kejian/codesearchnet-python-rebalanced · Datasets at Hugging Face

text stringlengths 75 104k	code_tokens list	avg_line_len float64 7.91 980	score float64 0 0.18
def _deserializeNT(data, glob): """ Deserialize special kinds of dicts from _serializeNT(). """ if isinstance(data, list): return [_deserializeNT(item, glob) for item in data] elif isinstance(data, tuple): return tuple(_deserializeNT(item, glob) for item in data) elif isinstanc...	[ "def", "_deserializeNT", "(", "data", ",", "glob", ")", ":", "if", "isinstance", "(", "data", ",", "list", ")", ":", "return", "[", "_deserializeNT", "(", "item", ",", "glob", ")", "for", "item", "in", "data", "]", "elif", "isinstance", "(", "data", ...	27.657143	0.000998
def simxSetIntegerParameter(clientID, paramIdentifier, paramValue, operationMode): ''' Please have a look at the function description/documentation in the V-REP user manual ''' return c_SetIntegerParameter(clientID, paramIdentifier, paramValue, operationMode)	[ "def", "simxSetIntegerParameter", "(", "clientID", ",", "paramIdentifier", ",", "paramValue", ",", "operationMode", ")", ":", "return", "c_SetIntegerParameter", "(", "clientID", ",", "paramIdentifier", ",", "paramValue", ",", "operationMode", ")" ]	45.166667	0.014493
def rank_environment_and_phenotypes(environment, phenotypes, k=15): """ Clusters sets of resources/tasks using a weighted hamming distance such that you can have few enough values to give each group of similar things a different color. This function is designed for cases when you want to color both ...	[ "def", "rank_environment_and_phenotypes", "(", "environment", ",", "phenotypes", ",", "k", "=", "15", ")", ":", "environment", "=", "convert_world_to_phenotype", "(", "environment", ")", "ranks", "=", "get_ranks_for_environment_and_phenotypes", "(", "environment", ",", ...	46.814815	0.000775
def get_session_key(limedict): """This function receive a dictionary with connection parameters. { "url": "full path for remote control", "username: "account name to be used" "password" "password for account"}""" url = limedict['url'] user = limedict['username'] password = li...	[ "def", "get_session_key", "(", "limedict", ")", ":", "url", "=", "limedict", "[", "'url'", "]", "user", "=", "limedict", "[", "'username'", "]", "password", "=", "limedict", "[", "'password'", "]", "params", "=", "{", "'username'", ":", "user", ",", "'pa...	46.333333	0.001764
def find_inputs_and_params(node): '''Walk a computation graph and extract root variables. Parameters ---------- node : Theano expression A symbolic Theano expression to walk. Returns ------- inputs : list Theano variables A list of candidate inputs for this graph. Inputs ar...	[ "def", "find_inputs_and_params", "(", "node", ")", ":", "queue", ",", "seen", ",", "inputs", ",", "params", "=", "[", "node", "]", ",", "set", "(", ")", ",", "set", "(", ")", ",", "set", "(", ")", "while", "queue", ":", "node", "=", "queue", ".",...	36.071429	0.001929
def os_deployment_servers(self): """ Gets the Os Deployment Servers API client. Returns: OsDeploymentServers: """ if not self.__os_deployment_servers: self.__os_deployment_servers = OsDeploymentServers(self.__connection) return self.__os_deploymen...	[ "def", "os_deployment_servers", "(", "self", ")", ":", "if", "not", "self", ".", "__os_deployment_servers", ":", "self", ".", "__os_deployment_servers", "=", "OsDeploymentServers", "(", "self", ".", "__connection", ")", "return", "self", ".", "__os_deployment_server...	32	0.009119
def downgrade(engine, desired_version): """Downgrades the assets db at the given engine to the desired version. Parameters ---------- engine : Engine An SQLAlchemy engine to the assets database. desired_version : int The desired resulting version for the assets database. """ ...	[ "def", "downgrade", "(", "engine", ",", "desired_version", ")", ":", "# Check the version of the db at the engine", "with", "engine", ".", "begin", "(", ")", "as", "conn", ":", "metadata", "=", "sa", ".", "MetaData", "(", "conn", ")", "metadata", ".", "reflect...	35.377778	0.000611
def _parse_posts(element): """ Returns a list with posts. """ posts = [] items = element.findall("item") for item in items: title = item.find("./title").text link = item.find("./link").text pub_date = item.find("./pubDate").text creator = item.find("./{%s}creato...	[ "def", "_parse_posts", "(", "element", ")", ":", "posts", "=", "[", "]", "items", "=", "element", ".", "findall", "(", "\"item\"", ")", "for", "item", "in", "items", ":", "title", "=", "item", ".", "find", "(", "\"./title\"", ")", ".", "text", "link"...	36.242857	0.000384
def save_collection(png_filename_base, numpy_data, start_layers_at=1): """ Export a numpy array to a set of png files, with each Z-index 2D array as its own 2D file. Arguments: png_filename_base: A filename template, such as "my-image-*.png" which will lead t...	[ "def", "save_collection", "(", "png_filename_base", ",", "numpy_data", ",", "start_layers_at", "=", "1", ")", ":", "file_ext", "=", "png_filename_base", ".", "split", "(", "'.'", ")", "[", "-", "1", "]", "if", "file_ext", "in", "[", "'png'", "]", ":", "#...	34.513514	0.000762
def find_mip(self, direction, mechanism, purview): """Return the minimum information partition for a mechanism over a purview. Args: direction (Direction): \|CAUSE\| or \|EFFECT\|. mechanism (tuple[int]): The nodes in the mechanism. purview (tuple[int]): The node...	[ "def", "find_mip", "(", "self", ",", "direction", ",", "mechanism", ",", "purview", ")", ":", "if", "not", "purview", ":", "return", "_null_ria", "(", "direction", ",", "mechanism", ",", "purview", ")", "# Calculate the unpartitioned repertoire to compare against th...	39.689655	0.000848
def _validate_config(config): """Verifies that a config dict for an attenuator device is valid. Args: config: A dict that is the configuration for an attenuator device. Raises: attenuator.Error: A config is not valid. """ required_keys = [KEY_ADDRESS, KEY_MODEL, KEY_PORT, KEY_PATHS...	[ "def", "_validate_config", "(", "config", ")", ":", "required_keys", "=", "[", "KEY_ADDRESS", ",", "KEY_MODEL", ",", "KEY_PORT", ",", "KEY_PATHS", "]", "for", "key", "in", "required_keys", ":", "if", "key", "not", "in", "config", ":", "raise", "Error", "("...	33.785714	0.002058
def get_fields(model_class, field_name='', path=''): """ Get fields and meta data from a model :param model_class: A django model class :param field_name: The field name to get sub fields from :param path: path of our field in format field_name__second_field_name__ect__ :returns: Returns fi...	[ "def", "get_fields", "(", "model_class", ",", "field_name", "=", "''", ",", "path", "=", "''", ")", ":", "fields", "=", "get_direct_fields_from_model", "(", "model_class", ")", "app_label", "=", "model_class", ".", "_meta", ".", "app_label", "if", "field_name"...	31.868421	0.000801
def hasannotation(self,Class,set=None): """Returns an integer indicating whether such as annotation exists, and if so, how many. See :meth:`AllowTokenAnnotation.annotations`` for a description of the parameters.""" return sum( 1 for _ in self.select(Class,set,True,default_ignore_annotations))	[ "def", "hasannotation", "(", "self", ",", "Class", ",", "set", "=", "None", ")", ":", "return", "sum", "(", "1", "for", "_", "in", "self", ".", "select", "(", "Class", ",", "set", ",", "True", ",", "default_ignore_annotations", ")", ")" ]	62.8	0.034591
def list(self): """List collection items.""" if self.is_fake: return for item in self.collection.list(): yield item.uid + self.content_suffix	[ "def", "list", "(", "self", ")", ":", "if", "self", ".", "is_fake", ":", "return", "for", "item", "in", "self", ".", "collection", ".", "list", "(", ")", ":", "yield", "item", ".", "uid", "+", "self", ".", "content_suffix" ]	26.285714	0.010526
def surface_intersections(edge_nodes1, edge_nodes2, all_intersections): """Find all intersections among edges of two surfaces. This treats intersections which have ``s == 1.0`` or ``t == 1.0`` as duplicates. The duplicates may be checked by the caller, e.g. by :func:`verify_duplicates`. Args: ...	[ "def", "surface_intersections", "(", "edge_nodes1", ",", "edge_nodes2", ",", "all_intersections", ")", ":", "# NOTE: There is no corresponding \"enable\", but the disable only applies", "# in this lexical scope.", "# pylint: disable=too-many-locals", "intersections", "=", "[", ...	40.327586	0.000417
def find_msvcrt(): """ Likely useless and will return None, see https://bugs.python.org/issue23606 Offered for full compatibility, though. """ # Compile Python command for wine-python command = '"from ctypes.util import find_msvcrt; print(find_msvcrt())"' # Start wine-python winepython_p = subprocess.Popen( ...	[ "def", "find_msvcrt", "(", ")", ":", "# Compile Python command for wine-python", "command", "=", "'\"from ctypes.util import find_msvcrt; print(find_msvcrt())\"'", "# Start wine-python", "winepython_p", "=", "subprocess", ".", "Popen", "(", "'wine-python -c'", "+", "command", "...	24.214286	0.042553
