", "format", "("...	32.333333	0.008016
def comments(self, update=True): """Fetch and return the comments for a single MoreComments object.""" if not self._comments: if self.count == 0: # Handle 'continue this thread' type return self._continue_comments(update) # pylint: disable=W0212 child...	[ "def", "comments", "(", "self", ",", "update", "=", "True", ")", ":", "if", "not", "self", ".", "_comments", ":", "if", "self", ".", "count", "==", "0", ":", "# Handle 'continue this thread' type", "return", "self", ".", "_continue_comments", "(", "update", ...	46	0.001521
def open_upload_stream(self, filename, chunk_size_bytes=None, metadata=None): """Opens a Stream that the application can write the contents of the file to. The user must specify the filename, and can choose to add any additional information in the metadata fie...	[ "def", "open_upload_stream", "(", "self", ",", "filename", ",", "chunk_size_bytes", "=", "None", ",", "metadata", "=", "None", ")", ":", "validate_string", "(", "\"filename\"", ",", "filename", ")", "opts", "=", "{", "\"filename\"", ":", "filename", ",", "\"...	41.95122	0.001705
def ModuleHelp(self, module): """Describe the key flags of a module. Args: module: A module object or a module name (a string). Returns: string describing the key flags of a module. """ helplist = [] self.__RenderOurModuleKeyFlags(module, helplist) return '\n'.join(helplist)	[ "def", "ModuleHelp", "(", "self", ",", "module", ")", ":", "helplist", "=", "[", "]", "self", ".", "__RenderOurModuleKeyFlags", "(", "module", ",", "helplist", ")", "return", "'\\n'", ".", "join", "(", "helplist", ")" ]	25.5	0.003155
def perform_permissions_check(self, user, obj, perms): """ Performs the permission check. """ return self.request.forum_permission_handler.can_edit_post(obj, user)	[ "def", "perform_permissions_check", "(", "self", ",", "user", ",", "obj", ",", "perms", ")", ":", "return", "self", ".", "request", ".", "forum_permission_handler", ".", "can_edit_post", "(", "obj", ",", "user", ")" ]	59	0.011173
def get_poll_option_formset_kwargs(self): """ Returns the keyword arguments for instantiating the poll option formset. """ kwargs = { 'prefix': 'poll', } if self.request.method in ('POST', 'PUT'): kwargs.update({ 'data': self.request.POST, ...	[ "def", "get_poll_option_formset_kwargs", "(", "self", ")", ":", "kwargs", "=", "{", "'prefix'", ":", "'poll'", ",", "}", "if", "self", ".", "request", ".", "method", "in", "(", "'POST'", ",", "'PUT'", ")", ":", "kwargs", ".", "update", "(", "{", "'data...	33.666667	0.006421
def cookie_attr_value_check(attr_name, attr_value): """ Check cookie attribute value for validity. Return True if value is valid :param attr_name: attribute name to check :param attr_value: attribute value to check :return: bool """ attr_value.encode('us-ascii') return WHTTPCookie.cookie_attr_value_compl...	[ "def", "cookie_attr_value_check", "(", "attr_name", ",", "attr_value", ")", ":", "attr_value", ".", "encode", "(", "'us-ascii'", ")", "return", "WHTTPCookie", ".", "cookie_attr_value_compliance", "[", "attr_name", "]", ".", "match", "(", "attr_value", ")", "is", ...	39.777778	0.027322
def __add_min_max_value( parser, basename, default_min, default_max, initial, help_template): """ Generates parser entries for options with a min, max, and default value. Args: parser: the parser to use. basename: the base option name. Gen...	[ "def", "__add_min_max_value", "(", "parser", ",", "basename", ",", "default_min", ",", "default_max", ",", "initial", ",", "help_template", ")", ":", "help_template", "=", "Template", "(", "help_template", ")", "parser", ".", "add", "(", "'--{0}-min'", ".", "f...	29.159091	0.000754
def _AssertIsLocal(path): ''' Checks if a given path is local, raise an exception if not. This is used in filesystem functions that do not support remote operations yet. :param unicode path: :raises NotImplementedForRemotePathError: If the given path is not local ''' from six.move...	[ "def", "_AssertIsLocal", "(", "path", ")", ":", "from", "six", ".", "moves", ".", "urllib", ".", "parse", "import", "urlparse", "if", "not", "_UrlIsLocal", "(", "urlparse", "(", "path", ")", ")", ":", "from", ".", "_exceptions", "import", "NotImplementedFo...	32.6	0.003976
def sonify(annotation, sr=22050, duration=None, **kwargs): '''Sonify a jams annotation through mir_eval Parameters ---------- annotation : jams.Annotation The annotation to sonify sr = : positive number The sampling rate of the output waveform duration : float (optional) ...	[ "def", "sonify", "(", "annotation", ",", "sr", "=", "22050", ",", "duration", "=", "None", ",", "", "", "kwargs", ")", ":", "length", "=", "None", "if", "duration", "is", "None", ":", "duration", "=", "annotation", ".", "duration", "if", "duration", ...	29.320755	0.000623
def getPosNew(data): """ get Fixed position """ pos = data.geno['col_header']['pos'][:] chrom= data.geno['col_header']['chrom'][:] n_chroms = chrom.max() pos_new = [] for chrom_i in range(1,n_chroms+1): I = chrom==chrom_i _pos = pos[I] for i in range(1,_pos.shape[...	[ "def", "getPosNew", "(", "data", ")", ":", "pos", "=", "data", ".", "geno", "[", "'col_header'", "]", "[", "'pos'", "]", "[", ":", "]", "chrom", "=", "data", ".", "geno", "[", "'col_header'", "]", "[", "'chrom'", "]", "[", ":", "]", "n_chroms", "...	28	0.01626
def run(self): """Start the collector worker thread. If running in standalone mode, the current thread will wait until the collector thread ends. """ self.collector.start() if self.standalone: self.collector.join()	[ "def", "run", "(", "self", ")", ":", "self", ".", "collector", ".", "start", "(", ")", "if", "self", ".", "standalone", ":", "self", ".", "collector", ".", "join", "(", ")" ]	29.666667	0.007273
def merge(profile, branch, merge_into): """Merge a branch into another branch. Args: profile A profile generated from ``simplygithub.authentication.profile``. Such profiles tell this module (i) the ``repo`` to connect to, and (ii) the ``token`` to connect with. ...	[ "def", "merge", "(", "profile", ",", "branch", ",", "merge_into", ")", ":", "data", "=", "merges", ".", "merge", "(", "profile", ",", "branch", ",", "merge_into", ")", "return", "data" ]	25.818182	0.001698
def handle(self, t_input: inference.TranslatorInput, t_output: inference.TranslatorOutput, t_walltime: float = 0.): """ :param t_input: Translator input. :param t_output: Translator output. :param t_walltime: Total walltime for translation. ...	[ "def", "handle", "(", "self", ",", "t_input", ":", "inference", ".", "TranslatorInput", ",", "t_output", ":", "inference", ".", "TranslatorOutput", ",", "t_walltime", ":", "float", "=", "0.", ")", ":", "self", ".", "stream", ".", "write", "(", "\"%s\\n\"",...	36.727273	0.012077
def _expand_libs_in_apps(specs): """ Expands specs.apps.depends.libs to include any indirectly required libs """ for app_name, app_spec in specs['apps'].iteritems(): if 'depends' in app_spec and 'libs' in app_spec['depends']: app_spec['depends']['libs'] = _get_dependent('libs', app_n...	[ "def", "_expand_libs_in_apps", "(", "specs", ")", ":", "for", "app_name", ",", "app_spec", "in", "specs", "[", "'apps'", "]", ".", "iteritems", "(", ")", ":", "if", "'depends'", "in", "app_spec", "and", "'libs'", "in", "app_spec", "[", "'depends'", "]", ...	47.571429	0.0059
def set_disk_timeout(timeout, power='ac', scheme=None): ''' Set the disk timeout in minutes for the given power scheme Args: timeout (int): The amount of time in minutes before the disk will timeout power (str): Set the value for AC or DC power. Default is ``ac``. V...	[ "def", "set_disk_timeout", "(", "timeout", ",", "power", "=", "'ac'", ",", "scheme", "=", "None", ")", ":", "return", "_set_powercfg_value", "(", "scheme", "=", "scheme", ",", "sub_group", "=", "'SUB_DISK'", ",", "setting_guid", "=", "'DISKIDLE'", ",", "powe...	28.4	0.000851
def find_feasible_flow(self): ''' API: find_feasible_flow(self) Description: Solves feasible flow problem, stores solution in 'flow' attribute or arcs. This method is used to get an initial feasible flow for simplex and cycle canceling algorithms. ...	[ "def", "find_feasible_flow", "(", "self", ")", ":", "# establish a feasible flow in the network, to do this add nodes s and", "# t and solve a max flow problem.", "nl", "=", "self", ".", "get_node_list", "(", ")", "for", "i", "in", "nl", ":", "b_i", "=", "self", ".", ...	41.404255	0.001004
def month_interval(year, month, return_str=False): """ Usage Example:: >>> timewrapper.day_interval(2014, 12) (datetime(2014, 12, 1, 0, 0, 0), datetime(2014, 12, 31, 23, 59, 59)) """ if month == 12: start, end = datetime(year, month, ...	[ "def", "month_interval", "(", "year", ",", "month", ",", "return_str", "=", "False", ")", ":", "if", "month", "==", "12", ":", "start", ",", "end", "=", "datetime", "(", "year", ",", "month", ",", "1", ")", ",", "datetime", "(", "year", "+", "1", ...	34.823529	0.013158
def refresh(self): """ Fetches all current container names from the client, along with their id. """ if not self._client: return current_containers = self._client.containers(all=True) self.clear() for container in current_containers: contai...	[ "def", "refresh", "(", "self", ")", ":", "if", "not", "self", ".", "_client", ":", "return", "current_containers", "=", "self", ".", "_client", ".", "containers", "(", "all", "=", "True", ")", "self", ".", "clear", "(", ")", "for", "container", "in", ...	36.714286	0.005693
def is_all_field_none(self): """ :rtype: bool """ if self._id_ is not None: return False if self._monetary_account_id is not None: return False if self._card_id is not None: return False if self._amount_local is not None: ...	[ "def", "is_all_field_none", "(", "self", ")", ":", "if", "self", ".", "_id_", "is", "not", "None", ":", "return", "False", "if", "self", ".", "_monetary_account_id", "is", "not", "None", ":", "return", "False", "if", "self", ".", "_card_id", "is", "not",...	22.791667	0.000876
def maketrans(fromstr, tostr): """maketrans(frm, to) -> string Return a translation table (a string of 256 bytes long) suitable for use in string.translate. The strings frm and to must be of the same length. """ if len(fromstr) != len(tostr): raise ValueError, "maketrans arguments mus...	[ "def", "maketrans", "(", "fromstr", ",", "tostr", ")", ":", "if", "len", "(", "fromstr", ")", "!=", "len", "(", "tostr", ")", ":", "raise", "ValueError", ",", "\"maketrans arguments must have same length\"", "global", "_idmapL", "if", "not", "_idmapL", ":", ...	29.555556	0.003643
def peek(self): '''Return (but do not consume) the next token At the end of input, ``None`` is returned. ''' if self.position >= len(self.tokens): return None return self.tokens[self.position]	[ "def", "peek", "(", "self", ")", ":", "if", "self", ".", "position", ">=", "len", "(", "self", ".", "tokens", ")", ":", "return", "None", "return", "self", ".", "tokens", "[", "self", ".", "position", "]" ]	23.8	0.008097
def _create_header(self): """ Function to create the GroupHeader (GrpHdr) in the CstmrCdtTrfInitn Node """ # Retrieve the node to which we will append the group header. CstmrCdtTrfInitn_node = self._xml.find('CstmrCdtTrfInitn') # Create the header nodes. ...	[ "def", "_create_header", "(", "self", ")", ":", "# Retrieve the node to which we will append the group header.", "CstmrCdtTrfInitn_node", "=", "self", ".", "_xml", ".", "find", "(", "'CstmrCdtTrfInitn'", ")", "# Create the header nodes.", "GrpHdr_node", "=", "ET", ".", "E...	35.9375	0.00254
def write_csv(self, path=None): """Write CSV file. Sorts the sections before calling the superclass write_csv""" # Sort the Sections self.sort_sections(['Root', 'Contacts', 'Documentation', 'References', 'Resources', 'Citations', 'Schema']) # Sort Terms in the root section # ...	[ "def", "write_csv", "(", "self", ",", "path", "=", "None", ")", ":", "# Sort the Sections", "self", ".", "sort_sections", "(", "[", "'Root'", ",", "'Contacts'", ",", "'Documentation'", ",", "'References'", ",", "'Resources'", ",", "'Citations'", ",", "'Schema'...	29.545455	0.005961
def _identify_heterogeneity_blocks_hmm(in_file, params, work_dir, somatic_info): """Use a HMM to identify blocks of heterogeneity to use for calculating allele frequencies. The goal is to subset the genome to a more reasonable section that contains potential loss of heterogeneity or other allele frequency ...	[ "def", "_identify_heterogeneity_blocks_hmm", "(", "in_file", ",", "params", ",", "work_dir", ",", "somatic_info", ")", ":", "def", "_segment_by_hmm", "(", "chrom", ",", "freqs", ",", "coords", ")", ":", "cur_coords", "=", "[", "]", "for", "j", ",", "state", ...	51.863636	0.005164
def update_record(self, dns_type, name, content, **kwargs): """ Update dns record :param dns_type: :param name: :param content: :param kwargs: :return: """ record = self.get_record(dns_type, name) data = { 'type': dns_type, ...	[ "def", "update_record", "(", "self", ",", "dns_type", ",", "name", ",", "content", ",", "", "", "kwargs", ")", ":", "record", "=", "self", ".", "get_record", "(", "dns_type", ",", "name", ")", "data", "=", "{", "'type'", ":", "dns_type", ",", "'nam...	29.928571	0.003468
def _map_arguments(self, args): """Map from the top-level arguments to the arguments provided to the indiviudal links """ data = args.get('data') comp = args.get('comp') library = args.get('library') dry_run = args.get('dry_run', False) self._set_link('sum-rings'...	[ "def", "_map_arguments", "(", "self", ",", "args", ")", ":", "data", "=", "args", ".", "get", "(", "'data'", ")", "comp", "=", "args", ".", "get", "(", "'comp'", ")", "library", "=", "args", ".", "get", "(", "'library'", ")", "dry_run", "=", "args"...	37.086957	0.002286
def print_attr_values( thing, all=False, heading=None, file=None ): ''' Print the attributes of thing which have non-empty values, as a vertical list of "name : value". When all=True, print all attributes even those with empty values. ''' if heading : if isinstance( heading, int ) : ...	[ "def", "print_attr_values", "(", "thing", ",", "all", "=", "False", ",", "heading", "=", "None", ",", "file", "=", "None", ")", ":", "if", "heading", ":", "if", "isinstance", "(", "heading", ",", "int", ")", ":", "# request for default heading", "heading",...	38.428571	0.025393
