kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def convert_softmax(net, node, module, builder): """Convert a softmax layer from mxnet to coreml. Parameters ---------- network: net A mxnet network object. layer: node Node to convert. module: module An module for MXNet builder: NeuralNetworkBuilder A neu...	[ "def", "convert_softmax", "(", "net", ",", "node", ",", "module", ",", "builder", ")", ":", "input_name", ",", "output_name", "=", "_get_input_output_name", "(", "net", ",", "node", ")", "name", "=", "node", "[", "'name'", "]", "builder", ".", "add_softmax...	25.136364	18
def update_screen(self): """Refresh the screen. You don't need to override this except to update only small portins of the screen.""" self.clock.tick(self.FPS) pygame.display.update()	[ "def", "update_screen", "(", "self", ")", ":", "self", ".", "clock", ".", "tick", "(", "self", ".", "FPS", ")", "pygame", ".", "display", ".", "update", "(", ")" ]	51	8
def path(self, which=None): """Extend ``nailgun.entity_mixins.Entity.path``. The format of the returned path depends on the value of ``which``: incremental_update /content_view_versions/incremental_update promote /content_view_versions/<id>/promote ``su...	[ "def", "path", "(", "self", ",", "which", "=", "None", ")", ":", "if", "which", "in", "(", "'incremental_update'", ",", "'promote'", ")", ":", "prefix", "=", "'base'", "if", "which", "==", "'incremental_update'", "else", "'self'", "return", "'{0}/{1}'", "....	33.1	20.15
def cross_v2(vec1, vec2): """Return the crossproduct of the two vectors as a Vec2. Cross product doesn't really make sense in 2D, but return the Z component of the 3d result. """ return vec1.y * vec2.x - vec1.x * vec2.y	[ "def", "cross_v2", "(", "vec1", ",", "vec2", ")", ":", "return", "vec1", ".", "y", "", "vec2", ".", "x", "-", "vec1", ".", "x", "", "vec2", ".", "y" ]	33.428571	16.428571
def _init_map(self, record_types=None, **kwargs): """Initialize form map""" osid_objects.OsidObjectForm._init_map(self, record_types=record_types) self._my_map['assignedAgencyIds'] = [str(kwargs['agency_id'])]	[ "def", "_init_map", "(", "self", ",", "record_types", "=", "None", ",", "", "", "kwargs", ")", ":", "osid_objects", ".", "OsidObjectForm", ".", "_init_map", "(", "self", ",", "record_types", "=", "record_types", ")", "self", ".", "_my_map", "[", "'assign...	57.5	19.25
def blockingSave(self, path): """ saved session to file - returns after finish only called by interactiveTutorial-save at the moment """ self.tmp_dir_save_session = self.tmp_dir_session.join('block').mkdir() state = {'session': dict(self.opts), 'di...	[ "def", "blockingSave", "(", "self", ",", "path", ")", ":", "self", ".", "tmp_dir_save_session", "=", "self", ".", "tmp_dir_session", ".", "join", "(", "'block'", ")", ".", "mkdir", "(", ")", "state", "=", "{", "'session'", ":", "dict", "(", "self", "."...	43.636364	14
def use_any_adapter(self, use_any_adapter): """ Allows GNS3 to use any VMware adapter on this instance. :param use_any_adapter: boolean """ if use_any_adapter: log.info("VMware VM '{name}' [{id}] is allowed to use any adapter".format(name=self.name, id=self.id)) ...	[ "def", "use_any_adapter", "(", "self", ",", "use_any_adapter", ")", ":", "if", "use_any_adapter", ":", "log", ".", "info", "(", "\"VMware VM '{name}' [{id}] is allowed to use any adapter\"", ".", "format", "(", "name", "=", "self", ".", "name", ",", "id", "=", "...	40.5	25.5
def shortened_character_name(self_or_cls, c, eliminations=[], substitutions={}, transforms=[]): """ Given a unicode character c, return the shortened unicode name (as a list of tokens) by applying the eliminations, substitutions and transforms. """ name = unicodedata.name...	[ "def", "shortened_character_name", "(", "self_or_cls", ",", "c", ",", "eliminations", "=", "[", "]", ",", "substitutions", "=", "{", "}", ",", "transforms", "=", "[", "]", ")", ":", "name", "=", "unicodedata", ".", "name", "(", "c", ")", ".", "lower", ...	41.6875	13.0625
def on_start(self, host, port, channel, nickname, password): """ A WebSocket session has started - create a greenlet to host the IRC client, and start it. """ self.client = WebSocketIRCClient(host, port, channel, nickname, password, self) ...	[ "def", "on_start", "(", "self", ",", "host", ",", "port", ",", "channel", ",", "nickname", ",", "password", ")", ":", "self", ".", "client", "=", "WebSocketIRCClient", "(", "host", ",", "port", ",", "channel", ",", "nickname", ",", "password", ",", "se...	43.75	12.5
def clone(self, newname, config_path=None, flags=0, bdevtype=None, bdevdata=None, newsize=0, hookargs=()): """ Clone the current container. """ args = {} args['newname'] = newname args['flags'] = flags args['newsize'] = newsize args['hoo...	[ "def", "clone", "(", "self", ",", "newname", ",", "config_path", "=", "None", ",", "flags", "=", "0", ",", "bdevtype", "=", "None", ",", "bdevdata", "=", "None", ",", "newsize", "=", "0", ",", "hookargs", "=", "(", ")", ")", ":", "args", "=", "{"...	29.954545	13.954545
def delete(self, path, data, options): """ Parses DELETE request options and dispatches a request """ data, options = self._update_request(data, options) return self.request('delete', path, data=data, options)	[ "def", "delete", "(", "self", ",", "path", ",", "data", ",", "", "", "options", ")", ":", "data", ",", "options", "=", "self", ".", "_update_request", "(", "data", ",", "options", ")", "return", "self", ".", "request", "(", "'delete'", ",", "path",...	41.333333	11
def _scan(positions): """get the region inside the vector with more expression""" scores = [] for start in range(0, len(positions) - 17, 5): end = start = 17 scores.add(_enrichment(positions[start:end], positions[:start], positions[end:]))	[ "def", "_scan", "(", "positions", ")", ":", "scores", "=", "[", "]", "for", "start", "in", "range", "(", "0", ",", "len", "(", "positions", ")", "-", "17", ",", "5", ")", ":", "end", "=", "start", "=", "17", "scores", ".", "add", "(", "_enrichm...	43.666667	19.833333
def kwargs_as_assignments(call_node, parent): """Yield NoDeclAssign nodes from kwargs in a Call node.""" if not isinstance(call_node, ast.Call): raise TypeError('node must be an ast.Call') if len(call_node.args) > 0: raise ValueError('positional args not allowed') for keyword in call_n...	[ "def", "kwargs_as_assignments", "(", "call_node", ",", "parent", ")", ":", "if", "not", "isinstance", "(", "call_node", ",", "ast", ".", "Call", ")", ":", "raise", "TypeError", "(", "'node must be an ast.Call'", ")", "if", "len", "(", "call_node", ".", "args...	37.45	17.35
def increment(self, key, value=1): """ Increment the value of an item in the cache. :param key: The cache key :type key: str :param value: The increment value :type value: int :rtype: int or bool """ self._store.increment(self.tagged_item_key(ke...	[ "def", "increment", "(", "self", ",", "key", ",", "value", "=", "1", ")", ":", "self", ".", "_store", ".", "increment", "(", "self", ".", "tagged_item_key", "(", "key", ")", ",", "value", ")" ]	24.461538	16.615385
def split_by_connected_component(self, idents): '''Split idents into equivalence classes based on connected components. ''' idents_remaining = set(idents) connected_components = [] for ident in idents: if ident not in idents_remaining: continue...	[ "def", "split_by_connected_component", "(", "self", ",", "idents", ")", ":", "idents_remaining", "=", "set", "(", "idents", ")", "connected_components", "=", "[", "]", "for", "ident", "in", "idents", ":", "if", "ident", "not", "in", "idents_remaining", ":", ...	36.363636	16.363636
def _paramiko_tunnel(lport, rport, server, remoteip, keyfile=None, password=None): """Function for actually starting a paramiko tunnel, to be passed to multiprocessing.Process(target=this), and not called directly. """ username, server, port = _split_server(server) client = paramiko.SSHClient() ...	[ "def", "_paramiko_tunnel", "(", "lport", ",", "rport", ",", "server", ",", "remoteip", ",", "keyfile", "=", "None", ",", "password", "=", "None", ")", ":", "username", ",", "server", ",", "port", "=", "_split_server", "(", "server", ")", "client", "=", ...	40.34375	22.71875
def validate(self, instance, value): """Check the class of the container and validate each element This returns a copy of the container to prevent unwanted sharing of pointers. """ if not self.coerce and not isinstance(value, self._class_container): self.error(instan...	[ "def", "validate", "(", "self", ",", "instance", ",", "value", ")", ":", "if", "not", "self", ".", "coerce", "and", "not", "isinstance", "(", "value", ",", "self", ".", "_class_container", ")", ":", "self", ".", "error", "(", "instance", ",", "value", ...	38.571429	16.952381
def scalar(cls, value): """Create an ArgumentType with a single scalar in range(value).""" return lambda i, name: cls(i, name, (value,), lambda a: a[0], None)	[ "def", "scalar", "(", "cls", ",", "value", ")", ":", "return", "lambda", "i", ",", "name", ":", "cls", "(", "i", ",", "name", ",", "(", "value", ",", ")", ",", "lambda", "a", ":", "a", "[", "0", "]", ",", "None", ")" ]	54.666667	16
def register_dependency(self, data_src, data_sink): """ registers a dependency of data_src -> data_sink by placing appropriate entries in provides_for and depends_on """ pdebug("registering dependency %s -> %s" % (data_src, data_sink)) if (data_src not in self._gettask(data...	[ "def", "register_dependency", "(", "self", ",", "data_src", ",", "data_sink", ")", ":", "pdebug", "(", "\"registering dependency %s -> %s\"", "%", "(", "data_src", ",", "data_sink", ")", ")", "if", "(", "data_src", "not", "in", "self", ".", "_gettask", "(", ...	44.083333	24.916667
def duration(cls, seconds, first=True): """ Constructs a human readable string to indicate the time duration for the given seconds :param int seconds: :param bool first: Just return the first unit instead of all :rtype: str """ num_units = [] for unit in...	[ "def", "duration", "(", "cls", ",", "seconds", ",", "first", "=", "True", ")", ":", "num_units", "=", "[", "]", "for", "unit", "in", "reversed", "(", "TimeUnit", ")", ":", "if", "seconds", ">=", "unit", ".", "seconds", ":", "name", "=", "unit", "."...	32.285714	17.52381
def remap_index_fn(ref_file): """minimap2 can build indexes on the fly but will also store commons ones. """ index_dir = os.path.join(os.path.dirname(ref_file), os.pardir, "minimap2") if os.path.exists(index_dir) and os.path.isdir(index_dir): return index_dir else: return os.path.dir...	[ "def", "remap_index_fn", "(", "ref_file", ")", ":", "index_dir", "=", "os", ".", "path", ".", "join", "(", "os", ".", "path", ".", "dirname", "(", "ref_file", ")", ",", "os", ".", "pardir", ",", "\"minimap2\"", ")", "if", "os", ".", "path", ".", "e...	40.875	14.75
def filename(self): """ Name of the file on the client file system, but normalized to ensure file system compatibility. An empty filename is returned as 'empty'. Only ASCII letters, digits, dashes, underscores and dots are allowed in the final filename. Accents are removed, ...	[ "def", "filename", "(", "self", ")", ":", "fname", "=", "self", ".", "raw_filename", "if", "not", "isinstance", "(", "fname", ",", "unicode", ")", ":", "fname", "=", "fname", ".", "decode", "(", "'utf8'", ",", "'ignore'", ")", "fname", "=", "normalize"...	52.333333	19.611111
def hide_zeroes(self): ''' Sometimes it makes sense to hide the labels for subsets whose size is zero. This utility method does this. ''' for v in self.subset_labels: if v is not None and v.get_text() == '0': v.set_visible(False)	[ "def", "hide_zeroes", "(", "self", ")", ":", "for", "v", "in", "self", ".", "subset_labels", ":", "if", "v", "is", "not", "None", "and", "v", ".", "get_text", "(", ")", "==", "'0'", ":", "v", ".", "set_visible", "(", "False", ")" ]	36.25	17.75
def _maybe_validate_rightmost_transposed_ndims( rightmost_transposed_ndims, validate_args, name=None): """Checks that `rightmost_transposed_ndims` is valid.""" with tf.name_scope(name or 'maybe_validate_rightmost_transposed_ndims'): assertions = [] if not dtype_util.is_integer(rightmost_transposed_ndims...	[ "def", "_maybe_validate_rightmost_transposed_ndims", "(", "rightmost_transposed_ndims", ",", "validate_args", ",", "name", "=", "None", ")", ":", "with", "tf", ".", "name_scope", "(", "name", "or", "'maybe_validate_rightmost_transposed_ndims'", ")", ":", "assertions", "...	44.741935	20.354839
def nonblock_recv(self): """Non blocking receive""" if self.buffered_frames(): # Get a frame from the buffer return self.get_frame() # Set the non blocking flag, read from the socket, and unset the flag self.set_nonblock(True) pkt = L2bpfListenSocket.rec...	[ "def", "nonblock_recv", "(", "self", ")", ":", "if", "self", ".", "buffered_frames", "(", ")", ":", "# Get a frame from the buffer", "return", "self", ".", "get_frame", "(", ")", "# Set the non blocking flag, read from the socket, and unset the flag", "self", ".", "set_...	30.666667	15.5
def _get_url(url): """Retrieve requested URL""" try: data = HTTP_SESSION.get(url, stream=True) data.raise_for_status() except requests.exceptions.RequestException as exc: raise FetcherException(exc) return data	[ "def", "_get_url", "(", "url", ")", ":", "try", ":", "data", "=", "HTTP_SESSION", ".", "get", "(", "url", ",", "stream", "=", "True", ")", "data", ".", "raise_for_status", "(", ")", "except", "requests", ".", "exceptions", ".", "RequestException", "as", ...	27	17.444444