def approximate_density( dist, xloc, parameters=None, cache=None, eps=1.e-7 ): """ Approximate the probability density function. Args: dist : Dist Distribution in question. May not be an advanced variable. xloc : numpy.ndarray ...	[ "def", "approximate_density", "(", "dist", ",", "xloc", ",", "parameters", "=", "None", ",", "cache", "=", "None", ",", "eps", "=", "1.e-7", ")", ":", "if", "parameters", "is", "None", ":", "parameters", "=", "dist", ".", "prm", ".", "copy", "(", ")"...	30.854545	0.000571
def other_object_webhook_handler(event): """Handle updates to transfer, charge, invoice, invoiceitem, plan, product and source objects. Docs for: - charge: https://stripe.com/docs/api#charges - coupon: https://stripe.com/docs/api#coupons - invoice: https://stripe.com/docs/api#invoices - invoiceitem: https://stri...	[ "def", "other_object_webhook_handler", "(", "event", ")", ":", "if", "event", ".", "parts", "[", ":", "2", "]", "==", "[", "\"charge\"", ",", "\"dispute\"", "]", ":", "# Do not attempt to handle charge.dispute.* events.", "# We do not have a Dispute model yet.", "target...	32.733333	0.027695
def _register_allocator(self, plugin_name, plugin_instance): """ Register an allocator. :param plugin_name: Allocator name :param plugin_instance: RunPluginBase :return: """ for allocator in plugin_instance.get_allocators().keys(): if allocator in sel...	[ "def", "_register_allocator", "(", "self", ",", "plugin_name", ",", "plugin_instance", ")", ":", "for", "allocator", "in", "plugin_instance", ".", "get_allocators", "(", ")", ".", "keys", "(", ")", ":", "if", "allocator", "in", "self", ".", "_allocators", ":...	46.461538	0.008117
def tags(self, where, archiver="", timeout=DEFAULT_TIMEOUT): """ Retrieves tags for all streams matching the given WHERE clause Arguments: [where]: the where clause (e.g. 'path like "keti"', 'SourceName = "TED Main"') [archiver]: if specified, this is the archiver to use. Else, ...	[ "def", "tags", "(", "self", ",", "where", ",", "archiver", "=", "\"\"", ",", "timeout", "=", "DEFAULT_TIMEOUT", ")", ":", "return", "self", ".", "query", "(", "\"select * where {0}\"", ".", "format", "(", "where", ")", ",", "archiver", ",", "timeout", ")...	54	0.009934
def update_instrument_config( instrument, measured_center) -> Tuple[Point, float]: """ Update config and pose tree with instrument's x and y offsets and tip length based on delta between probe center and measured_center, persist updated config and return it """ from copy import deepcopy ...	[ "def", "update_instrument_config", "(", "instrument", ",", "measured_center", ")", "->", "Tuple", "[", "Point", ",", "float", "]", ":", "from", "copy", "import", "deepcopy", "from", "opentrons", ".", "trackers", ".", "pose_tracker", "import", "update", "robot", ...	38.605263	0.000665
def write_maxjobs(self,fh,category): """ Write the DAG entry for this category's maxjobs to the DAG file descriptor. @param fh: descriptor of open DAG file. @param category: tuple containing type of jobs to set a maxjobs limit for and the maximum number of jobs of that type to run at once. "...	[ "def", "write_maxjobs", "(", "self", ",", "fh", ",", "category", ")", ":", "fh", ".", "write", "(", "'MAXJOBS '", "+", "str", "(", "category", "[", "0", "]", ")", "+", "' '", "+", "str", "(", "category", "[", "1", "]", ")", "+", "'\\n'", ")" ]	49.25	0.014963
def build_directories(root_dir): """Constructs the subdirectories output, stderr, stdout, and jobs in the passed root directory. These subdirectories have the following roles: jobs Stores the scripts for each job stderr Stores the stderr output from SGE stdout ...	[ "def", "build_directories", "(", "root_dir", ")", ":", "# If the root directory doesn't exist, create it", "if", "not", "os", ".", "path", ".", "exists", "(", "root_dir", ")", ":", "os", ".", "mkdir", "(", "root_dir", ")", "# Create subdirectories", "directories", ...	42.6	0.001148
def resolve_feats(feat_list, seqin, seqref, start, locus, missing, verbose=False, verbosity=0): """ resolve_feats - Resolves features from alignments :param feat_list: List of the found features :type feat_list: ``List`` :param seqin: The input sequence :type seqin: ``str`` :param locus: Th...	[ "def", "resolve_feats", "(", "feat_list", ",", "seqin", ",", "seqref", ",", "start", ",", "locus", ",", "missing", ",", "verbose", "=", "False", ",", "verbosity", "=", "0", ")", ":", "structures", "=", "get_structures", "(", ")", "logger", "=", "logging"...	38.405405	0.000915
def update_config(config): """Update bigchaindb.config with whatever is in the provided config dict, and then set bigchaindb.config['CONFIGURED'] = True Args: config (dict): the config dict to read for changes to the default config """ # Update the default config wit...	[ "def", "update_config", "(", "config", ")", ":", "# Update the default config with whatever is in the passed config", "update", "(", "bigchaindb", ".", "config", ",", "update_types", "(", "config", ",", "bigchaindb", ".", "config", ")", ")", "bigchaindb", ".", "config...	38.083333	0.002137
def show_lowstate(*kwargs): ''' List out the low data that will be applied to this minion CLI Example: .. code-block:: bash salt '' state.show_lowstate ''' __opts__['grains'] = __grains__ opts = salt.utils.state.get_sls_opts(__opts__, **kwargs) st_ = salt.client.ssh.state.SS...	[ "def", "show_lowstate", "(", "", "", "kwargs", ")", ":", "__opts__", "[", "'grains'", "]", "=", "__grains__", "opts", "=", "salt", ".", "utils", ".", "state", ".", "get_sls_opts", "(", "__opts__", ",", "", "", "kwargs", ")", "st_", "=", "salt", "...	25.190476	0.001821
def merge_base(self, left='master', right='HEAD'): """Returns the merge-base of master and HEAD in bash: `git merge-base left right`""" return self._check_output(['merge-base', left, right], raise_type=Scm.LocalException)	[ "def", "merge_base", "(", "self", ",", "left", "=", "'master'", ",", "right", "=", "'HEAD'", ")", ":", "return", "self", ".", "_check_output", "(", "[", "'merge-base'", ",", "left", ",", "right", "]", ",", "raise_type", "=", "Scm", ".", "LocalException",...	75.666667	0.0131
def returns_something(return_node): """Check if a return node returns a value other than None. :param return_node: The return node to check. :type return_node: astroid.Return :rtype: bool :return: True if the return node returns a value other than None, False otherwise. """ returns...	[ "def", "returns_something", "(", "return_node", ")", ":", "returns", "=", "return_node", ".", "value", "if", "returns", "is", "None", ":", "return", "False", "return", "not", "(", "isinstance", "(", "returns", ",", "astroid", ".", "Const", ")", "and", "ret...	28.125	0.002151
def transmit(self, channel, msg): r""" Transmit the message (or action) and return what was transmitted. >>> ap = LoggingCommandBot.action_pattern >>> ap.match('foo').groups() (None, 'foo') >>> ap.match('foo\nbar\n').group(2) 'foo\nbar\n' >>> is_action, msg = ap.match('/me is feeling fine today').grou...	[ "def", "transmit", "(", "self", ",", "channel", ",", "msg", ")", ":", "is_action", ",", "msg", "=", "self", ".", "action_pattern", ".", "match", "(", "msg", ")", ".", "groups", "(", ")", "func", "=", "self", ".", "_conn", ".", "action", "if", "is_a...	29.482759	0.032843
def create_commit(self, message, tree, parents, author={}, committer={}): """Create a commit on this repository. :param str message: (required), commit message :param str tree: (required), SHA of the tree object this commit points to :param list parents: (required), SHAs of ...	[ "def", "create_commit", "(", "self", ",", "message", ",", "tree", ",", "parents", ",", "author", "=", "{", "}", ",", "committer", "=", "{", "}", ")", ":", "json", "=", "None", "if", "message", "and", "tree", "and", "isinstance", "(", "parents", ",", ...	53.037037	0.001372
def clear(path): ''' Causes the all attributes on the file/directory to be removed :param str path: The file(s) to get attributes from :return: True if successful, otherwise False :raises: CommandExecutionError on file not found or any other unknown error CLI Example: .. code-block:: ba...	[ "def", "clear", "(", "path", ")", ":", "cmd", "=", "'xattr -c \"{0}\"'", ".", "format", "(", "path", ")", "try", ":", "salt", ".", "utils", ".", "mac_utils", ".", "execute_return_success", "(", "cmd", ")", "except", "CommandExecutionError", "as", "exc", ":...	29.68	0.001305
def get_flight_rules(vis: Number, ceiling: Cloud) -> int: """ Returns int based on current flight rules from parsed METAR data 0=VFR, 1=MVFR, 2=IFR, 3=LIFR Note: Common practice is to report IFR if visibility unavailable """ # Parse visibility if not vis: return 2 if vis.repr =...	[ "def", "get_flight_rules", "(", "vis", ":", "Number", ",", "ceiling", ":", "Cloud", ")", "->", "int", ":", "# Parse visibility", "if", "not", "vis", ":", "return", "2", "if", "vis", ".", "repr", "==", "'CAVOK'", "or", "vis", ".", "repr", ".", "startswi...	31.466667	0.001028
