kejian/codesearchnet-python-linelen40-full

text stringlengths 89 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 630
def location (self, pos): """Formats the location of the given SeqPos as: filename:line:col: """ result = '' if self.filename: result += self.filename + ':' if pos: result += str(pos) return result	[ "def", "location", "(", "self", ",", "pos", ")", ":", "result", "=", "''", "if", "self", ".", "filename", ":", "result", "+=", "self", ".", "filename", "+", "':'", "if", "pos", ":", "result", "+=", "str", "(", "pos", ")", "return", "result" ]	21.090909	16.909091
def _creation_options_for_cog(creation_options, source_profile, blocksize): """ it uses the profile of the source raster, override anything using the creation_options and guarantees we will have tiled raster and blocksize """ if not(creation_options): creation_options = {} creation_opti...	[ "def", "_creation_options_for_cog", "(", "creation_options", ",", "source_profile", ",", "blocksize", ")", ":", "if", "not", "(", "creation_options", ")", ":", "creation_options", "=", "{", "}", "creation_options", "[", "\"blocksize\"", "]", "=", "blocksize", "cre...	40.533333	15.866667
def create(self, set): """ Creates a new Set. """ target_url = self.client.get_url('SET', 'POST', 'create') r = self.client.request('POST', target_url, json=set._serialize()) return set._deserialize(r.json(), self)	[ "def", "create", "(", "self", ",", "set", ")", ":", "target_url", "=", "self", ".", "client", ".", "get_url", "(", "'SET'", ",", "'POST'", ",", "'create'", ")", "r", "=", "self", ".", "client", ".", "request", "(", "'POST'", ",", "target_url", ",", ...	36.571429	14
def load(file_or_path): """ Load a previously pickled model, using `m.pickle('path/to/file.pickle)'` :param file_name: path/to/file.pickle """ from pickle import UnpicklingError _python3 = True try: import cPickle as pickle _python3 = False except ImportError: #python3 ...	[ "def", "load", "(", "file_or_path", ")", ":", "from", "pickle", "import", "UnpicklingError", "_python3", "=", "True", "try", ":", "import", "cPickle", "as", "pickle", "_python3", "=", "False", "except", "ImportError", ":", "#python3", "import", "pickle", "try"...	27.703704	18.222222
def delete(self, filename=''): """Deletes given file or directory. If no filename is passed, current directory is removed. """ self._raise_if_none() fn = path_join(self.path, filename) try: if isfile(fn): remove(fn) else: ...	[ "def", "delete", "(", "self", ",", "filename", "=", "''", ")", ":", "self", ".", "_raise_if_none", "(", ")", "fn", "=", "path_join", "(", "self", ".", "path", ",", "filename", ")", "try", ":", "if", "isfile", "(", "fn", ")", ":", "remove", "(", "...	27.235294	13.705882
async def destroy(self, container = None): """ Destroy the created subqueue to change the behavior back to Lock """ if container is None: container = RoutineContainer(self.scheduler) if self.queue is not None: await container.syscall_noreturn(syscall_remov...	[ "async", "def", "destroy", "(", "self", ",", "container", "=", "None", ")", ":", "if", "container", "is", "None", ":", "container", "=", "RoutineContainer", "(", "self", ".", "scheduler", ")", "if", "self", ".", "queue", "is", "not", "None", ":", "awai...	42.555556	15.222222
def ace(args): """ %prog ace bamfile fastafile convert bam format to ace format. This often allows the remapping to be assessed as a denovo assembly format. bam file needs to be indexed. also creates a .mates file to be used in amos/bambus, and .astat file to mark whether the contig is unique o...	[ "def", "ace", "(", "args", ")", ":", "p", "=", "OptionParser", "(", "ace", ".", "__doc__", ")", "p", ".", "add_option", "(", "\"--splitdir\"", ",", "dest", "=", "\"splitdir\"", ",", "default", "=", "\"outRoot\"", ",", "help", "=", "\"split the ace per cont...	33.008696	21.686957
def pop_cell(self, idy=None, idx=None, tags=False): """Pops a cell, default the last of the last row""" idy = idy if idy is not None else len(self.body) - 1 idx = idx if idx is not None else len(self.body[idy]) - 1 cell = self.body[idy].pop(idx) return cell if tags else cell.chil...	[ "def", "pop_cell", "(", "self", ",", "idy", "=", "None", ",", "idx", "=", "None", ",", "tags", "=", "False", ")", ":", "idy", "=", "idy", "if", "idy", "is", "not", "None", "else", "len", "(", "self", ".", "body", ")", "-", "1", "idx", "=", "i...	53.333333	10.833333
def update_attr(self, attr): """Update input attr in self. Return list of attributes with changed values. """ changed_attr = [] for key, value in attr.items(): if value is None: continue if getattr(self, "_{0}".format(key), None) != value:...	[ "def", "update_attr", "(", "self", ",", "attr", ")", ":", "changed_attr", "=", "[", "]", "for", "key", ",", "value", "in", "attr", ".", "items", "(", ")", ":", "if", "value", "is", "None", ":", "continue", "if", "getattr", "(", "self", ",", "\"_{0}...	36.714286	14.428571
async def invoke(self, context): """Claims and processes Taskcluster work. Args: context (scriptworker.context.Context): context of worker Returns: status code of build """ try: # Note: claim_work(...) might not be safely interruptible! See ...	[ "async", "def", "invoke", "(", "self", ",", "context", ")", ":", "try", ":", "# Note: claim_work(...) might not be safely interruptible! See", "# https://bugzilla.mozilla.org/show_bug.cgi?id=1524069", "tasks", "=", "await", "self", ".", "_run_cancellable", "(", "claim_work", ...	48.357143	27.880952
def _compute_centers(self, X, sparse, rs): """Generate centers, then compute tau, dF and dN vals""" super(GRBFRandomLayer, self)._compute_centers(X, sparse, rs) centers = self.components_['centers'] sorted_distances = np.sort(squareform(pdist(centers))) self.dF_vals = sorted_di...	[ "def", "_compute_centers", "(", "self", ",", "X", ",", "sparse", ",", "rs", ")", ":", "super", "(", "GRBFRandomLayer", ",", "self", ")", ".", "_compute_centers", "(", "X", ",", "sparse", ",", "rs", ")", "centers", "=", "self", ".", "components_", "[", ...	35.894737	20
def epochs(self): """Get epochs as generator Returns ------- list of dict each epoch is defined by start_time and end_time (in s in reference to the start of the recordings) and a string of the sleep stage, and a string of the signal quality. ...	[ "def", "epochs", "(", "self", ")", ":", "if", "self", ".", "rater", "is", "None", ":", "raise", "IndexError", "(", "'You need to have at least one rater'", ")", "for", "one_epoch", "in", "self", ".", "rater", ".", "iterfind", "(", "'stages/epoch'", ")", ":",...	37.259259	23.148148
def pathsplit(value, sep=os.pathsep): ''' Get enviroment PATH elements as list. This function only cares about spliting across OSes. :param value: path string, as given by os.environ['PATH'] :type value: str :param sep: PATH separator, defaults to os.pathsep :type sep: str :yields: eve...	[ "def", "pathsplit", "(", "value", ",", "sep", "=", "os", ".", "pathsep", ")", ":", "for", "part", "in", "value", ".", "split", "(", "sep", ")", ":", "if", "part", "[", ":", "1", "]", "==", "part", "[", "-", "1", ":", "]", "==", "'\"'", "or", ...	28.941176	21.058824
def detect_credentials(config_name, extra_environ=None, filenames=None, aws_profile_name=None, default_value=Ellipsis): ''' detect_credentials(config_name) attempts to locate Amazon S3 Bucket credentials from the given configuration item config_name. The following optional argu...	[ "def", "detect_credentials", "(", "config_name", ",", "extra_environ", "=", "None", ",", "filenames", "=", "None", ",", "aws_profile_name", "=", "None", ",", "default_value", "=", "Ellipsis", ")", ":", "# Check the config first:", "if", "config_name", "is", "not",...	59.877778	28.344444
def wait_until(obj, att, desired, callback=None, interval=5, attempts=0, verbose=False, verbose_atts=None): """ When changing the state of an object, it will commonly be in a transitional state until the change is complete. This will reload the object every `interval` seconds, and check its `att...	[ "def", "wait_until", "(", "obj", ",", "att", ",", "desired", ",", "callback", "=", "None", ",", "interval", "=", "5", ",", "attempts", "=", "0", ",", "verbose", "=", "False", ",", "verbose_atts", "=", "None", ")", ":", "if", "callback", ":", "waiter"...	57.686275	30.235294
def get_jwt_secret(): """ Get the JWT secret :return: str """ secret_key = __options__.get("jwt_secret") or config("JWT_SECRET") or config("SECRET_KEY") if not secret_key: raise exceptions.AuthError("Missing config JWT/SECRET_KEY") return secret_key	[ "def", "get_jwt_secret", "(", ")", ":", "secret_key", "=", "__options__", ".", "get", "(", "\"jwt_secret\"", ")", "or", "config", "(", "\"JWT_SECRET\"", ")", "or", "config", "(", "\"SECRET_KEY\"", ")", "if", "not", "secret_key", ":", "raise", "exceptions", "...	30.777778	19.888889
def atlas_peer_getinfo( peer_hostport, timeout=None, peer_table=None ): """ Get host info Return the rpc_getinfo() response on success Return None on error """ if timeout is None: timeout = atlas_ping_timeout() host, port = url_to_host_port( peer_hostport ) RPC = get_rpc_client...	[ "def", "atlas_peer_getinfo", "(", "peer_hostport", ",", "timeout", "=", "None", ",", "peer_table", "=", "None", ")", ":", "if", "timeout", "is", "None", ":", "timeout", "=", "atlas_ping_timeout", "(", ")", "host", ",", "port", "=", "url_to_host_port", "(", ...	40.234568	30.283951
def req(self, method, params=()): """send request to ppcoind""" response = self.session.post( self.url, data=json.dumps({"method": method, "params": params, "jsonrpc": "1.1"}), ).json() if response["error"] is not None: return response["error"] ...	[ "def", "req", "(", "self", ",", "method", ",", "params", "=", "(", ")", ")", ":", "response", "=", "self", ".", "session", ".", "post", "(", "self", ".", "url", ",", "data", "=", "json", ".", "dumps", "(", "{", "\"method\"", ":", "method", ",", ...	29.583333	17.666667
def get_all_lower(self): """Return all parent GO IDs through both reverse 'is_a' and all relationships.""" all_lower = set() for lower in self.get_goterms_lower(): all_lower.add(lower.item_id) all_lower \|= lower.get_all_lower() return all_lower	[ "def", "get_all_lower", "(", "self", ")", ":", "all_lower", "=", "set", "(", ")", "for", "lower", "in", "self", ".", "get_goterms_lower", "(", ")", ":", "all_lower", ".", "add", "(", "lower", ".", "item_id", ")", "all_lower", "\|=", "lower", ".", "get_a...	42	8.428571
def extract_subset(self, input_data_tiles=None, out_tile=None): """ Extract subset from multiple tiles. input_data_tiles : list of (``Tile``, process data) tuples out_tile : ``Tile`` Returns ------- NumPy array or list of features. """ if self.ME...	[ "def", "extract_subset", "(", "self", ",", "input_data_tiles", "=", "None", ",", "out_tile", "=", "None", ")", ":", "if", "self", ".", "METADATA", "[", "\"data_type\"", "]", "==", "\"raster\"", ":", "mosaic", "=", "create_mosaic", "(", "input_data_tiles", ")...	34.586207	15.896552
def ko_bindings(model): """ Given a model, returns the Knockout data bindings. """ try: if isinstance(model, str): modelName = model else: modelName = model.__class__.__name__ modelBindingsString = "ko.applyBindings(new " + modelName + "ViewModel(), $('#...	[ "def", "ko_bindings", "(", "model", ")", ":", "try", ":", "if", "isinstance", "(", "model", ",", "str", ")", ":", "modelName", "=", "model", "else", ":", "modelName", "=", "model", ".", "__class__", ".", "__name__", "modelBindingsString", "=", "\"ko.applyB...	26.058824	22.058824
def add(message, level=0, user=None, message_short=None,log_file_name='%s/pyscada_daemon.log' % settings.BASE_DIR,): """ add a new massage/error notice to the log <0 - Debug 1 - Emergency 2 - Critical 3 - Errors 4 - Alerts 5 - Warnings 6 - Notification (webnotice) 7 - Information...	[ "def", "add", "(", "message", ",", "level", "=", "0", ",", "user", "=", "None", ",", "message_short", "=", "None", ",", "log_file_name", "=", "'%s/pyscada_daemon.log'", "%", "settings", ".", "BASE_DIR", ",", ")", ":", "#if not access(path.dirname(self.log_file_n...	32.388889	22
def reset_clipboard(self): """ Resets the clipboard, so that old elements do not pollute the new selection that is copied into the clipboard. :return: """ # reset selections for state_element_attr in ContainerState.state_element_attrs: self.model_copies[s...	[ "def", "reset_clipboard", "(", "self", ")", ":", "# reset selections", "for", "state_element_attr", "in", "ContainerState", ".", "state_element_attrs", ":", "self", ".", "model_copies", "[", "state_element_attr", "]", "=", "[", "]", "# reset parent state_id the copied e...	34.642857	18.785714
def get(tag: {str, 'Language'}, normalize=True) -> 'Language': """ Create a Language object from a language tag string. If normalize=True, non-standard or overlong tags will be replaced as they're interpreted. This is recommended. Here are several examples of language codes, wh...	[ "def", "get", "(", "tag", ":", "{", "str", ",", "'Language'", "}", ",", "normalize", "=", "True", ")", "->", "'Language'", ":", "if", "isinstance", "(", "tag", ",", "Language", ")", ":", "if", "not", "normalize", ":", "# shortcut: we have the tag already",...	39.39759	22.542169
def smart_cast2(var): r""" if the variable is a string tries to cast it to a reasonable value. maybe can just use eval. FIXME: funcname Args: var (unknown): Returns: unknown: some var CommandLine: python -m utool.util_type --test-smart_cast2 Example: >>> #...	[ "def", "smart_cast2", "(", "var", ")", ":", "if", "var", "is", "None", ":", "return", "None", "if", "isinstance", "(", "var", ",", "six", ".", "string_types", ")", ":", "castvar", "=", "None", "lower", "=", "var", ".", "lower", "(", ")", "if", "low...	31.053571	18.178571