def wait_while_reachable(self, servers, timeout=60): """wait while all servers be reachable Args: servers - list of servers """ t_start = time.time() while True: try: for server in servers: # TODO: use state code to chec...	[ "def", "wait_while_reachable", "(", "self", ",", "servers", ",", "timeout", "=", "60", ")", ":", "t_start", "=", "time", ".", "time", "(", ")", "while", "True", ":", "try", ":", "for", "server", "in", "servers", ":", "# TODO: use state code to check if serve...	48.2	0.005086
def add_arguments(parser, default_level=logging.INFO): """ Add arguments to an ArgumentParser or OptionParser for purposes of grabbing a logging level. """ adder = ( getattr(parser, 'add_argument', None) or getattr(parser, 'add_option') ) adder( '-l', '--log-level', default=default_level, type=lo...	[ "def", "add_arguments", "(", "parser", ",", "default_level", "=", "logging", ".", "INFO", ")", ":", "adder", "=", "(", "getattr", "(", "parser", ",", "'add_argument'", ",", "None", ")", "or", "getattr", "(", "parser", ",", "'add_option'", ")", ")", "adde...	31	0.031332
def _conn_ready(self, conn): """ There is a nice state diagram at the top of httplib.py. It indicates that once the response headers have been read (which _mexe does before adding the connection to the pool), a response is attached to the connection, and it stays there u...	[ "def", "_conn_ready", "(", "self", ",", "conn", ")", ":", "if", "ON_APP_ENGINE", ":", "# Google App Engine implementation of HTTPConnection doesn't contain", "# _HTTPConnection__response attribute. Moreover, it's not possible", "# to determine if given connection is ready. Reusing connecti...	51.318182	0.002609
def from_(self, selectable): """ Adds a table to the query. This function can only be called once and will raise an AttributeError if called a second time. :param selectable: Type: ``Table``, ``Query``, or ``str`` When a ``str`` is passed, a table with the name...	[ "def", "from_", "(", "self", ",", "selectable", ")", ":", "self", ".", "_from", ".", "append", "(", "Table", "(", "selectable", ")", "if", "isinstance", "(", "selectable", ",", "str", ")", "else", "selectable", ")", "if", "isinstance", "(", "selectable",...	38.24	0.006122
def start_threads(self, n_threads): """ Terminate existing threads and create a new set if the thread number doesn't match the desired number. Required: n_threads: (int) number of threads to spawn Returns: self """ if n_threads == len(self._threads): return self ...	[ "def", "start_threads", "(", "self", ",", "n_threads", ")", ":", "if", "n_threads", "==", "len", "(", "self", ".", "_threads", ")", ":", "return", "self", "# Terminate all previous tasks with the existing", "# event object, then create a new one for the next", "# generati...	25.4	0.010834
def _dist_version_url(self, dist): """ Get version and homepage for a pkg_resources.Distribution :param dist: the pkg_resources.Distribution to get information for :returns: 2-tuple of (version, homepage URL) :rtype: tuple """ ver = str(dist.version) url ...	[ "def", "_dist_version_url", "(", "self", ",", "dist", ")", ":", "ver", "=", "str", "(", "dist", ".", "version", ")", "url", "=", "None", "for", "line", "in", "dist", ".", "get_metadata_lines", "(", "dist", ".", "PKG_INFO", ")", ":", "line", "=", "lin...	32.722222	0.0033
def main(): """Executed on run""" args = parse_args() if args.version: from .__init__ import __version__, __release_date__ print('elkme %s (release date %s)' % (__version__, __release_date__)) print('(c) 2015-2017 46elks AB <hello@46elks.com>') print(small_elk) exit(...	[ "def", "main", "(", ")", ":", "args", "=", "parse_args", "(", ")", "if", "args", ".", "version", ":", "from", ".", "__init__", "import", "__version__", ",", "__release_date__", "print", "(", "'elkme %s (release date %s)'", "%", "(", "__version__", ",", "__re...	28.434783	0.006652
def movie(self, cycles, plotstyle='',movname='',fps=12,**kwargs): from matplotlib import animation ''' Make an interactive movie in the matplotlib window for a number of different plot types: Plot types ---------- 'iso_abund' : abundance distr...	[ "def", "movie", "(", "self", ",", "cycles", ",", "plotstyle", "=", "''", ",", "movname", "=", "''", ",", "fps", "=", "12", ",", "", "", "kwargs", ")", ":", "from", "matplotlib", "import", "animation", "modelself", "=", "self", "supported_styles", "="...	45.985577	0.013508
def schedule(identifier, kwargs): '''Schedule a harvest job to run periodically''' source = actions.schedule(identifier, kwargs) msg = 'Scheduled {source.name} with the following crontab: {cron}' log.info(msg.format(source=source, cron=source.periodic_task.crontab))	[ "def", "schedule", "(", "identifier", ",", "", "", "kwargs", ")", ":", "source", "=", "actions", ".", "schedule", "(", "identifier", ",", "", "", "kwargs", ")", "msg", "=", "'Scheduled {source.name} with the following crontab: {cron}'", "log", ".", "info", ...	56.4	0.003497
def decode_lazy(rlp, sedes=None, **sedes_kwargs): """Decode an RLP encoded object in a lazy fashion. If the encoded object is a bytestring, this function acts similar to :func:`rlp.decode`. If it is a list however, a :class:`LazyList` is returned instead. This object will decode the string lazily, avoi...	[ "def", "decode_lazy", "(", "rlp", ",", "sedes", "=", "None", ",", "", "", "sedes_kwargs", ")", ":", "item", ",", "end", "=", "consume_item_lazy", "(", "rlp", ",", "0", ")", "if", "end", "!=", "len", "(", "rlp", ")", ":", "raise", "DecodingError", ...	46.5	0.001859
def _build_tree_structure(cls): """ Build an in-memory representation of the item tree, trying to keep database accesses down to a minimum. The returned dictionary looks like this (as json dump): {"6": [7, 8, 10] "7": [12], "8": [], ... } """ all_node...	[ "def", "_build_tree_structure", "(", "cls", ")", ":", "all_nodes", "=", "{", "}", "for", "p_id", ",", "parent_id", "in", "cls", ".", "objects", ".", "order_by", "(", "cls", ".", "_mptt_meta", ".", "tree_id_attr", ",", "cls", ".", "_mptt_meta", ".", "left...	30.222222	0.003563
def GET_subdomain_ops(self, path_info, txid): """ Get all subdomain operations processed in a given transaction. Returns the list of subdomains on success (can be empty) Returns 502 on failure to get subdomains """ blockstackd_url = get_blockstackd_url() subdomain...	[ "def", "GET_subdomain_ops", "(", "self", ",", "path_info", ",", "txid", ")", ":", "blockstackd_url", "=", "get_blockstackd_url", "(", ")", "subdomain_ops", "=", "None", "try", ":", "subdomain_ops", "=", "blockstackd_client", ".", "get_subdomain_ops_at_txid", "(", ...	50	0.006543
def _bookToDF(b): '''internal''' quote = b.get('quote', []) asks = b.get('asks', []) bids = b.get('bids', []) trades = b.get('trades', []) df1 = pd.io.json.json_normalize(quote) df1['type'] = 'quote' df2 = pd.io.json.json_normalize(asks) df2['symbol'] = quote['symbol'] df2['typ...	[ "def", "_bookToDF", "(", "b", ")", ":", "quote", "=", "b", ".", "get", "(", "'quote'", ",", "[", "]", ")", "asks", "=", "b", ".", "get", "(", "'asks'", ",", "[", "]", ")", "bids", "=", "b", ".", "get", "(", "'bids'", ",", "[", "]", ")", "...	24.16	0.001592
def get_precision(self): """\ :returns: the ratio part of the dominant label for each unit. :rtype: 2D :class:`numpy.ndarray` """ assert self.classifier is not None, 'not calibrated' arr = np.zeros((self._som.nrows, self._som.ncols)) for ij, (lbl, p) in self.class...	[ "def", "get_precision", "(", "self", ")", ":", "assert", "self", ".", "classifier", "is", "not", "None", ",", "'not calibrated'", "arr", "=", "np", ".", "zeros", "(", "(", "self", ".", "_som", ".", "nrows", ",", "self", ".", "_som", ".", "ncols", ")"...	36.8	0.005305
def clean(self): """ Clean fields that depend on each other. In this case, the form can be used to link single user or bulk link multiple users. These are mutually exclusive modes, so this method checks that only one field is passed. """ cleaned_data = super(ManageLearne...	[ "def", "clean", "(", "self", ")", ":", "cleaned_data", "=", "super", "(", "ManageLearnersForm", ",", "self", ")", ".", "clean", "(", ")", "# Here we take values from `data` (and not `cleaned_data`) as we need raw values - field clean methods", "# might \"invalidate\" the value ...	41.685714	0.004019
def setbridgeprio(self, prio): """ Set bridge priority value. """ _runshell([brctlexe, 'setbridgeprio', self.name, str(prio)], "Could not set bridge priority in %s." % self.name)	[ "def", "setbridgeprio", "(", "self", ",", "prio", ")", ":", "_runshell", "(", "[", "brctlexe", ",", "'setbridgeprio'", ",", "self", ".", "name", ",", "str", "(", "prio", ")", "]", ",", "\"Could not set bridge priority in %s.\"", "%", "self", ".", "name", "...	50.75	0.014563
def get_long_description(): """ Strip the content index from the long description. """ import codecs with codecs.open('README.rst', encoding='UTF-8') as f: readme = [line for line in f if not line.startswith('.. contents::')] return ''.join(readme)	[ "def", "get_long_description", "(", ")", ":", "import", "codecs", "with", "codecs", ".", "open", "(", "'README.rst'", ",", "encoding", "=", "'UTF-8'", ")", "as", "f", ":", "readme", "=", "[", "line", "for", "line", "in", "f", "if", "not", "line", ".", ...	34.75	0.007018
def get_query_tables(query): """ :type query str :rtype: list[str] """ tables = [] last_keyword = None last_token = None table_syntax_keywords = [ # SELECT queries 'FROM', 'WHERE', 'JOIN', 'INNER JOIN', 'LEFT JOIN', 'RIGHT JOIN', 'ON', # INSERT queries 'I...	[ "def", "get_query_tables", "(", "query", ")", ":", "tables", "=", "[", "]", "last_keyword", "=", "None", "last_token", "=", "None", "table_syntax_keywords", "=", "[", "# SELECT queries", "'FROM'", ",", "'WHERE'", ",", "'JOIN'", ",", "'INNER JOIN'", ",", "'LEFT...	41.904762	0.002591
def CurrentNode(self): """Hacking interface allowing to get the xmlNodePtr correponding to the current node being accessed by the xmlTextReader. This is dangerous because the underlying node may be destroyed on the next Reads. """ ret = libxml2mod.xmlTextReaderCurrentNode(...	[ "def", "CurrentNode", "(", "self", ")", ":", "ret", "=", "libxml2mod", ".", "xmlTextReaderCurrentNode", "(", "self", ".", "_o", ")", "if", "ret", "is", "None", ":", "raise", "treeError", "(", "'xmlTextReaderCurrentNode() failed'", ")", "__tmp", "=", "xmlNode",...	50.111111	0.008715
def _mouseDown(x, y, button): """Send the mouse down event to Windows by calling the mouse_event() win32 function. Args: x (int): The x position of the mouse event. y (int): The y position of the mouse event. button (str): The mouse button, either 'left', 'middle', or 'right' Returns...	[ "def", "_mouseDown", "(", "x", ",", "y", ",", "button", ")", ":", "if", "button", "==", "'left'", ":", "try", ":", "_sendMouseEvent", "(", "MOUSEEVENTF_LEFTDOWN", ",", "x", ",", "y", ")", "except", "(", "PermissionError", ",", "OSError", ")", ":", "# T...	41.551724	0.005677
def N(u,i,p,knots): """Compute Spline Basis Evaluates the spline basis of order p defined by knots at knot i and point u. """ if p == 0: if knots[i] < u and u <=knots[i+1]: return 1.0 else: return 0.0 else: try: k = (( float((u-kn...	[ "def", "N", "(", "u", ",", "i", ",", "p", ",", "knots", ")", ":", "if", "p", "==", "0", ":", "if", "knots", "[", "i", "]", "<", "u", "and", "u", "<=", "knots", "[", "i", "+", "1", "]", ":", "return", "1.0", "else", ":", "return", "0.0", ...	28.434783	0.032544
def commit(self, force=False): """Commit data to couchdb Compared to threshold (unless forced) then sends data to couch """ self.log.debug('Bulk commit requested') size = sys.getsizeof(self.docs) self.log.debug('Size of docs in KB: %d', size) if size > self.comm...	[ "def", "commit", "(", "self", ",", "force", "=", "False", ")", ":", "self", ".", "log", ".", "debug", "(", "'Bulk commit requested'", ")", "size", "=", "sys", ".", "getsizeof", "(", "self", ".", "docs", ")", "self", ".", "log", ".", "debug", "(", "...	35.461538	0.004228
def locate(self, point): r"""Find a point on the current curve. Solves for :math:`s` in :math:`B(s) = p`. This method acts as a (partial) inverse to :meth:`evaluate`. .. note:: A unique solution is only guaranteed if the current curve has no self-intersections. ...	[ "def", "locate", "(", "self", ",", "point", ")", ":", "if", "point", ".", "shape", "!=", "(", "self", ".", "_dimension", ",", "1", ")", ":", "point_dimensions", "=", "\" x \"", ".", "join", "(", "str", "(", "dimension", ")", "for", "dimension", "in",...	31.902778	0.000845
def getPoly(rCut, nMax): """Used to calculate discrete vectors for the polynomial basis functions. Args: rCut(float): Radial cutoff nMax(int): Number of polynomial radial functions """ rCutVeryHard = rCut+5.0 rx = 0.5rCutVeryHard(x + 1) basisFunctions = [] for i in range(...	[ "def", "getPoly", "(", "rCut", ",", "nMax", ")", ":", "rCutVeryHard", "=", "rCut", "+", "5.0", "rx", "=", "0.5", "", "rCutVeryHard", "", "(", "x", "+", "1", ")", "basisFunctions", "=", "[", "]", "for", "i", "in", "range", "(", "1", ",", "nMax",...	36.55	0.001999
def high_cli(repo_name, login, with_blog, as_list, role): """Extract mails from stargazers, collaborators and people involved with issues of given repository. """ passw = getpass.getpass() github = gh_login(login, passw) repo = github.repository(login, repo_name) role = [ROLES[k] for k in ro...	[ "def", "high_cli", "(", "repo_name", ",", "login", ",", "with_blog", ",", "as_list", ",", "role", ")", ":", "passw", "=", "getpass", ".", "getpass", "(", ")", "github", "=", "gh_login", "(", "login", ",", "passw", ")", "repo", "=", "github", ".", "re...	31.526316	0.003241