def indent_text(text, nb_tabs=0, tab_str=" ", linebreak_input="\n", linebreak_output="\n", wrap=False): r"""Add tabs to each line of text. :param text: the text to indent :param nb_tabs: number of tabs to add :param tab_st...	[ "def", "indent_text", "(", "text", ",", "nb_tabs", "=", "0", ",", "tab_str", "=", "\" \"", ",", "linebreak_input", "=", "\"\\n\"", ",", "linebreak_output", "=", "\"\\n\"", ",", "wrap", "=", "False", ")", ":", "if", "not", "wrap", ":", "lines", "=", "t...	35.222222	0.001024
def validate(args): """ %prog validate outdir genome.fasta Validate current folder after MAKER run and check for failures. Failed batch will be written to a directory for additional work. """ from jcvi.utils.counter import Counter p = OptionParser(validate.__doc__) opts, args = p.parse...	[ "def", "validate", "(", "args", ")", ":", "from", "jcvi", ".", "utils", ".", "counter", "import", "Counter", "p", "=", "OptionParser", "(", "validate", ".", "__doc__", ")", "opts", ",", "args", "=", "p", ".", "parse_args", "(", "args", ")", "if", "le...	31.578947	0.001078
def run_zone(self, minutes, zone=None): """ Run or stop a zone or all zones for an amount of time. :param minutes: The number of minutes to run. :type minutes: int :param zone: The zone number to run. If no zone is specified then run all zones. :type...	[ "def", "run_zone", "(", "self", ",", "minutes", ",", "zone", "=", "None", ")", ":", "if", "zone", "is", "None", ":", "zone_cmd", "=", "'runall'", "relay_id", "=", "None", "else", ":", "if", "zone", "<", "0", "or", "zone", ">", "(", "len", "(", "s...	31.71875	0.001912
def generate_rest_view(config, model_cls, attrs=None, es_based=True, attr_view=False, singular=False): """ Generate REST view for a model class. :param model_cls: Generated DB model class. :param attr: List of strings that represent names of view methods, new generated view s...	[ "def", "generate_rest_view", "(", "config", ",", "model_cls", ",", "attrs", "=", "None", ",", "es_based", "=", "True", ",", "attr_view", "=", "False", ",", "singular", "=", "False", ")", ":", "valid_attrs", "=", "(", "list", "(", "collection_methods", ".",...	37.844444	0.000572
def start_(name): ''' Start a container name Container name or ID RETURN DATA A dictionary will be returned, containing the following keys: - ``status`` - A dictionary showing the prior state of the container as well as the new state - ``result`` - A boolean noting whet...	[ "def", "start_", "(", "name", ")", ":", "orig_state", "=", "state", "(", "name", ")", "if", "orig_state", "==", "'paused'", ":", "return", "{", "'result'", ":", "False", ",", "'state'", ":", "{", "'old'", ":", "orig_state", ",", "'new'", ":", "orig_sta...	26.483871	0.001175
def dock(self, other): ''' The opposite of concatenation. Remove a common suffix from the present pattern; that is, from each of its constituent concs. AYZ\|BYZ\|CYZ - YZ = A\|B\|C. ''' return pattern(*[c.dock(other) for c in self.concs])	[ "def", "dock", "(", "self", ",", "other", ")", ":", "return", "pattern", "(", "*", "[", "c", ".", "dock", "(", "other", ")", "for", "c", "in", "self", ".", "concs", "]", ")" ]	34.714286	0.032129
def get_attribute(self, app=None, key=None): """Returns an application attribute :param app: application id :param key: attribute key or None to retrieve all values for the given application :returns: attribute value if key was specified, or an array of tuples (k...	[ "def", "get_attribute", "(", "self", ",", "app", "=", "None", ",", "key", "=", "None", ")", ":", "path", "=", "'getattribute'", "if", "app", "is", "not", "None", ":", "path", "+=", "'/'", "+", "parse", ".", "quote", "(", "app", ",", "''", ")", "i...	38.525	0.001266
def svd_affine(inp, n_outmaps, r, base_axis=1, uv_init=None, b_init=None, fix_parameters=False, rng=None, with_bias=True): """SVD affine is a low rank approximation of the affine layer. It can be seen as two consecutive affine layers with a bottleneck. It computes: .. math...	[ "def", "svd_affine", "(", "inp", ",", "n_outmaps", ",", "r", ",", "base_axis", "=", "1", ",", "uv_init", "=", "None", ",", "b_init", "=", "None", ",", "fix_parameters", "=", "False", ",", "rng", "=", "None", ",", "with_bias", "=", "True", ")", ":", ...	38.233871	0.001645
def rescaleX(self): '''Rescales the horizontal axes to make the lengthscales equal.''' self.ratio = self.figure.get_size_inches()[0]/float(self.figure.get_size_inches()[1]) self.axes.set_xlim(-self.ratio,self.ratio) self.axes.set_ylim(-1,1)	[ "def", "rescaleX", "(", "self", ")", ":", "self", ".", "ratio", "=", "self", ".", "figure", ".", "get_size_inches", "(", ")", "[", "0", "]", "/", "float", "(", "self", ".", "figure", ".", "get_size_inches", "(", ")", "[", "1", "]", ")", "self", "...	53.6	0.018382
def generate_fixtures(datasets, reuses): '''Build sample fixture data (users, datasets and reuses).''' user = UserFactory() log.info('Generated user "{user.email}".'.format(user=user)) organization = OrganizationFactory(members=[Member(user=user)]) log.info('Generated organization "{org.name}".'.fo...	[ "def", "generate_fixtures", "(", "datasets", ",", "reuses", ")", ":", "user", "=", "UserFactory", "(", ")", "log", ".", "info", "(", "'Generated user \"{user.email}\".'", ".", "format", "(", "user", "=", "user", ")", ")", "organization", "=", "OrganizationFact...	44.4	0.001471
def classes_can_admin(self): """Return all the classes (sorted) that this user can admin.""" if self.is_admin: return sorted(Session.query(Class).all()) else: return sorted(self.admin_for)	[ "def", "classes_can_admin", "(", "self", ")", ":", "if", "self", ".", "is_admin", ":", "return", "sorted", "(", "Session", ".", "query", "(", "Class", ")", ".", "all", "(", ")", ")", "else", ":", "return", "sorted", "(", "self", ".", "admin_for", ")"...	38.5	0.008475
def mergecsv(args): """ %prog mergecsv *.tsv Merge a set of tsv files. """ p = OptionParser(mergecsv.__doc__) p.set_outfile() opts, args = p.parse_args(args) if len(args) < 2: sys.exit(not p.print_help()) tsvfiles = args outfile = opts.outfile if op.exists(outfile...	[ "def", "mergecsv", "(", "args", ")", ":", "p", "=", "OptionParser", "(", "mergecsv", ".", "__doc__", ")", "p", ".", "set_outfile", "(", ")", "opts", ",", "args", "=", "p", ".", "parse_args", "(", "args", ")", "if", "len", "(", "args", ")", "<", "...	20	0.001704
def addPathVariables(self, pathvars): """ Adds path variables to the pathvars map property""" if type(pathvars) is dict: self._pathvars = merge(self._pathvars, pathvars)	[ "def", "addPathVariables", "(", "self", ",", "pathvars", ")", ":", "if", "type", "(", "pathvars", ")", "is", "dict", ":", "self", ".", "_pathvars", "=", "merge", "(", "self", ".", "_pathvars", ",", "pathvars", ")" ]	48.5	0.010152
def bam_conversion(job, samfile, sample_type, univ_options): """ This module converts SAMFILE from sam to bam ARGUMENTS 1. samfile: <JSid for a sam file> 2. sample_type: string of 'tumor_dna' or 'normal_dna' 3. univ_options: Dict of universal arguments used by almost all tools univ_opt...	[ "def", "bam_conversion", "(", "job", ",", "samfile", ",", "sample_type", ",", "univ_options", ")", ":", "job", ".", "fileStore", ".", "logToMaster", "(", "'Running sam2bam on %s:%s'", "%", "(", "univ_options", "[", "'patient'", "]", ",", "sample_type", ")", ")...	42.34375	0.002165
def as_dictionary(self): """ Return the parameter as a dictionary. :return: dict """ return { "name": self.name, "type": self.type, "value": remove_0x_prefix(self.value) if self.type == 'bytes32' else self.value }	[ "def", "as_dictionary", "(", "self", ")", ":", "return", "{", "\"name\"", ":", "self", ".", "name", ",", "\"type\"", ":", "self", ".", "type", ",", "\"value\"", ":", "remove_0x_prefix", "(", "self", ".", "value", ")", "if", "self", ".", "type", "==", ...	26.181818	0.010067
def get_networks_by_name(self, name: str) -> List[Network]: """Get all networks with the given name. Useful for getting all versions of a given network.""" return self.session.query(Network).filter(Network.name.like(name)).all()	[ "def", "get_networks_by_name", "(", "self", ",", "name", ":", "str", ")", "->", "List", "[", "Network", "]", ":", "return", "self", ".", "session", ".", "query", "(", "Network", ")", ".", "filter", "(", "Network", ".", "name", ".", "like", "(", "name...	80.666667	0.016393
def IndexedDB_clearObjectStore(self, securityOrigin, databaseName, objectStoreName): """ Function path: IndexedDB.clearObjectStore Domain: IndexedDB Method name: clearObjectStore Parameters: Required arguments: 'securityOrigin' (type: string) -> Security origin. 'databaseName' (type: ...	[ "def", "IndexedDB_clearObjectStore", "(", "self", ",", "securityOrigin", ",", "databaseName", ",", "objectStoreName", ")", ":", "assert", "isinstance", "(", "securityOrigin", ",", "(", "str", ",", ")", ")", ",", "\"Argument 'securityOrigin' must be of type '['str']'. Re...	38.62069	0.043554