def set_cookie(self, key, value, expiration='Infinity', path='/', domain='', secure=False): """ expiration (int): seconds after with the cookie automatically gets deleted """ secure = 'true' if secure else 'false' self.app_instance.execute_javascript(""" var sKey = "...	[ "def", "set_cookie", "(", "self", ",", "key", ",", "value", ",", "expiration", "=", "'Infinity'", ",", "path", "=", "'/'", ",", "domain", "=", "''", ",", "secure", "=", "False", ")", ":", "secure", "=", "'true'", "if", "secure", "else", "'false'", "s...	50.064516	21.032258
def all_pairs(sets, similarity_func_name="jaccard", similarity_threshold=0.5): """Find all pairs of sets with similarity greater than a threshold. This is an implementation of the All-Pair-Binary algorithm in the paper "Scaling Up All Pairs Similarity Search" by Bayardo et al., with position fil...	[ "def", "all_pairs", "(", "sets", ",", "similarity_func_name", "=", "\"jaccard\"", ",", "similarity_threshold", "=", "0.5", ")", ":", "if", "not", "isinstance", "(", "sets", ",", "list", ")", "or", "len", "(", "sets", ")", "==", "0", ":", "raise", "ValueE...	47.898305	19.118644
def _addUserToGroup(self, username, group="Clients"): """Add user to the goup """ portal_groups = api.portal.get_tool("portal_groups") group = portal_groups.getGroupById('Clients') group.addMember(username)	[ "def", "_addUserToGroup", "(", "self", ",", "username", ",", "group", "=", "\"Clients\"", ")", ":", "portal_groups", "=", "api", ".", "portal", ".", "get_tool", "(", "\"portal_groups\"", ")", "group", "=", "portal_groups", ".", "getGroupById", "(", "'Clients'"...	40.166667	8.833333
def query_domain(self, domain, typenames, domainquerytype='list', count=False): """ Query by property domain values """ objects = self._get_repo_filter(Layer.objects) if domainquerytype == 'range': return [tuple(objects.aggregate(Min(domain), Max(domain)).values())]...	[ "def", "query_domain", "(", "self", ",", "domain", ",", "typenames", ",", "domainquerytype", "=", "'list'", ",", "count", "=", "False", ")", ":", "objects", "=", "self", ".", "_get_repo_filter", "(", "Layer", ".", "objects", ")", "if", "domainquerytype", "...	37.6	21.733333
def is_in_plane(self, pp, dist_tolerance): """ Determines if point pp is in the plane within the tolerance dist_tolerance :param pp: point to be tested :param dist_tolerance: tolerance on the distance to the plane within which point pp is considered in the plane :return: True if ...	[ "def", "is_in_plane", "(", "self", ",", "pp", ",", "dist_tolerance", ")", ":", "return", "np", ".", "abs", "(", "np", ".", "dot", "(", "self", ".", "normal_vector", ",", "pp", ")", "+", "self", ".", "_coefficients", "[", "3", "]", ")", "<=", "dist_...	57	25
def find_mean_vector(args, kwargs): """ Returns the mean vector for a set of measurments. By default, this expects the input to be plunges and bearings, but the type of input can be controlled through the ``measurement`` kwarg. Parameters ---------- args : 2 or 3 sequences of measureme...	[ "def", "find_mean_vector", "(", "", "args", ",", "", "*", "kwargs", ")", ":", "lon", ",", "lat", "=", "_convert_measurements", "(", "args", ",", "kwargs", ".", "get", "(", "'measurement'", ",", "'lines'", ")", ")", "vector", ",", "r_value", "=", "ste...	41.434783	23.478261
def calc_paired_insert_stats(in_bam, nsample=1000000): """Retrieve statistics for paired end read insert distances. """ dists = [] n = 0 with pysam.Samfile(in_bam, "rb") as in_pysam: for read in in_pysam: if read.is_proper_pair and read.is_read1: n += 1 ...	[ "def", "calc_paired_insert_stats", "(", "in_bam", ",", "nsample", "=", "1000000", ")", ":", "dists", "=", "[", "]", "n", "=", "0", "with", "pysam", ".", "Samfile", "(", "in_bam", ",", "\"rb\"", ")", "as", "in_pysam", ":", "for", "read", "in", "in_pysam...	33.692308	11.923077
def create_sysdig_capture(self, hostname, capture_name, duration, capture_filter='', folder='/'): '''Description Create a new sysdig capture. The capture will be immediately started. Arguments - hostname: the hostname of the instrumented host where the capture will b...	[ "def", "create_sysdig_capture", "(", "self", ",", "hostname", ",", "capture_name", ",", "duration", ",", "capture_filter", "=", "''", ",", "folder", "=", "'/'", ")", ":", "res", "=", "self", ".", "get_connected_agents", "(", ")", "if", "not", "res", "[", ...	37.255814	25.348837
def rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples): """ organizes RNA-seq and small-RNAseq samples, converting from BAM if necessary and trimming if necessary """ pipeline = dd.get_in_samples(samples, dd.get_analysis) trim_reads_set = any([tz.get_in(["algorithm", "trim_reads...	[ "def", "rnaseq_prep_samples", "(", "config", ",", "run_info_yaml", ",", "parallel", ",", "dirs", ",", "samples", ")", ":", "pipeline", "=", "dd", ".", "get_in_samples", "(", "samples", ",", "dd", ".", "get_analysis", ")", "trim_reads_set", "=", "any", "(", ...	52.2	22.28
def cursor_up(self, count=None): """Move cursor up the indicated # of lines in same column. Cursor stops at top margin. :param int count: number of lines to skip. """ top, _bottom = self.margins or Margins(0, self.lines - 1) self.cursor.y = max(self.cursor.y - (count or ...	[ "def", "cursor_up", "(", "self", ",", "count", "=", "None", ")", ":", "top", ",", "_bottom", "=", "self", ".", "margins", "or", "Margins", "(", "0", ",", "self", ".", "lines", "-", "1", ")", "self", ".", "cursor", ".", "y", "=", "max", "(", "se...	40.125	13.75
def is_instance_throughput_too_low(self, inst_id): """ Return whether the throughput of the master instance is greater than the acceptable threshold """ r = self.instance_throughput_ratio(inst_id) if r is None: logger.debug("{} instance {} throughput is not " ...	[ "def", "is_instance_throughput_too_low", "(", "self", ",", "inst_id", ")", ":", "r", "=", "self", ".", "instance_throughput_ratio", "(", "inst_id", ")", "if", "r", "is", "None", ":", "logger", ".", "debug", "(", "\"{} instance {} throughput is not \"", "\"measurab...	43.444444	20.222222
def get_source_code(items): """ Extract source code of given items, and concatenate and dedent it. """ sources = [] prev_class_name = None for func in items: try: lines, lineno = inspect.getsourcelines(func) except TypeError: continue if not line...	[ "def", "get_source_code", "(", "items", ")", ":", "sources", "=", "[", "]", "prev_class_name", "=", "None", "for", "func", "in", "items", ":", "try", ":", "lines", ",", "lineno", "=", "inspect", ".", "getsourcelines", "(", "func", ")", "except", "TypeErr...	28.75	17.1
def process(self): """Periodic nonblocking processes""" super(NativeBLEVirtualInterface, self).process() if (not self._stream_sm_running) and (not self.reports.empty()): self._stream_data() if (not self._trace_sm_running) and (not self.traces.empty()): self._se...	[ "def", "process", "(", "self", ")", ":", "super", "(", "NativeBLEVirtualInterface", ",", "self", ")", ".", "process", "(", ")", "if", "(", "not", "self", ".", "_stream_sm_running", ")", "and", "(", "not", "self", ".", "reports", ".", "empty", "(", ")",...	32.1	23.9
def _get_artifact_context(run, file_type): """Gets the artifact details for the given run and file_type.""" sha1sum = None image_file = False log_file = False config_file = False if request.path == '/image': image_file = True if file_type == 'before': sha1sum = run.r...	[ "def", "_get_artifact_context", "(", "run", ",", "file_type", ")", ":", "sha1sum", "=", "None", "image_file", "=", "False", "log_file", "=", "False", "config_file", "=", "False", "if", "request", ".", "path", "==", "'/image'", ":", "image_file", "=", "True",...	28.567568	13
def match(self, command_context=None, **command_env): """ Check if context request is compatible with adapters specification. True - if compatible, False - otherwise :param command_context: context to check :param command_env: command environment :return: bool """ spec = self.specification() if command...	[ "def", "match", "(", "self", ",", "command_context", "=", "None", ",", "", "", "command_env", ")", ":", "spec", "=", "self", ".", "specification", "(", ")", "if", "command_context", "is", "None", "and", "spec", "is", "None", ":", "return", "True", "e...	33	13.857143
def get_store_profile_by_id(cls, store_profile_id, **kwargs): """Find StoreProfile Return single instance of StoreProfile by its ID. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async=True >>> thread = api.get_store_p...	[ "def", "get_store_profile_by_id", "(", "cls", ",", "store_profile_id", ",", "", "", "kwargs", ")", ":", "kwargs", "[", "'_return_http_data_only'", "]", "=", "True", "if", "kwargs", ".", "get", "(", "'async'", ")", ":", "return", "cls", ".", "_get_store_pro...	44.095238	21.857143
def prototype(self, name, argtypes, restype=None): """Define argument / return types for the specified C function""" function = self.function(name) function.argtypes = argtypes if restype: function.restype = restype	[ "def", "prototype", "(", "self", ",", "name", ",", "argtypes", ",", "restype", "=", "None", ")", ":", "function", "=", "self", ".", "function", "(", "name", ")", "function", ".", "argtypes", "=", "argtypes", "if", "restype", ":", "function", ".", "rest...	42.333333	6.5
def read_umi_tools(filename: PathLike, dtype: str='float32') -> AnnData: """Read a gzipped condensed count matrix from umi_tools. Parameters ---------- filename File name to read from. """ # import pandas for conversion of a dict of dicts into a matrix # import gzip to read a gzippe...	[ "def", "read_umi_tools", "(", "filename", ":", "PathLike", ",", "dtype", ":", "str", "=", "'float32'", ")", "->", "AnnData", ":", "# import pandas for conversion of a dict of dicts into a matrix", "# import gzip to read a gzipped file :-)", "import", "gzip", "from", "pandas...	35.777778	22.259259
def from_filename(cls, filename, sync_from_start=True): """ Create a `Lexer` from a filename. """ # Inline imports: the Pygments dependency is optional! from pygments.util import ClassNotFound from pygments.lexers import get_lexer_for_filename try: py...	[ "def", "from_filename", "(", "cls", ",", "filename", ",", "sync_from_start", "=", "True", ")", ":", "# Inline imports: the Pygments dependency is optional!", "from", "pygments", ".", "util", "import", "ClassNotFound", "from", "pygments", ".", "lexers", "import", "get_...	36.642857	17.071429
def validate(self, value, add_comments=False, schema_name="map"): """ verbose - also return the jsonschema error details """ validator = self.get_schema_validator(schema_name) error_messages = [] if isinstance(value, list): for d in value: er...	[ "def", "validate", "(", "self", ",", "value", ",", "add_comments", "=", "False", ",", "schema_name", "=", "\"map\"", ")", ":", "validator", "=", "self", ".", "get_schema_validator", "(", "schema_name", ")", "error_messages", "=", "[", "]", "if", "isinstance"...	34.066667	23.133333
def sendMessage(self, data): """ Send websocket data frame to the client. If data is a unicode object then the frame is sent as Text. If the data is a bytearray object then the frame is sent as Binary. """ opcode = BINARY if _check_unicode(data): ...	[ "def", "sendMessage", "(", "self", ",", "data", ")", ":", "opcode", "=", "BINARY", "if", "_check_unicode", "(", "data", ")", ":", "opcode", "=", "TEXT", "self", ".", "_sendMessage", "(", "False", ",", "opcode", ",", "data", ")" ]	34.363636	16.363636
def import_submodules(name, submodules=None): """Import all submodules for a package/module name""" sys.path.insert(0, name) if submodules: for submodule in submodules: import_string('{0}.{1}'.format(name, submodule)) else: for item in pkgutil.walk_packages([name]): ...	[ "def", "import_submodules", "(", "name", ",", "submodules", "=", "None", ")", ":", "sys", ".", "path", ".", "insert", "(", "0", ",", "name", ")", "if", "submodules", ":", "for", "submodule", "in", "submodules", ":", "import_string", "(", "'{0}.{1}'", "."...	40.111111	13.555556
def next_release(major=False, minor=False, patch=True): """Get next release version (by major, minor or patch)""" import semantic_version prev = run('git describe --abbrev=0 --tags', warn=True, hide=True).stdout or '0.0.0' ver = semantic_version.Version.coerce(prev.strip()) print('current version:...	[ "def", "next_release", "(", "major", "=", "False", ",", "minor", "=", "False", ",", "patch", "=", "True", ")", ":", "import", "semantic_version", "prev", "=", "run", "(", "'git describe --abbrev=0 --tags'", ",", "warn", "=", "True", ",", "hide", "=", "True...	35.052632	18.684211
def get_property_names(self, is_allprop): """Return list of supported property names in Clark Notation. See DAVResource.get_property_names() """ # Let base class implementation add supported live and dead properties propNameList = super(VirtualResource, self).get_property_names(...	[ "def", "get_property_names", "(", "self", ",", "is_allprop", ")", ":", "# Let base class implementation add supported live and dead properties", "propNameList", "=", "super", "(", "VirtualResource", ",", "self", ")", ".", "get_property_names", "(", "is_allprop", ")", "# A...	48.6	19.2