def tf_action_exploration(self, action, exploration, action_spec): """ Applies optional exploration to the action (post-processor for action outputs). Args: action (tf.Tensor): The original output action tensor (to be post-processed). exploration (Exploration): The Exp...	[ "def", "tf_action_exploration", "(", "self", ",", "action", ",", "exploration", ",", "action_spec", ")", ":", "action_shape", "=", "tf", ".", "shape", "(", "input", "=", "action", ")", "exploration_value", "=", "exploration", ".", "tf_explore", "(", "episode",...	40.931818	22.386364
def load(stream, fmt='lha'): """Load a parameter file in DSixTools SLHA-like format or its JSON or YAML representation.""" if fmt == 'lha': return pylha.load(stream) elif fmt == 'json': if isinstance(stream, str): return json.loads(stream) else: return jso...	[ "def", "load", "(", "stream", ",", "fmt", "=", "'lha'", ")", ":", "if", "fmt", "==", "'lha'", ":", "return", "pylha", ".", "load", "(", "stream", ")", "elif", "fmt", "==", "'json'", ":", "if", "isinstance", "(", "stream", ",", "str", ")", ":", "r...	31.666667	10
def integer_list_file(cls, filename): """ Read a list of integers from a file. The file format is: - # anywhere in the line begins a comment - leading and trailing spaces are ignored - empty lines are ignored - integers can be specified as: - dec...	[ "def", "integer_list_file", "(", "cls", ",", "filename", ")", ":", "count", "=", "0", "result", "=", "list", "(", ")", "fd", "=", "open", "(", "filename", ",", "'r'", ")", "for", "line", "in", "fd", ":", "count", "=", "count", "+", "1", "if", "'#...	31.923077	12.282051
def calibrate_container_with_instrument(self, container: Container, instrument, save: bool ): '''Calibrates a container using the bottom...	[ "def", "calibrate_container_with_instrument", "(", "self", ",", "container", ":", "Container", ",", "instrument", ",", "save", ":", "bool", ")", ":", "well", "=", "container", "[", "0", "]", "# Get the relative position of well with respect to instrument", "delta", "=...	29.894737	18.842105
def groups_delete(self, room_id=None, group=None, **kwargs): """Delete a private group.""" if room_id: return self.__call_api_post('groups.delete', roomId=room_id, kwargs=kwargs) elif group: return self.__call_api_post('groups.delete', roomName=group, kwargs=kwargs) ...	[ "def", "groups_delete", "(", "self", ",", "room_id", "=", "None", ",", "group", "=", "None", ",", "", "", "kwargs", ")", ":", "if", "room_id", ":", "return", "self", ".", "__call_api_post", "(", "'groups.delete'", ",", "roomId", "=", "room_id", ",", ...	49.375	27
def fit(self, X, y=None, **fit_params): """Fit base estimators. Parameters ---------- X : array-like, shape = (n_samples, n_features) Training data. y : array-like, optional Target data if base estimators are supervised. Returns ------- ...	[ "def", "fit", "(", "self", ",", "X", ",", "y", "=", "None", ",", "", "", "fit_params", ")", ":", "X", "=", "numpy", ".", "asarray", "(", "X", ")", "self", ".", "_fit_estimators", "(", "X", ",", "y", ",", "", "", "fit_params", ")", "Xt", "...	23.952381	18.142857
def prepare_samples(job, fastqs, univ_options): """ This module will accept a dict object holding the 3 input prefixes and the patient id and will attempt to store the fastqs to the jobstore. The input files must satisfy the following 1. File extensions can only be fastq or fq (.gz is also allowed) ...	[ "def", "prepare_samples", "(", "job", ",", "fastqs", ",", "univ_options", ")", ":", "job", ".", "fileStore", ".", "logToMaster", "(", "'Downloading Inputs for %s'", "%", "univ_options", "[", "'patient'", "]", ")", "allowed_samples", "=", "{", "'tumor_dna_fastq_pre...	53.039474	23.828947
def writeWarp(self, warpDict): """ Write a list of (in, out) values for a warpmap """ warpElement = ET.Element("warp") axisNames = sorted(warpDict.keys()) for name in axisNames: axisElement = ET.Element("axis") axisElement.attrib['name'] = name for a, ...	[ "def", "writeWarp", "(", "self", ",", "warpDict", ")", ":", "warpElement", "=", "ET", ".", "Element", "(", "\"warp\"", ")", "axisNames", "=", "sorted", "(", "warpDict", ".", "keys", "(", ")", ")", "for", "name", "in", "axisNames", ":", "axisElement", "...	42.285714	4.142857
def rev(self, i): """Return a clone with a different revision.""" on = copy(self) on.revision = i return on	[ "def", "rev", "(", "self", ",", "i", ")", ":", "on", "=", "copy", "(", "self", ")", "on", ".", "revision", "=", "i", "return", "on" ]	27	16
def __select_nearest_ws(jsondata, latitude, longitude): """Select the nearest weatherstation.""" log.debug("__select_nearest_ws: latitude: %s, longitude: %s", latitude, longitude) dist = 0 dist2 = 0 loc_data = None try: ws_json = jsondata[__ACTUAL] ws_json = ws_jso...	[ "def", "__select_nearest_ws", "(", "jsondata", ",", "latitude", ",", "longitude", ")", ":", "log", ".", "debug", "(", "\"__select_nearest_ws: latitude: %s, longitude: %s\"", ",", "latitude", ",", "longitude", ")", "dist", "=", "0", "dist2", "=", "0", "loc_data", ...	32.948718	17.410256
def dict(self, iss_list=None): """ Return the bundle of keys as a dictionary with the issuer IDs as the keys and the key sets represented as JWKS instances. :param iss_list: List of Issuer IDs that should be part of the output :rtype: Dictionary """ ...	[ "def", "dict", "(", "self", ",", "iss_list", "=", "None", ")", ":", "_int", "=", "{", "}", "for", "iss", ",", "kj", "in", "self", ".", "bundle", ".", "items", "(", ")", ":", "if", "iss_list", "is", "None", "or", "iss", "in", "iss_list", ":", "t...	36.117647	17.294118
def create_message(self): """Returns a message body to send in this email. Should be from email.mime.*""" body = dedent("""\ Received exception {exception} on {queue} from worker {worker}: {traceback} Payload: {payload} """).format(exception=self._exception, ...	[ "def", "create_message", "(", "self", ")", ":", "body", "=", "dedent", "(", "\"\"\"\\\n Received exception {exception} on {queue} from worker {worker}:\n\n {traceback}\n\n Payload:\n {payload}\n\n \"\"\"", ")", ".", "format", "(", "exception", "=", ...	27.666667	18.611111
def make_proxy_method(cls, name): """Creates a proxy function that can be used by Flasks routing. The proxy instantiates the Mocha subclass and calls the appropriate method. :param name: the name of the method to create a proxy for """ i = cls() view = getattr(i,...	[ "def", "make_proxy_method", "(", "cls", ",", "name", ")", ":", "i", "=", "cls", "(", ")", "view", "=", "getattr", "(", "i", ",", "name", ")", "for", "decorator", "in", "cls", ".", "decorators", ":", "view", "=", "decorator", "(", "view", ")", "@", ...	38.971014	20.710145
def transaction_search(self, **kwargs): """Shortcut for the TransactionSearch method. Returns a PayPalResponseList object, which merges the L_ syntax list to a list of dictionaries with properly named keys. Note that the API will limit returned transactions to 100. Required Kwa...	[ "def", "transaction_search", "(", "self", ",", "", "", "kwargs", ")", ":", "plain", "=", "self", ".", "_call", "(", "'TransactionSearch'", ",", "", "", "kwargs", ")", "return", "PayPalResponseList", "(", "plain", ".", "raw", ",", "self", ".", "config...	33.722222	22.388889
def get(self, request, args, kwargs): """ Do the login and password protection. """ response = super(EntryProtectionMixin, self).get( request, args, **kwargs) if self.object.login_required and not request.user.is_authenticated: return self.login() ...	[ "def", "get", "(", "self", ",", "request", ",", "", "args", ",", "", "", "kwargs", ")", ":", "response", "=", "super", "(", "EntryProtectionMixin", ",", "self", ")", ".", "get", "(", "request", ",", "", "args", ",", "", "", "kwargs", ")", "...	41.833333	12.5
def transform(self, maps): """ This function transforms from component masses and caretsian spins to chi_p. Parameters ---------- maps : a mapping object Examples -------- Convert a dict of numpy.array: Returns ------- out : dict...	[ "def", "transform", "(", "self", ",", "maps", ")", ":", "out", "=", "{", "}", "out", "[", "\"chi_p\"", "]", "=", "conversions", ".", "chi_p", "(", "maps", "[", "parameters", ".", "mass1", "]", ",", "maps", "[", "parameters", ".", "mass2", "]", ",",...	31.791667	21.583333
def _do_subst(node, subs): """ Fetch the node contents and replace all instances of the keys with their values. For example, if subs is {'%VERSION%': '1.2345', '%BASE%': 'MyProg', '%prefix%': '/bin'}, then all instances of %VERSION% in the file will be replaced with 1.2345 and so forth. ...	[ "def", "_do_subst", "(", "node", ",", "subs", ")", ":", "contents", "=", "node", ".", "get_text_contents", "(", ")", "if", "subs", ":", "for", "(", "k", ",", "val", ")", "in", "subs", ":", "contents", "=", "re", ".", "sub", "(", "k", ",", "val", ...	34.238095	17
def date_map(doc, datemap_list, time_format=None): ''' For all the datetime fields in "datemap" find that key in doc and map the datetime object to a strftime string. This pprint and others will print out readable datetimes. ''' if datemap_list: for i in datemap_list:...	[ "def", "date_map", "(", "doc", ",", "datemap_list", ",", "time_format", "=", "None", ")", ":", "if", "datemap_list", ":", "for", "i", "in", "datemap_list", ":", "if", "isinstance", "(", "i", ",", "datetime", ")", ":", "doc", "=", "CursorFormatter", ".", ...	46.2	26.6
def stop_consumer(self): """Stop the consumer object and allow it to do a clean shutdown if it has the ability to do so. """ try: LOGGER.info('Shutting down the consumer') self.consumer.shutdown() except AttributeError: LOGGER.debug('Consumer ...	[ "def", "stop_consumer", "(", "self", ")", ":", "try", ":", "LOGGER", ".", "info", "(", "'Shutting down the consumer'", ")", "self", ".", "consumer", ".", "shutdown", "(", ")", "except", "AttributeError", ":", "LOGGER", ".", "debug", "(", "'Consumer does not ha...	34.4	14.6
def peng_mant(snum): r""" Return the mantissa of a number represented in engineering notation. :param snum: Number :type snum: :ref:`EngineeringNotationNumber` :rtype: float .. [[[cog cog.out(exobj_eng.get_sphinx_autodoc()) ]]] .. Auto-generated exceptions documentation for .. peng.f...	[ "def", "peng_mant", "(", "snum", ")", ":", "snum", "=", "snum", ".", "rstrip", "(", ")", "return", "float", "(", "snum", "if", "snum", "[", "-", "1", "]", ".", "isdigit", "(", ")", "else", "snum", "[", ":", "-", "1", "]", ")" ]	24.12	23.28
def iso_name_increment(name, is_dir=False, max_length=8): """Increment an ISO name to avoid name collision. Example: >>> iso_name_increment('foo.txt') 'foo1.txt' >>> iso_name_increment('bar10') 'bar11' >>> iso_name_increment('bar99', max_length=5) 'ba100' """...	[ "def", "iso_name_increment", "(", "name", ",", "is_dir", "=", "False", ",", "max_length", "=", "8", ")", ":", "# Split the extension if needed", "if", "not", "is_dir", "and", "'.'", "in", "name", ":", "name", ",", "ext", "=", "name", ".", "rsplit", "(", ...	29.333333	15.272727
def validate_bam(self, input_bam): """ Wrapper for Picard's ValidateSamFile. :param str input_bam: Path to file to validate. :return str: Command to run for the validation. """ cmd = self.tools.java + " -Xmx" + self.pm.javamem cmd += " -jar " + self.tools.picard ...	[ "def", "validate_bam", "(", "self", ",", "input_bam", ")", ":", "cmd", "=", "self", ".", "tools", ".", "java", "+", "\" -Xmx\"", "+", "self", ".", "pm", ".", "javamem", "cmd", "+=", "\" -jar \"", "+", "self", ".", "tools", ".", "picard", "+", "\" Val...	35.090909	13.454545
def format_mode(sres): """ Format a line in the directory list based on the file's type and other attributes. """ mode = sres.st_mode root = (mode & 0o700) >> 6 group = (mode & 0o070) >> 3 user = (mode & 0o7) def stat_type(md): ''' stat type''' if stat.S_ISDIR(md): return 'd' elif st...	[ "def", "format_mode", "(", "sres", ")", ":", "mode", "=", "sres", ".", "st_mode", "root", "=", "(", "mode", "&", "0o700", ")", ">>", "6", "group", "=", "(", "mode", "&", "0o070", ")", ">>", "3", "user", "=", "(", "mode", "&", "0o7", ")", "def",...	22.37037	21.111111
def com_google_fonts_check_kerning_for_non_ligated_sequences(ttFont, ligatures, has_kerning_info): """Is there kerning info for non-ligated sequences?""" def look_for_nonligated_kern_info(table): for pairpos in table.SubTable: for i, glyph in enumerate(pairpos.Coverage.glyphs): if not hasattr(pai...	[ "def", "com_google_fonts_check_kerning_for_non_ligated_sequences", "(", "ttFont", ",", "ligatures", ",", "has_kerning_info", ")", ":", "def", "look_for_nonligated_kern_info", "(", "table", ")", ":", "for", "pairpos", "in", "table", ".", "SubTable", ":", "for", "i", ...	40.145833	17.479167
def manager_required(func=None): """ Decorator for views that require not only a team but also that a user be logged in and be the manager or owner of that team. """ def decorator(view_func): @team_required @login_required @functools.wraps(view_func, assigned=available_attrs(...	[ "def", "manager_required", "(", "func", "=", "None", ")", ":", "def", "decorator", "(", "view_func", ")", ":", "@", "team_required", "@", "login_required", "@", "functools", ".", "wraps", "(", "view_func", ",", "assigned", "=", "available_attrs", "(", "view_...	37.777778	16.222222