def obtain_to(filename, compressed=True): """ Return the linke turbidity projected to the lat lon matrix coordenates. Keyword arguments: filename -- the name of a netcdf file. """ files = glob.glob(filename) root, _ = nc.open(filename) lat, lon = nc.getvar(root, 'lat')[0,:], nc.getvar(r...	[ "def", "obtain_to", "(", "filename", ",", "compressed", "=", "True", ")", ":", "files", "=", "glob", ".", "glob", "(", "filename", ")", "root", ",", "_", "=", "nc", ".", "open", "(", "filename", ")", "lat", ",", "lon", "=", "nc", ".", "getvar", "...	40.5	0.00905
def search(name): ''' Search for matches in the ports tree. Globs are supported, and the category is optional CLI Examples: .. code-block:: bash salt '' ports.search 'security/' salt '' ports.search 'security/n' salt '*' ports.search nmap .. warning:: Tak...	[ "def", "search", "(", "name", ")", ":", "name", "=", "six", ".", "text_type", "(", "name", ")", "all_ports", "=", "list_all", "(", ")", "if", "'/'", "in", "name", ":", "if", "name", ".", "count", "(", "'/'", ")", ">", "1", ":", "raise", "SaltInvo...	24.909091	0.001171
def get_location(opts=None, provider=None): ''' Return the region to use, in this order: opts['location'] provider['location'] get_region_from_metadata() DEFAULT_LOCATION ''' if opts is None: opts = {} ret = opts.get('location') if ret is None and provider...	[ "def", "get_location", "(", "opts", "=", "None", ",", "provider", "=", "None", ")", ":", "if", "opts", "is", "None", ":", "opts", "=", "{", "}", "ret", "=", "opts", ".", "get", "(", "'location'", ")", "if", "ret", "is", "None", "and", "provider", ...	26.777778	0.002004
def set_content_type (self): """Return URL content type, or an empty string if content type could not be found.""" if self.url: self.content_type = mimeutil.guess_mimetype(self.url, read=self.get_content) else: self.content_type = u""	[ "def", "set_content_type", "(", "self", ")", ":", "if", "self", ".", "url", ":", "self", ".", "content_type", "=", "mimeutil", ".", "guess_mimetype", "(", "self", ".", "url", ",", "read", "=", "self", ".", "get_content", ")", "else", ":", "self", ".", ...	40.571429	0.013793
def import_source(self, CachableSource): """Updates cache area and returns number of items updated with all available entries in ICachableSource""" _count = 0 for item in CachableSource.items(): if self.cache(item): _count += 1 return _count	[ "def", "import_source", "(", "self", ",", "CachableSource", ")", ":", "_count", "=", "0", "for", "item", "in", "CachableSource", ".", "items", "(", ")", ":", "if", "self", ".", "cache", "(", "item", ")", ":", "_count", "+=", "1", "return", "_count" ]	42.142857	0.009967
def _select_index(self, row, col): """Change the selection index, and make sure it stays in the right range A little more complicated than just dooing modulo the number of row columns to be sure to cycle through all element. horizontaly, the element are maped like this : to r <...	[ "def", "_select_index", "(", "self", ",", "row", ",", "col", ")", ":", "nr", ",", "nc", "=", "self", ".", "_size", "nr", "=", "nr", "-", "1", "nc", "=", "nc", "-", "1", "# case 1", "if", "(", "row", ">", "nr", "and", "col", ">=", "nc", ")", ...	31.431818	0.009818
def to_dict(self): """ Convert current Task into a dictionary :return: python dictionary """ task_desc_as_dict = { 'uid': self._uid, 'name': self._name, 'state': self._state, 'state_history': self._state_history, 'pre...	[ "def", "to_dict", "(", "self", ")", ":", "task_desc_as_dict", "=", "{", "'uid'", ":", "self", ".", "_uid", ",", "'name'", ":", "self", ".", "_name", ",", "'state'", ":", "self", ".", "_state", ",", "'state_history'", ":", "self", ".", "_state_history", ...	31.146341	0.001519
def _check_stream(self): """Determines which output stream (stdout, stderr, or custom) to use""" if self.stream: try: supported = ('PYCHARM_HOSTED' in os.environ or os.isatty(sys.stdout.fileno())) # a fix for IPython notebook "IOStre...	[ "def", "_check_stream", "(", "self", ")", ":", "if", "self", ".", "stream", ":", "try", ":", "supported", "=", "(", "'PYCHARM_HOSTED'", "in", "os", ".", "environ", "or", "os", ".", "isatty", "(", "sys", ".", "stdout", ".", "fileno", "(", ")", ")", ...	40.8	0.001596
def insert_vlan( self, environment_id, name, number, description, acl_file, acl_file_v6, network_ipv4, network_ipv6, vrf=None): """Create new VLAN :param environment_id: ID for Enviro...	[ "def", "insert_vlan", "(", "self", ",", "environment_id", ",", "name", ",", "number", ",", "description", ",", "acl_file", ",", "acl_file_v6", ",", "network_ipv4", ",", "network_ipv6", ",", "vrf", "=", "None", ")", ":", "if", "not", "is_valid_int_param", "("...	38.076923	0.002363
def get_jira_key_from_scenario(scenario): """Extract Jira Test Case key from scenario tags. Two tag formats are allowed: @jira('PROJECT-32') @jira=PROJECT-32 :param scenario: behave scenario :returns: Jira test case key """ jira_regex = re.compile('jira[=\(\']([A-Z]+\-[0-9]+)[\'\)]$')...	[ "def", "get_jira_key_from_scenario", "(", "scenario", ")", ":", "jira_regex", "=", "re", ".", "compile", "(", "'jira[=\\(\\']([A-Z]+\\-[0-9]+)[\\'\\)]$'", ")", "for", "tag", "in", "scenario", ".", "tags", ":", "match", "=", "jira_regex", ".", "search", "(", "t...	29.533333	0.008753
def parse_public(data): """ Loads a public key from a DER or PEM-formatted file. Supports RSA, DSA and EC public keys. For RSA keys, both the old RSAPublicKey and SubjectPublicKeyInfo structures are supported. Also allows extracting a public key from an X.509 certificate. :param data: A...	[ "def", "parse_public", "(", "data", ")", ":", "if", "not", "isinstance", "(", "data", ",", "byte_cls", ")", ":", "raise", "TypeError", "(", "pretty_message", "(", "'''\n data must be a byte string, not %s\n '''", ",", "type_name", "(", "data", ...	33.042254	0.001242
def declallfuncs(self): """generator on all declaration of function""" for f in self.body: if (hasattr(f, '_ctype') and isinstance(f._ctype, FuncType)): yield f	[ "def", "declallfuncs", "(", "self", ")", ":", "for", "f", "in", "self", ".", "body", ":", "if", "(", "hasattr", "(", "f", ",", "'_ctype'", ")", "and", "isinstance", "(", "f", ".", "_ctype", ",", "FuncType", ")", ")", ":", "yield", "f" ]	36.5	0.008929
def _get_enterprise_enrollment_api_admin_users_batch(self, start, end): # pylint: disable=invalid-name """ Returns a batched queryset of User objects. """ LOGGER.info('Fetching new batch of enterprise enrollment admin users from indexes: %s to %s', start, end) return User.obj...	[ "def", "_get_enterprise_enrollment_api_admin_users_batch", "(", "self", ",", "start", ",", "end", ")", ":", "# pylint: disable=invalid-name", "LOGGER", ".", "info", "(", "'Fetching new batch of enterprise enrollment admin users from indexes: %s to %s'", ",", "start", ",", "end"...	67.666667	0.012165
def from_btl(fname): """ DataFrame constructor to open Seabird CTD BTL-ASCII format. Examples -------- >>> from pathlib import Path >>> import ctd >>> data_path = Path(__file__).parents[1].joinpath("tests", "data") >>> bottles = ctd.from_btl(data_path.joinpath('btl', 'bottletest.btl')) ...	[ "def", "from_btl", "(", "fname", ")", ":", "f", "=", "_read_file", "(", "fname", ")", "metadata", "=", "_parse_seabird", "(", "f", ".", "readlines", "(", ")", ",", "ftype", "=", "\"btl\"", ")", "f", ".", "seek", "(", "0", ")", "df", "=", "pd", "....	29.708333	0.001357
def tangelo_import(args, *kwargs): """ When we are asked to import a module, if we get an import error and the calling script is one we are serving (not one in the python libraries), try again in the same directory as the script that is calling import. It seems like we should use sys.meta_path...	[ "def", "tangelo_import", "(", "", "args", ",", "", "", "kwargs", ")", ":", "try", ":", "return", "builtin_import", "(", "", "args", ",", "", "", "kwargs", ")", "except", "ImportError", ":", "if", "not", "hasattr", "(", "cherrypy", ".", "thread_da...	41.878788	0.001414
def get_context_data(self, kwargs): ''' Adds a 'base_template' attribute to context for the page_detail to extend from ''' context = super(PageList, self).get_context_data(kwargs) page_base_template = "nupages/base.html" # if MultiTenantMiddleware is used, us...	[ "def", "get_context_data", "(", "self", ",", "", "", "kwargs", ")", ":", "context", "=", "super", "(", "PageList", ",", "self", ")", ".", "get_context_data", "(", "", "", "kwargs", ")", "page_base_template", "=", "\"nupages/base.html\"", "# if MultiTenantM...	42.875	0.008559
def domain_xml(identifier, xml, mounts, network_name=None): """Fills the XML file with the required fields. @param identifier: (str) UUID of the Environment. @param xml: (str) XML configuration of the domain. @param filesystem: (tuple) ((source, target), (source, target)) * name * uuid ...	[ "def", "domain_xml", "(", "identifier", ",", "xml", ",", "mounts", ",", "network_name", "=", "None", ")", ":", "domain", "=", "etree", ".", "fromstring", "(", "xml", ")", "subelement", "(", "domain", ",", "'.//name'", ",", "'name'", ",", "identifier", ")...	34.766667	0.001866