def check(id_): """Check bibdocs.""" BibRecDocs, BibDoc = _import_bibdoc() try: BibDoc(id_).list_all_files() except Exception: click.secho("BibDoc {0} failed check.".format(id_), fg='red')	[ "def", "check", "(", "id_", ")", ":", "BibRecDocs", ",", "BibDoc", "=", "_import_bibdoc", "(", ")", "try", ":", "BibDoc", "(", "id_", ")", ".", "list_all_files", "(", ")", "except", "Exception", ":", "click", ".", "secho", "(", "\"BibDoc {0} failed check.\...	26.75	18.75
def set_command_attributes(self, name, attributes): """ Sets the xml attributes of a specified command. """ if self.command_exists(name): command = self.commands.get(name) command['attributes'] = attributes	[ "def", "set_command_attributes", "(", "self", ",", "name", ",", "attributes", ")", ":", "if", "self", ".", "command_exists", "(", "name", ")", ":", "command", "=", "self", ".", "commands", ".", "get", "(", "name", ")", "command", "[", "'attributes'", "]"...	48.4	5
def get_environ(self, key, default=None, cast=None): """Get value from environment variable using os.environ.get :param key: The name of the setting value, will always be upper case :param default: In case of not found it will be returned :param cast: Should cast in to @int, @float, @bo...	[ "def", "get_environ", "(", "self", ",", "key", ",", "default", "=", "None", ",", "cast", "=", "None", ")", ":", "key", "=", "key", ".", "upper", "(", ")", "data", "=", "self", ".", "environ", ".", "get", "(", "key", ",", "default", ")", "if", "...	42.058824	16.058824
def create_namespaced_deployment_rollback(self, name, namespace, body, **kwargs): # noqa: E501 """create_namespaced_deployment_rollback # noqa: E501 create rollback of a Deployment # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP requ...	[ "def", "create_namespaced_deployment_rollback", "(", "self", ",", "name", ",", "namespace", ",", "body", ",", "", "", "kwargs", ")", ":", "# noqa: E501", "kwargs", "[", "'_return_http_data_only'", "]", "=", "True", "if", "kwargs", ".", "get", "(", "'async_re...	66.653846	39.384615
def get_scrollbar_position_height(self): """Return the pixel span height of the scrollbar area in which the slider handle may move""" vsb = self.editor.verticalScrollBar() style = vsb.style() opt = QStyleOptionSlider() vsb.initStyleOption(opt) # Get the area in w...	[ "def", "get_scrollbar_position_height", "(", "self", ")", ":", "vsb", "=", "self", ".", "editor", ".", "verticalScrollBar", "(", ")", "style", "=", "vsb", ".", "style", "(", ")", "opt", "=", "QStyleOptionSlider", "(", ")", "vsb", ".", "initStyleOption", "(...	38.692308	13.076923
def addMenuLabel(menu, text): """Adds a QLabel contaning text to the given menu""" qaw = QWidgetAction(menu) lab = QLabel(text, menu) qaw.setDefaultWidget(lab) lab.setAlignment(Qt.AlignCenter) lab.setFrameShape(QFrame.StyledPanel) lab.setFrameShadow(QFrame.Sunken) menu.addAction(qaw) ...	[ "def", "addMenuLabel", "(", "menu", ",", "text", ")", ":", "qaw", "=", "QWidgetAction", "(", "menu", ")", "lab", "=", "QLabel", "(", "text", ",", "menu", ")", "qaw", ".", "setDefaultWidget", "(", "lab", ")", "lab", ".", "setAlignment", "(", "Qt", "."...	32.2	9.6
def read(self, vals): """Read values. Args: vals (list): list of strings representing values """ i = 0 if len(vals[i]) == 0: self.ground_temperature_depth = None else: self.ground_temperature_depth = vals[i] i += 1 if ...	[ "def", "read", "(", "self", ",", "vals", ")", ":", "i", "=", "0", "if", "len", "(", "vals", "[", "i", "]", ")", "==", "0", ":", "self", ".", "ground_temperature_depth", "=", "None", "else", ":", "self", ".", "ground_temperature_depth", "=", "vals", ...	33.761364	21.034091
def actualize (self, scanner = None): """ Generates all the actual targets and sets up build actions for this target. If 'scanner' is specified, creates an additional target with the same location as actual target, which will depend on the actual target and be as...	[ "def", "actualize", "(", "self", ",", "scanner", "=", "None", ")", ":", "if", "__debug__", ":", "from", ".", "scanner", "import", "Scanner", "assert", "scanner", "is", "None", "or", "isinstance", "(", "scanner", ",", "Scanner", ")", "actual_name", "=", "...	36.435897	25.384615
def update_edge_keys(G): """ Update the keys of edges that share a u, v with another edge but differ in geometry. For example, two one-way streets from u to v that bow away from each other as separate streets, rather than opposite direction edges of a single street. Parameters --------...	[ "def", "update_edge_keys", "(", "G", ")", ":", "# identify all the edges that are duplicates based on a sorted combination", "# of their origin, destination, and key. that is, edge uv will match edge vu", "# as a duplicate, but only if they have the same key", "edges", "=", "graph_to_gdfs", ...	42.654545	26.254545
def dlogpdf_dlink(self, link_f, y, Y_metadata=None): """ Gradient of the log likelihood function at y, given link(f) w.r.t link(f) .. math:: \\frac{d \\ln p(y_{i}\|\\lambda(f_{i}))}{d\\lambda(f)} = \\beta (\\log \\beta y_{i}) - \\Psi(\\alpha_{i})\\beta\\\\ \\alpha_{i} = \...	[ "def", "dlogpdf_dlink", "(", "self", ",", "link_f", ",", "y", ",", "Y_metadata", "=", "None", ")", ":", "grad", "=", "self", ".", "beta", "", "np", ".", "log", "(", "self", ".", "beta", "", "y", ")", "-", "special", ".", "psi", "(", "self", "...	42.47619	29.047619
def run_mp(songs): """ Concurrently calls get_lyrics to fetch the lyrics of a large list of songs. """ stats = Stats() if CONFIG['debug']: good = open('found', 'w') bad = open('notfound', 'w') logger.debug('Launching a pool of %d processes\n', CONFIG['jobcount']) chunksize =...	[ "def", "run_mp", "(", "songs", ")", ":", "stats", "=", "Stats", "(", ")", "if", "CONFIG", "[", "'debug'", "]", ":", "good", "=", "open", "(", "'found'", ",", "'w'", ")", "bad", "=", "open", "(", "'notfound'", ",", "'w'", ")", "logger", ".", "debu...	32.085714	20.257143
def write(self, filename=None): """Write array to xvg file filename in NXY format. .. Note:: Only plain files working at the moment, not compressed. """ self._init_filename(filename) with utilities.openany(self.real_filename, 'w') as xvg: xvg.write("# xmgrace compa...	[ "def", "write", "(", "self", ",", "filename", "=", "None", ")", ":", "self", ".", "_init_filename", "(", "filename", ")", "with", "utilities", ".", "openany", "(", "self", ".", "real_filename", ",", "'w'", ")", "as", "xvg", ":", "xvg", ".", "write", ...	48.692308	19.384615
def close(self, code=3000, message='Go away!'): """ Close session. @param code: Closing code @param message: Closing message """ if self.state != SESSION_STATE.CLOSED: # Notify handler if self.handler is not None: self.handler.send_pack(p...	[ "def", "close", "(", "self", ",", "code", "=", "3000", ",", "message", "=", "'Go away!'", ")", ":", "if", "self", ".", "state", "!=", "SESSION_STATE", ".", "CLOSED", ":", "# Notify handler", "if", "self", ".", "handler", "is", "not", "None", ":", "self...	30	14.846154
def infix(self, node, children): 'infix = "(" expr operator expr ")"' _, expr1, operator, expr2, _ = children return operator(expr1, expr2)	[ "def", "infix", "(", "self", ",", "node", ",", "children", ")", ":", "_", ",", "expr1", ",", "operator", ",", "expr2", ",", "_", "=", "children", "return", "operator", "(", "expr1", ",", "expr2", ")" ]	40	5.5
def should_skip_file(name): """ Checks if a file should be skipped based on its name. If it should be skipped, returns the reason, otherwise returns None. """ if name.startswith('.'): return 'Skipping hidden file %(filename)s' if name.endswith('~') or name.endswith('.bak'): ...	[ "def", "should_skip_file", "(", "name", ")", ":", "if", "name", ".", "startswith", "(", "'.'", ")", ":", "return", "'Skipping hidden file %(filename)s'", "if", "name", ".", "endswith", "(", "'~'", ")", "or", "name", ".", "endswith", "(", "'.bak'", ")", ":"...	38	16.555556
def get_default_config_help(self): """ Returns the help text for the configuration options for this handler """ config = super(NullHandler, self).get_default_config_help() config.update({ }) return config	[ "def", "get_default_config_help", "(", "self", ")", ":", "config", "=", "super", "(", "NullHandler", ",", "self", ")", ".", "get_default_config_help", "(", ")", "config", ".", "update", "(", "{", "}", ")", "return", "config" ]	25.3	21.5
def solve(self): """ Solve the OLL. Returns an Formula. """ if not isinstance(self.cube, Cube): raise ValueError("Use Solver.feed(cube) to feed the cube to solver.") self.recognise() self.cube(algo_dict[self.case]) return algo_dict[self.case]	[ "def", "solve", "(", "self", ")", ":", "if", "not", "isinstance", "(", "self", ".", "cube", ",", "Cube", ")", ":", "raise", "ValueError", "(", "\"Use Solver.feed(cube) to feed the cube to solver.\"", ")", "self", ".", "recognise", "(", ")", "self", ".", "cub...	33.555556	10.222222
def _set_raw_return(self, sep): """Set the output raw return section :param sep: the separator of current style """ raw = '' if self.dst.style['out'] == 'numpydoc': raw += '\n' spaces = ' ' * 4 with_space = lambda s: '\n'.join([self.docs['out...	[ "def", "_set_raw_return", "(", "self", ",", "sep", ")", ":", "raw", "=", "''", "if", "self", ".", "dst", ".", "style", "[", "'out'", "]", "==", "'numpydoc'", ":", "raw", "+=", "'\\n'", "spaces", "=", "' '", "*", "4", "with_space", "=", "lambda", "s...	54.47619	24.988095
def check_solver(self, image_x, image_y, kwargs_lens): """ returns the precision of the solver to match the image position :param kwargs_lens: full lens model (including solved parameters) :param image_x: point source in image :param image_y: point source in image :retur...	[ "def", "check_solver", "(", "self", ",", "image_x", ",", "image_y", ",", "kwargs_lens", ")", ":", "source_x", ",", "source_y", "=", "self", ".", "_lensModel", ".", "ray_shooting", "(", "image_x", ",", "image_y", ",", "kwargs_lens", ")", "dist", "=", "np", ...	50.833333	25.833333
def wsgi_wrap(app): ''' Wraps a standard wsgi application e.g.: def app(environ, start_response) It intercepts the start_response callback and grabs the results from it so it can return the status, headers, and body as a tuple ''' @wraps(app) def wrapped(environ, start_response): ...	[ "def", "wsgi_wrap", "(", "app", ")", ":", "@", "wraps", "(", "app", ")", "def", "wrapped", "(", "environ", ",", "start_response", ")", ":", "status_headers", "=", "[", "None", ",", "None", "]", "def", "_start_response", "(", "status", ",", "headers", "...	35.9375	15.8125
def override_tab_value(data, headers, new_value=' ', *_): """Override tab values in the data* with new_value. :param iterable data: An :term:`iterable` (e.g. list) of rows. :param iterable headers: The column headers. :param new_value: The new value to use for tab. :return: The processed dat...	[ "def", "override_tab_value", "(", "data", ",", "headers", ",", "new_value", "=", "' '", ",", "", "", "_", ")", ":", "return", "(", "(", "[", "v", ".", "replace", "(", "'\\t'", ",", "new_value", ")", "if", "isinstance", "(", "v", ",", "text_type"...	37.846154	17.923077
def _find_field(cls, field, doc): """Find the field in the document which matches the given field. The field may be in dot notation, eg "a.b.c". Returns a list with a single tuple (path, field_value) or the empty list if the field is not present. """ path = field.split("...	[ "def", "_find_field", "(", "cls", ",", "field", ",", "doc", ")", ":", "path", "=", "field", ".", "split", "(", "\".\"", ")", "try", ":", "for", "key", "in", "path", ":", "doc", "=", "doc", "[", "key", "]", "return", "[", "(", "path", ",", "doc"...	34	15.642857
def login(): """ This route has two purposes. First, it is used by the user to login. Second, it is used by the CAS to respond with the `ticket` after the user logs in successfully. When the user accesses this url, they are redirected to the CAS to login. If the login was successful, the CAS wi...	[ "def", "login", "(", ")", ":", "cas_token_session_key", "=", "current_app", ".", "config", "[", "'CAS_TOKEN_SESSION_KEY'", "]", "redirect_url", "=", "create_cas_login_url", "(", "current_app", ".", "config", "[", "'CAS_SERVER'", "]", ",", "current_app", ".", "conf...	41.121951	22.682927
def cumulative_sum(self): """ Return the cumulative sum of the elements in the SArray. Returns an SArray where each element in the output corresponds to the sum of all the elements preceding and including it. The SArray is expected to be of numeric type (int, float), or a numeri...	[ "def", "cumulative_sum", "(", "self", ")", ":", "from", ".", ".", "import", "extensions", "agg_op", "=", "\"__builtin__cum_sum__\"", "return", "SArray", "(", "_proxy", "=", "self", ".", "__proxy__", ".", "builtin_cumulative_aggregate", "(", "agg_op", ")", ")" ]	31.966667	22.166667
def create_rename_entry( step: 'projects.ProjectStep', insertion_index: int = None, stash_path: str = None ) -> typing.Union[None, STEP_RENAME]: """ Creates a STEP_RENAME for the given ProjectStep instance :param step: The ProjectStep instance for which the STEP_RENAME will ...	[ "def", "create_rename_entry", "(", "step", ":", "'projects.ProjectStep'", ",", "insertion_index", ":", "int", "=", "None", ",", "stash_path", ":", "str", "=", "None", ")", "->", "typing", ".", "Union", "[", "None", ",", "STEP_RENAME", "]", ":", "project", ...	29.226415	19.415094
def nonspeech_fragments(self): """ Iterates through the nonspeech fragments in the list (which are sorted). :rtype: generator of (int, :class:`~aeneas.syncmap.SyncMapFragment`) """ for i, fragment in enumerate(self.__fragments): if fragment.fragment_type == S...	[ "def", "nonspeech_fragments", "(", "self", ")", ":", "for", "i", ",", "fragment", "in", "enumerate", "(", "self", ".", "__fragments", ")", ":", "if", "fragment", ".", "fragment_type", "==", "SyncMapFragment", ".", "NONSPEECH", ":", "yield", "(", "i", ",", ...	37.2	16.6