def from_parameters3(cls, lengths, angles): """Construct a 3D unit cell with the given parameters The a vector is always parallel with the x-axis and they point in the same direction. The b vector is always in the xy plane and points towards the positive y-direction. The c vect...	[ "def", "from_parameters3", "(", "cls", ",", "lengths", ",", "angles", ")", ":", "for", "length", "in", "lengths", ":", "if", "length", "<=", "0", ":", "raise", "ValueError", "(", "\"The length parameters must be strictly positive.\"", ")", "for", "angle", "in", ...	41.880952	0.003333
def google(self): """Gets the tile in the Google format, converted from TMS""" tms_x, tms_y = self.tms return tms_x, (2 ** self.zoom - 1) - tms_y	[ "def", "google", "(", "self", ")", ":", "tms_x", ",", "tms_y", "=", "self", ".", "tms", "return", "tms_x", ",", "(", "2", "**", "self", ".", "zoom", "-", "1", ")", "-", "tms_y" ]	41.5	0.011834
def find_l50(contig_lengths_dict, genome_length_dict): """ Calculate the L50 for each strain. L50 is defined as the number of contigs required to achieve the N50 :param contig_lengths_dict: dictionary of strain name: reverse-sorted list of all contig lengths :param genome_length_dict: dictionary of stra...	[ "def", "find_l50", "(", "contig_lengths_dict", ",", "genome_length_dict", ")", ":", "# Initialise the dictionary", "l50_dict", "=", "dict", "(", ")", "for", "file_name", ",", "contig_lengths", "in", "contig_lengths_dict", ".", "items", "(", ")", ":", "currentlength"...	52.045455	0.005146
def check_response_code(resp): """ check if query quota has been surpassed or other errors occured :param resp: json response :return: """ if resp["status"] == "OK" or resp["status"] == "ZERO_RESULTS": return if resp["status"] == "REQUEST_DENIED": raise Exception("Google Pla...	[ "def", "check_response_code", "(", "resp", ")", ":", "if", "resp", "[", "\"status\"", "]", "==", "\"OK\"", "or", "resp", "[", "\"status\"", "]", "==", "\"ZERO_RESULTS\"", ":", "return", "if", "resp", "[", "\"status\"", "]", "==", "\"REQUEST_DENIED\"", ":", ...	43.192308	0.004355
def create_database(self, instance, body, project_id=None): """ Creates a new database inside a Cloud SQL instance. :param instance: Database instance ID. This does not include the project ID. :type instance: str :param body: The request body, as described in https:/...	[ "def", "create_database", "(", "self", ",", "instance", ",", "body", ",", "project_id", "=", "None", ")", ":", "response", "=", "self", ".", "get_conn", "(", ")", ".", "databases", "(", ")", ".", "insert", "(", "project", "=", "project_id", ",", "insta...	46.318182	0.004808
def spdhg_generic(x, f, g, A, tau, sigma, niter, *kwargs): r"""Computes a saddle point with a stochastic PDHG. This means, a solution (x, y), y = (y_1, ..., y_n) such that (x, y) in arg min_x max_y sum_i=1^n <y_i, A_i> - f*[i](y_i) + g(x) where g : X -> IR_infty and f[i] : Y[i] -> IR_infty ar...	[ "def", "spdhg_generic", "(", "x", ",", "f", ",", "g", ",", "A", ",", "tau", ",", "sigma", ",", "niter", ",", "", "", "kwargs", ")", ":", "# Callback object", "callback", "=", "kwargs", ".", "pop", "(", "'callback'", ",", "None", ")", "if", "callb...	32.88024	0.000177
def get_abstract(doi): """Get the abstract text of an article from Elsevier given a doi.""" xml_string = download_article(doi) if xml_string is None: return None assert isinstance(xml_string, str) xml_tree = ET.XML(xml_string.encode('utf-8'), parser=UTB()) if xml_tree is None: re...	[ "def", "get_abstract", "(", "doi", ")", ":", "xml_string", "=", "download_article", "(", "doi", ")", "if", "xml_string", "is", "None", ":", "return", "None", "assert", "isinstance", "(", "xml_string", ",", "str", ")", "xml_tree", "=", "ET", ".", "XML", "...	37.538462	0.002
def generateSortedChildListString(self, stream, sectionTitle, lst): ''' Helper method for :func:`~exhale.graph.ExhaleRoot.generateNamespaceChildrenString`. Used to build up a continuous string with all of the children separated out into titled sections. This generates a new titl...	[ "def", "generateSortedChildListString", "(", "self", ",", "stream", ",", "sectionTitle", ",", "lst", ")", ":", "if", "lst", ":", "lst", ".", "sort", "(", ")", "stream", ".", "write", "(", "textwrap", ".", "dedent", "(", "'''\n\n {heading}\n ...	36.102564	0.005533
def run(self, data, train_epochs=1000, test_epochs=1000, verbose=None, idx=0, lr=0.01, **kwargs): """Run the CGNN on a given graph.""" verbose = SETTINGS.get_default(verbose=verbose) optim = th.optim.Adam(self.parameters(), lr=lr) self.score.zero_() with trange(train_...	[ "def", "run", "(", "self", ",", "data", ",", "train_epochs", "=", "1000", ",", "test_epochs", "=", "1000", ",", "verbose", "=", "None", ",", "idx", "=", "0", ",", "lr", "=", "0.01", ",", "", "", "kwargs", ")", ":", "verbose", "=", "SETTINGS", "...	43.684211	0.003538
def proj_list(args): '''Retrieve the list of billing projects accessible to the caller/user, and show the level of access granted for each (e.g. Owner, User, ...)''' projects = fapi.list_billing_projects() fapi._check_response_code(projects, 200) projects = sorted(projects.json(), key=lambda d: d...	[ "def", "proj_list", "(", "args", ")", ":", "projects", "=", "fapi", ".", "list_billing_projects", "(", ")", "fapi", ".", "_check_response_code", "(", "projects", ",", "200", ")", "projects", "=", "sorted", "(", "projects", ".", "json", "(", ")", ",", "ke...	57.888889	0.003781
def run(self): """ Read lines while keep_reading is True. Calls process_dut for each received line. :return: Nothing """ self.keep_reading = True while self.keep_reading: line = self._readline() if line: self.input_queue.appendleft...	[ "def", "run", "(", "self", ")", ":", "self", ".", "keep_reading", "=", "True", "while", "self", ".", "keep_reading", ":", "line", "=", "self", ".", "_readline", "(", ")", "if", "line", ":", "self", ".", "input_queue", ".", "appendleft", "(", "line", ...	29.416667	0.008242
def object_patch_add_link(self, root, name, ref, create=False, **kwargs): """Creates a new merkledag object based on an existing one. The new object will have a link to the provided object. .. code-block:: python >>> c.object_patch_add_link( ... 'QmR79zQQj2aDfnrNgc...	[ "def", "object_patch_add_link", "(", "self", ",", "root", ",", "name", ",", "ref", ",", "create", "=", "False", ",", "", "", "kwargs", ")", ":", "kwargs", ".", "setdefault", "(", "\"opts\"", ",", "{", "\"create\"", ":", "create", "}", ")", "args", ...	32.441176	0.001761
def Norm2(self): """ Returns the L_2 (Euclidean) norm of self. """ sum = self.x * self.x + self.y * self.y + self.z * self.z return math.sqrt(float(sum))	[ "def", "Norm2", "(", "self", ")", ":", "sum", "=", "self", ".", "x", "", "self", ".", "x", "+", "self", ".", "y", "", "self", ".", "y", "+", "self", ".", "z", "*", "self", ".", "z", "return", "math", ".", "sqrt", "(", "float", "(", "sum",...	28	0.00578
def _resolve_image(ret, image, client_timeout): ''' Resolve the image ID and pull the image if necessary ''' image_id = __salt__['docker.resolve_image_id'](image) if image_id is False: if not __opts__['test']: # Image not pulled locally, so try pulling it try: ...	[ "def", "_resolve_image", "(", "ret", ",", "image", ",", "client_timeout", ")", ":", "image_id", "=", "__salt__", "[", "'docker.resolve_image_id'", "]", "(", "image", ")", "if", "image_id", "is", "False", ":", "if", "not", "__opts__", "[", "'test'", "]", ":...	38.862069	0.000866
def register_forward_pre_hook(self, hook): r"""Registers a forward pre-hook on the block. The hook function is called immediately before :func:`forward`. It should not modify the input or output. Parameters ---------- hook : callable The forward hook functio...	[ "def", "register_forward_pre_hook", "(", "self", ",", "hook", ")", ":", "handle", "=", "HookHandle", "(", ")", "handle", ".", "attach", "(", "self", ".", "_forward_pre_hooks", ",", "hook", ")", "return", "handle" ]	29.888889	0.003604
def calc_and_store_post_estimation_results(results_dict, estimator): """ Calculates and stores post-estimation results that require the use of the systematic utility transformation functions or the various derivative functions. Note that this function is only v...	[ "def", "calc_and_store_post_estimation_results", "(", "results_dict", ",", "estimator", ")", ":", "# Store the final log-likelihood", "final_log_likelihood", "=", "-", "1", "*", "results_dict", "[", "\"fun\"", "]", "results_dict", "[", "\"final_log_likelihood\"", "]", "="...	37.326733	0.000258
def insertFile(self, businput, qInserts=False): """ This method supports bulk insert of files performing other operations such as setting Block and Dataset parentages, setting mapping between OutputConfigModules and File(s) etc. :param qInserts: True means that inserts will be q...	[ "def", "insertFile", "(", "self", ",", "businput", ",", "qInserts", "=", "False", ")", ":", "# We do not want to go be beyond 10 files at a time", "# If user wants to insert over 10 files in one shot, we run into risks of locking the database", "# tables for longer time, and in case of e...	56.518939	0.010406
def get_resource(self, resource_id): """Gets the ``Resource`` specified by its ``Id``. In plenary mode, the exact ``Id`` is found or a ``NotFound`` results. Otherwise, the returned ``Resource`` may have a different ``Id`` than requested, such as the case where a duplicate ``Id``...	[ "def", "get_resource", "(", "self", ",", "resource_id", ")", ":", "# Implemented from template for", "# osid.resource.ResourceLookupSession.get_resource", "# NOTE: This implementation currently ignores plenary view", "collection", "=", "JSONClientValidated", "(", "'resource'", ",", ...	51	0.002654
def configure_retrieve(self, ns, definition): """ Register a retrieve endpoint. The definition's func should be a retrieve function, which must: - accept kwargs for path data - return an item or falsey :param ns: the namespace :param definition: the endpoint def...	[ "def", "configure_retrieve", "(", "self", ",", "ns", ",", "definition", ")", ":", "request_schema", "=", "definition", ".", "request_schema", "or", "Schema", "(", ")", "@", "self", ".", "add_route", "(", "ns", ".", "instance_path", ",", "Operation", ".", "...	37.96875	0.00321
def eye(n, d=None): """ Creates an identity TT-matrix""" c = _matrix.matrix() c.tt = _vector.vector() if d is None: n0 = _np.asanyarray(n, dtype=_np.int32) c.tt.d = n0.size else: n0 = _np.asanyarray([n] * d, dtype=_np.int32) c.tt.d = d c.n = n0.copy() c.m = n0...	[ "def", "eye", "(", "n", ",", "d", "=", "None", ")", ":", "c", "=", "_matrix", ".", "matrix", "(", ")", "c", ".", "tt", "=", "_vector", ".", "vector", "(", ")", "if", "d", "is", "None", ":", "n0", "=", "_np", ".", "asanyarray", "(", "n", ","...	24.64	0.004688
def _get_edge_date(self, date_field, sort): ''' This method is used to get start and end dates for the collection. ''' return self._source.query(self._source_coll, { 'q':':', 'rows':1, 'fq':'+{}:*'.format(date_field), ...	[ "def", "_get_edge_date", "(", "self", ",", "date_field", ",", "sort", ")", ":", "return", "self", ".", "_source", ".", "query", "(", "self", ".", "_source_coll", ",", "{", "'q'", ":", "':'", ",", "'rows'", ":", "1", ",", "'fq'", ":", "'+{}:*'", "."...	41.888889	0.015584
def device(self): """returns the device which owns the given stream""" splitted_path = self.path.split("/") return Device(self.db, splitted_path[0] + "/" + splitted_path[1])	[ "def", "device", "(", "self", ")", ":", "splitted_path", "=", "self", ".", "path", ".", "split", "(", "\"/\"", ")", "return", "Device", "(", "self", ".", "db", ",", "splitted_path", "[", "0", "]", "+", "\"/\"", "+", "splitted_path", "[", "1", "]", ...	35.833333	0.009091
def is_mod_class(mod, cls): """Checks if a class in a module was declared in that module. Args: mod: the module cls: the class """ return inspect.isclass(cls) and inspect.getmodule(cls) == mod	[ "def", "is_mod_class", "(", "mod", ",", "cls", ")", ":", "return", "inspect", ".", "isclass", "(", "cls", ")", "and", "inspect", ".", "getmodule", "(", "cls", ")", "==", "mod" ]	27.25	0.004444
def check_declared(self, node): """update the state of this Identifiers with the undeclared and declared identifiers of the given node.""" for ident in node.undeclared_identifiers(): if ident != 'context' and\ ident not in self.declared.union(self.locally_dec...	[ "def", "check_declared", "(", "self", ",", "node", ")", ":", "for", "ident", "in", "node", ".", "undeclared_identifiers", "(", ")", ":", "if", "ident", "!=", "'context'", "and", "ident", "not", "in", "self", ".", "declared", ".", "union", "(", "self", ...	45.6	0.004301
def search_stack_for_var(varname, verbose=util_arg.NOT_QUIET): """ Finds a varable (local or global) somewhere in the stack and returns the value Args: varname (str): variable name Returns: None if varname is not found else its value """ curr_frame = inspect.currentframe() ...	[ "def", "search_stack_for_var", "(", "varname", ",", "verbose", "=", "util_arg", ".", "NOT_QUIET", ")", ":", "curr_frame", "=", "inspect", ".", "currentframe", "(", ")", "if", "verbose", ":", "print", "(", "' * Searching parent frames for: '", "+", "six", ".", ...	36.178571	0.002885
def principals(geom, masses, on_tol=_DEF.ORTHONORM_TOL): """Principal axes and moments of inertia for the indicated geometry. Calculated by :func:`scipy.linalg.eigh`, since the moment of inertia tensor is symmetric (real-Hermitian) by construction. More convenient to compute both the axes and moments ...	[ "def", "principals", "(", "geom", ",", "masses", ",", "on_tol", "=", "_DEF", ".", "ORTHONORM_TOL", ")", ":", "# Imports", "import", "numpy", "as", "np", "from", "scipy", "import", "linalg", "as", "spla", "from", ".", ".", "const", "import", "PRM", ",", ...	39.753036	0.009538
def _get_types(type_): """ Gathers all types within the ``TYPE_MAPPINGS`` for a specific ``Types`` value. :param Types type_: The type to retrieve :return: All types within the ``TYPE_MAPPINGS`` :rtype: list """ return list( itertools.chain.from_iterable( map(lambda x: TYPE...	[ "def", "_get_types", "(", "type_", ")", ":", "return", "list", "(", "itertools", ".", "chain", ".", "from_iterable", "(", "map", "(", "lambda", "x", ":", "TYPE_MAPPINGS", "[", "x", "]", ".", "get", "(", "type_", ",", "[", "]", ")", ",", "TYPE_MAPPING...	28.230769	0.005277