def load_stylesheet_pyqt5(): """ Loads the stylesheet for use in a pyqt5 application. :param pyside: True to load the pyside rc file, False to load the PyQt rc file :return the stylesheet string """ # Smart import of the rc file import qdarkstyle.pyqt5_style_rc # Load the stylesheet c...	[ "def", "load_stylesheet_pyqt5", "(", ")", ":", "# Smart import of the rc file", "import", "qdarkstyle", ".", "pyqt5_style_rc", "# Load the stylesheet content from resources", "from", "PyQt5", ".", "QtCore", "import", "QFile", ",", "QTextStream", "f", "=", "QFile", "(", ...	29.676471	0.001919
def connection_string_parser(uri: str) -> list: """ Parse Connection string to extract host and port. :param uri: full URI for redis connection in the form of host:port :returns: list of RedisConnection objects """ redis_connections = [] raw_connections = uri.sp...	[ "def", "connection_string_parser", "(", "uri", ":", "str", ")", "->", "list", ":", "redis_connections", "=", "[", "]", "raw_connections", "=", "uri", ".", "split", "(", "','", ")", "connections", "=", "[", "connection", "for", "connection", "in", "raw_connec...	34.242424	0.001721
def replace(self, args, *kargs): """ lst.replace(<field>,[<oldvalue>,]<newvalue>) lst.replace( (fld,[ov],nv),(fld,[ov,]nv),...) if ov is None, all values are replaced ex: lst.replace( IP.src, "192.168.1.1", "10.0.0.1" ) lst.replace( IP.ttl, 64 ) ...	[ "def", "replace", "(", "self", ",", "", "args", ",", "", "*", "kargs", ")", ":", "delete_checksums", "=", "kargs", ".", "get", "(", "\"delete_checksums\"", ",", "False", ")", "x", "=", "PacketList", "(", "name", "=", "\"Replaced %s\"", "%", "self", "...	40.59375	0.001504
def run (self): """Handle keyboard interrupt and other errors.""" try: self.run_checked() except KeyboardInterrupt: thread.interrupt_main() except Exception: self.internal_error()	[ "def", "run", "(", "self", ")", ":", "try", ":", "self", ".", "run_checked", "(", ")", "except", "KeyboardInterrupt", ":", "thread", ".", "interrupt_main", "(", ")", "except", "Exception", ":", "self", ".", "internal_error", "(", ")" ]	30	0.012146
def request(self, method, url_parts, headers=None, data=None): """ Method for making requests to the Optimizely API """ if method in self.ALLOWED_REQUESTS: # add request token header headers = headers or {} # test if Oauth token if self.token_type...	[ "def", "request", "(", "self", ",", "method", ",", "url_parts", ",", "headers", "=", "None", ",", "data", "=", "None", ")", ":", "if", "method", "in", "self", ".", "ALLOWED_REQUESTS", ":", "# add request token header", "headers", "=", "headers", "or", "{",...	41.233333	0.00158
def get_blobstore(layout): """Return Blobstore instance for a given storage layout Args: layout (StorageLayout): Target storage layout. """ if layout.is_s3: from wal_e.blobstore import s3 blobstore = s3 elif layout.is_wabs: from wal_e.blobstore import wabs blo...	[ "def", "get_blobstore", "(", "layout", ")", ":", "if", "layout", ".", "is_s3", ":", "from", "wal_e", ".", "blobstore", "import", "s3", "blobstore", "=", "s3", "elif", "layout", ".", "is_wabs", ":", "from", "wal_e", ".", "blobstore", "import", "wabs", "bl...	28.761905	0.001603
def is_valid_intensity_measure_types(self): """ If the IMTs and levels are extracted from the risk models, they must not be set directly. Moreover, if `intensity_measure_types_and_levels` is set directly, `intensity_measure_types` must not be set. """ if self.grou...	[ "def", "is_valid_intensity_measure_types", "(", "self", ")", ":", "if", "self", ".", "ground_motion_correlation_model", ":", "for", "imt", "in", "self", ".", "imtls", ":", "if", "not", "(", "imt", ".", "startswith", "(", "'SA'", ")", "or", "imt", "==", "'P...	47.7	0.002055
def replace(text, old, new, count=None, strip=False): ''' Replace an ``old`` subset of ``text`` with ``new``. ``old`` type may be either a string or regular expression. If ``strip``, remove all leading/trailing whitespace. If ``count``, replace the specified number of occurence, other...	[ "def", "replace", "(", "text", ",", "old", ",", "new", ",", "count", "=", "None", ",", "strip", "=", "False", ")", ":", "if", "is_string", "(", "old", ")", ":", "text", "=", "text", ".", "replace", "(", "old", ",", "new", ",", "-", "1", "if", ...	31.315789	0.013051
def get_stats_str(list_=None, newlines=False, keys=None, exclude_keys=[], lbl=None, precision=None, axis=0, stat_dict=None, use_nan=False, align=False, use_median=False, **kwargs): """ Returns the string version of get_stats DEPRICATE in favor of ut.repr3(ut.get_stats(.....	[ "def", "get_stats_str", "(", "list_", "=", "None", ",", "newlines", "=", "False", ",", "keys", "=", "None", ",", "exclude_keys", "=", "[", "]", ",", "lbl", "=", "None", ",", "precision", "=", "None", ",", "axis", "=", "0", ",", "stat_dict", "=", "N...	35.813187	0.00209
def equals(self, data): """Adds new `IN` or `=` condition depending on if a list or string was provided :param data: string or list of values :raise: - QueryTypeError: if `data` is of an unexpected type """ if isinstance(data, six.string_types): return s...	[ "def", "equals", "(", "self", ",", "data", ")", ":", "if", "isinstance", "(", "data", ",", "six", ".", "string_types", ")", ":", "return", "self", ".", "_add_condition", "(", "'='", ",", "data", ",", "types", "=", "[", "int", ",", "str", "]", ")", ...	40.571429	0.008606
def seq_len(self,L): """set the length of the uncompressed sequence. its inverse 'one_mutation' is frequently used as a general length scale. This can't be changed once it is set. Parameters ---------- L : int length of the sequence alignment """ ...	[ "def", "seq_len", "(", "self", ",", "L", ")", ":", "if", "(", "not", "hasattr", "(", "self", ",", "'_seq_len'", ")", ")", "or", "self", ".", "_seq_len", "is", "None", ":", "if", "L", ":", "self", ".", "_seq_len", "=", "int", "(", "L", ")", "els...	35.133333	0.012939
def get_variable(self, variable_name, client=None): """API call: get a variable via a ``GET`` request. This will return None if the variable doesn't exist:: >>> from google.cloud import runtimeconfig >>> client = runtimeconfig.Client() >>> config = client.config('my-conf...	[ "def", "get_variable", "(", "self", ",", "variable_name", ",", "client", "=", "None", ")", ":", "client", "=", "self", ".", "_require_client", "(", "client", ")", "variable", "=", "Variable", "(", "config", "=", "self", ",", "name", "=", "variable_name", ...	38.709677	0.001626
def getRepositories(self): """Returns a list of repositories for this directory. """ if self.srcdir and not self.duplicate: return self.srcdir.get_all_rdirs() + self.repositories return self.repositories	[ "def", "getRepositories", "(", "self", ")", ":", "if", "self", ".", "srcdir", "and", "not", "self", ".", "duplicate", ":", "return", "self", ".", "srcdir", ".", "get_all_rdirs", "(", ")", "+", "self", ".", "repositories", "return", "self", ".", "reposito...	40.333333	0.008097
def replace(self, html): """Perform replacements on given HTML fragment.""" self.html = html text = html.text() positions = [] def perform_replacement(match): offset = sum(positions) start, stop = match.start() + offset, match.end() + offset ...	[ "def", "replace", "(", "self", ",", "html", ")", ":", "self", ".", "html", "=", "html", "text", "=", "html", ".", "text", "(", ")", "positions", "=", "[", "]", "def", "perform_replacement", "(", "match", ")", ":", "offset", "=", "sum", "(", "positi...	31.740741	0.002265
def new_thing(self, name, stats): """Create a new thing, located here, and return it.""" return self.character.new_thing( name, self.name, stats )	[ "def", "new_thing", "(", "self", ",", "name", ",", "", "", "stats", ")", ":", "return", "self", ".", "character", ".", "new_thing", "(", "name", ",", "self", ".", "name", ",", "", "", "stats", ")" ]	36.4	0.010753
def audio(self, audio, sample_rate, name=None, subdir=''): """Summary audio to listen on web browser. Args: audio (:class:`numpy.ndarray` or :class:`cupy.ndarray` or \ :class:`chainer.Variable`): sampled wave array. sample_rate (int): sampling rate. n...	[ "def", "audio", "(", "self", ",", "audio", ",", "sample_rate", ",", "name", "=", "None", ",", "subdir", "=", "''", ")", ":", "from", "chainerui", ".", "report", ".", "audio_report", "import", "check_available", "if", "not", "check_available", "(", ")", "...	41	0.002073
def _extend_str(class_node, rvalue): """function to extend builtin str/unicode class""" code = dedent( """ class whatever(object): def join(self, iterable): return {rvalue} def replace(self, old, new, count=None): return {rvalue} def format(self, *args...	[ "def", "_extend_str", "(", "class_node", ",", "rvalue", ")", ":", "code", "=", "dedent", "(", "\"\"\"\n class whatever(object):\n def join(self, iterable):\n return {rvalue}\n def replace(self, old, new, count=None):\n return {rvalue}\n def forma...	32.909091	0.000536