def get_pkg_module_names(package_path): """Returns module filenames from package. Args: package_path: Path to Python package. Returns: A set of module filenames. """ module_names = set() for fobj, modname, _ in pkgutil.iter_modules(path=[package_path]): filename = os.pat...	[ "def", "get_pkg_module_names", "(", "package_path", ")", ":", "module_names", "=", "set", "(", ")", "for", "fobj", ",", "modname", ",", "_", "in", "pkgutil", ".", "iter_modules", "(", "path", "=", "[", "package_path", "]", ")", ":", "filename", "=", "os"...	32.857143	15.285714
def _run_configure_script(self, script): """Run the script to install the Juju agent on the target machine. :param str script: The script returned by the ProvisioningScript API :raises: :class:`paramiko.ssh_exception.AuthenticationException` if the upload fails """ ...	[ "def", "_run_configure_script", "(", "self", ",", "script", ")", ":", "_", ",", "tmpFile", "=", "tempfile", ".", "mkstemp", "(", ")", "with", "open", "(", "tmpFile", ",", "'w'", ")", "as", "f", ":", "f", ".", "write", "(", "script", ")", "try", ":"...	30.026316	19.473684
def format_modified(self, modified, sep=" "): """Format modification date in UTC if it's not None. @param modified: modification date in UTC @ptype modified: datetime or None @return: formatted date or empty string @rtype: unicode """ if modified is not None: ...	[ "def", "format_modified", "(", "self", ",", "modified", ",", "sep", "=", "\" \"", ")", ":", "if", "modified", "is", "not", "None", ":", "return", "modified", ".", "strftime", "(", "\"%Y-%m-%d{0}%H:%M:%S.%fZ\"", ".", "format", "(", "sep", ")", ")", "return"...	40.1	10.4
def upgrade(self, flag): """Upgrade Slackware binary packages with new """ for pkg in self.binary: try: subprocess.call("upgradepkg {0} {1}".format(flag, pkg), shell=True) check = pkg[:-4].split("/")[-1] ...	[ "def", "upgrade", "(", "self", ",", "flag", ")", ":", "for", "pkg", "in", "self", ".", "binary", ":", "try", ":", "subprocess", ".", "call", "(", "\"upgradepkg {0} {1}\"", ".", "format", "(", "flag", ",", "pkg", ")", ",", "shell", "=", "True", ")", ...	40.533333	11.6
def extract_metainfo_files_from_package( package, output_folder, debug=False ): """ Extracts metdata files from the given package to the given folder, which may be referenced in any way that is permitted in a requirements.txt file or install_requires=[] listing. ...	[ "def", "extract_metainfo_files_from_package", "(", "package", ",", "output_folder", ",", "debug", "=", "False", ")", ":", "if", "package", "is", "None", ":", "raise", "ValueError", "(", "\"package cannot be None\"", ")", "if", "not", "os", ".", "path", ".", "e...	38.8	19.385714
def IntGreaterThanZero(n): """If n is an integer > 0, returns it, otherwise an error.""" try: n = int(n) except: raise ValueError("%s is not an integer" % n) if n <= 0: raise ValueError("%d is not > 0" % n) else: return n	[ "def", "IntGreaterThanZero", "(", "n", ")", ":", "try", ":", "n", "=", "int", "(", "n", ")", "except", ":", "raise", "ValueError", "(", "\"%s is not an integer\"", "%", "n", ")", "if", "n", "<=", "0", ":", "raise", "ValueError", "(", "\"%d is not > 0\"",...	26.6	19.5
def friendships_destroy(self, user_id=None, screen_name=None): """ Allows the authenticating user to unfollow the specified user. https://dev.twitter.com/docs/api/1.1/post/friendships/destroy :param str user_id: The screen name of the user for whom to unfollow. Required if ...	[ "def", "friendships_destroy", "(", "self", ",", "user_id", "=", "None", ",", "screen_name", "=", "None", ")", ":", "params", "=", "{", "}", "set_str_param", "(", "params", ",", "'user_id'", ",", "user_id", ")", "set_str_param", "(", "params", ",", "'screen...	37.85	20.95
def get_active_choices(self, language_code=None, site_id=None): """ Find out which translations should be visible in the site. It returns a list with either a single choice (the current language), or a list with the current language + fallback language. """ if language_co...	[ "def", "get_active_choices", "(", "self", ",", "language_code", "=", "None", ",", "site_id", "=", "None", ")", ":", "if", "language_code", "is", "None", ":", "language_code", "=", "get_language", "(", ")", "lang_dict", "=", "self", ".", "get_language", "(", ...	45.142857	20.714286
def install_programmer(programmer_id, programmer_options, replace_existing=False): """install programmer in programmers.txt. :param programmer_id: string identifier :param programmer_options: dict like :param replace_existing: bool :rtype: None """ doaction = 0 if programmer_id in prog...	[ "def", "install_programmer", "(", "programmer_id", ",", "programmer_options", ",", "replace_existing", "=", "False", ")", ":", "doaction", "=", "0", "if", "programmer_id", "in", "programmers", "(", ")", ".", "keys", "(", ")", ":", "log", ".", "debug", "(", ...	32.818182	19.363636
def _set_ip_acl_interface(self, v, load=False): """ Setter method for ip_acl_interface, mapped from YANG variable /interface/tengigabitethernet/ip_acl_interface (container) If this variable is read-only (config: false) in the source YANG file, then _set_ip_acl_interface is considered as a private me...	[ "def", "_set_ip_acl_interface", "(", "self", ",", "v", ",", "load", "=", "False", ")", ":", "if", "hasattr", "(", "v", ",", "\"_utype\"", ")", ":", "v", "=", "v", ".", "_utype", "(", "v", ")", "try", ":", "t", "=", "YANGDynClass", "(", "v", ",", ...	78.863636	37
def indent_func(input_): """ Takes either no arguments or an alias label """ if isinstance(input_, six.string_types): # A label was specified lbl = input_ return _indent_decor(lbl) elif isinstance(input_, (bool, tuple)): # Allow individually turning of of this decorat...	[ "def", "indent_func", "(", "input_", ")", ":", "if", "isinstance", "(", "input_", ",", "six", ".", "string_types", ")", ":", "# A label was specified", "lbl", "=", "input_", "return", "_indent_decor", "(", "lbl", ")", "elif", "isinstance", "(", "input_", ","...	30.823529	11.529412
def get_current_time(self): """ Get current time :return: datetime.time """ hms = [int(self.get_current_controller_value(i)) for i in range(406, 409)] return datetime.time(*hms)	[ "def", "get_current_time", "(", "self", ")", ":", "hms", "=", "[", "int", "(", "self", ".", "get_current_controller_value", "(", "i", ")", ")", "for", "i", "in", "range", "(", "406", ",", "409", ")", "]", "return", "datetime", ".", "time", "(", "*", ...	27.375	15.875
def _to_dict(self): """Return a json dictionary representing this model.""" _dict = {} if hasattr(self, 'text') and self.text is not None: _dict['text'] = self.text return _dict	[ "def", "_to_dict", "(", "self", ")", ":", "_dict", "=", "{", "}", "if", "hasattr", "(", "self", ",", "'text'", ")", "and", "self", ".", "text", "is", "not", "None", ":", "_dict", "[", "'text'", "]", "=", "self", ".", "text", "return", "_dict" ]	36	14.166667
def add(self, bounds1, label1, bounds2, label2, bin3, label3, data_label): """ Combines signals from multiple instruments within given bounds. Parameters ---------- bounds1 : (min, max) Bounds for selecting data on the axis of label1 D...	[ "def", "add", "(", "self", ",", "bounds1", ",", "label1", ",", "bounds2", ",", "label2", ",", "bin3", ",", "label3", ",", "data_label", ")", ":", "# TODO Update for 2.7 compatability.", "if", "isinstance", "(", "data_label", ",", "str", ")", ":", "data_label...	38.25	19.75
def write_connection_file(fname=None, shell_port=0, iopub_port=0, stdin_port=0, hb_port=0, ip=LOCALHOST, key=b''): """Generates a JSON config file, including the selection of random ports. Parameters ---------- fname : unicode The path to the file to write she...	[ "def", "write_connection_file", "(", "fname", "=", "None", ",", "shell_port", "=", "0", ",", "iopub_port", "=", "0", ",", "stdin_port", "=", "0", ",", "hb_port", "=", "0", ",", "ip", "=", "LOCALHOST", ",", "key", "=", "b''", ")", ":", "# default to tem...	27.469697	17.5
def get_id(id_or_obj): """ Returns the 'id' attribute of 'id_or_obj' if present; if not, returns 'id_or_obj'. """ if isinstance(id_or_obj, six.string_types + (int,)): # It's an ID return id_or_obj try: return id_or_obj.id except AttributeError: return id_or_ob...	[ "def", "get_id", "(", "id_or_obj", ")", ":", "if", "isinstance", "(", "id_or_obj", ",", "six", ".", "string_types", "+", "(", "int", ",", ")", ")", ":", "# It's an ID", "return", "id_or_obj", "try", ":", "return", "id_or_obj", ".", "id", "except", "Attri...	25.833333	15.5
def get_data(self, compact=True): ''' Returns data representing current state of the form. While Form.raw_data may contain alien fields and invalid data, this method returns only valid fields that belong to this form only. It's designed to pass somewhere current state of the form...	[ "def", "get_data", "(", "self", ",", "compact", "=", "True", ")", ":", "data", "=", "MultiDict", "(", ")", "for", "field", "in", "self", ".", "fields", ":", "raw_value", "=", "field", ".", "from_python", "(", "self", ".", "python_data", "[", "field", ...	43.6	23.2
def update_pop(self): """Assigns fitnesses to particles that are within bounds.""" valid_particles = [] invalid_particles = [] for part in self.population: if any(x > 1 or x < -1 for x in part): invalid_particles.append(part) else: ...	[ "def", "update_pop", "(", "self", ")", ":", "valid_particles", "=", "[", "]", "invalid_particles", "=", "[", "]", "for", "part", "in", "self", ".", "population", ":", "if", "any", "(", "x", ">", "1", "or", "x", "<", "-", "1", "for", "x", "in", "p...	42.47619	8.952381
def get_parameter(self): """ get the parameter object from the system for this var needs to be backend safe (not passing or storing bundle) """ if not self.is_param: raise ValueError("this var does not point to a parameter") # this is quite expensive, so let...	[ "def", "get_parameter", "(", "self", ")", ":", "if", "not", "self", ".", "is_param", ":", "raise", "ValueError", "(", "\"this var does not point to a parameter\"", ")", "# this is quite expensive, so let's cache the parameter object so we only", "# have to filter on the first tim...	39.933333	25.4
def sendcontrol(self, char): '''Helper method that wraps send() with mnemonic access for sending control character to the child (such as Ctrl-C or Ctrl-D). For example, to send Ctrl-G (ASCII 7, bell, '\a'):: child.sendcontrol('g') See also, sendintr() and sendeof(). ...	[ "def", "sendcontrol", "(", "self", ",", "char", ")", ":", "char", "=", "char", ".", "lower", "(", ")", "a", "=", "ord", "(", "char", ")", "if", "97", "<=", "a", "<=", "122", ":", "a", "=", "a", "-", "ord", "(", "'a'", ")", "+", "1", "byte",...	29.518519	17.074074
def get_max_instability(self, min_voltage=None, max_voltage=None): """ The maximum instability along a path for a specific voltage range. Args: min_voltage: The minimum allowable voltage. max_voltage: The maximum allowable voltage. Returns: Maximum d...	[ "def", "get_max_instability", "(", "self", ",", "min_voltage", "=", "None", ",", "max_voltage", "=", "None", ")", ":", "data", "=", "[", "]", "for", "pair", "in", "self", ".", "_select_in_voltage_range", "(", "min_voltage", ",", "max_voltage", ")", ":", "i...	42.157895	21.421053
def storage_command(self, name, method_name=None, command_type=None, oauth=False, generic_update=None, **kwargs): """ Registers an Azure CLI Storage Data Plane command. These commands always include the four parameters which can be used to obtain a storage client: account-name, account-key, connection-s...	[ "def", "storage_command", "(", "self", ",", "name", ",", "method_name", "=", "None", ",", "command_type", "=", "None", ",", "oauth", "=", "False", ",", "generic_update", "=", "None", ",", "", "", "kwargs", ")", ":", "if", "generic_update", ":", "comman...	66.769231	27.230769
def cull_edges(self, stat, threshold=0.5, comparator=ge): """Delete edges whose stat >= ``threshold`` (default 0.5). Optional argument ``comparator`` will replace >= as the test for whether to cull. You can use the name of a stored function. """ return self.cull_portals(stat, t...	[ "def", "cull_edges", "(", "self", ",", "stat", ",", "threshold", "=", "0.5", ",", "comparator", "=", "ge", ")", ":", "return", "self", ".", "cull_portals", "(", "stat", ",", "threshold", ",", "comparator", ")" ]	41.75	22.125
def _get_grammar_errors(self,pos,text,tokens): """ Internal function to get the number of grammar errors in given text pos - part of speech tagged text (list) text - normal text (list) tokens - list of lists of tokenized text """ word_counts = [max(len(t),1) for t...	[ "def", "_get_grammar_errors", "(", "self", ",", "pos", ",", "text", ",", "tokens", ")", ":", "word_counts", "=", "[", "max", "(", "len", "(", "t", ")", ",", "1", ")", "for", "t", "in", "tokens", "]", "good_pos_tags", "=", "[", "]", "min_pos_seq", "...	48.820513	20.25641
def resetAndRejoin(self, timeout): """reset and join back Thread Network with a given timeout delay Args: timeout: a timeout interval before rejoin Thread Network Returns: True: successful to reset and rejoin Thread Network False: fail to reset and rejoin th...	[ "def", "resetAndRejoin", "(", "self", ",", "timeout", ")", ":", "print", "'%s call resetAndRejoin'", "%", "self", ".", "port", "print", "timeout", "try", ":", "if", "self", ".", "__sendCommand", "(", "WPANCTL_CMD", "+", "'setprop Daemon:AutoAssociateAfterReset false...	38	24.075