def makedirs_safe(fulldir): """Creates a directory if it does not exists. Takes into consideration concurrent access support. Works like the shell's 'mkdir -p'. """ try: if not os.path.exists(fulldir): os.makedirs(fulldir) except OSError as exc: # Python >2.5 import errno if exc.errno == errno.EE...	[ "def", "makedirs_safe", "(", "fulldir", ")", ":", "try", ":", "if", "not", "os", ".", "path", ".", "exists", "(", "fulldir", ")", ":", "os", ".", "makedirs", "(", "fulldir", ")", "except", "OSError", "as", "exc", ":", "# Python >2.5", "import", "errno"...	30.545455	16.272727
def sanitize(self, table_name, column_name, value): """ Sanitizes given value extracted from the database according to the sanitation configuration. TODO: Add support for dates, booleans and other types found in SQL than string. :param table_name: Name of the database t...	[ "def", "sanitize", "(", "self", ",", "table_name", ",", "column_name", ",", "value", ")", ":", "sanitizer_callback", "=", "self", ".", "get_sanitizer_for", "(", "table_name", ",", "column_name", ")", "return", "sanitizer_callback", "(", "value", ")", "if", "sa...	37.08	23
def _UnserializableObjectFallback(self, obj): """Handles sanitizing of unserializable objects for Json. For instances of heap types, we take the class dict, augment it with the instance's __dict__, tag it and transmit it over to the RPC client to be reconstructed there. (Works with both old and new sty...	[ "def", "_UnserializableObjectFallback", "(", "self", ",", "obj", ")", ":", "if", "isinstance", "(", "obj", ",", "libpython", ".", "PyInstanceObjectPtr", ")", ":", "# old-style classes use 'classobj'/'instance'", "# get class attribute dictionary", "in_class", "=", "obj", ...	44.015625	22.515625
def loadXMLGenericData(filename): # not tested """Read any type of vtk data object encoded in XML format. Return an ``Actor(vtkActor)`` object.""" reader = vtk.vtkXMLGenericDataObjectReader() reader.SetFileName(filename) reader.Update() return Actor(reader.GetOutput())	[ "def", "loadXMLGenericData", "(", "filename", ")", ":", "# not tested", "reader", "=", "vtk", ".", "vtkXMLGenericDataObjectReader", "(", ")", "reader", ".", "SetFileName", "(", "filename", ")", "reader", ".", "Update", "(", ")", "return", "Actor", "(", "reader...	47.5	8
def parse_ls(out): """ Parser for Android's ls -lR output. Takes a string, returns parsed structure. """ # assumed ls -lR line format: # -rw-r--r-- root shell 0 2013-07-05 02:26 tasks # drwxr-xr-x root root 2013-07-05 02:26 log # brw------- root root ...	[ "def", "parse_ls", "(", "out", ")", ":", "# assumed ls -lR line format:", "# -rw-r--r-- root shell 0 2013-07-05 02:26 tasks", "# drwxr-xr-x root root 2013-07-05 02:26 log", "# brw------- root root 179, 0 2013-07-05 02:26 mmcblk0", "# lrwxrwxrwx root r...	35.412371	14.443299
def verify_mass_range_options(opts, parser, nonSpin=False): """ Parses the metric calculation options given and verifies that they are correct. Parameters ---------- opts : argparse.Values instance Result of parsing the input options with OptionParser parser : object The Opt...	[ "def", "verify_mass_range_options", "(", "opts", ",", "parser", ",", "nonSpin", "=", "False", ")", ":", "# Mass1 must be the heavier!", "if", "opts", ".", "min_mass1", "<", "opts", ".", "min_mass2", ":", "parser", ".", "error", "(", "\"min-mass1 cannot be less tha...	53.512739	21.33121
def get_source(self, objtxt): """Get object source""" from spyder_kernels.utils.dochelpers import getsource obj, valid = self._eval(objtxt) if valid: return getsource(obj)	[ "def", "get_source", "(", "self", ",", "objtxt", ")", ":", "from", "spyder_kernels", ".", "utils", ".", "dochelpers", "import", "getsource", "obj", ",", "valid", "=", "self", ".", "_eval", "(", "objtxt", ")", "if", "valid", ":", "return", "getsource", "(...	30	14.714286
def kill(self, exit_code: Any = None): """ Stops the behaviour Args: exit_code (object, optional): the exit code of the behaviour (Default value = None) """ self._force_kill.set() if exit_code is not None: self._exit_code = exit_code logger...	[ "def", "kill", "(", "self", ",", "exit_code", ":", "Any", "=", "None", ")", ":", "self", ".", "_force_kill", ".", "set", "(", ")", "if", "exit_code", "is", "not", "None", ":", "self", ".", "_exit_code", "=", "exit_code", "logger", ".", "info", "(", ...	31.833333	20
def add_in_filter(self, *values): """ Add a filter using "IN" logic. This is typically the primary filter that will be used to find a match and generally combines other filters to get more granular. An example of usage would be searching for an IP address (or addresses) in a spec...	[ "def", "add_in_filter", "(", "self", ",", "", "values", ")", ":", "filt", "=", "InFilter", "(", "", "values", ")", "self", ".", "update_filter", "(", "filt", ")", "return", "filt" ]	42.176471	20.176471
def _create_command_file(self, expect, send): """Internal function. Do not use. Takes a long command, and puts it in an executable file ready to run. Returns the filename. """ shutit = self.shutit random_id = shutit_util.random_id() fname = shutit_global.shutit_global_object.shutit_state_dir + '/tmp_' + ra...	[ "def", "_create_command_file", "(", "self", ",", "expect", ",", "send", ")", ":", "shutit", "=", "self", ".", "shutit", "random_id", "=", "shutit_util", ".", "random_id", "(", ")", "fname", "=", "shutit_global", ".", "shutit_global_object", ".", "shutit_state_...	51.518519	22.037037
def config_value_keys(self, sortkey = False): """ Return configuration keys directly stored in this node. Configurations in child nodes are not included. """ if sortkey: items = sorted(self.items()) else: items = self.items() return (k for k,v in i...	[ "def", "config_value_keys", "(", "self", ",", "sortkey", "=", "False", ")", ":", "if", "sortkey", ":", "items", "=", "sorted", "(", "self", ".", "items", "(", ")", ")", "else", ":", "items", "=", "self", ".", "items", "(", ")", "return", "(", "k", ...	38.777778	17.666667
def wait_lock(path, lock_fn=None, timeout=5, sleep=0.1, time_start=None): ''' Obtain a write lock. If one exists, wait for it to release first ''' if not isinstance(path, six.string_types): raise FileLockError('path must be a string') if lock_fn is None: lock_fn = path + '.w' if ...	[ "def", "wait_lock", "(", "path", ",", "lock_fn", "=", "None", ",", "timeout", "=", "5", ",", "sleep", "=", "0.1", ",", "time_start", "=", "None", ")", ":", "if", "not", "isinstance", "(", "path", ",", "six", ".", "string_types", ")", ":", "raise", ...	33.445946	21.364865
def cmd_up(self, args): '''adjust TRIM_PITCH_CD up by 5 degrees''' if len(args) == 0: adjust = 5.0 else: adjust = float(args[0]) old_trim = self.get_mav_param('TRIM_PITCH_CD', None) if old_trim is None: print("Existing trim value unknown!") ...	[ "def", "cmd_up", "(", "self", ",", "args", ")", ":", "if", "len", "(", "args", ")", "==", "0", ":", "adjust", "=", "5.0", "else", ":", "adjust", "=", "float", "(", "args", "[", "0", "]", ")", "old_trim", "=", "self", ".", "get_mav_param", "(", ...	41.5	18.375
def register(cls, name, klass, content_type='text/plain'): """ Register an emitter. Parameters:: - `name`: The name of the emitter ('json', 'xml', 'yaml', ...) - `klass`: The emitter class. - `content_type`: The content type to serve response as. """ c...	[ "def", "register", "(", "cls", ",", "name", ",", "klass", ",", "content_type", "=", "'text/plain'", ")", ":", "cls", ".", "EMITTERS", "[", "name", "]", "=", "(", "klass", ",", "content_type", ")" ]	35.2	15.8
def commit_hash(dir='.'): """ Return commit hash for HEAD of checked out branch of the specified directory. """ cmd = ['git', 'rev-parse', 'HEAD'] try: with open(os.devnull, 'w') as devnull: revision_hash = subprocess.check_output( cmd, cwd=d...	[ "def", "commit_hash", "(", "dir", "=", "'.'", ")", ":", "cmd", "=", "[", "'git'", ",", "'rev-parse'", ",", "'HEAD'", "]", "try", ":", "with", "open", "(", "os", ".", "devnull", ",", "'w'", ")", "as", "devnull", ":", "revision_hash", "=", "subprocess"...	24.772727	17.318182
def read(self, uri=None, resources=None, index_only=False): """Read sitemap from a URI including handling sitemapindexes. If index_only is True then individual sitemaps references in a sitemapindex will not be read. This will result in no resources being returned and is useful only to r...	[ "def", "read", "(", "self", ",", "uri", "=", "None", ",", "resources", "=", "None", ",", "index_only", "=", "False", ")", ":", "try", ":", "fh", "=", "URLopener", "(", ")", ".", "open", "(", "uri", ")", "self", ".", "num_files", "+=", "1", "excep...	44.483333	18.216667
def get_prefix(): """Global prefix to identify ncluster created resources name used to identify ncluster created resources, (name of EFS, VPC, keypair prefixes), can be changed through $NCLUSTER_PREFIX for debugging purposes. """ name = os.environ.get('NCLUSTER_PREFIX', DEFAULT_PREFIX) if name != DEFAULT_PREFI...	[ "def", "get_prefix", "(", ")", ":", "name", "=", "os", ".", "environ", ".", "get", "(", "'NCLUSTER_PREFIX'", ",", "DEFAULT_PREFIX", ")", "if", "name", "!=", "DEFAULT_PREFIX", ":", "validate_prefix", "(", "name", ")", "return", "name" ]	44.375	16.875
def rgb_to_name(rgb_triplet, spec=u'css3'): """ Convert a 3-tuple of integers, suitable for use in an ``rgb()`` color triplet, to its corresponding normalized color name, if any such name exists. The optional keyword argument ``spec`` determines which specification's list of color names will be...	[ "def", "rgb_to_name", "(", "rgb_triplet", ",", "spec", "=", "u'css3'", ")", ":", "return", "hex_to_name", "(", "rgb_to_hex", "(", "normalize_integer_triplet", "(", "rgb_triplet", ")", ")", ",", "spec", "=", "spec", ")" ]	28.818182	22.181818
def get_change(self, change_id): """ Get information about a proposed set of changes, as submitted by the change_rrsets method. Returns a Python data structure with status information about the changes. :type change_id: str :param change_id: The unique identifier...	[ "def", "get_change", "(", "self", ",", "change_id", ")", ":", "uri", "=", "'/%s/change/%s'", "%", "(", "self", ".", "Version", ",", "change_id", ")", "response", "=", "self", ".", "make_request", "(", "'GET'", ",", "uri", ")", "body", "=", "response", ...	37.958333	17.041667
def GET_AUTH(self): """ GET request """ return self.template_helper.get_renderer().queue(*self.submission_manager.get_job_queue_snapshot(), datetime.fromtimestamp)	[ "def", "GET_AUTH", "(", "self", ")", ":", "return", "self", ".", "template_helper", ".", "get_renderer", "(", ")", ".", "queue", "(", "*", "self", ".", "submission_manager", ".", "get_job_queue_snapshot", "(", ")", ",", "datetime", ".", "fromtimestamp", ")" ...	59	37.333333
def _upsert(context, params, data): """Insert or update data and add/update appropriate timestamps""" table = params.get("table") table = datastore.get_table(table, primary_id=False) unique_keys = ensure_list(params.get("unique")) data["__last_seen"] = datetime.datetime.utcnow() if len(unique_ke...	[ "def", "_upsert", "(", "context", ",", "params", ",", "data", ")", ":", "table", "=", "params", ".", "get", "(", "\"table\"", ")", "table", "=", "datastore", ".", "get_table", "(", "table", ",", "primary_id", "=", "False", ")", "unique_keys", "=", "ens...	40.916667	13.666667
def _make_pkh_address(pubkey_hash, witness=False, cashaddr=True): ''' bytes, bool -> str ''' addr_bytes = bytearray() if riemann.network.CASHADDR_P2PKH is not None and cashaddr: addr_bytes.extend(riemann.network.CASHADDR_P2PKH) addr_bytes.extend(pubkey_hash) return riemann.ne...	[ "def", "_make_pkh_address", "(", "pubkey_hash", ",", "witness", "=", "False", ",", "cashaddr", "=", "True", ")", ":", "addr_bytes", "=", "bytearray", "(", ")", "if", "riemann", ".", "network", ".", "CASHADDR_P2PKH", "is", "not", "None", "and", "cashaddr", ...	40.705882	19.294118
def gen_random_mobile(): """ 随机生成一个手机号 :return: * str: (string) 手机号举例如下:: print('--- gen_random_mobile demo ---') print(gen_random_mobile()) print(gen_random_mobile()) print('---') 执行结果:: --- gen_random_mobile demo --- 16706146773 ...	[ "def", "gen_random_mobile", "(", ")", ":", "prefix_list", "=", "[", "\"13\"", ",", "\"1400\"", ",", "\"1410\"", ",", "\"1440\"", ",", "\"145\"", ",", "\"146\"", ",", "\"147\"", ",", "\"148\"", ",", "\"15\"", ",", "\"162\"", ",", "\"165\"", ",", "\"166\"", ...	25.193548	22.032258
def create_cylinder(rows, cols, radius=[1.0, 1.0], length=1.0, offset=False): """Create a cylinder Parameters ---------- rows : int Number of rows. cols : int Number of columns. radius : tuple of float Cylinder radii. length : float Length of the cylinder. ...	[ "def", "create_cylinder", "(", "rows", ",", "cols", ",", "radius", "=", "[", "1.0", ",", "1.0", "]", ",", "length", "=", "1.0", ",", "offset", "=", "False", ")", ":", "verts", "=", "np", ".", "empty", "(", "(", "rows", "+", "1", ",", "cols", ",...	36.365385	17.346154