def cleaned_date(day, keep_datetime=False): """ Return a "clean" date type. * keep a `date` unchanged * convert a datetime into a date, * convert any "duck date" type into a date using its `date()` method. """ if not isinstance(day, (date, datetime)): raise UnsupportedDateType( ...	[ "def", "cleaned_date", "(", "day", ",", "keep_datetime", "=", "False", ")", ":", "if", "not", "isinstance", "(", "day", ",", "(", "date", ",", "datetime", ")", ")", ":", "raise", "UnsupportedDateType", "(", "\"`{}` is of unsupported type ({})\"", ".", "format"...	33.2	0.001953
def parse_cmd_arguments(): """Parse command line arguments.""" parser = argparse.ArgumentParser() parser.add_argument('file', type=str, help='Filename to be staticfied') parser.add_argument('--static-endpoint', help='Static endpoint which is "static" by de...	[ "def", "parse_cmd_arguments", "(", ")", ":", "parser", "=", "argparse", ".", "ArgumentParser", "(", ")", "parser", ".", "add_argument", "(", "'file'", ",", "type", "=", "str", ",", "help", "=", "'Filename to be staticfied'", ")", "parser", ".", "add_argument",...	47.368421	0.001089
def add_aggregated_lv_components(network, components): """ Aggregates LV load and generation at LV stations Use this function if you aim for MV calculation only. The according DataFrames of `components` are extended by load and generators representing these aggregated respecting the technology type...	[ "def", "add_aggregated_lv_components", "(", "network", ",", "components", ")", ":", "generators", "=", "{", "}", "loads", "=", "{", "}", "# collect aggregated generation capacity by type and subtype", "# collect aggregated load grouped by sector", "for", "lv_grid", "in", "n...	38.851852	0.00031
def slice(self, who): "return the slice entry (in a bed6 format), AS IS in the chain header" assert who in ('t', 'q'), "who should be 't' or 'q'" if who == 't': return (self.tName, self.tStart, self.tEnd, self.id, self.score, self.tStrand) else: return (self.qNa...	[ "def", "slice", "(", "self", ",", "who", ")", ":", "assert", "who", "in", "(", "'t'", ",", "'q'", ")", ",", "\"who should be 't' or 'q'\"", "if", "who", "==", "'t'", ":", "return", "(", "self", ".", "tName", ",", "self", ".", "tStart", ",", "self", ...	41.555556	0.010471
def skewvT(self,R,romberg=False,nsigma=None,phi=0.): """ NAME: skewvT PURPOSE: calculate skew in vT at R by marginalizing over velocity INPUT: R - radius at which to calculate <vR> (can be Quantity) OPTIONAL INPUT: nsigma - numbe...	[ "def", "skewvT", "(", "self", ",", "R", ",", "romberg", "=", "False", ",", "nsigma", "=", "None", ",", "phi", "=", "0.", ")", ":", "surfmass", "=", "self", ".", "surfacemass", "(", "R", ",", "romberg", "=", "romberg", ",", "nsigma", "=", "nsigma", ...	24.853659	0.02644
def get_id_for_extra_dim_type(type_str): """ Returns the index of the type as defined in the LAS Specification Parameters ---------- type_str: str Returns ------- int index of the type """ try: return _type_to_extra_dim_id_style_1[type_str] except KeyError: ...	[ "def", "get_id_for_extra_dim_type", "(", "type_str", ")", ":", "try", ":", "return", "_type_to_extra_dim_id_style_1", "[", "type_str", "]", "except", "KeyError", ":", "try", ":", "return", "_type_to_extra_dim_id_style_2", "[", "type_str", "]", "except", "KeyError", ...	22.3	0.002151
def from_scene_coords(self, x=0, y=0): """Converts x, y given in the scene coordinates to sprite's local ones coordinates""" matrix = self.get_matrix() matrix.invert() return matrix.transform_point(x, y)	[ "def", "from_scene_coords", "(", "self", ",", "x", "=", "0", ",", "y", "=", "0", ")", ":", "matrix", "=", "self", ".", "get_matrix", "(", ")", "matrix", ".", "invert", "(", ")", "return", "matrix", ".", "transform_point", "(", "x", ",", "y", ")" ]	39.666667	0.00823
def is_obtuse(p1, v, p2): '''Determine whether the angle, p1 - v - p2 is obtuse p1 - N x 2 array of coordinates of first point on edge v - N x 2 array of vertex coordinates p2 - N x 2 array of coordinates of second point on edge returns vector of booleans ''' p1x = p1[:,1] p1y ...	[ "def", "is_obtuse", "(", "p1", ",", "v", ",", "p2", ")", ":", "p1x", "=", "p1", "[", ":", ",", "1", "]", "p1y", "=", "p1", "[", ":", ",", "0", "]", "p2x", "=", "p2", "[", ":", ",", "1", "]", "p2y", "=", "p2", "[", ":", ",", "0", "]", ...	24.75	0.01751
def _format_output(selected_number, raw_data): """Format data to get a readable output""" tmp_data = {} data = collections.defaultdict(lambda: 0) balance = raw_data.pop('balance') for number in raw_data.keys(): tmp_data = dict([(k, int(v) if v is not None else "No limit") ...	[ "def", "_format_output", "(", "selected_number", ",", "raw_data", ")", ":", "tmp_data", "=", "{", "}", "data", "=", "collections", ".", "defaultdict", "(", "lambda", ":", "0", ")", "balance", "=", "raw_data", ".", "pop", "(", "'balance'", ")", "for", "nu...	33	0.001473
def to_html(self): """Render a Table MessageElement as html. :returns: The html representation of the Table MessageElement :rtype: basestring """ table = '<table%s>\n' % self.html_attributes() if self.caption is not None: if isinstance(self.caption, MessageEl...	[ "def", "to_html", "(", "self", ")", ":", "table", "=", "'<table%s>\\n'", "%", "self", ".", "html_attributes", "(", ")", "if", "self", ".", "caption", "is", "not", "None", ":", "if", "isinstance", "(", "self", ".", "caption", ",", "MessageElement", ")", ...	34.16	0.002278
def parse_package(package_string, arch_included=True): """Parse an RPM version string to get name, version, and arch Splits most (all tested) RPM version strings into name, epoch, version, release, and architecture. Epoch (also called serial) is an optional component of RPM versioning and is also optio...	[ "def", "parse_package", "(", "package_string", ",", "arch_included", "=", "True", ")", ":", "# Yum sets epoch values to 0 if they are not specified", "logger", ".", "debug", "(", "'parse_package(%s, %s)'", ",", "package_string", ",", "arch_included", ")", "default_epoch", ...	41.390244	0.000576
def _convert(self, args): '''convert '(1,1)' to 'B2' and 'B2' to '(1,1)' auto-recongnize''' if args.find(",") > -1: b, a = args.replace("(", "").replace(")", "").split(",") a = chr(int(a)+65)#chr(65) is "A" and ord("A") is 65 b = str(int(b)+1) return a+b ...	[ "def", "_convert", "(", "self", ",", "args", ")", ":", "if", "args", ".", "find", "(", "\",\"", ")", ">", "-", "1", ":", "b", ",", "a", "=", "args", ".", "replace", "(", "\"(\"", ",", "\"\"", ")", ".", "replace", "(", "\")\"", ",", "\"\"", ")...	47.636364	0.009363
def scroll_to(self, line): """ Scroll the abstract canvas to make a specific line. :param line: The line to scroll to. """ self._buffer.scroll(line - self._start_line) self._start_line = line	[ "def", "scroll_to", "(", "self", ",", "line", ")", ":", "self", ".", "_buffer", ".", "scroll", "(", "line", "-", "self", ".", "_start_line", ")", "self", ".", "_start_line", "=", "line" ]	29.125	0.008333
def create_folder(self, name, parent_folder_id=0): """Create a folder If the folder exists, a BoxError will be raised. Args: folder_id (int): Name of the folder. parent_folder_id (int): ID of the folder where to create the new one. Returns: dict. R...	[ "def", "create_folder", "(", "self", ",", "name", ",", "parent_folder_id", "=", "0", ")", ":", "return", "self", ".", "__request", "(", "\"POST\"", ",", "\"folders\"", ",", "data", "=", "{", "\"name\"", ":", "name", ",", "\"parent\"", ":", "{", "\"id\"",...	31.913043	0.009259
def condense_otus(otuF, nuniqueF): """ Traverse the input otu-sequence file, collect the non-unique OTU IDs and file the sequences associated with then under the unique OTU ID as defined by the input matrix. :@type otuF: file :@param otuF: The output file from QIIME's pick_otus.py :@type nu...	[ "def", "condense_otus", "(", "otuF", ",", "nuniqueF", ")", ":", "uniqueOTUs", "=", "set", "(", ")", "nuOTUs", "=", "{", "}", "# parse non-unique otu matrix", "for", "line", "in", "nuniqueF", ":", "line", "=", "line", ".", "split", "(", ")", "uOTU", "=", ...	30.236842	0.000843
def get_distribution(cls, ctx, name=None, recipes=[], ndk_api=None, force_build=False, extra_dist_dirs=[], require_perfect_match=False, allow_replace_dist=True): '''Takes information abou...	[ "def", "get_distribution", "(", "cls", ",", "ctx", ",", "name", "=", "None", ",", "recipes", "=", "[", "]", ",", "ndk_api", "=", "None", ",", "force_build", "=", "False", ",", "extra_dist_dirs", "=", "[", "]", ",", "require_perfect_match", "=", "False", ...	38.426087	0.001985
def remove_other_cflags(self, flags, target_name=None, configuration_name=None): """ Removes the given flags from the OTHER_CFLAGS section of the target on the configurations :param flags: A string or array of strings. If none, removes all values from the flag. :param target_name: Target...	[ "def", "remove_other_cflags", "(", "self", ",", "flags", ",", "target_name", "=", "None", ",", "configuration_name", "=", "None", ")", ":", "self", ".", "remove_flags", "(", "XCBuildConfigurationFlags", ".", "OTHER_CFLAGS", ",", "flags", ",", "target_name", ",",...	70.555556	0.012442