def location (self, pos): """Formats the location of the given SeqPos as: filename:line:col: """ result = '' if self.filename: result += self.filename + ':' if pos: result += str(pos) return result

[ "def", "location", "(", "self", ",", "pos", ")", ":", "result", "=", "''", "if", "self", ".", "filename", ":", "result", "+=", "self", ".", "filename", "+", "':'", "if", "pos", ":", "result", "+=", "str", "(", "pos", ")", "return", "result" ]

21.090909

16.909091

def _creation_options_for_cog(creation_options, source_profile, blocksize): """ it uses the profile of the source raster, override anything using the creation_options and guarantees we will have tiled raster and blocksize """ if not(creation_options): creation_options = {} creation_opti...

[ "def", "_creation_options_for_cog", "(", "creation_options", ",", "source_profile", ",", "blocksize", ")", ":", "if", "not", "(", "creation_options", ")", ":", "creation_options", "=", "{", "}", "creation_options", "[", "\"blocksize\"", "]", "=", "blocksize", "cre...

40.533333

15.866667

def create(self, set): """ Creates a new Set. """ target_url = self.client.get_url('SET', 'POST', 'create') r = self.client.request('POST', target_url, json=set._serialize()) return set._deserialize(r.json(), self)

[ "def", "create", "(", "self", ",", "set", ")", ":", "target_url", "=", "self", ".", "client", ".", "get_url", "(", "'SET'", ",", "'POST'", ",", "'create'", ")", "r", "=", "self", ".", "client", ".", "request", "(", "'POST'", ",", "target_url", ",", ...

36.571429

14

def load(file_or_path): """ Load a previously pickled model, using `m.pickle('path/to/file.pickle)'` :param file_name: path/to/file.pickle """ from pickle import UnpicklingError _python3 = True try: import cPickle as pickle _python3 = False except ImportError: #python3 ...

[ "def", "load", "(", "file_or_path", ")", ":", "from", "pickle", "import", "UnpicklingError", "_python3", "=", "True", "try", ":", "import", "cPickle", "as", "pickle", "_python3", "=", "False", "except", "ImportError", ":", "#python3", "import", "pickle", "try"...

27.703704

18.222222

def delete(self, filename=''): """Deletes given file or directory. If no filename is passed, current directory is removed. """ self._raise_if_none() fn = path_join(self.path, filename) try: if isfile(fn): remove(fn) else: ...

[ "def", "delete", "(", "self", ",", "filename", "=", "''", ")", ":", "self", ".", "_raise_if_none", "(", ")", "fn", "=", "path_join", "(", "self", ".", "path", ",", "filename", ")", "try", ":", "if", "isfile", "(", "fn", ")", ":", "remove", "(", "...

27.235294

13.705882

async def destroy(self, container = None): """ Destroy the created subqueue to change the behavior back to Lock """ if container is None: container = RoutineContainer(self.scheduler) if self.queue is not None: await container.syscall_noreturn(syscall_remov...

[ "async", "def", "destroy", "(", "self", ",", "container", "=", "None", ")", ":", "if", "container", "is", "None", ":", "container", "=", "RoutineContainer", "(", "self", ".", "scheduler", ")", "if", "self", ".", "queue", "is", "not", "None", ":", "awai...

42.555556

15.222222

def ace(args): """ %prog ace bamfile fastafile convert bam format to ace format. This often allows the remapping to be assessed as a denovo assembly format. bam file needs to be indexed. also creates a .mates file to be used in amos/bambus, and .astat file to mark whether the contig is unique o...

[ "def", "ace", "(", "args", ")", ":", "p", "=", "OptionParser", "(", "ace", ".", "__doc__", ")", "p", ".", "add_option", "(", "\"--splitdir\"", ",", "dest", "=", "\"splitdir\"", ",", "default", "=", "\"outRoot\"", ",", "help", "=", "\"split the ace per cont...

33.008696

21.686957

def pop_cell(self, idy=None, idx=None, tags=False): """Pops a cell, default the last of the last row""" idy = idy if idy is not None else len(self.body) - 1 idx = idx if idx is not None else len(self.body[idy]) - 1 cell = self.body[idy].pop(idx) return cell if tags else cell.chil...

[ "def", "pop_cell", "(", "self", ",", "idy", "=", "None", ",", "idx", "=", "None", ",", "tags", "=", "False", ")", ":", "idy", "=", "idy", "if", "idy", "is", "not", "None", "else", "len", "(", "self", ".", "body", ")", "-", "1", "idx", "=", "i...

53.333333

10.833333

def update_attr(self, attr): """Update input attr in self. Return list of attributes with changed values. """ changed_attr = [] for key, value in attr.items(): if value is None: continue if getattr(self, "_{0}".format(key), None) != value:...

[ "def", "update_attr", "(", "self", ",", "attr", ")", ":", "changed_attr", "=", "[", "]", "for", "key", ",", "value", "in", "attr", ".", "items", "(", ")", ":", "if", "value", "is", "None", ":", "continue", "if", "getattr", "(", "self", ",", "\"_{0}...

36.714286

14.428571

async def invoke(self, context): """Claims and processes Taskcluster work. Args: context (scriptworker.context.Context): context of worker Returns: status code of build """ try: # Note: claim_work(...) might not be safely interruptible! See ...

[ "async", "def", "invoke", "(", "self", ",", "context", ")", ":", "try", ":", "# Note: claim_work(...) might not be safely interruptible! See", "# https://bugzilla.mozilla.org/show_bug.cgi?id=1524069", "tasks", "=", "await", "self", ".", "_run_cancellable", "(", "claim_work", ...

48.357143

27.880952

def _compute_centers(self, X, sparse, rs): """Generate centers, then compute tau, dF and dN vals""" super(GRBFRandomLayer, self)._compute_centers(X, sparse, rs) centers = self.components_['centers'] sorted_distances = np.sort(squareform(pdist(centers))) self.dF_vals = sorted_di...

[ "def", "_compute_centers", "(", "self", ",", "X", ",", "sparse", ",", "rs", ")", ":", "super", "(", "GRBFRandomLayer", ",", "self", ")", ".", "_compute_centers", "(", "X", ",", "sparse", ",", "rs", ")", "centers", "=", "self", ".", "components_", "[", ...

35.894737

20

def epochs(self): """Get epochs as generator Returns ------- list of dict each epoch is defined by start_time and end_time (in s in reference to the start of the recordings) and a string of the sleep stage, and a string of the signal quality. ...

[ "def", "epochs", "(", "self", ")", ":", "if", "self", ".", "rater", "is", "None", ":", "raise", "IndexError", "(", "'You need to have at least one rater'", ")", "for", "one_epoch", "in", "self", ".", "rater", ".", "iterfind", "(", "'stages/epoch'", ")", ":",...

37.259259

23.148148

def pathsplit(value, sep=os.pathsep): ''' Get enviroment PATH elements as list. This function only cares about spliting across OSes. :param value: path string, as given by os.environ['PATH'] :type value: str :param sep: PATH separator, defaults to os.pathsep :type sep: str :yields: eve...

[ "def", "pathsplit", "(", "value", ",", "sep", "=", "os", ".", "pathsep", ")", ":", "for", "part", "in", "value", ".", "split", "(", "sep", ")", ":", "if", "part", "[", ":", "1", "]", "==", "part", "[", "-", "1", ":", "]", "==", "'\"'", "or", ...

28.941176

21.058824

def detect_credentials(config_name, extra_environ=None, filenames=None, aws_profile_name=None, default_value=Ellipsis): ''' detect_credentials(config_name) attempts to locate Amazon S3 Bucket credentials from the given configuration item config_name. The following optional argu...

[ "def", "detect_credentials", "(", "config_name", ",", "extra_environ", "=", "None", ",", "filenames", "=", "None", ",", "aws_profile_name", "=", "None", ",", "default_value", "=", "Ellipsis", ")", ":", "# Check the config first:", "if", "config_name", "is", "not",...

59.877778

28.344444

def wait_until(obj, att, desired, callback=None, interval=5, attempts=0, verbose=False, verbose_atts=None): """ When changing the state of an object, it will commonly be in a transitional state until the change is complete. This will reload the object every `interval` seconds, and check its `att...

[ "def", "wait_until", "(", "obj", ",", "att", ",", "desired", ",", "callback", "=", "None", ",", "interval", "=", "5", ",", "attempts", "=", "0", ",", "verbose", "=", "False", ",", "verbose_atts", "=", "None", ")", ":", "if", "callback", ":", "waiter"...

57.686275

30.235294

def get_jwt_secret(): """ Get the JWT secret :return: str """ secret_key = __options__.get("jwt_secret") or config("JWT_SECRET") or config("SECRET_KEY") if not secret_key: raise exceptions.AuthError("Missing config JWT/SECRET_KEY") return secret_key

[ "def", "get_jwt_secret", "(", ")", ":", "secret_key", "=", "__options__", ".", "get", "(", "\"jwt_secret\"", ")", "or", "config", "(", "\"JWT_SECRET\"", ")", "or", "config", "(", "\"SECRET_KEY\"", ")", "if", "not", "secret_key", ":", "raise", "exceptions", "...

30.777778

19.888889

def atlas_peer_getinfo( peer_hostport, timeout=None, peer_table=None ): """ Get host info Return the rpc_getinfo() response on success Return None on error """ if timeout is None: timeout = atlas_ping_timeout() host, port = url_to_host_port( peer_hostport ) RPC = get_rpc_client...

[ "def", "atlas_peer_getinfo", "(", "peer_hostport", ",", "timeout", "=", "None", ",", "peer_table", "=", "None", ")", ":", "if", "timeout", "is", "None", ":", "timeout", "=", "atlas_ping_timeout", "(", ")", "host", ",", "port", "=", "url_to_host_port", "(", ...

40.234568

30.283951

def req(self, method, params=()): """send request to ppcoind""" response = self.session.post( self.url, data=json.dumps({"method": method, "params": params, "jsonrpc": "1.1"}), ).json() if response["error"] is not None: return response["error"] ...

[ "def", "req", "(", "self", ",", "method", ",", "params", "=", "(", ")", ")", ":", "response", "=", "self", ".", "session", ".", "post", "(", "self", ".", "url", ",", "data", "=", "json", ".", "dumps", "(", "{", "\"method\"", ":", "method", ",", ...

29.583333

17.666667

def get_all_lower(self): """Return all parent GO IDs through both reverse 'is_a' and all relationships.""" all_lower = set() for lower in self.get_goterms_lower(): all_lower.add(lower.item_id) all_lower |= lower.get_all_lower() return all_lower

[ "def", "get_all_lower", "(", "self", ")", ":", "all_lower", "=", "set", "(", ")", "for", "lower", "in", "self", ".", "get_goterms_lower", "(", ")", ":", "all_lower", ".", "add", "(", "lower", ".", "item_id", ")", "all_lower", "|=", "lower", ".", "get_a...

42

8.428571

def extract_subset(self, input_data_tiles=None, out_tile=None): """ Extract subset from multiple tiles. input_data_tiles : list of (``Tile``, process data) tuples out_tile : ``Tile`` Returns ------- NumPy array or list of features. """ if self.ME...

[ "def", "extract_subset", "(", "self", ",", "input_data_tiles", "=", "None", ",", "out_tile", "=", "None", ")", ":", "if", "self", ".", "METADATA", "[", "\"data_type\"", "]", "==", "\"raster\"", ":", "mosaic", "=", "create_mosaic", "(", "input_data_tiles", ")...

34.586207

15.896552

def ko_bindings(model): """ Given a model, returns the Knockout data bindings. """ try: if isinstance(model, str): modelName = model else: modelName = model.__class__.__name__ modelBindingsString = "ko.applyBindings(new " + modelName + "ViewModel(), $('#...

[ "def", "ko_bindings", "(", "model", ")", ":", "try", ":", "if", "isinstance", "(", "model", ",", "str", ")", ":", "modelName", "=", "model", "else", ":", "modelName", "=", "model", ".", "__class__", ".", "__name__", "modelBindingsString", "=", "\"ko.applyB...

26.058824

22.058824

def add(message, level=0, user=None, message_short=None,log_file_name='%s/pyscada_daemon.log' % settings.BASE_DIR,): """ add a new massage/error notice to the log <0 - Debug 1 - Emergency 2 - Critical 3 - Errors 4 - Alerts 5 - Warnings 6 - Notification (webnotice) 7 - Information...

[ "def", "add", "(", "message", ",", "level", "=", "0", ",", "user", "=", "None", ",", "message_short", "=", "None", ",", "log_file_name", "=", "'%s/pyscada_daemon.log'", "%", "settings", ".", "BASE_DIR", ",", ")", ":", "#if not access(path.dirname(self.log_file_n...

32.388889

22

def reset_clipboard(self): """ Resets the clipboard, so that old elements do not pollute the new selection that is copied into the clipboard. :return: """ # reset selections for state_element_attr in ContainerState.state_element_attrs: self.model_copies[s...

[ "def", "reset_clipboard", "(", "self", ")", ":", "# reset selections", "for", "state_element_attr", "in", "ContainerState", ".", "state_element_attrs", ":", "self", ".", "model_copies", "[", "state_element_attr", "]", "=", "[", "]", "# reset parent state_id the copied e...

34.642857

18.785714

def get(tag: {str, 'Language'}, normalize=True) -> 'Language': """ Create a Language object from a language tag string. If normalize=True, non-standard or overlong tags will be replaced as they're interpreted. This is recommended. Here are several examples of language codes, wh...

[ "def", "get", "(", "tag", ":", "{", "str", ",", "'Language'", "}", ",", "normalize", "=", "True", ")", "->", "'Language'", ":", "if", "isinstance", "(", "tag", ",", "Language", ")", ":", "if", "not", "normalize", ":", "# shortcut: we have the tag already",...

39.39759

22.542169

def smart_cast2(var): r""" if the variable is a string tries to cast it to a reasonable value. maybe can just use eval. FIXME: funcname Args: var (unknown): Returns: unknown: some var CommandLine: python -m utool.util_type --test-smart_cast2 Example: >>> #...

[ "def", "smart_cast2", "(", "var", ")", ":", "if", "var", "is", "None", ":", "return", "None", "if", "isinstance", "(", "var", ",", "six", ".", "string_types", ")", ":", "castvar", "=", "None", "lower", "=", "var", ".", "lower", "(", ")", "if", "low...