def make_frame(self, frame, birthframe, startframe, stopframe, deathframe, noiseframe=None): """ :param frame: current frame :param birthframe: frame where this animation starts returning something other than None :param startframe: frame where animation starts to evolve :param ...	[ "def", "make_frame", "(", "self", ",", "frame", ",", "birthframe", ",", "startframe", ",", "stopframe", ",", "deathframe", ",", "noiseframe", "=", "None", ")", ":", "newx", "=", "self", ".", "anim_x", ".", "make_frame", "(", "frame", ",", "birthframe", "...	47.047619	23.238095
def get_valid_statements_for_modeling(sts: List[Influence]) -> List[Influence]: """ Select INDRA statements that can be used to construct a Delphi model from a given list of statements. """ return [ s for s in sts if is_grounded_statement(s) and (s.subj_delta["polarity"] is ...	[ "def", "get_valid_statements_for_modeling", "(", "sts", ":", "List", "[", "Influence", "]", ")", "->", "List", "[", "Influence", "]", ":", "return", "[", "s", "for", "s", "in", "sts", "if", "is_grounded_statement", "(", "s", ")", "and", "(", "s", ".", ...	34.090909	19.727273
def fulltext(search, lang=Lang.English, ignore_case=True): """Full text search. Example:: filters = Text.fulltext("python pymongo_mate") .. note:: This field doesn't need to specify field. """ return { "$text": { "$search": ...	[ "def", "fulltext", "(", "search", ",", "lang", "=", "Lang", ".", "English", ",", "ignore_case", "=", "True", ")", ":", "return", "{", "\"$text\"", ":", "{", "\"$search\"", ":", "search", ",", "\"$language\"", ":", "lang", ",", "\"$caseSensitive\"", ":", ...	24.473684	20.105263
def get_version_details(path): """Parses version file :param path: path to version file :return: version details """ with open(path, "r") as reader: lines = reader.readlines() data = { line.split(" = ")[0].replace("__", ""): line.split(" = ")[1].strip()....	[ "def", "get_version_details", "(", "path", ")", ":", "with", "open", "(", "path", ",", "\"r\"", ")", "as", "reader", ":", "lines", "=", "reader", ".", "readlines", "(", ")", "data", "=", "{", "line", ".", "split", "(", "\" = \"", ")", "[", "0", "]"...	25.466667	15.666667
def get_snapshot(self, hosts, macromodulations, timeperiods): # pragma: no cover, not yet! """ Raise snapshot event handlers if NONE of the following conditions is met:: * snapshot_command is None * snapshot_enabled is disabled * snapshot_criteria does not matches current state...	[ "def", "get_snapshot", "(", "self", ",", "hosts", ",", "macromodulations", ",", "timeperiods", ")", ":", "# pragma: no cover, not yet!", "# We should have a snapshot_command, to be enabled and of course", "# in the good time and state :D", "if", "self", ".", "snapshot_command", ...	39.6875	22
def run(self): """ Run the EventHubClient in blocking mode. Opens the connection and starts running all Sender/Receiver clients. Returns a list of the start up results. For a succcesful client start the result will be `None`, otherwise the exception raised. If all clients...	[ "def", "run", "(", "self", ")", ":", "log", ".", "info", "(", "\"%r: Starting %r clients\"", ",", "self", ".", "container_id", ",", "len", "(", "self", ".", "clients", ")", ")", "try", ":", "self", ".", "_start_clients", "(", ")", "redirects", "=", "["...	44.16129	22.032258
def add_pool(arg, opts, shell_opts): """ Add a pool. """ p = Pool() p.name = opts.get('name') p.description = opts.get('description') p.default_type = opts.get('default-type') p.ipv4_default_prefix_length = opts.get('ipv4_default_prefix_length') p.ipv6_default_prefix_length = opts.get('...	[ "def", "add_pool", "(", "arg", ",", "opts", ",", "shell_opts", ")", ":", "p", "=", "Pool", "(", ")", "p", ".", "name", "=", "opts", ".", "get", "(", "'name'", ")", "p", ".", "description", "=", "opts", ".", "get", "(", "'description'", ")", "p", ...	30.941176	20.764706
def lint(fix_imports): """ Run flake8. """ from glob import glob from subprocess import call # FIXME: should support passing these in an option skip = [ 'ansible', 'db', 'flask_sessions', 'node_modules', 'requirements', ] root_files = glob('*....	[ "def", "lint", "(", "fix_imports", ")", ":", "from", "glob", "import", "glob", "from", "subprocess", "import", "call", "# FIXME: should support passing these in an option", "skip", "=", "[", "'ansible'", ",", "'db'", ",", "'flask_sessions'", ",", "'node_modules'", "...	26.866667	18.266667
def mark(self, value=1): """Updates the dictionary.""" self['count'] += value for m in self._meters: m.update(value)	[ "def", "mark", "(", "self", ",", "value", "=", "1", ")", ":", "self", "[", "'count'", "]", "+=", "value", "for", "m", "in", "self", ".", "_meters", ":", "m", ".", "update", "(", "value", ")" ]	21.666667	17.166667
def retrieve_outputs(self): """ Declare the outputs of the algorithms as attributes: x_final, y_final, metrics. """ metrics = {} for obs in self._observers['cv_metrics']: metrics[obs.name] = obs.retrieve_metrics() self.metrics = metrics	[ "def", "retrieve_outputs", "(", "self", ")", ":", "metrics", "=", "{", "}", "for", "obs", "in", "self", ".", "_observers", "[", "'cv_metrics'", "]", ":", "metrics", "[", "obs", ".", "name", "]", "=", "obs", ".", "retrieve_metrics", "(", ")", "self", ...	32.111111	13.444444
def read(self, length=1000, blocking=False): """ Read ``length`` bytes from current process output stream. Note: This method is not fully non-blocking, however it behaves like one. """ size_p = PLARGE_INTEGER(LARGE_INTEGER(0)) if not blocking: windll....	[ "def", "read", "(", "self", ",", "length", "=", "1000", ",", "blocking", "=", "False", ")", ":", "size_p", "=", "PLARGE_INTEGER", "(", "LARGE_INTEGER", "(", "0", ")", ")", "if", "not", "blocking", ":", "windll", ".", "kernel32", ".", "GetFileSizeEx", "...	38.058824	15.352941
def if_then_else(cls, condition: 'TensorFluent', true_case: 'TensorFluent', false_case: 'TensorFluent') -> 'TensorFluent': '''Returns a TensorFluent for the control op if-then-else. Args: condition: Boolean fluent for the if condition. true_ca...	[ "def", "if_then_else", "(", "cls", ",", "condition", ":", "'TensorFluent'", ",", "true_case", ":", "'TensorFluent'", ",", "false_case", ":", "'TensorFluent'", ")", "->", "'TensorFluent'", ":", "true", "=", "TensorFluent", ".", "constant", "(", "True", ",", "tf...	38.565217	22.478261
def svm_score(self, x): x = x[1:] ''' original_X = self.svm_processor.train_X[:, 1:] score = 0 for i in range(len(self.svm_processor.sv_alpha)): score += self.svm_processor.sv_alpha[i] * self.svm_processor.sv_Y[i] * utility.Kernel.gaussian_kernel(self, original_X[se...	[ "def", "svm_score", "(", "self", ",", "x", ")", ":", "x", "=", "x", "[", "1", ":", "]", "score", "=", "np", ".", "sum", "(", "self", ".", "svm_processor", ".", "sv_alpha", "", "self", ".", "svm_processor", ".", "sv_Y", "", "utility", ".", "Kern...	40.133333	40.266667
def add_edge(self, id1, id2, weight=0.0, length=1.0, label="", properties={}): """ Add weighted (0.0-1.0) edge between nodes, creating them if necessary. The weight represents the importance of the connection (not the cost). """ if id1 == id2: return None ...	[ "def", "add_edge", "(", "self", ",", "id1", ",", "id2", ",", "weight", "=", "0.0", ",", "length", "=", "1.0", ",", "label", "=", "\"\"", ",", "properties", "=", "{", "}", ")", ":", "if", "id1", "==", "id2", ":", "return", "None", "if", "not", "...	32.518519	18.481481
def pseudo_with_symbol(self, symbol, allow_multi=False): """ Return the pseudo with the given chemical symbol. Args: symbols: String with the chemical symbol of the element allow_multi: By default, the method raises ValueError if multiple occurrences are ...	[ "def", "pseudo_with_symbol", "(", "self", ",", "symbol", ",", "allow_multi", "=", "False", ")", ":", "pseudos", "=", "self", ".", "select_symbols", "(", "symbol", ",", "ret_list", "=", "True", ")", "if", "not", "pseudos", "or", "(", "len", "(", "pseudos"...	39.4	26
def is_consecutive(self): """ Determine whether or not the non-zero labels in the segmentation image are consecutive (i.e. no missing values). """ if (self.labels[-1] - self.labels[0] + 1) == self.nlabels: return True else: return False	[ "def", "is_consecutive", "(", "self", ")", ":", "if", "(", "self", ".", "labels", "[", "-", "1", "]", "-", "self", ".", "labels", "[", "0", "]", "+", "1", ")", "==", "self", ".", "nlabels", ":", "return", "True", "else", ":", "return", "False" ]	30	18.8
def get_stored_cert_serials(store): ''' Get all of the certificate serials in the specified store store The store to get all the certificate serials from CLI Example: .. code-block:: bash salt '*' certutil.get_stored_cert_serials <store> ''' cmd = "certutil.exe -store {0}...	[ "def", "get_stored_cert_serials", "(", "store", ")", ":", "cmd", "=", "\"certutil.exe -store {0}\"", ".", "format", "(", "store", ")", "out", "=", "__salt__", "[", "'cmd.run'", "]", "(", "cmd", ")", "# match serial numbers by header position to work with multiple langua...	28.277778	24.944444
def add_ref_annotation(self, id_tier, tier2, time, value='', prev=None, svg=None): """Add a reference annotation. .. note:: When a timepoint matches two annotations the new reference annotation will reference to the first annotation. To circumvent this it's alw...	[ "def", "add_ref_annotation", "(", "self", ",", "id_tier", ",", "tier2", ",", "time", ",", "value", "=", "''", ",", "prev", "=", "None", ",", "svg", "=", "None", ")", ":", "if", "self", ".", "tiers", "[", "id_tier", "]", "[", "0", "]", ":", "raise...	47.6875	17.78125
def C(w, Xs): '''Calculate the cylinder center given the cylinder direction and a list of data points. ''' n = len(Xs) P = projection_matrix(w) Ys = [np.dot(P, X) for X in Xs] A = calc_A(Ys) A_hat = calc_A_hat(A, skew_matrix(w)) return np.dot(A_hat, sum(np.dot(Y, Y) * Y for Y in Ys...	[ "def", "C", "(", "w", ",", "Xs", ")", ":", "n", "=", "len", "(", "Xs", ")", "P", "=", "projection_matrix", "(", "w", ")", "Ys", "=", "[", "np", ".", "dot", "(", "P", ",", "X", ")", "for", "X", "in", "Xs", "]", "A", "=", "calc_A", "(", "...	31	23.363636
def firmware_download_input_protocol_type_usb_protocol_usb_directory(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") firmware_download = ET.Element("firmware_download") config = firmware_download input = ET.SubElement(firmware_download, "input") ...	[ "def", "firmware_download_input_protocol_type_usb_protocol_usb_directory", "(", "self", ",", "", "", "kwargs", ")", ":", "config", "=", "ET", ".", "Element", "(", "\"config\"", ")", "firmware_download", "=", "ET", ".", "Element", "(", "\"firmware_download\"", ")",...	45.066667	15.4
def request(self, req_and_resp, opt=None, headers=None): """ preprocess before performing a request, usually some patching. authorization also applied here. :param req_and_resp: tuple of Request and Response :type req_and_resp: (Request, Response) :param opt: customized options ...	[ "def", "request", "(", "self", ",", "req_and_resp", ",", "opt", "=", "None", ",", "headers", "=", "None", ")", ":", "req", ",", "resp", "=", "req_and_resp", "# dump info for debugging", "logger", ".", "info", "(", "'request.url: {0}'", ".", "format", "(", ...	38.814815	17
def make_class_method_decorator(classkey, modname=None): """ register a class to be injectable classkey is a key that identifies the injected class REMEMBER to call inject_instance in __init__ Args: classkey : the class to be injected into modname : the global __name__ of the module...	[ "def", "make_class_method_decorator", "(", "classkey", ",", "modname", "=", "None", ")", ":", "global", "__APP_MODNAME_REGISTER__", "#if util_arg.VERBOSE or VERBOSE_CLASS:", "if", "VERBOSE_CLASS", ":", "print", "(", "'[util_class] register via make_class_method_decorator classkey...	42.830508	17.644068
def use_comparative_agent_view(self): """Pass through to provider ResourceAgentSession.use_comparative_agent_view""" self._object_views['agent'] = COMPARATIVE # self._get_provider_session('resource_agent_session') # To make sure the session is tracked for session in self._get_provider_se...	[ "def", "use_comparative_agent_view", "(", "self", ")", ":", "self", ".", "_object_views", "[", "'agent'", "]", "=", "COMPARATIVE", "# self._get_provider_session('resource_agent_session') # To make sure the session is tracked", "for", "session", "in", "self", ".", "_get_provid...	49.666667	16.333333
def async_mail_task(subject_or_message, to=None, template=None, kwargs): """ Celery task to send emails asynchronously using the mail bundle. """ to = to or kwargs.pop('recipients', []) msg = make_message(subject_or_message, to, template, kwargs) with mail.connect() as connection: co...	[ "def", "async_mail_task", "(", "subject_or_message", ",", "to", "=", "None", ",", "template", "=", "None", ",", "", "", "kwargs", ")", ":", "to", "=", "to", "or", "kwargs", ".", "pop", "(", "'recipients'", ",", "[", "]", ")", "msg", "=", "make_mess...	41.375	13.125
def wait(self, task_id): """ Blocking method which wait end of task. It's prefered to use :class:`carotte.Task` object directly :param string task_id: Task ID :returns: Task dict :rtype: dict """ data = { 'action': 'wait', 'id': t...	[ "def", "wait", "(", "self", ",", "task_id", ")", ":", "data", "=", "{", "'action'", ":", "'wait'", ",", "'id'", ":", "task_id", "}", "self", ".", "__send_pyobj", "(", "data", ")", "task", "=", "self", ".", "__recv_pyobj", "(", "notimeout", "=", "True...	24.764706	16.647059