def disttar(target, source, env): """tar archive builder""" import tarfile env_dict = env.Dictionary() if env_dict.get("DISTTAR_FORMAT") in ["gz", "bz2"]: tar_format = env_dict["DISTTAR_FORMAT"] else: tar_format = "" # split the target ...

[ "def", "disttar", "(", "target", ",", "source", ",", "env", ")", ":", "import", "tarfile", "env_dict", "=", "env", ".", "Dictionary", "(", ")", "if", "env_dict", ".", "get", "(", "\"DISTTAR_FORMAT\"", ")", "in", "[", "\"gz\"", ",", "\"bz2\"", "]", ":",...

34.257143

0.008921

def discard_config(self): """Discard changes (rollback 0).""" self.device.cu.rollback(rb_id=0) if not self.config_lock: self._unlock()

[ "def", "discard_config", "(", "self", ")", ":", "self", ".", "device", ".", "cu", ".", "rollback", "(", "rb_id", "=", "0", ")", "if", "not", "self", ".", "config_lock", ":", "self", ".", "_unlock", "(", ")" ]

33.2

0.011765

def start(self, max_value=None, init=True): '''Starts measuring time, and prints the bar at 0%. It returns self so you can use it like this: Args: max_value (int): The maximum value of the progressbar reinit (bool): Initialize the progressbar, this is useful if you ...

[ "def", "start", "(", "self", ",", "max_value", "=", "None", ",", "init", "=", "True", ")", ":", "if", "init", ":", "self", ".", "init", "(", ")", "# Prevent multiple starts", "if", "self", ".", "start_time", "is", "not", "None", ":", "# pragma: no cover"...

32.753846

0.000912

def append(self, data): """Append data to a file.""" data_length = len(data) if self._size + data_length > self._flush_size: self.flush() if not self._exclusive and data_length > _FILE_POOL_MAX_SIZE: raise errors.Error( "Too big input %s (%s)." % (data_length, _FILE_POOL_MAX_SIZE...

[ "def", "append", "(", "self", ",", "data", ")", ":", "data_length", "=", "len", "(", "data", ")", "if", "self", ".", "_size", "+", "data_length", ">", "self", ".", "_flush_size", ":", "self", ".", "flush", "(", ")", "if", "not", "self", ".", "_excl...

29.333333

0.015419

def time_average(rho, t): r"""Return a time-averaged density matrix (using trapezium rule). We test a basic two-level system. >>> import numpy as np >>> from scipy.constants import physical_constants >>> from sympy import Matrix, symbols >>> from fast.electric_field import electric_field_ampli...

[ "def", "time_average", "(", "rho", ",", "t", ")", ":", "T", "=", "t", "[", "-", "1", "]", "-", "t", "[", "0", "]", "dt", "=", "t", "[", "1", "]", "-", "t", "[", "0", "]", "rhoav", "=", "np", ".", "sum", "(", "rho", "[", "1", ":", "-",...

33.54386

0.000508

def _recv_loop(self): """Sits in tight loop collecting data received from peer and processing it. """ required_len = BGP_MIN_MSG_LEN conn_lost_reason = "Connection lost as protocol is no longer active" try: while True: next_bytes = self._socket...

[ "def", "_recv_loop", "(", "self", ")", ":", "required_len", "=", "BGP_MIN_MSG_LEN", "conn_lost_reason", "=", "\"Connection lost as protocol is no longer active\"", "try", ":", "while", "True", ":", "next_bytes", "=", "self", ".", "_socket", ".", "recv", "(", "requir...

40.5

0.002193

def list(self, **params): """ Retrieve all lead unqualified reasons Returns all lead unqualified reasons available to the user according to the parameters provided :calls: ``get /lead_unqualified_reasons`` :param dict params: (optional) Search options. :return: List of ...

[ "def", "list", "(", "self", ",", "*", "*", "params", ")", ":", "_", ",", "_", ",", "lead_unqualified_reasons", "=", "self", ".", "http_client", ".", "get", "(", "\"/lead_unqualified_reasons\"", ",", "params", "=", "params", ")", "return", "lead_unqualified_r...

42.142857

0.008292

def set_local(self, key=None, value=None, data=None, **kwdata): """ Locally store some data associated with this conversation. Data can be passed in either as a single dict, or as key-word args. For example, if you need to store the previous value of a remote field to determine...

[ "def", "set_local", "(", "self", ",", "key", "=", "None", ",", "value", "=", "None", ",", "data", "=", "None", ",", "*", "*", "kwdata", ")", ":", "if", "data", "is", "None", ":", "data", "=", "{", "}", "if", "key", "is", "not", "None", ":", "...

39.870968

0.00158

def reset_params(self): """(Re)set all parameters.""" units = [self.input_units] units += [self.hidden_units] * self.num_hidden units += [self.output_units] sequence = [] for u0, u1 in zip(units, units[1:]): sequence.append(nn.Linear(u0, u1)) sequ...

[ "def", "reset_params", "(", "self", ")", ":", "units", "=", "[", "self", ".", "input_units", "]", "units", "+=", "[", "self", ".", "hidden_units", "]", "*", "self", ".", "num_hidden", "units", "+=", "[", "self", ".", "output_units", "]", "sequence", "=...

32.176471

0.003552

def find_page_of_state_m(self, state_m): """Return the identifier and page of a given state model :param state_m: The state model to be searched :return: page containing the state and the state_identifier """ for state_identifier, page_info in list(self.tabs.items()): ...

[ "def", "find_page_of_state_m", "(", "self", ",", "state_m", ")", ":", "for", "state_identifier", ",", "page_info", "in", "list", "(", "self", ".", "tabs", ".", "items", "(", ")", ")", ":", "if", "page_info", "[", "'state_m'", "]", "is", "state_m", ":", ...

43.3

0.004525

def get_model(self, model_name): """ TODO: Need to validate model name has 2x '.' chars """ klass = None try: module_name, class_name = model_name.rsplit('.', 1) mod = __import__(module_name, fromlist=[class_name]) klass = getattr(mod, class_na...