def _deserializeNT(data, glob): """ Deserialize special kinds of dicts from _serializeNT(). """ if isinstance(data, list): return [_deserializeNT(item, glob) for item in data] elif isinstance(data, tuple): return tuple(_deserializeNT(item, glob) for item in data) elif isinstanc...

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def simxSetIntegerParameter(clientID, paramIdentifier, paramValue, operationMode): ''' Please have a look at the function description/documentation in the V-REP user manual ''' return c_SetIntegerParameter(clientID, paramIdentifier, paramValue, operationMode)

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def rank_environment_and_phenotypes(environment, phenotypes, k=15): """ Clusters sets of resources/tasks using a weighted hamming distance such that you can have few enough values to give each group of similar things a different color. This function is designed for cases when you want to color both ...

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def get_session_key(limedict): """This function receive a dictionary with connection parameters. { "url": "full path for remote control", "username: "account name to be used" "password" "password for account"}""" url = limedict['url'] user = limedict['username'] password = li...

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def find_inputs_and_params(node): '''Walk a computation graph and extract root variables. Parameters ---------- node : Theano expression A symbolic Theano expression to walk. Returns ------- inputs : list Theano variables A list of candidate inputs for this graph. Inputs ar...

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def os_deployment_servers(self): """ Gets the Os Deployment Servers API client. Returns: OsDeploymentServers: """ if not self.__os_deployment_servers: self.__os_deployment_servers = OsDeploymentServers(self.__connection) return self.__os_deploymen...

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def downgrade(engine, desired_version): """Downgrades the assets db at the given engine to the desired version. Parameters ---------- engine : Engine An SQLAlchemy engine to the assets database. desired_version : int The desired resulting version for the assets database. """ ...

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def _parse_posts(element): """ Returns a list with posts. """ posts = [] items = element.findall("item") for item in items: title = item.find("./title").text link = item.find("./link").text pub_date = item.find("./pubDate").text creator = item.find("./{%s}creato...

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def save_collection(png_filename_base, numpy_data, start_layers_at=1): """ Export a numpy array to a set of png files, with each Z-index 2D array as its own 2D file. Arguments: png_filename_base: A filename template, such as "my-image-*.png" which will lead t...

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def find_mip(self, direction, mechanism, purview): """Return the minimum information partition for a mechanism over a purview. Args: direction (Direction): |CAUSE| or |EFFECT|. mechanism (tuple[int]): The nodes in the mechanism. purview (tuple[int]): The node...

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def _validate_config(config): """Verifies that a config dict for an attenuator device is valid. Args: config: A dict that is the configuration for an attenuator device. Raises: attenuator.Error: A config is not valid. """ required_keys = [KEY_ADDRESS, KEY_MODEL, KEY_PORT, KEY_PATHS...

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def get_fields(model_class, field_name='', path=''): """ Get fields and meta data from a model :param model_class: A django model class :param field_name: The field name to get sub fields from :param path: path of our field in format field_name__second_field_name__ect__ :returns: Returns fi...

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def hasannotation(self,Class,set=None): """Returns an integer indicating whether such as annotation exists, and if so, how many. See :meth:`AllowTokenAnnotation.annotations`` for a description of the parameters.""" return sum( 1 for _ in self.select(Class,set,True,default_ignore_annotations))

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def list(self): """List collection items.""" if self.is_fake: return for item in self.collection.list(): yield item.uid + self.content_suffix

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def surface_intersections(edge_nodes1, edge_nodes2, all_intersections): """Find all intersections among edges of two surfaces. This treats intersections which have ``s == 1.0`` or ``t == 1.0`` as duplicates. The duplicates may be checked by the caller, e.g. by :func:`verify_duplicates`. Args: ...

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def find_msvcrt(): """ Likely useless and will return None, see https://bugs.python.org/issue23606 Offered for full compatibility, though. """ # Compile Python command for wine-python command = '"from ctypes.util import find_msvcrt; print(find_msvcrt())"' # Start wine-python winepython_p = subprocess.Popen( ...

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def approximate_density( dist, xloc, parameters=None, cache=None, eps=1.e-7 ): """ Approximate the probability density function. Args: dist : Dist Distribution in question. May not be an advanced variable. xloc : numpy.ndarray ...

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def other_object_webhook_handler(event): """Handle updates to transfer, charge, invoice, invoiceitem, plan, product and source objects. Docs for: - charge: https://stripe.com/docs/api#charges - coupon: https://stripe.com/docs/api#coupons - invoice: https://stripe.com/docs/api#invoices - invoiceitem: https://stri...

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def _register_allocator(self, plugin_name, plugin_instance): """ Register an allocator. :param plugin_name: Allocator name :param plugin_instance: RunPluginBase :return: """ for allocator in plugin_instance.get_allocators().keys(): if allocator in sel...

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def tags(self, where, archiver="", timeout=DEFAULT_TIMEOUT): """ Retrieves tags for all streams matching the given WHERE clause Arguments: [where]: the where clause (e.g. 'path like "keti"', 'SourceName = "TED Main"') [archiver]: if specified, this is the archiver to use. Else, ...

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def update_instrument_config( instrument, measured_center) -> Tuple[Point, float]: """ Update config and pose tree with instrument's x and y offsets and tip length based on delta between probe center and measured_center, persist updated config and return it """ from copy import deepcopy ...

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def write_maxjobs(self,fh,category): """ Write the DAG entry for this category's maxjobs to the DAG file descriptor. @param fh: descriptor of open DAG file. @param category: tuple containing type of jobs to set a maxjobs limit for and the maximum number of jobs of that type to run at once. "...

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def build_directories(root_dir): """Constructs the subdirectories output, stderr, stdout, and jobs in the passed root directory. These subdirectories have the following roles: jobs Stores the scripts for each job stderr Stores the stderr output from SGE stdout ...

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def resolve_feats(feat_list, seqin, seqref, start, locus, missing, verbose=False, verbosity=0): """ resolve_feats - Resolves features from alignments :param feat_list: List of the found features :type feat_list: ``List`` :param seqin: The input sequence :type seqin: ``str`` :param locus: Th...

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def update_config(config): """Update bigchaindb.config with whatever is in the provided config dict, and then set bigchaindb.config['CONFIGURED'] = True Args: config (dict): the config dict to read for changes to the default config """ # Update the default config wit...

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def show_lowstate(**kwargs): ''' List out the low data that will be applied to this minion CLI Example: .. code-block:: bash salt '*' state.show_lowstate ''' __opts__['grains'] = __grains__ opts = salt.utils.state.get_sls_opts(__opts__, **kwargs) st_ = salt.client.ssh.state.SS...

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def merge_base(self, left='master', right='HEAD'): """Returns the merge-base of master and HEAD in bash: `git merge-base left right`""" return self._check_output(['merge-base', left, right], raise_type=Scm.LocalException)

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def returns_something(return_node): """Check if a return node returns a value other than None. :param return_node: The return node to check. :type return_node: astroid.Return :rtype: bool :return: True if the return node returns a value other than None, False otherwise. """ returns...

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def transmit(self, channel, msg): r""" Transmit the message (or action) and return what was transmitted. >>> ap = LoggingCommandBot.action_pattern >>> ap.match('foo').groups() (None, 'foo') >>> ap.match('foo\nbar\n').group(2) 'foo\nbar\n' >>> is_action, msg = ap.match('/me is feeling fine today').grou...