def convert_softmax(net, node, module, builder): """Convert a softmax layer from mxnet to coreml. Parameters ---------- network: net A mxnet network object. layer: node Node to convert. module: module An module for MXNet builder: NeuralNetworkBuilder A neu...

[ "def", "convert_softmax", "(", "net", ",", "node", ",", "module", ",", "builder", ")", ":", "input_name", ",", "output_name", "=", "_get_input_output_name", "(", "net", ",", "node", ")", "name", "=", "node", "[", "'name'", "]", "builder", ".", "add_softmax...

25.136364

18

def update_screen(self): """Refresh the screen. You don't need to override this except to update only small portins of the screen.""" self.clock.tick(self.FPS) pygame.display.update()

[ "def", "update_screen", "(", "self", ")", ":", "self", ".", "clock", ".", "tick", "(", "self", ".", "FPS", ")", "pygame", ".", "display", ".", "update", "(", ")" ]

51

8

def path(self, which=None): """Extend ``nailgun.entity_mixins.Entity.path``. The format of the returned path depends on the value of ``which``: incremental_update /content_view_versions/incremental_update promote /content_view_versions/<id>/promote ``su...

[ "def", "path", "(", "self", ",", "which", "=", "None", ")", ":", "if", "which", "in", "(", "'incremental_update'", ",", "'promote'", ")", ":", "prefix", "=", "'base'", "if", "which", "==", "'incremental_update'", "else", "'self'", "return", "'{0}/{1}'", "....

33.1

20.15

def cross_v2(vec1, vec2): """Return the crossproduct of the two vectors as a Vec2. Cross product doesn't really make sense in 2D, but return the Z component of the 3d result. """ return vec1.y * vec2.x - vec1.x * vec2.y

[ "def", "cross_v2", "(", "vec1", ",", "vec2", ")", ":", "return", "vec1", ".", "y", "*", "vec2", ".", "x", "-", "vec1", ".", "x", "*", "vec2", ".", "y" ]

33.428571

16.428571

def _init_map(self, record_types=None, **kwargs): """Initialize form map""" osid_objects.OsidObjectForm._init_map(self, record_types=record_types) self._my_map['assignedAgencyIds'] = [str(kwargs['agency_id'])]

[ "def", "_init_map", "(", "self", ",", "record_types", "=", "None", ",", "*", "*", "kwargs", ")", ":", "osid_objects", ".", "OsidObjectForm", ".", "_init_map", "(", "self", ",", "record_types", "=", "record_types", ")", "self", ".", "_my_map", "[", "'assign...

57.5

19.25

def blockingSave(self, path): """ saved session to file - returns after finish only called by interactiveTutorial-save at the moment """ self.tmp_dir_save_session = self.tmp_dir_session.join('block').mkdir() state = {'session': dict(self.opts), 'di...

[ "def", "blockingSave", "(", "self", ",", "path", ")", ":", "self", ".", "tmp_dir_save_session", "=", "self", ".", "tmp_dir_session", ".", "join", "(", "'block'", ")", ".", "mkdir", "(", ")", "state", "=", "{", "'session'", ":", "dict", "(", "self", "."...

43.636364

14

def use_any_adapter(self, use_any_adapter): """ Allows GNS3 to use any VMware adapter on this instance. :param use_any_adapter: boolean """ if use_any_adapter: log.info("VMware VM '{name}' [{id}] is allowed to use any adapter".format(name=self.name, id=self.id)) ...

[ "def", "use_any_adapter", "(", "self", ",", "use_any_adapter", ")", ":", "if", "use_any_adapter", ":", "log", ".", "info", "(", "\"VMware VM '{name}' [{id}] is allowed to use any adapter\"", ".", "format", "(", "name", "=", "self", ".", "name", ",", "id", "=", "...

40.5

25.5

def shortened_character_name(self_or_cls, c, eliminations=[], substitutions={}, transforms=[]): """ Given a unicode character c, return the shortened unicode name (as a list of tokens) by applying the eliminations, substitutions and transforms. """ name = unicodedata.name...

[ "def", "shortened_character_name", "(", "self_or_cls", ",", "c", ",", "eliminations", "=", "[", "]", ",", "substitutions", "=", "{", "}", ",", "transforms", "=", "[", "]", ")", ":", "name", "=", "unicodedata", ".", "name", "(", "c", ")", ".", "lower", ...

41.6875

13.0625

def on_start(self, host, port, channel, nickname, password): """ A WebSocket session has started - create a greenlet to host the IRC client, and start it. """ self.client = WebSocketIRCClient(host, port, channel, nickname, password, self) ...

[ "def", "on_start", "(", "self", ",", "host", ",", "port", ",", "channel", ",", "nickname", ",", "password", ")", ":", "self", ".", "client", "=", "WebSocketIRCClient", "(", "host", ",", "port", ",", "channel", ",", "nickname", ",", "password", ",", "se...

43.75

12.5

def clone(self, newname, config_path=None, flags=0, bdevtype=None, bdevdata=None, newsize=0, hookargs=()): """ Clone the current container. """ args = {} args['newname'] = newname args['flags'] = flags args['newsize'] = newsize args['hoo...

[ "def", "clone", "(", "self", ",", "newname", ",", "config_path", "=", "None", ",", "flags", "=", "0", ",", "bdevtype", "=", "None", ",", "bdevdata", "=", "None", ",", "newsize", "=", "0", ",", "hookargs", "=", "(", ")", ")", ":", "args", "=", "{"...

29.954545

13.954545

def delete(self, path, data, **options): """ Parses DELETE request options and dispatches a request """ data, options = self._update_request(data, options) return self.request('delete', path, data=data, **options)

[ "def", "delete", "(", "self", ",", "path", ",", "data", ",", "*", "*", "options", ")", ":", "data", ",", "options", "=", "self", ".", "_update_request", "(", "data", ",", "options", ")", "return", "self", ".", "request", "(", "'delete'", ",", "path",...

41.333333

11

def _scan(positions): """get the region inside the vector with more expression""" scores = [] for start in range(0, len(positions) - 17, 5): end = start = 17 scores.add(_enrichment(positions[start:end], positions[:start], positions[end:]))

[ "def", "_scan", "(", "positions", ")", ":", "scores", "=", "[", "]", "for", "start", "in", "range", "(", "0", ",", "len", "(", "positions", ")", "-", "17", ",", "5", ")", ":", "end", "=", "start", "=", "17", "scores", ".", "add", "(", "_enrichm...

43.666667

19.833333

def kwargs_as_assignments(call_node, parent): """Yield NoDeclAssign nodes from kwargs in a Call node.""" if not isinstance(call_node, ast.Call): raise TypeError('node must be an ast.Call') if len(call_node.args) > 0: raise ValueError('positional args not allowed') for keyword in call_n...

[ "def", "kwargs_as_assignments", "(", "call_node", ",", "parent", ")", ":", "if", "not", "isinstance", "(", "call_node", ",", "ast", ".", "Call", ")", ":", "raise", "TypeError", "(", "'node must be an ast.Call'", ")", "if", "len", "(", "call_node", ".", "args...

37.45

17.35

def increment(self, key, value=1): """ Increment the value of an item in the cache. :param key: The cache key :type key: str :param value: The increment value :type value: int :rtype: int or bool """ self._store.increment(self.tagged_item_key(ke...

[ "def", "increment", "(", "self", ",", "key", ",", "value", "=", "1", ")", ":", "self", ".", "_store", ".", "increment", "(", "self", ".", "tagged_item_key", "(", "key", ")", ",", "value", ")" ]

24.461538

16.615385

def split_by_connected_component(self, idents): '''Split idents into equivalence classes based on connected components. ''' idents_remaining = set(idents) connected_components = [] for ident in idents: if ident not in idents_remaining: continue...

[ "def", "split_by_connected_component", "(", "self", ",", "idents", ")", ":", "idents_remaining", "=", "set", "(", "idents", ")", "connected_components", "=", "[", "]", "for", "ident", "in", "idents", ":", "if", "ident", "not", "in", "idents_remaining", ":", ...

36.363636

16.363636

def _paramiko_tunnel(lport, rport, server, remoteip, keyfile=None, password=None): """Function for actually starting a paramiko tunnel, to be passed to multiprocessing.Process(target=this), and not called directly. """ username, server, port = _split_server(server) client = paramiko.SSHClient() ...

[ "def", "_paramiko_tunnel", "(", "lport", ",", "rport", ",", "server", ",", "remoteip", ",", "keyfile", "=", "None", ",", "password", "=", "None", ")", ":", "username", ",", "server", ",", "port", "=", "_split_server", "(", "server", ")", "client", "=", ...

40.34375

22.71875

def validate(self, instance, value): """Check the class of the container and validate each element This returns a copy of the container to prevent unwanted sharing of pointers. """ if not self.coerce and not isinstance(value, self._class_container): self.error(instan...

[ "def", "validate", "(", "self", ",", "instance", ",", "value", ")", ":", "if", "not", "self", ".", "coerce", "and", "not", "isinstance", "(", "value", ",", "self", ".", "_class_container", ")", ":", "self", ".", "error", "(", "instance", ",", "value", ...

38.571429

16.952381

def scalar(cls, value): """Create an ArgumentType with a single scalar in range(value).""" return lambda i, name: cls(i, name, (value,), lambda a: a[0], None)

[ "def", "scalar", "(", "cls", ",", "value", ")", ":", "return", "lambda", "i", ",", "name", ":", "cls", "(", "i", ",", "name", ",", "(", "value", ",", ")", ",", "lambda", "a", ":", "a", "[", "0", "]", ",", "None", ")" ]

54.666667

16

def register_dependency(self, data_src, data_sink): """ registers a dependency of data_src -> data_sink by placing appropriate entries in provides_for and depends_on """ pdebug("registering dependency %s -> %s" % (data_src, data_sink)) if (data_src not in self._gettask(data...

[ "def", "register_dependency", "(", "self", ",", "data_src", ",", "data_sink", ")", ":", "pdebug", "(", "\"registering dependency %s -> %s\"", "%", "(", "data_src", ",", "data_sink", ")", ")", "if", "(", "data_src", "not", "in", "self", ".", "_gettask", "(", ...

44.083333

24.916667

def duration(cls, seconds, first=True): """ Constructs a human readable string to indicate the time duration for the given seconds :param int seconds: :param bool first: Just return the first unit instead of all :rtype: str """ num_units = [] for unit in...

[ "def", "duration", "(", "cls", ",", "seconds", ",", "first", "=", "True", ")", ":", "num_units", "=", "[", "]", "for", "unit", "in", "reversed", "(", "TimeUnit", ")", ":", "if", "seconds", ">=", "unit", ".", "seconds", ":", "name", "=", "unit", "."...

32.285714

17.52381

def remap_index_fn(ref_file): """minimap2 can build indexes on the fly but will also store commons ones. """ index_dir = os.path.join(os.path.dirname(ref_file), os.pardir, "minimap2") if os.path.exists(index_dir) and os.path.isdir(index_dir): return index_dir else: return os.path.dir...

[ "def", "remap_index_fn", "(", "ref_file", ")", ":", "index_dir", "=", "os", ".", "path", ".", "join", "(", "os", ".", "path", ".", "dirname", "(", "ref_file", ")", ",", "os", ".", "pardir", ",", "\"minimap2\"", ")", "if", "os", ".", "path", ".", "e...

40.875

14.75

def filename(self): """ Name of the file on the client file system, but normalized to ensure file system compatibility. An empty filename is returned as 'empty'. Only ASCII letters, digits, dashes, underscores and dots are allowed in the final filename. Accents are removed, ...

[ "def", "filename", "(", "self", ")", ":", "fname", "=", "self", ".", "raw_filename", "if", "not", "isinstance", "(", "fname", ",", "unicode", ")", ":", "fname", "=", "fname", ".", "decode", "(", "'utf8'", ",", "'ignore'", ")", "fname", "=", "normalize"...

52.333333

19.611111

def hide_zeroes(self): ''' Sometimes it makes sense to hide the labels for subsets whose size is zero. This utility method does this. ''' for v in self.subset_labels: if v is not None and v.get_text() == '0': v.set_visible(False)

[ "def", "hide_zeroes", "(", "self", ")", ":", "for", "v", "in", "self", ".", "subset_labels", ":", "if", "v", "is", "not", "None", "and", "v", ".", "get_text", "(", ")", "==", "'0'", ":", "v", ".", "set_visible", "(", "False", ")" ]

36.25

17.75

def _maybe_validate_rightmost_transposed_ndims( rightmost_transposed_ndims, validate_args, name=None): """Checks that `rightmost_transposed_ndims` is valid.""" with tf.name_scope(name or 'maybe_validate_rightmost_transposed_ndims'): assertions = [] if not dtype_util.is_integer(rightmost_transposed_ndims...

[ "def", "_maybe_validate_rightmost_transposed_ndims", "(", "rightmost_transposed_ndims", ",", "validate_args", ",", "name", "=", "None", ")", ":", "with", "tf", ".", "name_scope", "(", "name", "or", "'maybe_validate_rightmost_transposed_ndims'", ")", ":", "assertions", "...

44.741935

20.354839

def nonblock_recv(self): """Non blocking receive""" if self.buffered_frames(): # Get a frame from the buffer return self.get_frame() # Set the non blocking flag, read from the socket, and unset the flag self.set_nonblock(True) pkt = L2bpfListenSocket.rec...

[ "def", "nonblock_recv", "(", "self", ")", ":", "if", "self", ".", "buffered_frames", "(", ")", ":", "# Get a frame from the buffer", "return", "self", ".", "get_frame", "(", ")", "# Set the non blocking flag, read from the socket, and unset the flag", "self", ".", "set_...

30.666667

15.5

def _get_url(url): """Retrieve requested URL""" try: data = HTTP_SESSION.get(url, stream=True) data.raise_for_status() except requests.exceptions.RequestException as exc: raise FetcherException(exc) return data

[ "def", "_get_url", "(", "url", ")", ":", "try", ":", "data", "=", "HTTP_SESSION", ".", "get", "(", "url", ",", "stream", "=", "True", ")", "data", ".", "raise_for_status", "(", ")", "except", "requests", ".", "exceptions", ".", "RequestException", "as", ...

27

17.444444

def tf_action_exploration(self, action, exploration, action_spec): """ Applies optional exploration to the action (post-processor for action outputs). Args: action (tf.Tensor): The original output action tensor (to be post-processed). exploration (Exploration): The Exp...