[ "def", "get_model", "(", "self", ",", "model_name", ")", ":", "klass", "=", "None", "try", ":", "module_name", ",", "class_name", "=", "model_name", ".", "rsplit", "(", "'.'", ",", "1", ")", "mod", "=", "__import__", "(", "module_name", ",", "fromlist", ...

33.076923

0.004525

def to_bytes(s): """ 将字符串转换成字节数组 :param s: 要转换成字节数组的字符串 :return: 转换成字节数组的字符串 """ if bytes != str: if type(s) == str: return s.encode('utf-8') return s

[ "def", "to_bytes", "(", "s", ")", ":", "if", "bytes", "!=", "str", ":", "if", "type", "(", "s", ")", "==", "str", ":", "return", "s", ".", "encode", "(", "'utf-8'", ")", "return", "s" ]

18.9

0.005051

def _init(self): """Read the line number.""" self._line_number = next_line( self._communication.last_requested_line_number, self._file.read(1)[0])

[ "def", "_init", "(", "self", ")", ":", "self", ".", "_line_number", "=", "next_line", "(", "self", ".", "_communication", ".", "last_requested_line_number", ",", "self", ".", "_file", ".", "read", "(", "1", ")", "[", "0", "]", ")" ]

36.4

0.010753

def log_the_survey_settings( log, pathToYamlFile): """ *Create a MD log of the survey settings* **Key Arguments:** - ``log`` -- logger - ``pathToYamlFile`` -- yaml results file **Return:** - None """ ################ > IMPORTS ################ ## STA...

[ "def", "log_the_survey_settings", "(", "log", ",", "pathToYamlFile", ")", ":", "################ > IMPORTS ################", "## STANDARD LIB ##", "## THIRD PARTY ##", "import", "yaml", "## LOCAL APPLICATION ##", "from", "datetime", "import", "datetime", ",", "date", ",", ...

42.777108

0.003441

def connection_exists(self, from_obj, to_obj): """ Returns ``True`` if a connection between the given objects exists, else ``False``. """ self._validate_ctypes(from_obj, to_obj) return self.connections.filter(from_pk=from_obj.pk, to_pk=to_obj.pk).exists()

[ "def", "connection_exists", "(", "self", ",", "from_obj", ",", "to_obj", ")", ":", "self", ".", "_validate_ctypes", "(", "from_obj", ",", "to_obj", ")", "return", "self", ".", "connections", ".", "filter", "(", "from_pk", "=", "from_obj", ".", "pk", ",", ...

42.428571

0.009901

def setTerms( self, terms ): """ Sets a simple rule list by accepting a list of strings for terms. \ This is a convenience method for the setRules method. :param rules | [<str> term, ..] """ return self.setRules([XQueryRule(term = term) for term in terms])

[ "def", "setTerms", "(", "self", ",", "terms", ")", ":", "return", "self", ".", "setRules", "(", "[", "XQueryRule", "(", "term", "=", "term", ")", "for", "term", "in", "terms", "]", ")" ]

39

0.021944

def response_hook(self, r, **kwargs): """The actual hook handler.""" if r.status_code == 401: # Handle server auth. www_authenticate = r.headers.get('www-authenticate', '').lower() auth_type = _auth_type_from_header(www_authenticate) if auth_type is not N...

[ "def", "response_hook", "(", "self", ",", "r", ",", "*", "*", "kwargs", ")", ":", "if", "r", ".", "status_code", "==", "401", ":", "# Handle server auth.", "www_authenticate", "=", "r", ".", "headers", ".", "get", "(", "'www-authenticate'", ",", "''", ")...

35.322581

0.001778

def _str_extract_noexpand(arr, pat, flags=0): """ Find groups in each string in the Series using passed regular expression. This function is called from str_extract(expand=False), and can return Series, DataFrame, or Index. """ from pandas import DataFrame, Index regex = re.compile(pat...

[ "def", "_str_extract_noexpand", "(", "arr", ",", "pat", ",", "flags", "=", "0", ")", ":", "from", "pandas", "import", "DataFrame", ",", "Index", "regex", "=", "re", ".", "compile", "(", "pat", ",", "flags", "=", "flags", ")", "groups_or_na", "=", "_gro...

35.16129

0.000893

def summary(self): """ A succinct summary of the argument specifier. Unlike the repr, a summary does not have to be complete but must supply the most relevant information about the object to the user. """ print("Items: %s" % len(self)) varying_keys = ', '.join('%r...

[ "def", "summary", "(", "self", ")", ":", "print", "(", "\"Items: %s\"", "%", "len", "(", "self", ")", ")", "varying_keys", "=", "', '", ".", "join", "(", "'%r'", "%", "k", "for", "k", "in", "self", ".", "varying_keys", ")", "print", "(", "\"Varying K...

44.230769

0.006814

def queue(self, blogname, **kwargs): """ Gets posts that are currently in the blog's queue :param limit: an int, the number of posts you want returned :param offset: an int, the post you want to start at, for pagination. :param filter: the post format that you want returned: HTM...

[ "def", "queue", "(", "self", ",", "blogname", ",", "*", "*", "kwargs", ")", ":", "url", "=", "\"/v2/blog/{}/posts/queue\"", ".", "format", "(", "blogname", ")", "return", "self", ".", "send_api_request", "(", "\"get\"", ",", "url", ",", "kwargs", ",", "[...

44.666667

0.005484

def get_reports(): """ Returns energy data from 1960 to 2014 across various factors. """ if False: # If there was a Test version of this method, it would go here. But alas. pass else: rows = _Constants._DATABASE.execute("SELECT data FROM energy".format( hardw...

[ "def", "get_reports", "(", ")", ":", "if", "False", ":", "# If there was a Test version of this method, it would go here. But alas.", "pass", "else", ":", "rows", "=", "_Constants", ".", "_DATABASE", ".", "execute", "(", "\"SELECT data FROM energy\"", ".", "format", "("...

32.333333

0.008016

def comments(self, update=True): """Fetch and return the comments for a single MoreComments object.""" if not self._comments: if self.count == 0: # Handle 'continue this thread' type return self._continue_comments(update) # pylint: disable=W0212 child...

[ "def", "comments", "(", "self", ",", "update", "=", "True", ")", ":", "if", "not", "self", ".", "_comments", ":", "if", "self", ".", "count", "==", "0", ":", "# Handle 'continue this thread' type", "return", "self", ".", "_continue_comments", "(", "update", ...

46

0.001521

def open_upload_stream(self, filename, chunk_size_bytes=None, metadata=None): """Opens a Stream that the application can write the contents of the file to. The user must specify the filename, and can choose to add any additional information in the metadata fie...

[ "def", "open_upload_stream", "(", "self", ",", "filename", ",", "chunk_size_bytes", "=", "None", ",", "metadata", "=", "None", ")", ":", "validate_string", "(", "\"filename\"", ",", "filename", ")", "opts", "=", "{", "\"filename\"", ":", "filename", ",", "\"...

41.95122

0.001705

def ModuleHelp(self, module): """Describe the key flags of a module. Args: module: A module object or a module name (a string). Returns: string describing the key flags of a module. """ helplist = [] self.__RenderOurModuleKeyFlags(module, helplist) return '\n'.join(helplist)

[ "def", "ModuleHelp", "(", "self", ",", "module", ")", ":", "helplist", "=", "[", "]", "self", ".", "__RenderOurModuleKeyFlags", "(", "module", ",", "helplist", ")", "return", "'\\n'", ".", "join", "(", "helplist", ")" ]

25.5

0.003155

def perform_permissions_check(self, user, obj, perms): """ Performs the permission check. """ return self.request.forum_permission_handler.can_edit_post(obj, user)

[ "def", "perform_permissions_check", "(", "self", ",", "user", ",", "obj", ",", "perms", ")", ":", "return", "self", ".", "request", ".", "forum_permission_handler", ".", "can_edit_post", "(", "obj", ",", "user", ")" ]

59

0.011173

def get_poll_option_formset_kwargs(self): """ Returns the keyword arguments for instantiating the poll option formset. """ kwargs = { 'prefix': 'poll', } if self.request.method in ('POST', 'PUT'): kwargs.update({ 'data': self.request.POST, ...

[ "def", "get_poll_option_formset_kwargs", "(", "self", ")", ":", "kwargs", "=", "{", "'prefix'", ":", "'poll'", ",", "}", "if", "self", ".", "request", ".", "method", "in", "(", "'POST'", ",", "'PUT'", ")", ":", "kwargs", ".", "update", "(", "{", "'data...

33.666667

0.006421

def cookie_attr_value_check(attr_name, attr_value): """ Check cookie attribute value for validity. Return True if value is valid :param attr_name: attribute name to check :param attr_value: attribute value to check :return: bool """ attr_value.encode('us-ascii') return WHTTPCookie.cookie_attr_value_compl...

[ "def", "cookie_attr_value_check", "(", "attr_name", ",", "attr_value", ")", ":", "attr_value", ".", "encode", "(", "'us-ascii'", ")", "return", "WHTTPCookie", ".", "cookie_attr_value_compliance", "[", "attr_name", "]", ".", "match", "(", "attr_value", ")", "is", ...

39.777778

0.027322

def __add_min_max_value( parser, basename, default_min, default_max, initial, help_template): """ Generates parser entries for options with a min, max, and default value. Args: parser: the parser to use. basename: the base option name. Gen...

[ "def", "__add_min_max_value", "(", "parser", ",", "basename", ",", "default_min", ",", "default_max", ",", "initial", ",", "help_template", ")", ":", "help_template", "=", "Template", "(", "help_template", ")", "parser", ".", "add", "(", "'--{0}-min'", ".", "f...

29.159091

0.000754

def _AssertIsLocal(path): ''' Checks if a given path is local, raise an exception if not. This is used in filesystem functions that do not support remote operations yet. :param unicode path: :raises NotImplementedForRemotePathError: If the given path is not local ''' from six.move...

[ "def", "_AssertIsLocal", "(", "path", ")", ":", "from", "six", ".", "moves", ".", "urllib", ".", "parse", "import", "urlparse", "if", "not", "_UrlIsLocal", "(", "urlparse", "(", "path", ")", ")", ":", "from", ".", "_exceptions", "import", "NotImplementedFo...

32.6

0.003976

def sonify(annotation, sr=22050, duration=None, **kwargs): '''Sonify a jams annotation through mir_eval Parameters ---------- annotation : jams.Annotation The annotation to sonify sr = : positive number The sampling rate of the output waveform duration : float (optional) ...

[ "def", "sonify", "(", "annotation", ",", "sr", "=", "22050", ",", "duration", "=", "None", ",", "*", "*", "kwargs", ")", ":", "length", "=", "None", "if", "duration", "is", "None", ":", "duration", "=", "annotation", ".", "duration", "if", "duration", ...

29.320755

0.000623

def getPosNew(data): """ get Fixed position """ pos = data.geno['col_header']['pos'][:] chrom= data.geno['col_header']['chrom'][:] n_chroms = chrom.max() pos_new = [] for chrom_i in range(1,n_chroms+1): I = chrom==chrom_i _pos = pos[I] for i in range(1,_pos.shape[...

[ "def", "getPosNew", "(", "data", ")", ":", "pos", "=", "data", ".", "geno", "[", "'col_header'", "]", "[", "'pos'", "]", "[", ":", "]", "chrom", "=", "data", ".", "geno", "[", "'col_header'", "]", "[", "'chrom'", "]", "[", ":", "]", "n_chroms", "...

28

0.01626

def run(self): """Start the collector worker thread. If running in standalone mode, the current thread will wait until the collector thread ends. """ self.collector.start() if self.standalone: self.collector.join()

[ "def", "run", "(", "self", ")", ":", "self", ".", "collector", ".", "start", "(", ")", "if", "self", ".", "standalone", ":", "self", ".", "collector", ".", "join", "(", ")" ]

29.666667

0.007273

def merge(profile, branch, merge_into): """Merge a branch into another branch. Args: profile A profile generated from ``simplygithub.authentication.profile``. Such profiles tell this module (i) the ``repo`` to connect to, and (ii) the ``token`` to connect with. ...

[ "def", "merge", "(", "profile", ",", "branch", ",", "merge_into", ")", ":", "data", "=", "merges", ".", "merge", "(", "profile", ",", "branch", ",", "merge_into", ")", "return", "data" ]

25.818182

0.001698

def handle(self, t_input: inference.TranslatorInput, t_output: inference.TranslatorOutput, t_walltime: float = 0.): """ :param t_input: Translator input. :param t_output: Translator output. :param t_walltime: Total walltime for translation. ...

[ "def", "handle", "(", "self", ",", "t_input", ":", "inference", ".", "TranslatorInput", ",", "t_output", ":", "inference", ".", "TranslatorOutput", ",", "t_walltime", ":", "float", "=", "0.", ")", ":", "self", ".", "stream", ".", "write", "(", "\"%s\\n\"",...