31.053571

18.178571

def set_cookie(self, key, value, expiration='Infinity', path='/', domain='', secure=False): """ expiration (int): seconds after with the cookie automatically gets deleted """ secure = 'true' if secure else 'false' self.app_instance.execute_javascript(""" var sKey = "...

[ "def", "set_cookie", "(", "self", ",", "key", ",", "value", ",", "expiration", "=", "'Infinity'", ",", "path", "=", "'/'", ",", "domain", "=", "''", ",", "secure", "=", "False", ")", ":", "secure", "=", "'true'", "if", "secure", "else", "'false'", "s...

50.064516

21.032258

def all_pairs(sets, similarity_func_name="jaccard", similarity_threshold=0.5): """Find all pairs of sets with similarity greater than a threshold. This is an implementation of the All-Pair-Binary algorithm in the paper "Scaling Up All Pairs Similarity Search" by Bayardo et al., with position fil...

[ "def", "all_pairs", "(", "sets", ",", "similarity_func_name", "=", "\"jaccard\"", ",", "similarity_threshold", "=", "0.5", ")", ":", "if", "not", "isinstance", "(", "sets", ",", "list", ")", "or", "len", "(", "sets", ")", "==", "0", ":", "raise", "ValueE...

47.898305

19.118644

def _addUserToGroup(self, username, group="Clients"): """Add user to the goup """ portal_groups = api.portal.get_tool("portal_groups") group = portal_groups.getGroupById('Clients') group.addMember(username)

[ "def", "_addUserToGroup", "(", "self", ",", "username", ",", "group", "=", "\"Clients\"", ")", ":", "portal_groups", "=", "api", ".", "portal", ".", "get_tool", "(", "\"portal_groups\"", ")", "group", "=", "portal_groups", ".", "getGroupById", "(", "'Clients'"...

40.166667

8.833333

def query_domain(self, domain, typenames, domainquerytype='list', count=False): """ Query by property domain values """ objects = self._get_repo_filter(Layer.objects) if domainquerytype == 'range': return [tuple(objects.aggregate(Min(domain), Max(domain)).values())]...

[ "def", "query_domain", "(", "self", ",", "domain", ",", "typenames", ",", "domainquerytype", "=", "'list'", ",", "count", "=", "False", ")", ":", "objects", "=", "self", ".", "_get_repo_filter", "(", "Layer", ".", "objects", ")", "if", "domainquerytype", "...

37.6

21.733333

def is_in_plane(self, pp, dist_tolerance): """ Determines if point pp is in the plane within the tolerance dist_tolerance :param pp: point to be tested :param dist_tolerance: tolerance on the distance to the plane within which point pp is considered in the plane :return: True if ...

[ "def", "is_in_plane", "(", "self", ",", "pp", ",", "dist_tolerance", ")", ":", "return", "np", ".", "abs", "(", "np", ".", "dot", "(", "self", ".", "normal_vector", ",", "pp", ")", "+", "self", ".", "_coefficients", "[", "3", "]", ")", "<=", "dist_...

57

25

def find_mean_vector(*args, **kwargs): """ Returns the mean vector for a set of measurments. By default, this expects the input to be plunges and bearings, but the type of input can be controlled through the ``measurement`` kwarg. Parameters ---------- *args : 2 or 3 sequences of measureme...

[ "def", "find_mean_vector", "(", "*", "args", ",", "*", "*", "kwargs", ")", ":", "lon", ",", "lat", "=", "_convert_measurements", "(", "args", ",", "kwargs", ".", "get", "(", "'measurement'", ",", "'lines'", ")", ")", "vector", ",", "r_value", "=", "ste...

41.434783

23.478261

def calc_paired_insert_stats(in_bam, nsample=1000000): """Retrieve statistics for paired end read insert distances. """ dists = [] n = 0 with pysam.Samfile(in_bam, "rb") as in_pysam: for read in in_pysam: if read.is_proper_pair and read.is_read1: n += 1 ...

[ "def", "calc_paired_insert_stats", "(", "in_bam", ",", "nsample", "=", "1000000", ")", ":", "dists", "=", "[", "]", "n", "=", "0", "with", "pysam", ".", "Samfile", "(", "in_bam", ",", "\"rb\"", ")", "as", "in_pysam", ":", "for", "read", "in", "in_pysam...

33.692308

11.923077

def create_sysdig_capture(self, hostname, capture_name, duration, capture_filter='', folder='/'): '''**Description** Create a new sysdig capture. The capture will be immediately started. **Arguments** - **hostname**: the hostname of the instrumented host where the capture will b...

[ "def", "create_sysdig_capture", "(", "self", ",", "hostname", ",", "capture_name", ",", "duration", ",", "capture_filter", "=", "''", ",", "folder", "=", "'/'", ")", ":", "res", "=", "self", ".", "get_connected_agents", "(", ")", "if", "not", "res", "[", ...

37.255814

25.348837

def rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples): """ organizes RNA-seq and small-RNAseq samples, converting from BAM if necessary and trimming if necessary """ pipeline = dd.get_in_samples(samples, dd.get_analysis) trim_reads_set = any([tz.get_in(["algorithm", "trim_reads...

[ "def", "rnaseq_prep_samples", "(", "config", ",", "run_info_yaml", ",", "parallel", ",", "dirs", ",", "samples", ")", ":", "pipeline", "=", "dd", ".", "get_in_samples", "(", "samples", ",", "dd", ".", "get_analysis", ")", "trim_reads_set", "=", "any", "(", ...

52.2

22.28

def cursor_up(self, count=None): """Move cursor up the indicated # of lines in same column. Cursor stops at top margin. :param int count: number of lines to skip. """ top, _bottom = self.margins or Margins(0, self.lines - 1) self.cursor.y = max(self.cursor.y - (count or ...

[ "def", "cursor_up", "(", "self", ",", "count", "=", "None", ")", ":", "top", ",", "_bottom", "=", "self", ".", "margins", "or", "Margins", "(", "0", ",", "self", ".", "lines", "-", "1", ")", "self", ".", "cursor", ".", "y", "=", "max", "(", "se...

40.125

13.75

def is_instance_throughput_too_low(self, inst_id): """ Return whether the throughput of the master instance is greater than the acceptable threshold """ r = self.instance_throughput_ratio(inst_id) if r is None: logger.debug("{} instance {} throughput is not " ...

[ "def", "is_instance_throughput_too_low", "(", "self", ",", "inst_id", ")", ":", "r", "=", "self", ".", "instance_throughput_ratio", "(", "inst_id", ")", "if", "r", "is", "None", ":", "logger", ".", "debug", "(", "\"{} instance {} throughput is not \"", "\"measurab...

43.444444

20.222222

def get_source_code(items): """ Extract source code of given items, and concatenate and dedent it. """ sources = [] prev_class_name = None for func in items: try: lines, lineno = inspect.getsourcelines(func) except TypeError: continue if not line...

[ "def", "get_source_code", "(", "items", ")", ":", "sources", "=", "[", "]", "prev_class_name", "=", "None", "for", "func", "in", "items", ":", "try", ":", "lines", ",", "lineno", "=", "inspect", ".", "getsourcelines", "(", "func", ")", "except", "TypeErr...

28.75

17.1

def process(self): """Periodic nonblocking processes""" super(NativeBLEVirtualInterface, self).process() if (not self._stream_sm_running) and (not self.reports.empty()): self._stream_data() if (not self._trace_sm_running) and (not self.traces.empty()): self._se...

[ "def", "process", "(", "self", ")", ":", "super", "(", "NativeBLEVirtualInterface", ",", "self", ")", ".", "process", "(", ")", "if", "(", "not", "self", ".", "_stream_sm_running", ")", "and", "(", "not", "self", ".", "reports", ".", "empty", "(", ")",...

32.1

23.9

def _get_artifact_context(run, file_type): """Gets the artifact details for the given run and file_type.""" sha1sum = None image_file = False log_file = False config_file = False if request.path == '/image': image_file = True if file_type == 'before': sha1sum = run.r...

[ "def", "_get_artifact_context", "(", "run", ",", "file_type", ")", ":", "sha1sum", "=", "None", "image_file", "=", "False", "log_file", "=", "False", "config_file", "=", "False", "if", "request", ".", "path", "==", "'/image'", ":", "image_file", "=", "True",...

28.567568

13

def match(self, command_context=None, **command_env): """ Check if context request is compatible with adapters specification. True - if compatible, False - otherwise :param command_context: context to check :param command_env: command environment :return: bool """ spec = self.specification() if command...

[ "def", "match", "(", "self", ",", "command_context", "=", "None", ",", "*", "*", "command_env", ")", ":", "spec", "=", "self", ".", "specification", "(", ")", "if", "command_context", "is", "None", "and", "spec", "is", "None", ":", "return", "True", "e...

33

13.857143

def get_store_profile_by_id(cls, store_profile_id, **kwargs): """Find StoreProfile Return single instance of StoreProfile by its ID. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async=True >>> thread = api.get_store_p...

[ "def", "get_store_profile_by_id", "(", "cls", ",", "store_profile_id", ",", "*", "*", "kwargs", ")", ":", "kwargs", "[", "'_return_http_data_only'", "]", "=", "True", "if", "kwargs", ".", "get", "(", "'async'", ")", ":", "return", "cls", ".", "_get_store_pro...

44.095238

21.857143

def prototype(self, name, argtypes, restype=None): """Define argument / return types for the specified C function""" function = self.function(name) function.argtypes = argtypes if restype: function.restype = restype

[ "def", "prototype", "(", "self", ",", "name", ",", "argtypes", ",", "restype", "=", "None", ")", ":", "function", "=", "self", ".", "function", "(", "name", ")", "function", ".", "argtypes", "=", "argtypes", "if", "restype", ":", "function", ".", "rest...

42.333333

6.5

def read_umi_tools(filename: PathLike, dtype: str='float32') -> AnnData: """Read a gzipped condensed count matrix from umi_tools. Parameters ---------- filename File name to read from. """ # import pandas for conversion of a dict of dicts into a matrix # import gzip to read a gzippe...

[ "def", "read_umi_tools", "(", "filename", ":", "PathLike", ",", "dtype", ":", "str", "=", "'float32'", ")", "->", "AnnData", ":", "# import pandas for conversion of a dict of dicts into a matrix", "# import gzip to read a gzipped file :-)", "import", "gzip", "from", "pandas...

35.777778

22.259259

def from_filename(cls, filename, sync_from_start=True): """ Create a `Lexer` from a filename. """ # Inline imports: the Pygments dependency is optional! from pygments.util import ClassNotFound from pygments.lexers import get_lexer_for_filename try: py...

[ "def", "from_filename", "(", "cls", ",", "filename", ",", "sync_from_start", "=", "True", ")", ":", "# Inline imports: the Pygments dependency is optional!", "from", "pygments", ".", "util", "import", "ClassNotFound", "from", "pygments", ".", "lexers", "import", "get_...

36.642857

17.071429

def validate(self, value, add_comments=False, schema_name="map"): """ verbose - also return the jsonschema error details """ validator = self.get_schema_validator(schema_name) error_messages = [] if isinstance(value, list): for d in value: er...

[ "def", "validate", "(", "self", ",", "value", ",", "add_comments", "=", "False", ",", "schema_name", "=", "\"map\"", ")", ":", "validator", "=", "self", ".", "get_schema_validator", "(", "schema_name", ")", "error_messages", "=", "[", "]", "if", "isinstance"...

34.066667

23.133333

def sendMessage(self, data): """ Send websocket data frame to the client. If data is a unicode object then the frame is sent as Text. If the data is a bytearray object then the frame is sent as Binary. """ opcode = BINARY if _check_unicode(data): ...

[ "def", "sendMessage", "(", "self", ",", "data", ")", ":", "opcode", "=", "BINARY", "if", "_check_unicode", "(", "data", ")", ":", "opcode", "=", "TEXT", "self", ".", "_sendMessage", "(", "False", ",", "opcode", ",", "data", ")" ]

34.363636

16.363636

def import_submodules(name, submodules=None): """Import all submodules for a package/module name""" sys.path.insert(0, name) if submodules: for submodule in submodules: import_string('{0}.{1}'.format(name, submodule)) else: for item in pkgutil.walk_packages([name]): ...

[ "def", "import_submodules", "(", "name", ",", "submodules", "=", "None", ")", ":", "sys", ".", "path", ".", "insert", "(", "0", ",", "name", ")", "if", "submodules", ":", "for", "submodule", "in", "submodules", ":", "import_string", "(", "'{0}.{1}'", "."...

40.111111

13.555556

def next_release(major=False, minor=False, patch=True): """Get next release version (by major, minor or patch)""" import semantic_version prev = run('git describe --abbrev=0 --tags', warn=True, hide=True).stdout or '0.0.0' ver = semantic_version.Version.coerce(prev.strip()) print('current version:...

[ "def", "next_release", "(", "major", "=", "False", ",", "minor", "=", "False", ",", "patch", "=", "True", ")", ":", "import", "semantic_version", "prev", "=", "run", "(", "'git describe --abbrev=0 --tags'", ",", "warn", "=", "True", ",", "hide", "=", "True...

35.052632

18.684211

def get_property_names(self, is_allprop): """Return list of supported property names in Clark Notation. See DAVResource.get_property_names() """ # Let base class implementation add supported live and dead properties propNameList = super(VirtualResource, self).get_property_names(...

[ "def", "get_property_names", "(", "self", ",", "is_allprop", ")", ":", "# Let base class implementation add supported live and dead properties", "propNameList", "=", "super", "(", "VirtualResource", ",", "self", ")", ".", "get_property_names", "(", "is_allprop", ")", "# A...

48.6

19.2

def check(id_): """Check bibdocs.""" BibRecDocs, BibDoc = _import_bibdoc() try: BibDoc(id_).list_all_files() except Exception: click.secho("BibDoc {0} failed check.".format(id_), fg='red')

[ "def", "check", "(", "id_", ")", ":", "BibRecDocs", ",", "BibDoc", "=", "_import_bibdoc", "(", ")", "try", ":", "BibDoc", "(", "id_", ")", ".", "list_all_files", "(", ")", "except", "Exception", ":", "click", ".", "secho", "(", "\"BibDoc {0} failed check.\...