[ "def", "tf_action_exploration", "(", "self", ",", "action", ",", "exploration", ",", "action_spec", ")", ":", "action_shape", "=", "tf", ".", "shape", "(", "input", "=", "action", ")", "exploration_value", "=", "exploration", ".", "tf_explore", "(", "episode",...

40.931818

22.386364

def load(stream, fmt='lha'): """Load a parameter file in DSixTools SLHA-like format or its JSON or YAML representation.""" if fmt == 'lha': return pylha.load(stream) elif fmt == 'json': if isinstance(stream, str): return json.loads(stream) else: return jso...

[ "def", "load", "(", "stream", ",", "fmt", "=", "'lha'", ")", ":", "if", "fmt", "==", "'lha'", ":", "return", "pylha", ".", "load", "(", "stream", ")", "elif", "fmt", "==", "'json'", ":", "if", "isinstance", "(", "stream", ",", "str", ")", ":", "r...

31.666667

10

def integer_list_file(cls, filename): """ Read a list of integers from a file. The file format is: - # anywhere in the line begins a comment - leading and trailing spaces are ignored - empty lines are ignored - integers can be specified as: - dec...

[ "def", "integer_list_file", "(", "cls", ",", "filename", ")", ":", "count", "=", "0", "result", "=", "list", "(", ")", "fd", "=", "open", "(", "filename", ",", "'r'", ")", "for", "line", "in", "fd", ":", "count", "=", "count", "+", "1", "if", "'#...

31.923077

12.282051

def calibrate_container_with_instrument(self, container: Container, instrument, save: bool ): '''Calibrates a container using the bottom...

[ "def", "calibrate_container_with_instrument", "(", "self", ",", "container", ":", "Container", ",", "instrument", ",", "save", ":", "bool", ")", ":", "well", "=", "container", "[", "0", "]", "# Get the relative position of well with respect to instrument", "delta", "=...

29.894737

18.842105

def groups_delete(self, room_id=None, group=None, **kwargs): """Delete a private group.""" if room_id: return self.__call_api_post('groups.delete', roomId=room_id, kwargs=kwargs) elif group: return self.__call_api_post('groups.delete', roomName=group, kwargs=kwargs) ...

[ "def", "groups_delete", "(", "self", ",", "room_id", "=", "None", ",", "group", "=", "None", ",", "*", "*", "kwargs", ")", ":", "if", "room_id", ":", "return", "self", ".", "__call_api_post", "(", "'groups.delete'", ",", "roomId", "=", "room_id", ",", ...

49.375

27

def fit(self, X, y=None, **fit_params): """Fit base estimators. Parameters ---------- X : array-like, shape = (n_samples, n_features) Training data. y : array-like, optional Target data if base estimators are supervised. Returns ------- ...

[ "def", "fit", "(", "self", ",", "X", ",", "y", "=", "None", ",", "*", "*", "fit_params", ")", ":", "X", "=", "numpy", ".", "asarray", "(", "X", ")", "self", ".", "_fit_estimators", "(", "X", ",", "y", ",", "*", "*", "fit_params", ")", "Xt", "...

23.952381

18.142857

def prepare_samples(job, fastqs, univ_options): """ This module will accept a dict object holding the 3 input prefixes and the patient id and will attempt to store the fastqs to the jobstore. The input files must satisfy the following 1. File extensions can only be fastq or fq (.gz is also allowed) ...

[ "def", "prepare_samples", "(", "job", ",", "fastqs", ",", "univ_options", ")", ":", "job", ".", "fileStore", ".", "logToMaster", "(", "'Downloading Inputs for %s'", "%", "univ_options", "[", "'patient'", "]", ")", "allowed_samples", "=", "{", "'tumor_dna_fastq_pre...

53.039474

23.828947

def writeWarp(self, warpDict): """ Write a list of (in, out) values for a warpmap """ warpElement = ET.Element("warp") axisNames = sorted(warpDict.keys()) for name in axisNames: axisElement = ET.Element("axis") axisElement.attrib['name'] = name for a, ...

[ "def", "writeWarp", "(", "self", ",", "warpDict", ")", ":", "warpElement", "=", "ET", ".", "Element", "(", "\"warp\"", ")", "axisNames", "=", "sorted", "(", "warpDict", ".", "keys", "(", ")", ")", "for", "name", "in", "axisNames", ":", "axisElement", "...

42.285714

4.142857

def rev(self, i): """Return a clone with a different revision.""" on = copy(self) on.revision = i return on

[ "def", "rev", "(", "self", ",", "i", ")", ":", "on", "=", "copy", "(", "self", ")", "on", ".", "revision", "=", "i", "return", "on" ]

27

16

def __select_nearest_ws(jsondata, latitude, longitude): """Select the nearest weatherstation.""" log.debug("__select_nearest_ws: latitude: %s, longitude: %s", latitude, longitude) dist = 0 dist2 = 0 loc_data = None try: ws_json = jsondata[__ACTUAL] ws_json = ws_jso...

[ "def", "__select_nearest_ws", "(", "jsondata", ",", "latitude", ",", "longitude", ")", ":", "log", ".", "debug", "(", "\"__select_nearest_ws: latitude: %s, longitude: %s\"", ",", "latitude", ",", "longitude", ")", "dist", "=", "0", "dist2", "=", "0", "loc_data", ...

32.948718

17.410256

def dict(self, iss_list=None): """ Return the bundle of keys as a dictionary with the issuer IDs as the keys and the key sets represented as JWKS instances. :param iss_list: List of Issuer IDs that should be part of the output :rtype: Dictionary """ ...

[ "def", "dict", "(", "self", ",", "iss_list", "=", "None", ")", ":", "_int", "=", "{", "}", "for", "iss", ",", "kj", "in", "self", ".", "bundle", ".", "items", "(", ")", ":", "if", "iss_list", "is", "None", "or", "iss", "in", "iss_list", ":", "t...

36.117647

17.294118

def create_message(self): """Returns a message body to send in this email. Should be from email.mime.*""" body = dedent("""\ Received exception {exception} on {queue} from worker {worker}: {traceback} Payload: {payload} """).format(exception=self._exception, ...

[ "def", "create_message", "(", "self", ")", ":", "body", "=", "dedent", "(", "\"\"\"\\\n Received exception {exception} on {queue} from worker {worker}:\n\n {traceback}\n\n Payload:\n {payload}\n\n \"\"\"", ")", ".", "format", "(", "exception", "=", ...

27.666667

18.611111

def make_proxy_method(cls, name): """Creates a proxy function that can be used by Flasks routing. The proxy instantiates the Mocha subclass and calls the appropriate method. :param name: the name of the method to create a proxy for """ i = cls() view = getattr(i,...

[ "def", "make_proxy_method", "(", "cls", ",", "name", ")", ":", "i", "=", "cls", "(", ")", "view", "=", "getattr", "(", "i", ",", "name", ")", "for", "decorator", "in", "cls", ".", "decorators", ":", "view", "=", "decorator", "(", "view", ")", "@", ...

38.971014

20.710145

def transaction_search(self, **kwargs): """Shortcut for the TransactionSearch method. Returns a PayPalResponseList object, which merges the L_ syntax list to a list of dictionaries with properly named keys. Note that the API will limit returned transactions to 100. Required Kwa...

[ "def", "transaction_search", "(", "self", ",", "*", "*", "kwargs", ")", ":", "plain", "=", "self", ".", "_call", "(", "'TransactionSearch'", ",", "*", "*", "kwargs", ")", "return", "PayPalResponseList", "(", "plain", ".", "raw", ",", "self", ".", "config...

33.722222

22.388889

def get(self, request, *args, **kwargs): """ Do the login and password protection. """ response = super(EntryProtectionMixin, self).get( request, *args, **kwargs) if self.object.login_required and not request.user.is_authenticated: return self.login() ...

[ "def", "get", "(", "self", ",", "request", ",", "*", "args", ",", "*", "*", "kwargs", ")", ":", "response", "=", "super", "(", "EntryProtectionMixin", ",", "self", ")", ".", "get", "(", "request", ",", "*", "args", ",", "*", "*", "kwargs", ")", "...

41.833333

12.5

def transform(self, maps): """ This function transforms from component masses and caretsian spins to chi_p. Parameters ---------- maps : a mapping object Examples -------- Convert a dict of numpy.array: Returns ------- out : dict...

[ "def", "transform", "(", "self", ",", "maps", ")", ":", "out", "=", "{", "}", "out", "[", "\"chi_p\"", "]", "=", "conversions", ".", "chi_p", "(", "maps", "[", "parameters", ".", "mass1", "]", ",", "maps", "[", "parameters", ".", "mass2", "]", ",",...

31.791667

21.583333

def _do_subst(node, subs): """ Fetch the node contents and replace all instances of the keys with their values. For example, if subs is {'%VERSION%': '1.2345', '%BASE%': 'MyProg', '%prefix%': '/bin'}, then all instances of %VERSION% in the file will be replaced with 1.2345 and so forth. ...

[ "def", "_do_subst", "(", "node", ",", "subs", ")", ":", "contents", "=", "node", ".", "get_text_contents", "(", ")", "if", "subs", ":", "for", "(", "k", ",", "val", ")", "in", "subs", ":", "contents", "=", "re", ".", "sub", "(", "k", ",", "val", ...

34.238095

17

def date_map(doc, datemap_list, time_format=None): ''' For all the datetime fields in "datemap" find that key in doc and map the datetime object to a strftime string. This pprint and others will print out readable datetimes. ''' if datemap_list: for i in datemap_list:...

[ "def", "date_map", "(", "doc", ",", "datemap_list", ",", "time_format", "=", "None", ")", ":", "if", "datemap_list", ":", "for", "i", "in", "datemap_list", ":", "if", "isinstance", "(", "i", ",", "datetime", ")", ":", "doc", "=", "CursorFormatter", ".", ...

46.2

26.6

def stop_consumer(self): """Stop the consumer object and allow it to do a clean shutdown if it has the ability to do so. """ try: LOGGER.info('Shutting down the consumer') self.consumer.shutdown() except AttributeError: LOGGER.debug('Consumer ...

[ "def", "stop_consumer", "(", "self", ")", ":", "try", ":", "LOGGER", ".", "info", "(", "'Shutting down the consumer'", ")", "self", ".", "consumer", ".", "shutdown", "(", ")", "except", "AttributeError", ":", "LOGGER", ".", "debug", "(", "'Consumer does not ha...

34.4

14.6

def peng_mant(snum): r""" Return the mantissa of a number represented in engineering notation. :param snum: Number :type snum: :ref:`EngineeringNotationNumber` :rtype: float .. [[[cog cog.out(exobj_eng.get_sphinx_autodoc()) ]]] .. Auto-generated exceptions documentation for .. peng.f...

[ "def", "peng_mant", "(", "snum", ")", ":", "snum", "=", "snum", ".", "rstrip", "(", ")", "return", "float", "(", "snum", "if", "snum", "[", "-", "1", "]", ".", "isdigit", "(", ")", "else", "snum", "[", ":", "-", "1", "]", ")" ]

24.12

23.28

def iso_name_increment(name, is_dir=False, max_length=8): """Increment an ISO name to avoid name collision. Example: >>> iso_name_increment('foo.txt') 'foo1.txt' >>> iso_name_increment('bar10') 'bar11' >>> iso_name_increment('bar99', max_length=5) 'ba100' """...

[ "def", "iso_name_increment", "(", "name", ",", "is_dir", "=", "False", ",", "max_length", "=", "8", ")", ":", "# Split the extension if needed", "if", "not", "is_dir", "and", "'.'", "in", "name", ":", "name", ",", "ext", "=", "name", ".", "rsplit", "(", ...

29.333333

15.272727

def validate_bam(self, input_bam): """ Wrapper for Picard's ValidateSamFile. :param str input_bam: Path to file to validate. :return str: Command to run for the validation. """ cmd = self.tools.java + " -Xmx" + self.pm.javamem cmd += " -jar " + self.tools.picard ...

[ "def", "validate_bam", "(", "self", ",", "input_bam", ")", ":", "cmd", "=", "self", ".", "tools", ".", "java", "+", "\" -Xmx\"", "+", "self", ".", "pm", ".", "javamem", "cmd", "+=", "\" -jar \"", "+", "self", ".", "tools", ".", "picard", "+", "\" Val...

35.090909

13.454545

def format_mode(sres): """ Format a line in the directory list based on the file's type and other attributes. """ mode = sres.st_mode root = (mode & 0o700) >> 6 group = (mode & 0o070) >> 3 user = (mode & 0o7) def stat_type(md): ''' stat type''' if stat.S_ISDIR(md): return 'd' elif st...

[ "def", "format_mode", "(", "sres", ")", ":", "mode", "=", "sres", ".", "st_mode", "root", "=", "(", "mode", "&", "0o700", ")", ">>", "6", "group", "=", "(", "mode", "&", "0o070", ")", ">>", "3", "user", "=", "(", "mode", "&", "0o7", ")", "def",...

22.37037

21.111111

def com_google_fonts_check_kerning_for_non_ligated_sequences(ttFont, ligatures, has_kerning_info): """Is there kerning info for non-ligated sequences?""" def look_for_nonligated_kern_info(table): for pairpos in table.SubTable: for i, glyph in enumerate(pairpos.Coverage.glyphs): if not hasattr(pai...

[ "def", "com_google_fonts_check_kerning_for_non_ligated_sequences", "(", "ttFont", ",", "ligatures", ",", "has_kerning_info", ")", ":", "def", "look_for_nonligated_kern_info", "(", "table", ")", ":", "for", "pairpos", "in", "table", ".", "SubTable", ":", "for", "i", ...

40.145833

17.479167

def manager_required(func=None): """ Decorator for views that require not only a team but also that a user be logged in and be the manager or owner of that team. """ def decorator(view_func): @team_required @login_required @functools.wraps(view_func, assigned=available_attrs(...

[ "def", "manager_required", "(", "func", "=", "None", ")", ":", "def", "decorator", "(", "view_func", ")", ":", "@", "team_required", "@", "login_required", "@", "functools", ".", "wraps", "(", "view_func", ",", "assigned", "=", "available_attrs", "(", "view_...

37.777778

16.222222

def makedirs_safe(fulldir): """Creates a directory if it does not exists. Takes into consideration concurrent access support. Works like the shell's 'mkdir -p'. """ try: if not os.path.exists(fulldir): os.makedirs(fulldir) except OSError as exc: # Python >2.5 import errno if exc.errno == errno.EE...