36.727273

0.012077

def _expand_libs_in_apps(specs): """ Expands specs.apps.depends.libs to include any indirectly required libs """ for app_name, app_spec in specs['apps'].iteritems(): if 'depends' in app_spec and 'libs' in app_spec['depends']: app_spec['depends']['libs'] = _get_dependent('libs', app_n...

[ "def", "_expand_libs_in_apps", "(", "specs", ")", ":", "for", "app_name", ",", "app_spec", "in", "specs", "[", "'apps'", "]", ".", "iteritems", "(", ")", ":", "if", "'depends'", "in", "app_spec", "and", "'libs'", "in", "app_spec", "[", "'depends'", "]", ...

47.571429

0.0059

def set_disk_timeout(timeout, power='ac', scheme=None): ''' Set the disk timeout in minutes for the given power scheme Args: timeout (int): The amount of time in minutes before the disk will timeout power (str): Set the value for AC or DC power. Default is ``ac``. V...

[ "def", "set_disk_timeout", "(", "timeout", ",", "power", "=", "'ac'", ",", "scheme", "=", "None", ")", ":", "return", "_set_powercfg_value", "(", "scheme", "=", "scheme", ",", "sub_group", "=", "'SUB_DISK'", ",", "setting_guid", "=", "'DISKIDLE'", ",", "powe...

28.4

0.000851

def find_feasible_flow(self): ''' API: find_feasible_flow(self) Description: Solves feasible flow problem, stores solution in 'flow' attribute or arcs. This method is used to get an initial feasible flow for simplex and cycle canceling algorithms. ...

[ "def", "find_feasible_flow", "(", "self", ")", ":", "# establish a feasible flow in the network, to do this add nodes s and", "# t and solve a max flow problem.", "nl", "=", "self", ".", "get_node_list", "(", ")", "for", "i", "in", "nl", ":", "b_i", "=", "self", ".", ...

41.404255

0.001004

def month_interval(year, month, return_str=False): """ Usage Example:: >>> timewrapper.day_interval(2014, 12) (datetime(2014, 12, 1, 0, 0, 0), datetime(2014, 12, 31, 23, 59, 59)) """ if month == 12: start, end = datetime(year, month, ...

[ "def", "month_interval", "(", "year", ",", "month", ",", "return_str", "=", "False", ")", ":", "if", "month", "==", "12", ":", "start", ",", "end", "=", "datetime", "(", "year", ",", "month", ",", "1", ")", ",", "datetime", "(", "year", "+", "1", ...

34.823529

0.013158

def refresh(self): """ Fetches all current container names from the client, along with their id. """ if not self._client: return current_containers = self._client.containers(all=True) self.clear() for container in current_containers: contai...

[ "def", "refresh", "(", "self", ")", ":", "if", "not", "self", ".", "_client", ":", "return", "current_containers", "=", "self", ".", "_client", ".", "containers", "(", "all", "=", "True", ")", "self", ".", "clear", "(", ")", "for", "container", "in", ...

36.714286

0.005693

def is_all_field_none(self): """ :rtype: bool """ if self._id_ is not None: return False if self._monetary_account_id is not None: return False if self._card_id is not None: return False if self._amount_local is not None: ...

[ "def", "is_all_field_none", "(", "self", ")", ":", "if", "self", ".", "_id_", "is", "not", "None", ":", "return", "False", "if", "self", ".", "_monetary_account_id", "is", "not", "None", ":", "return", "False", "if", "self", ".", "_card_id", "is", "not",...

22.791667

0.000876

def maketrans(fromstr, tostr): """maketrans(frm, to) -> string Return a translation table (a string of 256 bytes long) suitable for use in string.translate. The strings frm and to must be of the same length. """ if len(fromstr) != len(tostr): raise ValueError, "maketrans arguments mus...

[ "def", "maketrans", "(", "fromstr", ",", "tostr", ")", ":", "if", "len", "(", "fromstr", ")", "!=", "len", "(", "tostr", ")", ":", "raise", "ValueError", ",", "\"maketrans arguments must have same length\"", "global", "_idmapL", "if", "not", "_idmapL", ":", ...

29.555556

0.003643

def peek(self): '''Return (but do not consume) the next token At the end of input, ``None`` is returned. ''' if self.position >= len(self.tokens): return None return self.tokens[self.position]

[ "def", "peek", "(", "self", ")", ":", "if", "self", ".", "position", ">=", "len", "(", "self", ".", "tokens", ")", ":", "return", "None", "return", "self", ".", "tokens", "[", "self", ".", "position", "]" ]

23.8

0.008097

def _create_header(self): """ Function to create the GroupHeader (GrpHdr) in the CstmrCdtTrfInitn Node """ # Retrieve the node to which we will append the group header. CstmrCdtTrfInitn_node = self._xml.find('CstmrCdtTrfInitn') # Create the header nodes. ...

[ "def", "_create_header", "(", "self", ")", ":", "# Retrieve the node to which we will append the group header.", "CstmrCdtTrfInitn_node", "=", "self", ".", "_xml", ".", "find", "(", "'CstmrCdtTrfInitn'", ")", "# Create the header nodes.", "GrpHdr_node", "=", "ET", ".", "E...

35.9375

0.00254

def write_csv(self, path=None): """Write CSV file. Sorts the sections before calling the superclass write_csv""" # Sort the Sections self.sort_sections(['Root', 'Contacts', 'Documentation', 'References', 'Resources', 'Citations', 'Schema']) # Sort Terms in the root section # ...

[ "def", "write_csv", "(", "self", ",", "path", "=", "None", ")", ":", "# Sort the Sections", "self", ".", "sort_sections", "(", "[", "'Root'", ",", "'Contacts'", ",", "'Documentation'", ",", "'References'", ",", "'Resources'", ",", "'Citations'", ",", "'Schema'...

29.545455

0.005961

def _identify_heterogeneity_blocks_hmm(in_file, params, work_dir, somatic_info): """Use a HMM to identify blocks of heterogeneity to use for calculating allele frequencies. The goal is to subset the genome to a more reasonable section that contains potential loss of heterogeneity or other allele frequency ...

[ "def", "_identify_heterogeneity_blocks_hmm", "(", "in_file", ",", "params", ",", "work_dir", ",", "somatic_info", ")", ":", "def", "_segment_by_hmm", "(", "chrom", ",", "freqs", ",", "coords", ")", ":", "cur_coords", "=", "[", "]", "for", "j", ",", "state", ...

51.863636

0.005164

def update_record(self, dns_type, name, content, **kwargs): """ Update dns record :param dns_type: :param name: :param content: :param kwargs: :return: """ record = self.get_record(dns_type, name) data = { 'type': dns_type, ...

[ "def", "update_record", "(", "self", ",", "dns_type", ",", "name", ",", "content", ",", "*", "*", "kwargs", ")", ":", "record", "=", "self", ".", "get_record", "(", "dns_type", ",", "name", ")", "data", "=", "{", "'type'", ":", "dns_type", ",", "'nam...

29.928571

0.003468

def _map_arguments(self, args): """Map from the top-level arguments to the arguments provided to the indiviudal links """ data = args.get('data') comp = args.get('comp') library = args.get('library') dry_run = args.get('dry_run', False) self._set_link('sum-rings'...

[ "def", "_map_arguments", "(", "self", ",", "args", ")", ":", "data", "=", "args", ".", "get", "(", "'data'", ")", "comp", "=", "args", ".", "get", "(", "'comp'", ")", "library", "=", "args", ".", "get", "(", "'library'", ")", "dry_run", "=", "args"...

37.086957

0.002286

def print_attr_values( thing, all=False, heading=None, file=None ): ''' Print the attributes of thing which have non-empty values, as a vertical list of "name : value". When all=True, print all attributes even those with empty values. ''' if heading : if isinstance( heading, int ) : ...

[ "def", "print_attr_values", "(", "thing", ",", "all", "=", "False", ",", "heading", "=", "None", ",", "file", "=", "None", ")", ":", "if", "heading", ":", "if", "isinstance", "(", "heading", ",", "int", ")", ":", "# request for default heading", "heading",...

38.428571

0.025393

def wait_while_reachable(self, servers, timeout=60): """wait while all servers be reachable Args: servers - list of servers """ t_start = time.time() while True: try: for server in servers: # TODO: use state code to chec...

[ "def", "wait_while_reachable", "(", "self", ",", "servers", ",", "timeout", "=", "60", ")", ":", "t_start", "=", "time", ".", "time", "(", ")", "while", "True", ":", "try", ":", "for", "server", "in", "servers", ":", "# TODO: use state code to check if serve...

48.2

0.005086

def add_arguments(parser, default_level=logging.INFO): """ Add arguments to an ArgumentParser or OptionParser for purposes of grabbing a logging level. """ adder = ( getattr(parser, 'add_argument', None) or getattr(parser, 'add_option') ) adder( '-l', '--log-level', default=default_level, type=lo...

[ "def", "add_arguments", "(", "parser", ",", "default_level", "=", "logging", ".", "INFO", ")", ":", "adder", "=", "(", "getattr", "(", "parser", ",", "'add_argument'", ",", "None", ")", "or", "getattr", "(", "parser", ",", "'add_option'", ")", ")", "adde...

31

0.031332

def _conn_ready(self, conn): """ There is a nice state diagram at the top of httplib.py. It indicates that once the response headers have been read (which _mexe does before adding the connection to the pool), a response is attached to the connection, and it stays there u...

[ "def", "_conn_ready", "(", "self", ",", "conn", ")", ":", "if", "ON_APP_ENGINE", ":", "# Google App Engine implementation of HTTPConnection doesn't contain", "# _HTTPConnection__response attribute. Moreover, it's not possible", "# to determine if given connection is ready. Reusing connecti...

51.318182

0.002609

def from_(self, selectable): """ Adds a table to the query. This function can only be called once and will raise an AttributeError if called a second time. :param selectable: Type: ``Table``, ``Query``, or ``str`` When a ``str`` is passed, a table with the name...

[ "def", "from_", "(", "self", ",", "selectable", ")", ":", "self", ".", "_from", ".", "append", "(", "Table", "(", "selectable", ")", "if", "isinstance", "(", "selectable", ",", "str", ")", "else", "selectable", ")", "if", "isinstance", "(", "selectable",...

38.24

0.006122

def start_threads(self, n_threads): """ Terminate existing threads and create a new set if the thread number doesn't match the desired number. Required: n_threads: (int) number of threads to spawn Returns: self """ if n_threads == len(self._threads): return self ...

[ "def", "start_threads", "(", "self", ",", "n_threads", ")", ":", "if", "n_threads", "==", "len", "(", "self", ".", "_threads", ")", ":", "return", "self", "# Terminate all previous tasks with the existing", "# event object, then create a new one for the next", "# generati...

25.4

0.010834

def _dist_version_url(self, dist): """ Get version and homepage for a pkg_resources.Distribution :param dist: the pkg_resources.Distribution to get information for :returns: 2-tuple of (version, homepage URL) :rtype: tuple """ ver = str(dist.version) url ...

[ "def", "_dist_version_url", "(", "self", ",", "dist", ")", ":", "ver", "=", "str", "(", "dist", ".", "version", ")", "url", "=", "None", "for", "line", "in", "dist", ".", "get_metadata_lines", "(", "dist", ".", "PKG_INFO", ")", ":", "line", "=", "lin...

32.722222

0.0033

def main(): """Executed on run""" args = parse_args() if args.version: from .__init__ import __version__, __release_date__ print('elkme %s (release date %s)' % (__version__, __release_date__)) print('(c) 2015-2017 46elks AB <hello@46elks.com>') print(small_elk) exit(...

[ "def", "main", "(", ")", ":", "args", "=", "parse_args", "(", ")", "if", "args", ".", "version", ":", "from", ".", "__init__", "import", "__version__", ",", "__release_date__", "print", "(", "'elkme %s (release date %s)'", "%", "(", "__version__", ",", "__re...

28.434783

0.006652

def movie(self, cycles, plotstyle='',movname='',fps=12,**kwargs): from matplotlib import animation ''' Make an interactive movie in the matplotlib window for a number of different plot types: Plot types ---------- 'iso_abund' : abundance distr...

[ "def", "movie", "(", "self", ",", "cycles", ",", "plotstyle", "=", "''", ",", "movname", "=", "''", ",", "fps", "=", "12", ",", "*", "*", "kwargs", ")", ":", "from", "matplotlib", "import", "animation", "modelself", "=", "self", "supported_styles", "="...

45.985577

0.013508

def schedule(identifier, **kwargs): '''Schedule a harvest job to run periodically''' source = actions.schedule(identifier, **kwargs) msg = 'Scheduled {source.name} with the following crontab: {cron}' log.info(msg.format(source=source, cron=source.periodic_task.crontab))

[ "def", "schedule", "(", "identifier", ",", "*", "*", "kwargs", ")", ":", "source", "=", "actions", ".", "schedule", "(", "identifier", ",", "*", "*", "kwargs", ")", "msg", "=", "'Scheduled {source.name} with the following crontab: {cron}'", "log", ".", "info", ...