26.75

18.75

def set_command_attributes(self, name, attributes): """ Sets the xml attributes of a specified command. """ if self.command_exists(name): command = self.commands.get(name) command['attributes'] = attributes

[ "def", "set_command_attributes", "(", "self", ",", "name", ",", "attributes", ")", ":", "if", "self", ".", "command_exists", "(", "name", ")", ":", "command", "=", "self", ".", "commands", ".", "get", "(", "name", ")", "command", "[", "'attributes'", "]"...

48.4

5

def get_environ(self, key, default=None, cast=None): """Get value from environment variable using os.environ.get :param key: The name of the setting value, will always be upper case :param default: In case of not found it will be returned :param cast: Should cast in to @int, @float, @bo...

[ "def", "get_environ", "(", "self", ",", "key", ",", "default", "=", "None", ",", "cast", "=", "None", ")", ":", "key", "=", "key", ".", "upper", "(", ")", "data", "=", "self", ".", "environ", ".", "get", "(", "key", ",", "default", ")", "if", "...

42.058824

16.058824

def create_namespaced_deployment_rollback(self, name, namespace, body, **kwargs): # noqa: E501 """create_namespaced_deployment_rollback # noqa: E501 create rollback of a Deployment # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP requ...

[ "def", "create_namespaced_deployment_rollback", "(", "self", ",", "name", ",", "namespace", ",", "body", ",", "*", "*", "kwargs", ")", ":", "# noqa: E501", "kwargs", "[", "'_return_http_data_only'", "]", "=", "True", "if", "kwargs", ".", "get", "(", "'async_re...

66.653846

39.384615

def get_scrollbar_position_height(self): """Return the pixel span height of the scrollbar area in which the slider handle may move""" vsb = self.editor.verticalScrollBar() style = vsb.style() opt = QStyleOptionSlider() vsb.initStyleOption(opt) # Get the area in w...

[ "def", "get_scrollbar_position_height", "(", "self", ")", ":", "vsb", "=", "self", ".", "editor", ".", "verticalScrollBar", "(", ")", "style", "=", "vsb", ".", "style", "(", ")", "opt", "=", "QStyleOptionSlider", "(", ")", "vsb", ".", "initStyleOption", "(...

38.692308

13.076923

def addMenuLabel(menu, text): """Adds a QLabel contaning text to the given menu""" qaw = QWidgetAction(menu) lab = QLabel(text, menu) qaw.setDefaultWidget(lab) lab.setAlignment(Qt.AlignCenter) lab.setFrameShape(QFrame.StyledPanel) lab.setFrameShadow(QFrame.Sunken) menu.addAction(qaw) ...

[ "def", "addMenuLabel", "(", "menu", ",", "text", ")", ":", "qaw", "=", "QWidgetAction", "(", "menu", ")", "lab", "=", "QLabel", "(", "text", ",", "menu", ")", "qaw", ".", "setDefaultWidget", "(", "lab", ")", "lab", ".", "setAlignment", "(", "Qt", "."...

32.2

9.6

def read(self, vals): """Read values. Args: vals (list): list of strings representing values """ i = 0 if len(vals[i]) == 0: self.ground_temperature_depth = None else: self.ground_temperature_depth = vals[i] i += 1 if ...

[ "def", "read", "(", "self", ",", "vals", ")", ":", "i", "=", "0", "if", "len", "(", "vals", "[", "i", "]", ")", "==", "0", ":", "self", ".", "ground_temperature_depth", "=", "None", "else", ":", "self", ".", "ground_temperature_depth", "=", "vals", ...

33.761364

21.034091

def actualize (self, scanner = None): """ Generates all the actual targets and sets up build actions for this target. If 'scanner' is specified, creates an additional target with the same location as actual target, which will depend on the actual target and be as...

[ "def", "actualize", "(", "self", ",", "scanner", "=", "None", ")", ":", "if", "__debug__", ":", "from", ".", "scanner", "import", "Scanner", "assert", "scanner", "is", "None", "or", "isinstance", "(", "scanner", ",", "Scanner", ")", "actual_name", "=", "...

36.435897

25.384615

def update_edge_keys(G): """ Update the keys of edges that share a u, v with another edge but differ in geometry. For example, two one-way streets from u to v that bow away from each other as separate streets, rather than opposite direction edges of a single street. Parameters --------...

[ "def", "update_edge_keys", "(", "G", ")", ":", "# identify all the edges that are duplicates based on a sorted combination", "# of their origin, destination, and key. that is, edge uv will match edge vu", "# as a duplicate, but only if they have the same key", "edges", "=", "graph_to_gdfs", ...

42.654545

26.254545

def dlogpdf_dlink(self, link_f, y, Y_metadata=None): """ Gradient of the log likelihood function at y, given link(f) w.r.t link(f) .. math:: \\frac{d \\ln p(y_{i}|\\lambda(f_{i}))}{d\\lambda(f)} = \\beta (\\log \\beta y_{i}) - \\Psi(\\alpha_{i})\\beta\\\\ \\alpha_{i} = \...

[ "def", "dlogpdf_dlink", "(", "self", ",", "link_f", ",", "y", ",", "Y_metadata", "=", "None", ")", ":", "grad", "=", "self", ".", "beta", "*", "np", ".", "log", "(", "self", ".", "beta", "*", "y", ")", "-", "special", ".", "psi", "(", "self", "...

42.47619

29.047619

def run_mp(songs): """ Concurrently calls get_lyrics to fetch the lyrics of a large list of songs. """ stats = Stats() if CONFIG['debug']: good = open('found', 'w') bad = open('notfound', 'w') logger.debug('Launching a pool of %d processes\n', CONFIG['jobcount']) chunksize =...

[ "def", "run_mp", "(", "songs", ")", ":", "stats", "=", "Stats", "(", ")", "if", "CONFIG", "[", "'debug'", "]", ":", "good", "=", "open", "(", "'found'", ",", "'w'", ")", "bad", "=", "open", "(", "'notfound'", ",", "'w'", ")", "logger", ".", "debu...

32.085714

20.257143

def write(self, filename=None): """Write array to xvg file *filename* in NXY format. .. Note:: Only plain files working at the moment, not compressed. """ self._init_filename(filename) with utilities.openany(self.real_filename, 'w') as xvg: xvg.write("# xmgrace compa...

[ "def", "write", "(", "self", ",", "filename", "=", "None", ")", ":", "self", ".", "_init_filename", "(", "filename", ")", "with", "utilities", ".", "openany", "(", "self", ".", "real_filename", ",", "'w'", ")", "as", "xvg", ":", "xvg", ".", "write", ...

48.692308

19.384615

def close(self, code=3000, message='Go away!'): """ Close session. @param code: Closing code @param message: Closing message """ if self.state != SESSION_STATE.CLOSED: # Notify handler if self.handler is not None: self.handler.send_pack(p...

[ "def", "close", "(", "self", ",", "code", "=", "3000", ",", "message", "=", "'Go away!'", ")", ":", "if", "self", ".", "state", "!=", "SESSION_STATE", ".", "CLOSED", ":", "# Notify handler", "if", "self", ".", "handler", "is", "not", "None", ":", "self...

30

14.846154

def infix(self, node, children): 'infix = "(" expr operator expr ")"' _, expr1, operator, expr2, _ = children return operator(expr1, expr2)

[ "def", "infix", "(", "self", ",", "node", ",", "children", ")", ":", "_", ",", "expr1", ",", "operator", ",", "expr2", ",", "_", "=", "children", "return", "operator", "(", "expr1", ",", "expr2", ")" ]

40

5.5

def should_skip_file(name): """ Checks if a file should be skipped based on its name. If it should be skipped, returns the reason, otherwise returns None. """ if name.startswith('.'): return 'Skipping hidden file %(filename)s' if name.endswith('~') or name.endswith('.bak'): ...

[ "def", "should_skip_file", "(", "name", ")", ":", "if", "name", ".", "startswith", "(", "'.'", ")", ":", "return", "'Skipping hidden file %(filename)s'", "if", "name", ".", "endswith", "(", "'~'", ")", "or", "name", ".", "endswith", "(", "'.bak'", ")", ":"...

38

16.555556

def get_default_config_help(self): """ Returns the help text for the configuration options for this handler """ config = super(NullHandler, self).get_default_config_help() config.update({ }) return config

[ "def", "get_default_config_help", "(", "self", ")", ":", "config", "=", "super", "(", "NullHandler", ",", "self", ")", ".", "get_default_config_help", "(", ")", "config", ".", "update", "(", "{", "}", ")", "return", "config" ]

25.3

21.5

def solve(self): """ Solve the OLL. Returns an Formula. """ if not isinstance(self.cube, Cube): raise ValueError("Use Solver.feed(cube) to feed the cube to solver.") self.recognise() self.cube(algo_dict[self.case]) return algo_dict[self.case]

[ "def", "solve", "(", "self", ")", ":", "if", "not", "isinstance", "(", "self", ".", "cube", ",", "Cube", ")", ":", "raise", "ValueError", "(", "\"Use Solver.feed(cube) to feed the cube to solver.\"", ")", "self", ".", "recognise", "(", ")", "self", ".", "cub...

33.555556

10.222222

def _set_raw_return(self, sep): """Set the output raw return section :param sep: the separator of current style """ raw = '' if self.dst.style['out'] == 'numpydoc': raw += '\n' spaces = ' ' * 4 with_space = lambda s: '\n'.join([self.docs['out...

[ "def", "_set_raw_return", "(", "self", ",", "sep", ")", ":", "raw", "=", "''", "if", "self", ".", "dst", ".", "style", "[", "'out'", "]", "==", "'numpydoc'", ":", "raw", "+=", "'\\n'", "spaces", "=", "' '", "*", "4", "with_space", "=", "lambda", "s...

54.47619

24.988095

def check_solver(self, image_x, image_y, kwargs_lens): """ returns the precision of the solver to match the image position :param kwargs_lens: full lens model (including solved parameters) :param image_x: point source in image :param image_y: point source in image :retur...

[ "def", "check_solver", "(", "self", ",", "image_x", ",", "image_y", ",", "kwargs_lens", ")", ":", "source_x", ",", "source_y", "=", "self", ".", "_lensModel", ".", "ray_shooting", "(", "image_x", ",", "image_y", ",", "kwargs_lens", ")", "dist", "=", "np", ...

50.833333

25.833333

def wsgi_wrap(app): ''' Wraps a standard wsgi application e.g.: def app(environ, start_response) It intercepts the start_response callback and grabs the results from it so it can return the status, headers, and body as a tuple ''' @wraps(app) def wrapped(environ, start_response): ...

[ "def", "wsgi_wrap", "(", "app", ")", ":", "@", "wraps", "(", "app", ")", "def", "wrapped", "(", "environ", ",", "start_response", ")", ":", "status_headers", "=", "[", "None", ",", "None", "]", "def", "_start_response", "(", "status", ",", "headers", "...

35.9375

15.8125

def override_tab_value(data, headers, new_value=' ', **_): """Override tab values in the *data* with *new_value*. :param iterable data: An :term:`iterable` (e.g. list) of rows. :param iterable headers: The column headers. :param new_value: The new value to use for tab. :return: The processed dat...

[ "def", "override_tab_value", "(", "data", ",", "headers", ",", "new_value", "=", "' '", ",", "*", "*", "_", ")", ":", "return", "(", "(", "[", "v", ".", "replace", "(", "'\\t'", ",", "new_value", ")", "if", "isinstance", "(", "v", ",", "text_type"...

37.846154

17.923077

def _find_field(cls, field, doc): """Find the field in the document which matches the given field. The field may be in dot notation, eg "a.b.c". Returns a list with a single tuple (path, field_value) or the empty list if the field is not present. """ path = field.split("...

[ "def", "_find_field", "(", "cls", ",", "field", ",", "doc", ")", ":", "path", "=", "field", ".", "split", "(", "\".\"", ")", "try", ":", "for", "key", "in", "path", ":", "doc", "=", "doc", "[", "key", "]", "return", "[", "(", "path", ",", "doc"...

34

15.642857

def login(): """ This route has two purposes. First, it is used by the user to login. Second, it is used by the CAS to respond with the `ticket` after the user logs in successfully. When the user accesses this url, they are redirected to the CAS to login. If the login was successful, the CAS wi...

[ "def", "login", "(", ")", ":", "cas_token_session_key", "=", "current_app", ".", "config", "[", "'CAS_TOKEN_SESSION_KEY'", "]", "redirect_url", "=", "create_cas_login_url", "(", "current_app", ".", "config", "[", "'CAS_SERVER'", "]", ",", "current_app", ".", "conf...

41.121951

22.682927

def cumulative_sum(self): """ Return the cumulative sum of the elements in the SArray. Returns an SArray where each element in the output corresponds to the sum of all the elements preceding and including it. The SArray is expected to be of numeric type (int, float), or a numeri...

[ "def", "cumulative_sum", "(", "self", ")", ":", "from", ".", ".", "import", "extensions", "agg_op", "=", "\"__builtin__cum_sum__\"", "return", "SArray", "(", "_proxy", "=", "self", ".", "__proxy__", ".", "builtin_cumulative_aggregate", "(", "agg_op", ")", ")" ]

31.966667

22.166667

def create_rename_entry( step: 'projects.ProjectStep', insertion_index: int = None, stash_path: str = None ) -> typing.Union[None, STEP_RENAME]: """ Creates a STEP_RENAME for the given ProjectStep instance :param step: The ProjectStep instance for which the STEP_RENAME will ...

[ "def", "create_rename_entry", "(", "step", ":", "'projects.ProjectStep'", ",", "insertion_index", ":", "int", "=", "None", ",", "stash_path", ":", "str", "=", "None", ")", "->", "typing", ".", "Union", "[", "None", ",", "STEP_RENAME", "]", ":", "project", ...

29.226415

19.415094

def nonspeech_fragments(self): """ Iterates through the nonspeech fragments in the list (which are sorted). :rtype: generator of (int, :class:`~aeneas.syncmap.SyncMapFragment`) """ for i, fragment in enumerate(self.__fragments): if fragment.fragment_type == S...

[ "def", "nonspeech_fragments", "(", "self", ")", ":", "for", "i", ",", "fragment", "in", "enumerate", "(", "self", ".", "__fragments", ")", ":", "if", "fragment", ".", "fragment_type", "==", "SyncMapFragment", ".", "NONSPEECH", ":", "yield", "(", "i", ",", ...