[ "def", "makedirs_safe", "(", "fulldir", ")", ":", "try", ":", "if", "not", "os", ".", "path", ".", "exists", "(", "fulldir", ")", ":", "os", ".", "makedirs", "(", "fulldir", ")", "except", "OSError", "as", "exc", ":", "# Python >2.5", "import", "errno"...

30.545455

16.272727

def sanitize(self, table_name, column_name, value): """ Sanitizes given value extracted from the database according to the sanitation configuration. TODO: Add support for dates, booleans and other types found in SQL than string. :param table_name: Name of the database t...

[ "def", "sanitize", "(", "self", ",", "table_name", ",", "column_name", ",", "value", ")", ":", "sanitizer_callback", "=", "self", ".", "get_sanitizer_for", "(", "table_name", ",", "column_name", ")", "return", "sanitizer_callback", "(", "value", ")", "if", "sa...

37.08

23

def _UnserializableObjectFallback(self, obj): """Handles sanitizing of unserializable objects for Json. For instances of heap types, we take the class dict, augment it with the instance's __dict__, tag it and transmit it over to the RPC client to be reconstructed there. (Works with both old and new sty...

[ "def", "_UnserializableObjectFallback", "(", "self", ",", "obj", ")", ":", "if", "isinstance", "(", "obj", ",", "libpython", ".", "PyInstanceObjectPtr", ")", ":", "# old-style classes use 'classobj'/'instance'", "# get class attribute dictionary", "in_class", "=", "obj", ...

44.015625

22.515625

def loadXMLGenericData(filename): # not tested """Read any type of vtk data object encoded in XML format. Return an ``Actor(vtkActor)`` object.""" reader = vtk.vtkXMLGenericDataObjectReader() reader.SetFileName(filename) reader.Update() return Actor(reader.GetOutput())

[ "def", "loadXMLGenericData", "(", "filename", ")", ":", "# not tested", "reader", "=", "vtk", ".", "vtkXMLGenericDataObjectReader", "(", ")", "reader", ".", "SetFileName", "(", "filename", ")", "reader", ".", "Update", "(", ")", "return", "Actor", "(", "reader...

47.5

8

def parse_ls(out): """ Parser for Android's ls -lR output. Takes a string, returns parsed structure. """ # assumed ls -lR line format: # -rw-r--r-- root shell 0 2013-07-05 02:26 tasks # drwxr-xr-x root root 2013-07-05 02:26 log # brw------- root root ...

[ "def", "parse_ls", "(", "out", ")", ":", "# assumed ls -lR line format:", "# -rw-r--r-- root shell 0 2013-07-05 02:26 tasks", "# drwxr-xr-x root root 2013-07-05 02:26 log", "# brw------- root root 179, 0 2013-07-05 02:26 mmcblk0", "# lrwxrwxrwx root r...

35.412371

14.443299

def verify_mass_range_options(opts, parser, nonSpin=False): """ Parses the metric calculation options given and verifies that they are correct. Parameters ---------- opts : argparse.Values instance Result of parsing the input options with OptionParser parser : object The Opt...

[ "def", "verify_mass_range_options", "(", "opts", ",", "parser", ",", "nonSpin", "=", "False", ")", ":", "# Mass1 must be the heavier!", "if", "opts", ".", "min_mass1", "<", "opts", ".", "min_mass2", ":", "parser", ".", "error", "(", "\"min-mass1 cannot be less tha...

53.512739

21.33121

def get_source(self, objtxt): """Get object source""" from spyder_kernels.utils.dochelpers import getsource obj, valid = self._eval(objtxt) if valid: return getsource(obj)

[ "def", "get_source", "(", "self", ",", "objtxt", ")", ":", "from", "spyder_kernels", ".", "utils", ".", "dochelpers", "import", "getsource", "obj", ",", "valid", "=", "self", ".", "_eval", "(", "objtxt", ")", "if", "valid", ":", "return", "getsource", "(...

30

14.714286

def kill(self, exit_code: Any = None): """ Stops the behaviour Args: exit_code (object, optional): the exit code of the behaviour (Default value = None) """ self._force_kill.set() if exit_code is not None: self._exit_code = exit_code logger...

[ "def", "kill", "(", "self", ",", "exit_code", ":", "Any", "=", "None", ")", ":", "self", ".", "_force_kill", ".", "set", "(", ")", "if", "exit_code", "is", "not", "None", ":", "self", ".", "_exit_code", "=", "exit_code", "logger", ".", "info", "(", ...

31.833333

20

def add_in_filter(self, *values): """ Add a filter using "IN" logic. This is typically the primary filter that will be used to find a match and generally combines other filters to get more granular. An example of usage would be searching for an IP address (or addresses) in a spec...

[ "def", "add_in_filter", "(", "self", ",", "*", "values", ")", ":", "filt", "=", "InFilter", "(", "*", "values", ")", "self", ".", "update_filter", "(", "filt", ")", "return", "filt" ]

42.176471

20.176471

def _create_command_file(self, expect, send): """Internal function. Do not use. Takes a long command, and puts it in an executable file ready to run. Returns the filename. """ shutit = self.shutit random_id = shutit_util.random_id() fname = shutit_global.shutit_global_object.shutit_state_dir + '/tmp_' + ra...

[ "def", "_create_command_file", "(", "self", ",", "expect", ",", "send", ")", ":", "shutit", "=", "self", ".", "shutit", "random_id", "=", "shutit_util", ".", "random_id", "(", ")", "fname", "=", "shutit_global", ".", "shutit_global_object", ".", "shutit_state_...

51.518519

22.037037

def config_value_keys(self, sortkey = False): """ Return configuration keys directly stored in this node. Configurations in child nodes are not included. """ if sortkey: items = sorted(self.items()) else: items = self.items() return (k for k,v in i...

[ "def", "config_value_keys", "(", "self", ",", "sortkey", "=", "False", ")", ":", "if", "sortkey", ":", "items", "=", "sorted", "(", "self", ".", "items", "(", ")", ")", "else", ":", "items", "=", "self", ".", "items", "(", ")", "return", "(", "k", ...

38.777778

17.666667

def wait_lock(path, lock_fn=None, timeout=5, sleep=0.1, time_start=None): ''' Obtain a write lock. If one exists, wait for it to release first ''' if not isinstance(path, six.string_types): raise FileLockError('path must be a string') if lock_fn is None: lock_fn = path + '.w' if ...

[ "def", "wait_lock", "(", "path", ",", "lock_fn", "=", "None", ",", "timeout", "=", "5", ",", "sleep", "=", "0.1", ",", "time_start", "=", "None", ")", ":", "if", "not", "isinstance", "(", "path", ",", "six", ".", "string_types", ")", ":", "raise", ...

33.445946

21.364865

def cmd_up(self, args): '''adjust TRIM_PITCH_CD up by 5 degrees''' if len(args) == 0: adjust = 5.0 else: adjust = float(args[0]) old_trim = self.get_mav_param('TRIM_PITCH_CD', None) if old_trim is None: print("Existing trim value unknown!") ...

[ "def", "cmd_up", "(", "self", ",", "args", ")", ":", "if", "len", "(", "args", ")", "==", "0", ":", "adjust", "=", "5.0", "else", ":", "adjust", "=", "float", "(", "args", "[", "0", "]", ")", "old_trim", "=", "self", ".", "get_mav_param", "(", ...

41.5

18.375

def register(cls, name, klass, content_type='text/plain'): """ Register an emitter. Parameters:: - `name`: The name of the emitter ('json', 'xml', 'yaml', ...) - `klass`: The emitter class. - `content_type`: The content type to serve response as. """ c...

[ "def", "register", "(", "cls", ",", "name", ",", "klass", ",", "content_type", "=", "'text/plain'", ")", ":", "cls", ".", "EMITTERS", "[", "name", "]", "=", "(", "klass", ",", "content_type", ")" ]

35.2

15.8

def commit_hash(dir='.'): """ Return commit hash for HEAD of checked out branch of the specified directory. """ cmd = ['git', 'rev-parse', 'HEAD'] try: with open(os.devnull, 'w') as devnull: revision_hash = subprocess.check_output( cmd, cwd=d...

[ "def", "commit_hash", "(", "dir", "=", "'.'", ")", ":", "cmd", "=", "[", "'git'", ",", "'rev-parse'", ",", "'HEAD'", "]", "try", ":", "with", "open", "(", "os", ".", "devnull", ",", "'w'", ")", "as", "devnull", ":", "revision_hash", "=", "subprocess"...

24.772727

17.318182

def read(self, uri=None, resources=None, index_only=False): """Read sitemap from a URI including handling sitemapindexes. If index_only is True then individual sitemaps references in a sitemapindex will not be read. This will result in no resources being returned and is useful only to r...

[ "def", "read", "(", "self", ",", "uri", "=", "None", ",", "resources", "=", "None", ",", "index_only", "=", "False", ")", ":", "try", ":", "fh", "=", "URLopener", "(", ")", ".", "open", "(", "uri", ")", "self", ".", "num_files", "+=", "1", "excep...

44.483333

18.216667

def get_prefix(): """Global prefix to identify ncluster created resources name used to identify ncluster created resources, (name of EFS, VPC, keypair prefixes), can be changed through $NCLUSTER_PREFIX for debugging purposes. """ name = os.environ.get('NCLUSTER_PREFIX', DEFAULT_PREFIX) if name != DEFAULT_PREFI...

[ "def", "get_prefix", "(", ")", ":", "name", "=", "os", ".", "environ", ".", "get", "(", "'NCLUSTER_PREFIX'", ",", "DEFAULT_PREFIX", ")", "if", "name", "!=", "DEFAULT_PREFIX", ":", "validate_prefix", "(", "name", ")", "return", "name" ]

44.375

16.875

def rgb_to_name(rgb_triplet, spec=u'css3'): """ Convert a 3-tuple of integers, suitable for use in an ``rgb()`` color triplet, to its corresponding normalized color name, if any such name exists. The optional keyword argument ``spec`` determines which specification's list of color names will be...

[ "def", "rgb_to_name", "(", "rgb_triplet", ",", "spec", "=", "u'css3'", ")", ":", "return", "hex_to_name", "(", "rgb_to_hex", "(", "normalize_integer_triplet", "(", "rgb_triplet", ")", ")", ",", "spec", "=", "spec", ")" ]

28.818182

22.181818

def get_change(self, change_id): """ Get information about a proposed set of changes, as submitted by the change_rrsets method. Returns a Python data structure with status information about the changes. :type change_id: str :param change_id: The unique identifier...

[ "def", "get_change", "(", "self", ",", "change_id", ")", ":", "uri", "=", "'/%s/change/%s'", "%", "(", "self", ".", "Version", ",", "change_id", ")", "response", "=", "self", ".", "make_request", "(", "'GET'", ",", "uri", ")", "body", "=", "response", ...

37.958333

17.041667

def GET_AUTH(self): """ GET request """ return self.template_helper.get_renderer().queue(*self.submission_manager.get_job_queue_snapshot(), datetime.fromtimestamp)

[ "def", "GET_AUTH", "(", "self", ")", ":", "return", "self", ".", "template_helper", ".", "get_renderer", "(", ")", ".", "queue", "(", "*", "self", ".", "submission_manager", ".", "get_job_queue_snapshot", "(", ")", ",", "datetime", ".", "fromtimestamp", ")" ...

59

37.333333

def _upsert(context, params, data): """Insert or update data and add/update appropriate timestamps""" table = params.get("table") table = datastore.get_table(table, primary_id=False) unique_keys = ensure_list(params.get("unique")) data["__last_seen"] = datetime.datetime.utcnow() if len(unique_ke...

[ "def", "_upsert", "(", "context", ",", "params", ",", "data", ")", ":", "table", "=", "params", ".", "get", "(", "\"table\"", ")", "table", "=", "datastore", ".", "get_table", "(", "table", ",", "primary_id", "=", "False", ")", "unique_keys", "=", "ens...

40.916667

13.666667

def _make_pkh_address(pubkey_hash, witness=False, cashaddr=True): ''' bytes, bool -> str ''' addr_bytes = bytearray() if riemann.network.CASHADDR_P2PKH is not None and cashaddr: addr_bytes.extend(riemann.network.CASHADDR_P2PKH) addr_bytes.extend(pubkey_hash) return riemann.ne...

[ "def", "_make_pkh_address", "(", "pubkey_hash", ",", "witness", "=", "False", ",", "cashaddr", "=", "True", ")", ":", "addr_bytes", "=", "bytearray", "(", ")", "if", "riemann", ".", "network", ".", "CASHADDR_P2PKH", "is", "not", "None", "and", "cashaddr", ...

40.705882

19.294118

def gen_random_mobile(): """ 随机生成一个手机号 :return: * str: (string) 手机号举例如下:: print('--- gen_random_mobile demo ---') print(gen_random_mobile()) print(gen_random_mobile()) print('---') 执行结果:: --- gen_random_mobile demo --- 16706146773 ...

[ "def", "gen_random_mobile", "(", ")", ":", "prefix_list", "=", "[", "\"13\"", ",", "\"1400\"", ",", "\"1410\"", ",", "\"1440\"", ",", "\"145\"", ",", "\"146\"", ",", "\"147\"", ",", "\"148\"", ",", "\"15\"", ",", "\"162\"", ",", "\"165\"", ",", "\"166\"", ...

25.193548

22.032258

def create_cylinder(rows, cols, radius=[1.0, 1.0], length=1.0, offset=False): """Create a cylinder Parameters ---------- rows : int Number of rows. cols : int Number of columns. radius : tuple of float Cylinder radii. length : float Length of the cylinder. ...

[ "def", "create_cylinder", "(", "rows", ",", "cols", ",", "radius", "=", "[", "1.0", ",", "1.0", "]", ",", "length", "=", "1.0", ",", "offset", "=", "False", ")", ":", "verts", "=", "np", ".", "empty", "(", "(", "rows", "+", "1", ",", "cols", ",...

36.365385

17.346154

def make_frame(self, frame, birthframe, startframe, stopframe, deathframe, noiseframe=None): """ :param frame: current frame :param birthframe: frame where this animation starts returning something other than None :param startframe: frame where animation starts to evolve :param ...