56.4

0.003497

def decode_lazy(rlp, sedes=None, **sedes_kwargs): """Decode an RLP encoded object in a lazy fashion. If the encoded object is a bytestring, this function acts similar to :func:`rlp.decode`. If it is a list however, a :class:`LazyList` is returned instead. This object will decode the string lazily, avoi...

[ "def", "decode_lazy", "(", "rlp", ",", "sedes", "=", "None", ",", "*", "*", "sedes_kwargs", ")", ":", "item", ",", "end", "=", "consume_item_lazy", "(", "rlp", ",", "0", ")", "if", "end", "!=", "len", "(", "rlp", ")", ":", "raise", "DecodingError", ...

46.5

0.001859

def _build_tree_structure(cls): """ Build an in-memory representation of the item tree, trying to keep database accesses down to a minimum. The returned dictionary looks like this (as json dump): {"6": [7, 8, 10] "7": [12], "8": [], ... } """ all_node...

[ "def", "_build_tree_structure", "(", "cls", ")", ":", "all_nodes", "=", "{", "}", "for", "p_id", ",", "parent_id", "in", "cls", ".", "objects", ".", "order_by", "(", "cls", ".", "_mptt_meta", ".", "tree_id_attr", ",", "cls", ".", "_mptt_meta", ".", "left...

30.222222

0.003563

def GET_subdomain_ops(self, path_info, txid): """ Get all subdomain operations processed in a given transaction. Returns the list of subdomains on success (can be empty) Returns 502 on failure to get subdomains """ blockstackd_url = get_blockstackd_url() subdomain...

[ "def", "GET_subdomain_ops", "(", "self", ",", "path_info", ",", "txid", ")", ":", "blockstackd_url", "=", "get_blockstackd_url", "(", ")", "subdomain_ops", "=", "None", "try", ":", "subdomain_ops", "=", "blockstackd_client", ".", "get_subdomain_ops_at_txid", "(", ...

50

0.006543

def _bookToDF(b): '''internal''' quote = b.get('quote', []) asks = b.get('asks', []) bids = b.get('bids', []) trades = b.get('trades', []) df1 = pd.io.json.json_normalize(quote) df1['type'] = 'quote' df2 = pd.io.json.json_normalize(asks) df2['symbol'] = quote['symbol'] df2['typ...

[ "def", "_bookToDF", "(", "b", ")", ":", "quote", "=", "b", ".", "get", "(", "'quote'", ",", "[", "]", ")", "asks", "=", "b", ".", "get", "(", "'asks'", ",", "[", "]", ")", "bids", "=", "b", ".", "get", "(", "'bids'", ",", "[", "]", ")", "...

24.16

0.001592

def get_precision(self): """\ :returns: the ratio part of the dominant label for each unit. :rtype: 2D :class:`numpy.ndarray` """ assert self.classifier is not None, 'not calibrated' arr = np.zeros((self._som.nrows, self._som.ncols)) for ij, (lbl, p) in self.class...

[ "def", "get_precision", "(", "self", ")", ":", "assert", "self", ".", "classifier", "is", "not", "None", ",", "'not calibrated'", "arr", "=", "np", ".", "zeros", "(", "(", "self", ".", "_som", ".", "nrows", ",", "self", ".", "_som", ".", "ncols", ")"...

36.8

0.005305

def clean(self): """ Clean fields that depend on each other. In this case, the form can be used to link single user or bulk link multiple users. These are mutually exclusive modes, so this method checks that only one field is passed. """ cleaned_data = super(ManageLearne...

[ "def", "clean", "(", "self", ")", ":", "cleaned_data", "=", "super", "(", "ManageLearnersForm", ",", "self", ")", ".", "clean", "(", ")", "# Here we take values from `data` (and not `cleaned_data`) as we need raw values - field clean methods", "# might \"invalidate\" the value ...

41.685714

0.004019

def setbridgeprio(self, prio): """ Set bridge priority value. """ _runshell([brctlexe, 'setbridgeprio', self.name, str(prio)], "Could not set bridge priority in %s." % self.name)

[ "def", "setbridgeprio", "(", "self", ",", "prio", ")", ":", "_runshell", "(", "[", "brctlexe", ",", "'setbridgeprio'", ",", "self", ".", "name", ",", "str", "(", "prio", ")", "]", ",", "\"Could not set bridge priority in %s.\"", "%", "self", ".", "name", "...

50.75

0.014563

def get_long_description(): """ Strip the content index from the long description. """ import codecs with codecs.open('README.rst', encoding='UTF-8') as f: readme = [line for line in f if not line.startswith('.. contents::')] return ''.join(readme)

[ "def", "get_long_description", "(", ")", ":", "import", "codecs", "with", "codecs", ".", "open", "(", "'README.rst'", ",", "encoding", "=", "'UTF-8'", ")", "as", "f", ":", "readme", "=", "[", "line", "for", "line", "in", "f", "if", "not", "line", ".", ...

34.75

0.007018

def get_query_tables(query): """ :type query str :rtype: list[str] """ tables = [] last_keyword = None last_token = None table_syntax_keywords = [ # SELECT queries 'FROM', 'WHERE', 'JOIN', 'INNER JOIN', 'LEFT JOIN', 'RIGHT JOIN', 'ON', # INSERT queries 'I...

[ "def", "get_query_tables", "(", "query", ")", ":", "tables", "=", "[", "]", "last_keyword", "=", "None", "last_token", "=", "None", "table_syntax_keywords", "=", "[", "# SELECT queries", "'FROM'", ",", "'WHERE'", ",", "'JOIN'", ",", "'INNER JOIN'", ",", "'LEFT...

41.904762

0.002591

def CurrentNode(self): """Hacking interface allowing to get the xmlNodePtr correponding to the current node being accessed by the xmlTextReader. This is dangerous because the underlying node may be destroyed on the next Reads. """ ret = libxml2mod.xmlTextReaderCurrentNode(...

[ "def", "CurrentNode", "(", "self", ")", ":", "ret", "=", "libxml2mod", ".", "xmlTextReaderCurrentNode", "(", "self", ".", "_o", ")", "if", "ret", "is", "None", ":", "raise", "treeError", "(", "'xmlTextReaderCurrentNode() failed'", ")", "__tmp", "=", "xmlNode",...

50.111111

0.008715

def _mouseDown(x, y, button): """Send the mouse down event to Windows by calling the mouse_event() win32 function. Args: x (int): The x position of the mouse event. y (int): The y position of the mouse event. button (str): The mouse button, either 'left', 'middle', or 'right' Returns...

[ "def", "_mouseDown", "(", "x", ",", "y", ",", "button", ")", ":", "if", "button", "==", "'left'", ":", "try", ":", "_sendMouseEvent", "(", "MOUSEEVENTF_LEFTDOWN", ",", "x", ",", "y", ")", "except", "(", "PermissionError", ",", "OSError", ")", ":", "# T...

41.551724

0.005677

def N(u,i,p,knots): """Compute Spline Basis Evaluates the spline basis of order p defined by knots at knot i and point u. """ if p == 0: if knots[i] < u and u <=knots[i+1]: return 1.0 else: return 0.0 else: try: k = (( float((u-kn...

[ "def", "N", "(", "u", ",", "i", ",", "p", ",", "knots", ")", ":", "if", "p", "==", "0", ":", "if", "knots", "[", "i", "]", "<", "u", "and", "u", "<=", "knots", "[", "i", "+", "1", "]", ":", "return", "1.0", "else", ":", "return", "0.0", ...

28.434783

0.032544

def commit(self, force=False): """Commit data to couchdb Compared to threshold (unless forced) then sends data to couch """ self.log.debug('Bulk commit requested') size = sys.getsizeof(self.docs) self.log.debug('Size of docs in KB: %d', size) if size > self.comm...

[ "def", "commit", "(", "self", ",", "force", "=", "False", ")", ":", "self", ".", "log", ".", "debug", "(", "'Bulk commit requested'", ")", "size", "=", "sys", ".", "getsizeof", "(", "self", ".", "docs", ")", "self", ".", "log", ".", "debug", "(", "...

35.461538

0.004228

def locate(self, point): r"""Find a point on the current curve. Solves for :math:`s` in :math:`B(s) = p`. This method acts as a (partial) inverse to :meth:`evaluate`. .. note:: A unique solution is only guaranteed if the current curve has no self-intersections. ...

[ "def", "locate", "(", "self", ",", "point", ")", ":", "if", "point", ".", "shape", "!=", "(", "self", ".", "_dimension", ",", "1", ")", ":", "point_dimensions", "=", "\" x \"", ".", "join", "(", "str", "(", "dimension", ")", "for", "dimension", "in",...

31.902778

0.000845

def getPoly(rCut, nMax): """Used to calculate discrete vectors for the polynomial basis functions. Args: rCut(float): Radial cutoff nMax(int): Number of polynomial radial functions """ rCutVeryHard = rCut+5.0 rx = 0.5*rCutVeryHard*(x + 1) basisFunctions = [] for i in range(...

[ "def", "getPoly", "(", "rCut", ",", "nMax", ")", ":", "rCutVeryHard", "=", "rCut", "+", "5.0", "rx", "=", "0.5", "*", "rCutVeryHard", "*", "(", "x", "+", "1", ")", "basisFunctions", "=", "[", "]", "for", "i", "in", "range", "(", "1", ",", "nMax",...

36.55

0.001999

def high_cli(repo_name, login, with_blog, as_list, role): """Extract mails from stargazers, collaborators and people involved with issues of given repository. """ passw = getpass.getpass() github = gh_login(login, passw) repo = github.repository(login, repo_name) role = [ROLES[k] for k in ro...

[ "def", "high_cli", "(", "repo_name", ",", "login", ",", "with_blog", ",", "as_list", ",", "role", ")", ":", "passw", "=", "getpass", ".", "getpass", "(", ")", "github", "=", "gh_login", "(", "login", ",", "passw", ")", "repo", "=", "github", ".", "re...

31.526316

0.003241

def from_parameters3(cls, lengths, angles): """Construct a 3D unit cell with the given parameters The a vector is always parallel with the x-axis and they point in the same direction. The b vector is always in the xy plane and points towards the positive y-direction. The c vect...

[ "def", "from_parameters3", "(", "cls", ",", "lengths", ",", "angles", ")", ":", "for", "length", "in", "lengths", ":", "if", "length", "<=", "0", ":", "raise", "ValueError", "(", "\"The length parameters must be strictly positive.\"", ")", "for", "angle", "in", ...

41.880952

0.003333

def google(self): """Gets the tile in the Google format, converted from TMS""" tms_x, tms_y = self.tms return tms_x, (2 ** self.zoom - 1) - tms_y

[ "def", "google", "(", "self", ")", ":", "tms_x", ",", "tms_y", "=", "self", ".", "tms", "return", "tms_x", ",", "(", "2", "**", "self", ".", "zoom", "-", "1", ")", "-", "tms_y" ]

41.5

0.011834

def find_l50(contig_lengths_dict, genome_length_dict): """ Calculate the L50 for each strain. L50 is defined as the number of contigs required to achieve the N50 :param contig_lengths_dict: dictionary of strain name: reverse-sorted list of all contig lengths :param genome_length_dict: dictionary of stra...

[ "def", "find_l50", "(", "contig_lengths_dict", ",", "genome_length_dict", ")", ":", "# Initialise the dictionary", "l50_dict", "=", "dict", "(", ")", "for", "file_name", ",", "contig_lengths", "in", "contig_lengths_dict", ".", "items", "(", ")", ":", "currentlength"...

52.045455

0.005146

def check_response_code(resp): """ check if query quota has been surpassed or other errors occured :param resp: json response :return: """ if resp["status"] == "OK" or resp["status"] == "ZERO_RESULTS": return if resp["status"] == "REQUEST_DENIED": raise Exception("Google Pla...

[ "def", "check_response_code", "(", "resp", ")", ":", "if", "resp", "[", "\"status\"", "]", "==", "\"OK\"", "or", "resp", "[", "\"status\"", "]", "==", "\"ZERO_RESULTS\"", ":", "return", "if", "resp", "[", "\"status\"", "]", "==", "\"REQUEST_DENIED\"", ":", ...

43.192308

0.004355

def create_database(self, instance, body, project_id=None): """ Creates a new database inside a Cloud SQL instance. :param instance: Database instance ID. This does not include the project ID. :type instance: str :param body: The request body, as described in https:/...

[ "def", "create_database", "(", "self", ",", "instance", ",", "body", ",", "project_id", "=", "None", ")", ":", "response", "=", "self", ".", "get_conn", "(", ")", ".", "databases", "(", ")", ".", "insert", "(", "project", "=", "project_id", ",", "insta...