37.2

16.6

def get_pkg_module_names(package_path): """Returns module filenames from package. Args: package_path: Path to Python package. Returns: A set of module filenames. """ module_names = set() for fobj, modname, _ in pkgutil.iter_modules(path=[package_path]): filename = os.pat...

[ "def", "get_pkg_module_names", "(", "package_path", ")", ":", "module_names", "=", "set", "(", ")", "for", "fobj", ",", "modname", ",", "_", "in", "pkgutil", ".", "iter_modules", "(", "path", "=", "[", "package_path", "]", ")", ":", "filename", "=", "os"...

32.857143

15.285714

def _run_configure_script(self, script): """Run the script to install the Juju agent on the target machine. :param str script: The script returned by the ProvisioningScript API :raises: :class:`paramiko.ssh_exception.AuthenticationException` if the upload fails """ ...

[ "def", "_run_configure_script", "(", "self", ",", "script", ")", ":", "_", ",", "tmpFile", "=", "tempfile", ".", "mkstemp", "(", ")", "with", "open", "(", "tmpFile", ",", "'w'", ")", "as", "f", ":", "f", ".", "write", "(", "script", ")", "try", ":"...

30.026316

19.473684

def format_modified(self, modified, sep=" "): """Format modification date in UTC if it's not None. @param modified: modification date in UTC @ptype modified: datetime or None @return: formatted date or empty string @rtype: unicode """ if modified is not None: ...

[ "def", "format_modified", "(", "self", ",", "modified", ",", "sep", "=", "\" \"", ")", ":", "if", "modified", "is", "not", "None", ":", "return", "modified", ".", "strftime", "(", "\"%Y-%m-%d{0}%H:%M:%S.%fZ\"", ".", "format", "(", "sep", ")", ")", "return"...

40.1

10.4

def upgrade(self, flag): """Upgrade Slackware binary packages with new """ for pkg in self.binary: try: subprocess.call("upgradepkg {0} {1}".format(flag, pkg), shell=True) check = pkg[:-4].split("/")[-1] ...

[ "def", "upgrade", "(", "self", ",", "flag", ")", ":", "for", "pkg", "in", "self", ".", "binary", ":", "try", ":", "subprocess", ".", "call", "(", "\"upgradepkg {0} {1}\"", ".", "format", "(", "flag", ",", "pkg", ")", ",", "shell", "=", "True", ")", ...

40.533333

11.6

def extract_metainfo_files_from_package( package, output_folder, debug=False ): """ Extracts metdata files from the given package to the given folder, which may be referenced in any way that is permitted in a requirements.txt file or install_requires=[] listing. ...

[ "def", "extract_metainfo_files_from_package", "(", "package", ",", "output_folder", ",", "debug", "=", "False", ")", ":", "if", "package", "is", "None", ":", "raise", "ValueError", "(", "\"package cannot be None\"", ")", "if", "not", "os", ".", "path", ".", "e...

38.8

19.385714

def IntGreaterThanZero(n): """If *n* is an integer > 0, returns it, otherwise an error.""" try: n = int(n) except: raise ValueError("%s is not an integer" % n) if n <= 0: raise ValueError("%d is not > 0" % n) else: return n

[ "def", "IntGreaterThanZero", "(", "n", ")", ":", "try", ":", "n", "=", "int", "(", "n", ")", "except", ":", "raise", "ValueError", "(", "\"%s is not an integer\"", "%", "n", ")", "if", "n", "<=", "0", ":", "raise", "ValueError", "(", "\"%d is not > 0\"",...

26.6

19.5

def friendships_destroy(self, user_id=None, screen_name=None): """ Allows the authenticating user to unfollow the specified user. https://dev.twitter.com/docs/api/1.1/post/friendships/destroy :param str user_id: The screen name of the user for whom to unfollow. Required if ...

[ "def", "friendships_destroy", "(", "self", ",", "user_id", "=", "None", ",", "screen_name", "=", "None", ")", ":", "params", "=", "{", "}", "set_str_param", "(", "params", ",", "'user_id'", ",", "user_id", ")", "set_str_param", "(", "params", ",", "'screen...

37.85

20.95

def get_active_choices(self, language_code=None, site_id=None): """ Find out which translations should be visible in the site. It returns a list with either a single choice (the current language), or a list with the current language + fallback language. """ if language_co...

[ "def", "get_active_choices", "(", "self", ",", "language_code", "=", "None", ",", "site_id", "=", "None", ")", ":", "if", "language_code", "is", "None", ":", "language_code", "=", "get_language", "(", ")", "lang_dict", "=", "self", ".", "get_language", "(", ...

45.142857

20.714286

def install_programmer(programmer_id, programmer_options, replace_existing=False): """install programmer in programmers.txt. :param programmer_id: string identifier :param programmer_options: dict like :param replace_existing: bool :rtype: None """ doaction = 0 if programmer_id in prog...

[ "def", "install_programmer", "(", "programmer_id", ",", "programmer_options", ",", "replace_existing", "=", "False", ")", ":", "doaction", "=", "0", "if", "programmer_id", "in", "programmers", "(", ")", ".", "keys", "(", ")", ":", "log", ".", "debug", "(", ...

32.818182

19.363636

def _set_ip_acl_interface(self, v, load=False): """ Setter method for ip_acl_interface, mapped from YANG variable /interface/tengigabitethernet/ip_acl_interface (container) If this variable is read-only (config: false) in the source YANG file, then _set_ip_acl_interface is considered as a private me...

[ "def", "_set_ip_acl_interface", "(", "self", ",", "v", ",", "load", "=", "False", ")", ":", "if", "hasattr", "(", "v", ",", "\"_utype\"", ")", ":", "v", "=", "v", ".", "_utype", "(", "v", ")", "try", ":", "t", "=", "YANGDynClass", "(", "v", ",", ...

78.863636

37

def indent_func(input_): """ Takes either no arguments or an alias label """ if isinstance(input_, six.string_types): # A label was specified lbl = input_ return _indent_decor(lbl) elif isinstance(input_, (bool, tuple)): # Allow individually turning of of this decorat...

[ "def", "indent_func", "(", "input_", ")", ":", "if", "isinstance", "(", "input_", ",", "six", ".", "string_types", ")", ":", "# A label was specified", "lbl", "=", "input_", "return", "_indent_decor", "(", "lbl", ")", "elif", "isinstance", "(", "input_", ","...

30.823529

11.529412

def get_current_time(self): """ Get current time :return: datetime.time """ hms = [int(self.get_current_controller_value(i)) for i in range(406, 409)] return datetime.time(*hms)

[ "def", "get_current_time", "(", "self", ")", ":", "hms", "=", "[", "int", "(", "self", ".", "get_current_controller_value", "(", "i", ")", ")", "for", "i", "in", "range", "(", "406", ",", "409", ")", "]", "return", "datetime", ".", "time", "(", "*", ...

27.375

15.875

def _to_dict(self): """Return a json dictionary representing this model.""" _dict = {} if hasattr(self, 'text') and self.text is not None: _dict['text'] = self.text return _dict

[ "def", "_to_dict", "(", "self", ")", ":", "_dict", "=", "{", "}", "if", "hasattr", "(", "self", ",", "'text'", ")", "and", "self", ".", "text", "is", "not", "None", ":", "_dict", "[", "'text'", "]", "=", "self", ".", "text", "return", "_dict" ]

36

14.166667

def add(self, bounds1, label1, bounds2, label2, bin3, label3, data_label): """ Combines signals from multiple instruments within given bounds. Parameters ---------- bounds1 : (min, max) Bounds for selecting data on the axis of label1 D...

[ "def", "add", "(", "self", ",", "bounds1", ",", "label1", ",", "bounds2", ",", "label2", ",", "bin3", ",", "label3", ",", "data_label", ")", ":", "# TODO Update for 2.7 compatability.", "if", "isinstance", "(", "data_label", ",", "str", ")", ":", "data_label...

38.25

19.75

def write_connection_file(fname=None, shell_port=0, iopub_port=0, stdin_port=0, hb_port=0, ip=LOCALHOST, key=b''): """Generates a JSON config file, including the selection of random ports. Parameters ---------- fname : unicode The path to the file to write she...

[ "def", "write_connection_file", "(", "fname", "=", "None", ",", "shell_port", "=", "0", ",", "iopub_port", "=", "0", ",", "stdin_port", "=", "0", ",", "hb_port", "=", "0", ",", "ip", "=", "LOCALHOST", ",", "key", "=", "b''", ")", ":", "# default to tem...

27.469697

17.5

def get_id(id_or_obj): """ Returns the 'id' attribute of 'id_or_obj' if present; if not, returns 'id_or_obj'. """ if isinstance(id_or_obj, six.string_types + (int,)): # It's an ID return id_or_obj try: return id_or_obj.id except AttributeError: return id_or_ob...

[ "def", "get_id", "(", "id_or_obj", ")", ":", "if", "isinstance", "(", "id_or_obj", ",", "six", ".", "string_types", "+", "(", "int", ",", ")", ")", ":", "# It's an ID", "return", "id_or_obj", "try", ":", "return", "id_or_obj", ".", "id", "except", "Attri...

25.833333

15.5

def get_data(self, compact=True): ''' Returns data representing current state of the form. While Form.raw_data may contain alien fields and invalid data, this method returns only valid fields that belong to this form only. It's designed to pass somewhere current state of the form...

[ "def", "get_data", "(", "self", ",", "compact", "=", "True", ")", ":", "data", "=", "MultiDict", "(", ")", "for", "field", "in", "self", ".", "fields", ":", "raw_value", "=", "field", ".", "from_python", "(", "self", ".", "python_data", "[", "field", ...

43.6

23.2

def update_pop(self): """Assigns fitnesses to particles that are within bounds.""" valid_particles = [] invalid_particles = [] for part in self.population: if any(x > 1 or x < -1 for x in part): invalid_particles.append(part) else: ...

[ "def", "update_pop", "(", "self", ")", ":", "valid_particles", "=", "[", "]", "invalid_particles", "=", "[", "]", "for", "part", "in", "self", ".", "population", ":", "if", "any", "(", "x", ">", "1", "or", "x", "<", "-", "1", "for", "x", "in", "p...

42.47619

8.952381

def get_parameter(self): """ get the parameter object from the system for this var needs to be backend safe (not passing or storing bundle) """ if not self.is_param: raise ValueError("this var does not point to a parameter") # this is quite expensive, so let...

[ "def", "get_parameter", "(", "self", ")", ":", "if", "not", "self", ".", "is_param", ":", "raise", "ValueError", "(", "\"this var does not point to a parameter\"", ")", "# this is quite expensive, so let's cache the parameter object so we only", "# have to filter on the first tim...

39.933333

25.4

def sendcontrol(self, char): '''Helper method that wraps send() with mnemonic access for sending control character to the child (such as Ctrl-C or Ctrl-D). For example, to send Ctrl-G (ASCII 7, bell, '\a'):: child.sendcontrol('g') See also, sendintr() and sendeof(). ...

[ "def", "sendcontrol", "(", "self", ",", "char", ")", ":", "char", "=", "char", ".", "lower", "(", ")", "a", "=", "ord", "(", "char", ")", "if", "97", "<=", "a", "<=", "122", ":", "a", "=", "a", "-", "ord", "(", "'a'", ")", "+", "1", "byte",...

29.518519

17.074074

def get_max_instability(self, min_voltage=None, max_voltage=None): """ The maximum instability along a path for a specific voltage range. Args: min_voltage: The minimum allowable voltage. max_voltage: The maximum allowable voltage. Returns: Maximum d...

[ "def", "get_max_instability", "(", "self", ",", "min_voltage", "=", "None", ",", "max_voltage", "=", "None", ")", ":", "data", "=", "[", "]", "for", "pair", "in", "self", ".", "_select_in_voltage_range", "(", "min_voltage", ",", "max_voltage", ")", ":", "i...

42.157895

21.421053

def storage_command(self, name, method_name=None, command_type=None, oauth=False, generic_update=None, **kwargs): """ Registers an Azure CLI Storage Data Plane command. These commands always include the four parameters which can be used to obtain a storage client: account-name, account-key, connection-s...

[ "def", "storage_command", "(", "self", ",", "name", ",", "method_name", "=", "None", ",", "command_type", "=", "None", ",", "oauth", "=", "False", ",", "generic_update", "=", "None", ",", "*", "*", "kwargs", ")", ":", "if", "generic_update", ":", "comman...

66.769231

27.230769

def cull_edges(self, stat, threshold=0.5, comparator=ge): """Delete edges whose stat >= ``threshold`` (default 0.5). Optional argument ``comparator`` will replace >= as the test for whether to cull. You can use the name of a stored function. """ return self.cull_portals(stat, t...

[ "def", "cull_edges", "(", "self", ",", "stat", ",", "threshold", "=", "0.5", ",", "comparator", "=", "ge", ")", ":", "return", "self", ".", "cull_portals", "(", "stat", ",", "threshold", ",", "comparator", ")" ]

41.75

22.125

def _get_grammar_errors(self,pos,text,tokens): """ Internal function to get the number of grammar errors in given text pos - part of speech tagged text (list) text - normal text (list) tokens - list of lists of tokenized text """ word_counts = [max(len(t),1) for t...

[ "def", "_get_grammar_errors", "(", "self", ",", "pos", ",", "text", ",", "tokens", ")", ":", "word_counts", "=", "[", "max", "(", "len", "(", "t", ")", ",", "1", ")", "for", "t", "in", "tokens", "]", "good_pos_tags", "=", "[", "]", "min_pos_seq", "...

48.820513

20.25641

def resetAndRejoin(self, timeout): """reset and join back Thread Network with a given timeout delay Args: timeout: a timeout interval before rejoin Thread Network Returns: True: successful to reset and rejoin Thread Network False: fail to reset and rejoin th...

[ "def", "resetAndRejoin", "(", "self", ",", "timeout", ")", ":", "print", "'%s call resetAndRejoin'", "%", "self", ".", "port", "print", "timeout", "try", ":", "if", "self", ".", "__sendCommand", "(", "WPANCTL_CMD", "+", "'setprop Daemon:AutoAssociateAfterReset false...

38

24.075