[ "def", "make_frame", "(", "self", ",", "frame", ",", "birthframe", ",", "startframe", ",", "stopframe", ",", "deathframe", ",", "noiseframe", "=", "None", ")", ":", "newx", "=", "self", ".", "anim_x", ".", "make_frame", "(", "frame", ",", "birthframe", "...

47.047619

23.238095

def get_valid_statements_for_modeling(sts: List[Influence]) -> List[Influence]: """ Select INDRA statements that can be used to construct a Delphi model from a given list of statements. """ return [ s for s in sts if is_grounded_statement(s) and (s.subj_delta["polarity"] is ...

[ "def", "get_valid_statements_for_modeling", "(", "sts", ":", "List", "[", "Influence", "]", ")", "->", "List", "[", "Influence", "]", ":", "return", "[", "s", "for", "s", "in", "sts", "if", "is_grounded_statement", "(", "s", ")", "and", "(", "s", ".", ...

34.090909

19.727273

def fulltext(search, lang=Lang.English, ignore_case=True): """Full text search. Example:: filters = Text.fulltext("python pymongo_mate") .. note:: This field doesn't need to specify field. """ return { "$text": { "$search": ...

[ "def", "fulltext", "(", "search", ",", "lang", "=", "Lang", ".", "English", ",", "ignore_case", "=", "True", ")", ":", "return", "{", "\"$text\"", ":", "{", "\"$search\"", ":", "search", ",", "\"$language\"", ":", "lang", ",", "\"$caseSensitive\"", ":", ...

24.473684

20.105263

def get_version_details(path): """Parses version file :param path: path to version file :return: version details """ with open(path, "r") as reader: lines = reader.readlines() data = { line.split(" = ")[0].replace("__", ""): line.split(" = ")[1].strip()....

[ "def", "get_version_details", "(", "path", ")", ":", "with", "open", "(", "path", ",", "\"r\"", ")", "as", "reader", ":", "lines", "=", "reader", ".", "readlines", "(", ")", "data", "=", "{", "line", ".", "split", "(", "\" = \"", ")", "[", "0", "]"...

25.466667

15.666667

def get_snapshot(self, hosts, macromodulations, timeperiods): # pragma: no cover, not yet! """ Raise snapshot event handlers if NONE of the following conditions is met:: * snapshot_command is None * snapshot_enabled is disabled * snapshot_criteria does not matches current state...

[ "def", "get_snapshot", "(", "self", ",", "hosts", ",", "macromodulations", ",", "timeperiods", ")", ":", "# pragma: no cover, not yet!", "# We should have a snapshot_command, to be enabled and of course", "# in the good time and state :D", "if", "self", ".", "snapshot_command", ...

39.6875

22

def run(self): """ Run the EventHubClient in blocking mode. Opens the connection and starts running all Sender/Receiver clients. Returns a list of the start up results. For a succcesful client start the result will be `None`, otherwise the exception raised. If all clients...

[ "def", "run", "(", "self", ")", ":", "log", ".", "info", "(", "\"%r: Starting %r clients\"", ",", "self", ".", "container_id", ",", "len", "(", "self", ".", "clients", ")", ")", "try", ":", "self", ".", "_start_clients", "(", ")", "redirects", "=", "["...

44.16129

22.032258

def add_pool(arg, opts, shell_opts): """ Add a pool. """ p = Pool() p.name = opts.get('name') p.description = opts.get('description') p.default_type = opts.get('default-type') p.ipv4_default_prefix_length = opts.get('ipv4_default_prefix_length') p.ipv6_default_prefix_length = opts.get('...

[ "def", "add_pool", "(", "arg", ",", "opts", ",", "shell_opts", ")", ":", "p", "=", "Pool", "(", ")", "p", ".", "name", "=", "opts", ".", "get", "(", "'name'", ")", "p", ".", "description", "=", "opts", ".", "get", "(", "'description'", ")", "p", ...

30.941176

20.764706

def lint(fix_imports): """ Run flake8. """ from glob import glob from subprocess import call # FIXME: should support passing these in an option skip = [ 'ansible', 'db', 'flask_sessions', 'node_modules', 'requirements', ] root_files = glob('*....

[ "def", "lint", "(", "fix_imports", ")", ":", "from", "glob", "import", "glob", "from", "subprocess", "import", "call", "# FIXME: should support passing these in an option", "skip", "=", "[", "'ansible'", ",", "'db'", ",", "'flask_sessions'", ",", "'node_modules'", "...

26.866667

18.266667

def mark(self, value=1): """Updates the dictionary.""" self['count'] += value for m in self._meters: m.update(value)

[ "def", "mark", "(", "self", ",", "value", "=", "1", ")", ":", "self", "[", "'count'", "]", "+=", "value", "for", "m", "in", "self", ".", "_meters", ":", "m", ".", "update", "(", "value", ")" ]

21.666667

17.166667

def retrieve_outputs(self): """ Declare the outputs of the algorithms as attributes: x_final, y_final, metrics. """ metrics = {} for obs in self._observers['cv_metrics']: metrics[obs.name] = obs.retrieve_metrics() self.metrics = metrics

[ "def", "retrieve_outputs", "(", "self", ")", ":", "metrics", "=", "{", "}", "for", "obs", "in", "self", ".", "_observers", "[", "'cv_metrics'", "]", ":", "metrics", "[", "obs", ".", "name", "]", "=", "obs", ".", "retrieve_metrics", "(", ")", "self", ...

32.111111

13.444444

def read(self, length=1000, blocking=False): """ Read ``length`` bytes from current process output stream. Note: This method is not fully non-blocking, however it behaves like one. """ size_p = PLARGE_INTEGER(LARGE_INTEGER(0)) if not blocking: windll....

[ "def", "read", "(", "self", ",", "length", "=", "1000", ",", "blocking", "=", "False", ")", ":", "size_p", "=", "PLARGE_INTEGER", "(", "LARGE_INTEGER", "(", "0", ")", ")", "if", "not", "blocking", ":", "windll", ".", "kernel32", ".", "GetFileSizeEx", "...

38.058824

15.352941

def if_then_else(cls, condition: 'TensorFluent', true_case: 'TensorFluent', false_case: 'TensorFluent') -> 'TensorFluent': '''Returns a TensorFluent for the control op if-then-else. Args: condition: Boolean fluent for the if condition. true_ca...

[ "def", "if_then_else", "(", "cls", ",", "condition", ":", "'TensorFluent'", ",", "true_case", ":", "'TensorFluent'", ",", "false_case", ":", "'TensorFluent'", ")", "->", "'TensorFluent'", ":", "true", "=", "TensorFluent", ".", "constant", "(", "True", ",", "tf...

38.565217

22.478261

def svm_score(self, x): x = x[1:] ''' original_X = self.svm_processor.train_X[:, 1:] score = 0 for i in range(len(self.svm_processor.sv_alpha)): score += self.svm_processor.sv_alpha[i] * self.svm_processor.sv_Y[i] * utility.Kernel.gaussian_kernel(self, original_X[se...

[ "def", "svm_score", "(", "self", ",", "x", ")", ":", "x", "=", "x", "[", "1", ":", "]", "score", "=", "np", ".", "sum", "(", "self", ".", "svm_processor", ".", "sv_alpha", "*", "self", ".", "svm_processor", ".", "sv_Y", "*", "utility", ".", "Kern...

40.133333

40.266667

def add_edge(self, id1, id2, weight=0.0, length=1.0, label="", properties={}): """ Add weighted (0.0-1.0) edge between nodes, creating them if necessary. The weight represents the importance of the connection (not the cost). """ if id1 == id2: return None ...

[ "def", "add_edge", "(", "self", ",", "id1", ",", "id2", ",", "weight", "=", "0.0", ",", "length", "=", "1.0", ",", "label", "=", "\"\"", ",", "properties", "=", "{", "}", ")", ":", "if", "id1", "==", "id2", ":", "return", "None", "if", "not", "...

32.518519

18.481481

def pseudo_with_symbol(self, symbol, allow_multi=False): """ Return the pseudo with the given chemical symbol. Args: symbols: String with the chemical symbol of the element allow_multi: By default, the method raises ValueError if multiple occurrences are ...

[ "def", "pseudo_with_symbol", "(", "self", ",", "symbol", ",", "allow_multi", "=", "False", ")", ":", "pseudos", "=", "self", ".", "select_symbols", "(", "symbol", ",", "ret_list", "=", "True", ")", "if", "not", "pseudos", "or", "(", "len", "(", "pseudos"...

39.4

26

def is_consecutive(self): """ Determine whether or not the non-zero labels in the segmentation image are consecutive (i.e. no missing values). """ if (self.labels[-1] - self.labels[0] + 1) == self.nlabels: return True else: return False

[ "def", "is_consecutive", "(", "self", ")", ":", "if", "(", "self", ".", "labels", "[", "-", "1", "]", "-", "self", ".", "labels", "[", "0", "]", "+", "1", ")", "==", "self", ".", "nlabels", ":", "return", "True", "else", ":", "return", "False" ]

30

18.8

def get_stored_cert_serials(store): ''' Get all of the certificate serials in the specified store store The store to get all the certificate serials from CLI Example: .. code-block:: bash salt '*' certutil.get_stored_cert_serials <store> ''' cmd = "certutil.exe -store {0}...

[ "def", "get_stored_cert_serials", "(", "store", ")", ":", "cmd", "=", "\"certutil.exe -store {0}\"", ".", "format", "(", "store", ")", "out", "=", "__salt__", "[", "'cmd.run'", "]", "(", "cmd", ")", "# match serial numbers by header position to work with multiple langua...

28.277778

24.944444

def add_ref_annotation(self, id_tier, tier2, time, value='', prev=None, svg=None): """Add a reference annotation. .. note:: When a timepoint matches two annotations the new reference annotation will reference to the first annotation. To circumvent this it's alw...

[ "def", "add_ref_annotation", "(", "self", ",", "id_tier", ",", "tier2", ",", "time", ",", "value", "=", "''", ",", "prev", "=", "None", ",", "svg", "=", "None", ")", ":", "if", "self", ".", "tiers", "[", "id_tier", "]", "[", "0", "]", ":", "raise...

47.6875

17.78125

def C(w, Xs): '''Calculate the cylinder center given the cylinder direction and a list of data points. ''' n = len(Xs) P = projection_matrix(w) Ys = [np.dot(P, X) for X in Xs] A = calc_A(Ys) A_hat = calc_A_hat(A, skew_matrix(w)) return np.dot(A_hat, sum(np.dot(Y, Y) * Y for Y in Ys...

[ "def", "C", "(", "w", ",", "Xs", ")", ":", "n", "=", "len", "(", "Xs", ")", "P", "=", "projection_matrix", "(", "w", ")", "Ys", "=", "[", "np", ".", "dot", "(", "P", ",", "X", ")", "for", "X", "in", "Xs", "]", "A", "=", "calc_A", "(", "...

31

23.363636

def firmware_download_input_protocol_type_usb_protocol_usb_directory(self, **kwargs): """Auto Generated Code """ config = ET.Element("config") firmware_download = ET.Element("firmware_download") config = firmware_download input = ET.SubElement(firmware_download, "input") ...

[ "def", "firmware_download_input_protocol_type_usb_protocol_usb_directory", "(", "self", ",", "*", "*", "kwargs", ")", ":", "config", "=", "ET", ".", "Element", "(", "\"config\"", ")", "firmware_download", "=", "ET", ".", "Element", "(", "\"firmware_download\"", ")",...

45.066667

15.4

def request(self, req_and_resp, opt=None, headers=None): """ preprocess before performing a request, usually some patching. authorization also applied here. :param req_and_resp: tuple of Request and Response :type req_and_resp: (Request, Response) :param opt: customized options ...

[ "def", "request", "(", "self", ",", "req_and_resp", ",", "opt", "=", "None", ",", "headers", "=", "None", ")", ":", "req", ",", "resp", "=", "req_and_resp", "# dump info for debugging", "logger", ".", "info", "(", "'request.url: {0}'", ".", "format", "(", ...

38.814815

17

def make_class_method_decorator(classkey, modname=None): """ register a class to be injectable classkey is a key that identifies the injected class REMEMBER to call inject_instance in __init__ Args: classkey : the class to be injected into modname : the global __name__ of the module...

[ "def", "make_class_method_decorator", "(", "classkey", ",", "modname", "=", "None", ")", ":", "global", "__APP_MODNAME_REGISTER__", "#if util_arg.VERBOSE or VERBOSE_CLASS:", "if", "VERBOSE_CLASS", ":", "print", "(", "'[util_class] register via make_class_method_decorator classkey...

42.830508

17.644068

def use_comparative_agent_view(self): """Pass through to provider ResourceAgentSession.use_comparative_agent_view""" self._object_views['agent'] = COMPARATIVE # self._get_provider_session('resource_agent_session') # To make sure the session is tracked for session in self._get_provider_se...

[ "def", "use_comparative_agent_view", "(", "self", ")", ":", "self", ".", "_object_views", "[", "'agent'", "]", "=", "COMPARATIVE", "# self._get_provider_session('resource_agent_session') # To make sure the session is tracked", "for", "session", "in", "self", ".", "_get_provid...

49.666667

16.333333

def async_mail_task(subject_or_message, to=None, template=None, **kwargs): """ Celery task to send emails asynchronously using the mail bundle. """ to = to or kwargs.pop('recipients', []) msg = make_message(subject_or_message, to, template, **kwargs) with mail.connect() as connection: co...

[ "def", "async_mail_task", "(", "subject_or_message", ",", "to", "=", "None", ",", "template", "=", "None", ",", "*", "*", "kwargs", ")", ":", "to", "=", "to", "or", "kwargs", ".", "pop", "(", "'recipients'", ",", "[", "]", ")", "msg", "=", "make_mess...

41.375

13.125

def wait(self, task_id): """ Blocking method which wait end of task. It's prefered to use :class:`carotte.Task` object directly :param string task_id: Task ID :returns: Task dict :rtype: dict """ data = { 'action': 'wait', 'id': t...

[ "def", "wait", "(", "self", ",", "task_id", ")", ":", "data", "=", "{", "'action'", ":", "'wait'", ",", "'id'", ":", "task_id", "}", "self", ".", "__send_pyobj", "(", "data", ")", "task", "=", "self", ".", "__recv_pyobj", "(", "notimeout", "=", "True...

24.764706

16.647059