46.318182

0.004808

def spdhg_generic(x, f, g, A, tau, sigma, niter, **kwargs): r"""Computes a saddle point with a stochastic PDHG. This means, a solution (x*, y*), y* = (y*_1, ..., y*_n) such that (x*, y*) in arg min_x max_y sum_i=1^n <y_i, A_i> - f*[i](y_i) + g(x) where g : X -> IR_infty and f[i] : Y[i] -> IR_infty ar...

[ "def", "spdhg_generic", "(", "x", ",", "f", ",", "g", ",", "A", ",", "tau", ",", "sigma", ",", "niter", ",", "*", "*", "kwargs", ")", ":", "# Callback object", "callback", "=", "kwargs", ".", "pop", "(", "'callback'", ",", "None", ")", "if", "callb...

32.88024

0.000177

def get_abstract(doi): """Get the abstract text of an article from Elsevier given a doi.""" xml_string = download_article(doi) if xml_string is None: return None assert isinstance(xml_string, str) xml_tree = ET.XML(xml_string.encode('utf-8'), parser=UTB()) if xml_tree is None: re...

[ "def", "get_abstract", "(", "doi", ")", ":", "xml_string", "=", "download_article", "(", "doi", ")", "if", "xml_string", "is", "None", ":", "return", "None", "assert", "isinstance", "(", "xml_string", ",", "str", ")", "xml_tree", "=", "ET", ".", "XML", "...

37.538462

0.002

def generateSortedChildListString(self, stream, sectionTitle, lst): ''' Helper method for :func:`~exhale.graph.ExhaleRoot.generateNamespaceChildrenString`. Used to build up a continuous string with all of the children separated out into titled sections. This generates a new titl...

[ "def", "generateSortedChildListString", "(", "self", ",", "stream", ",", "sectionTitle", ",", "lst", ")", ":", "if", "lst", ":", "lst", ".", "sort", "(", ")", "stream", ".", "write", "(", "textwrap", ".", "dedent", "(", "'''\n\n {heading}\n ...

36.102564

0.005533

def run(self, data, train_epochs=1000, test_epochs=1000, verbose=None, idx=0, lr=0.01, **kwargs): """Run the CGNN on a given graph.""" verbose = SETTINGS.get_default(verbose=verbose) optim = th.optim.Adam(self.parameters(), lr=lr) self.score.zero_() with trange(train_...

[ "def", "run", "(", "self", ",", "data", ",", "train_epochs", "=", "1000", ",", "test_epochs", "=", "1000", ",", "verbose", "=", "None", ",", "idx", "=", "0", ",", "lr", "=", "0.01", ",", "*", "*", "kwargs", ")", ":", "verbose", "=", "SETTINGS", "...

43.684211

0.003538

def proj_list(args): '''Retrieve the list of billing projects accessible to the caller/user, and show the level of access granted for each (e.g. Owner, User, ...)''' projects = fapi.list_billing_projects() fapi._check_response_code(projects, 200) projects = sorted(projects.json(), key=lambda d: d...

[ "def", "proj_list", "(", "args", ")", ":", "projects", "=", "fapi", ".", "list_billing_projects", "(", ")", "fapi", ".", "_check_response_code", "(", "projects", ",", "200", ")", "projects", "=", "sorted", "(", "projects", ".", "json", "(", ")", ",", "ke...

57.888889

0.003781

def run(self): """ Read lines while keep_reading is True. Calls process_dut for each received line. :return: Nothing """ self.keep_reading = True while self.keep_reading: line = self._readline() if line: self.input_queue.appendleft...

[ "def", "run", "(", "self", ")", ":", "self", ".", "keep_reading", "=", "True", "while", "self", ".", "keep_reading", ":", "line", "=", "self", ".", "_readline", "(", ")", "if", "line", ":", "self", ".", "input_queue", ".", "appendleft", "(", "line", ...

29.416667

0.008242

def object_patch_add_link(self, root, name, ref, create=False, **kwargs): """Creates a new merkledag object based on an existing one. The new object will have a link to the provided object. .. code-block:: python >>> c.object_patch_add_link( ... 'QmR79zQQj2aDfnrNgc...

[ "def", "object_patch_add_link", "(", "self", ",", "root", ",", "name", ",", "ref", ",", "create", "=", "False", ",", "*", "*", "kwargs", ")", ":", "kwargs", ".", "setdefault", "(", "\"opts\"", ",", "{", "\"create\"", ":", "create", "}", ")", "args", ...

32.441176

0.001761

def Norm2(self): """ Returns the L_2 (Euclidean) norm of self. """ sum = self.x * self.x + self.y * self.y + self.z * self.z return math.sqrt(float(sum))

[ "def", "Norm2", "(", "self", ")", ":", "sum", "=", "self", ".", "x", "*", "self", ".", "x", "+", "self", ".", "y", "*", "self", ".", "y", "+", "self", ".", "z", "*", "self", ".", "z", "return", "math", ".", "sqrt", "(", "float", "(", "sum",...

28

0.00578

def _resolve_image(ret, image, client_timeout): ''' Resolve the image ID and pull the image if necessary ''' image_id = __salt__['docker.resolve_image_id'](image) if image_id is False: if not __opts__['test']: # Image not pulled locally, so try pulling it try: ...

[ "def", "_resolve_image", "(", "ret", ",", "image", ",", "client_timeout", ")", ":", "image_id", "=", "__salt__", "[", "'docker.resolve_image_id'", "]", "(", "image", ")", "if", "image_id", "is", "False", ":", "if", "not", "__opts__", "[", "'test'", "]", ":...

38.862069

0.000866

def register_forward_pre_hook(self, hook): r"""Registers a forward pre-hook on the block. The hook function is called immediately before :func:`forward`. It should not modify the input or output. Parameters ---------- hook : callable The forward hook functio...

[ "def", "register_forward_pre_hook", "(", "self", ",", "hook", ")", ":", "handle", "=", "HookHandle", "(", ")", "handle", ".", "attach", "(", "self", ".", "_forward_pre_hooks", ",", "hook", ")", "return", "handle" ]

29.888889

0.003604

def calc_and_store_post_estimation_results(results_dict, estimator): """ Calculates and stores post-estimation results that require the use of the systematic utility transformation functions or the various derivative functions. Note that this function is only v...

[ "def", "calc_and_store_post_estimation_results", "(", "results_dict", ",", "estimator", ")", ":", "# Store the final log-likelihood", "final_log_likelihood", "=", "-", "1", "*", "results_dict", "[", "\"fun\"", "]", "results_dict", "[", "\"final_log_likelihood\"", "]", "="...

37.326733

0.000258

def insertFile(self, businput, qInserts=False): """ This method supports bulk insert of files performing other operations such as setting Block and Dataset parentages, setting mapping between OutputConfigModules and File(s) etc. :param qInserts: True means that inserts will be q...

[ "def", "insertFile", "(", "self", ",", "businput", ",", "qInserts", "=", "False", ")", ":", "# We do not want to go be beyond 10 files at a time", "# If user wants to insert over 10 files in one shot, we run into risks of locking the database", "# tables for longer time, and in case of e...

56.518939

0.010406

def get_resource(self, resource_id): """Gets the ``Resource`` specified by its ``Id``. In plenary mode, the exact ``Id`` is found or a ``NotFound`` results. Otherwise, the returned ``Resource`` may have a different ``Id`` than requested, such as the case where a duplicate ``Id``...

[ "def", "get_resource", "(", "self", ",", "resource_id", ")", ":", "# Implemented from template for", "# osid.resource.ResourceLookupSession.get_resource", "# NOTE: This implementation currently ignores plenary view", "collection", "=", "JSONClientValidated", "(", "'resource'", ",", ...

51

0.002654

def configure_retrieve(self, ns, definition): """ Register a retrieve endpoint. The definition's func should be a retrieve function, which must: - accept kwargs for path data - return an item or falsey :param ns: the namespace :param definition: the endpoint def...

[ "def", "configure_retrieve", "(", "self", ",", "ns", ",", "definition", ")", ":", "request_schema", "=", "definition", ".", "request_schema", "or", "Schema", "(", ")", "@", "self", ".", "add_route", "(", "ns", ".", "instance_path", ",", "Operation", ".", "...

37.96875

0.00321

def eye(n, d=None): """ Creates an identity TT-matrix""" c = _matrix.matrix() c.tt = _vector.vector() if d is None: n0 = _np.asanyarray(n, dtype=_np.int32) c.tt.d = n0.size else: n0 = _np.asanyarray([n] * d, dtype=_np.int32) c.tt.d = d c.n = n0.copy() c.m = n0...

[ "def", "eye", "(", "n", ",", "d", "=", "None", ")", ":", "c", "=", "_matrix", ".", "matrix", "(", ")", "c", ".", "tt", "=", "_vector", ".", "vector", "(", ")", "if", "d", "is", "None", ":", "n0", "=", "_np", ".", "asanyarray", "(", "n", ","...

24.64

0.004688

def _get_edge_date(self, date_field, sort): ''' This method is used to get start and end dates for the collection. ''' return self._source.query(self._source_coll, { 'q':'*:*', 'rows':1, 'fq':'+{}:*'.format(date_field), ...

[ "def", "_get_edge_date", "(", "self", ",", "date_field", ",", "sort", ")", ":", "return", "self", ".", "_source", ".", "query", "(", "self", ".", "_source_coll", ",", "{", "'q'", ":", "'*:*'", ",", "'rows'", ":", "1", ",", "'fq'", ":", "'+{}:*'", "."...

41.888889

0.015584

def device(self): """returns the device which owns the given stream""" splitted_path = self.path.split("/") return Device(self.db, splitted_path[0] + "/" + splitted_path[1])

[ "def", "device", "(", "self", ")", ":", "splitted_path", "=", "self", ".", "path", ".", "split", "(", "\"/\"", ")", "return", "Device", "(", "self", ".", "db", ",", "splitted_path", "[", "0", "]", "+", "\"/\"", "+", "splitted_path", "[", "1", "]", ...

35.833333

0.009091

def is_mod_class(mod, cls): """Checks if a class in a module was declared in that module. Args: mod: the module cls: the class """ return inspect.isclass(cls) and inspect.getmodule(cls) == mod

[ "def", "is_mod_class", "(", "mod", ",", "cls", ")", ":", "return", "inspect", ".", "isclass", "(", "cls", ")", "and", "inspect", ".", "getmodule", "(", "cls", ")", "==", "mod" ]

27.25

0.004444

def check_declared(self, node): """update the state of this Identifiers with the undeclared and declared identifiers of the given node.""" for ident in node.undeclared_identifiers(): if ident != 'context' and\ ident not in self.declared.union(self.locally_dec...

[ "def", "check_declared", "(", "self", ",", "node", ")", ":", "for", "ident", "in", "node", ".", "undeclared_identifiers", "(", ")", ":", "if", "ident", "!=", "'context'", "and", "ident", "not", "in", "self", ".", "declared", ".", "union", "(", "self", ...

45.6

0.004301

def search_stack_for_var(varname, verbose=util_arg.NOT_QUIET): """ Finds a varable (local or global) somewhere in the stack and returns the value Args: varname (str): variable name Returns: None if varname is not found else its value """ curr_frame = inspect.currentframe() ...

[ "def", "search_stack_for_var", "(", "varname", ",", "verbose", "=", "util_arg", ".", "NOT_QUIET", ")", ":", "curr_frame", "=", "inspect", ".", "currentframe", "(", ")", "if", "verbose", ":", "print", "(", "' * Searching parent frames for: '", "+", "six", ".", ...

36.178571

0.002885

def principals(geom, masses, on_tol=_DEF.ORTHONORM_TOL): """Principal axes and moments of inertia for the indicated geometry. Calculated by :func:`scipy.linalg.eigh`, since the moment of inertia tensor is symmetric (real-Hermitian) by construction. More convenient to compute both the axes and moments ...

[ "def", "principals", "(", "geom", ",", "masses", ",", "on_tol", "=", "_DEF", ".", "ORTHONORM_TOL", ")", ":", "# Imports", "import", "numpy", "as", "np", "from", "scipy", "import", "linalg", "as", "spla", "from", ".", ".", "const", "import", "PRM", ",", ...

39.753036

0.009538

def _get_types(type_): """ Gathers all types within the ``TYPE_MAPPINGS`` for a specific ``Types`` value. :param Types type_: The type to retrieve :return: All types within the ``TYPE_MAPPINGS`` :rtype: list """ return list( itertools.chain.from_iterable( map(lambda x: TYPE...

[ "def", "_get_types", "(", "type_", ")", ":", "return", "list", "(", "itertools", ".", "chain", ".", "from_iterable", "(", "map", "(", "lambda", "x", ":", "TYPE_MAPPINGS", "[", "x", "]", ".", "get", "(", "type_", ",", "[", "]", ")", ",", "TYPE_MAPPING...

28.230769

0.005277