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def create_commit(self, message, tree, parents, author={}, committer={}): """Create a commit on this repository. :param str message: (required), commit message :param str tree: (required), SHA of the tree object this commit points to :param list parents: (required), SHAs of ...

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def clear(path): ''' Causes the all attributes on the file/directory to be removed :param str path: The file(s) to get attributes from :return: True if successful, otherwise False :raises: CommandExecutionError on file not found or any other unknown error CLI Example: .. code-block:: ba...

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def get_flight_rules(vis: Number, ceiling: Cloud) -> int: """ Returns int based on current flight rules from parsed METAR data 0=VFR, 1=MVFR, 2=IFR, 3=LIFR Note: Common practice is to report IFR if visibility unavailable """ # Parse visibility if not vis: return 2 if vis.repr =...

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def indent_text(text, nb_tabs=0, tab_str=" ", linebreak_input="\n", linebreak_output="\n", wrap=False): r"""Add tabs to each line of text. :param text: the text to indent :param nb_tabs: number of tabs to add :param tab_st...

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def validate(args): """ %prog validate outdir genome.fasta Validate current folder after MAKER run and check for failures. Failed batch will be written to a directory for additional work. """ from jcvi.utils.counter import Counter p = OptionParser(validate.__doc__) opts, args = p.parse...

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def run_zone(self, minutes, zone=None): """ Run or stop a zone or all zones for an amount of time. :param minutes: The number of minutes to run. :type minutes: int :param zone: The zone number to run. If no zone is specified then run all zones. :type...

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def generate_rest_view(config, model_cls, attrs=None, es_based=True, attr_view=False, singular=False): """ Generate REST view for a model class. :param model_cls: Generated DB model class. :param attr: List of strings that represent names of view methods, new generated view s...

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def start_(name): ''' Start a container name Container name or ID **RETURN DATA** A dictionary will be returned, containing the following keys: - ``status`` - A dictionary showing the prior state of the container as well as the new state - ``result`` - A boolean noting whet...

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def dock(self, other): ''' The opposite of concatenation. Remove a common suffix from the present pattern; that is, from each of its constituent concs. AYZ|BYZ|CYZ - YZ = A|B|C. ''' return pattern(*[c.dock(other) for c in self.concs])

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def get_attribute(self, app=None, key=None): """Returns an application attribute :param app: application id :param key: attribute key or None to retrieve all values for the given application :returns: attribute value if key was specified, or an array of tuples (k...

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def svd_affine(inp, n_outmaps, r, base_axis=1, uv_init=None, b_init=None, fix_parameters=False, rng=None, with_bias=True): """SVD affine is a low rank approximation of the affine layer. It can be seen as two consecutive affine layers with a bottleneck. It computes: .. math...

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def rescaleX(self): '''Rescales the horizontal axes to make the lengthscales equal.''' self.ratio = self.figure.get_size_inches()[0]/float(self.figure.get_size_inches()[1]) self.axes.set_xlim(-self.ratio,self.ratio) self.axes.set_ylim(-1,1)

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def generate_fixtures(datasets, reuses): '''Build sample fixture data (users, datasets and reuses).''' user = UserFactory() log.info('Generated user "{user.email}".'.format(user=user)) organization = OrganizationFactory(members=[Member(user=user)]) log.info('Generated organization "{org.name}".'.fo...

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def classes_can_admin(self): """Return all the classes (sorted) that this user can admin.""" if self.is_admin: return sorted(Session.query(Class).all()) else: return sorted(self.admin_for)

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def mergecsv(args): """ %prog mergecsv *.tsv Merge a set of tsv files. """ p = OptionParser(mergecsv.__doc__) p.set_outfile() opts, args = p.parse_args(args) if len(args) < 2: sys.exit(not p.print_help()) tsvfiles = args outfile = opts.outfile if op.exists(outfile...

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def addPathVariables(self, pathvars): """ Adds path variables to the pathvars map property""" if type(pathvars) is dict: self._pathvars = merge(self._pathvars, pathvars)

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def bam_conversion(job, samfile, sample_type, univ_options): """ This module converts SAMFILE from sam to bam ARGUMENTS 1. samfile: <JSid for a sam file> 2. sample_type: string of 'tumor_dna' or 'normal_dna' 3. univ_options: Dict of universal arguments used by almost all tools univ_opt...

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def as_dictionary(self): """ Return the parameter as a dictionary. :return: dict """ return { "name": self.name, "type": self.type, "value": remove_0x_prefix(self.value) if self.type == 'bytes32' else self.value }

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def get_networks_by_name(self, name: str) -> List[Network]: """Get all networks with the given name. Useful for getting all versions of a given network.""" return self.session.query(Network).filter(Network.name.like(name)).all()

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def IndexedDB_clearObjectStore(self, securityOrigin, databaseName, objectStoreName): """ Function path: IndexedDB.clearObjectStore Domain: IndexedDB Method name: clearObjectStore Parameters: Required arguments: 'securityOrigin' (type: string) -> Security origin. 'databaseName' (type: ...

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def obtain_to(filename, compressed=True): """ Return the linke turbidity projected to the lat lon matrix coordenates. Keyword arguments: filename -- the name of a netcdf file. """ files = glob.glob(filename) root, _ = nc.open(filename) lat, lon = nc.getvar(root, 'lat')[0,:], nc.getvar(r...

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def search(name): ''' Search for matches in the ports tree. Globs are supported, and the category is optional CLI Examples: .. code-block:: bash salt '*' ports.search 'security/*' salt '*' ports.search 'security/n*' salt '*' ports.search nmap .. warning:: Tak...

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def get_location(opts=None, provider=None): ''' Return the region to use, in this order: opts['location'] provider['location'] get_region_from_metadata() DEFAULT_LOCATION ''' if opts is None: opts = {} ret = opts.get('location') if ret is None and provider...

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def set_content_type (self): """Return URL content type, or an empty string if content type could not be found.""" if self.url: self.content_type = mimeutil.guess_mimetype(self.url, read=self.get_content) else: self.content_type = u""

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def import_source(self, CachableSource): """Updates cache area and returns number of items updated with all available entries in ICachableSource""" _count = 0 for item in CachableSource.items(): if self.cache(item): _count += 1 return _count

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def _select_index(self, row, col): """Change the selection index, and make sure it stays in the right range A little more complicated than just dooing modulo the number of row columns to be sure to cycle through all element. horizontaly, the element are maped like this : to r <...

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def to_dict(self): """ Convert current Task into a dictionary :return: python dictionary """ task_desc_as_dict = { 'uid': self._uid, 'name': self._name, 'state': self._state, 'state_history': self._state_history, 'pre...

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def _check_stream(self): """Determines which output stream (stdout, stderr, or custom) to use""" if self.stream: try: supported = ('PYCHARM_HOSTED' in os.environ or os.isatty(sys.stdout.fileno())) # a fix for IPython notebook "IOStre...

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def insert_vlan( self, environment_id, name, number, description, acl_file, acl_file_v6, network_ipv4, network_ipv6, vrf=None): """Create new VLAN :param environment_id: ID for Enviro...

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def get_jira_key_from_scenario(scenario): """Extract Jira Test Case key from scenario tags. Two tag formats are allowed: @jira('PROJECT-32') @jira=PROJECT-32 :param scenario: behave scenario :returns: Jira test case key """ jira_regex = re.compile('jira[=$\']*([A-Z]+\-[0-9]+)[\'$]*$')...

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def parse_public(data): """ Loads a public key from a DER or PEM-formatted file. Supports RSA, DSA and EC public keys. For RSA keys, both the old RSAPublicKey and SubjectPublicKeyInfo structures are supported. Also allows extracting a public key from an X.509 certificate. :param data: A...

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def declallfuncs(self): """generator on all declaration of function""" for f in self.body: if (hasattr(f, '_ctype') and isinstance(f._ctype, FuncType)): yield f

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def _get_enterprise_enrollment_api_admin_users_batch(self, start, end): # pylint: disable=invalid-name """ Returns a batched queryset of User objects. """ LOGGER.info('Fetching new batch of enterprise enrollment admin users from indexes: %s to %s', start, end) return User.obj...

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def from_btl(fname): """ DataFrame constructor to open Seabird CTD BTL-ASCII format. Examples -------- >>> from pathlib import Path >>> import ctd >>> data_path = Path(__file__).parents[1].joinpath("tests", "data") >>> bottles = ctd.from_btl(data_path.joinpath('btl', 'bottletest.btl')) ...

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def tangelo_import(*args, **kwargs): """ When we are asked to import a module, if we get an import error and the calling script is one we are serving (not one in the python libraries), try again in the same directory as the script that is calling import. It seems like we should use sys.meta_path...

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def get_context_data(self, **kwargs): ''' Adds a 'base_template' attribute to context for the page_detail to extend from ''' context = super(PageList, self).get_context_data(**kwargs) page_base_template = "nupages/base.html" # if MultiTenantMiddleware is used, us...

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def domain_xml(identifier, xml, mounts, network_name=None): """Fills the XML file with the required fields. @param identifier: (str) UUID of the Environment. @param xml: (str) XML configuration of the domain. @param filesystem: (tuple) ((source, target), (source, target)) * name * uuid ...

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def load_stylesheet_pyqt5(): """ Loads the stylesheet for use in a pyqt5 application. :param pyside: True to load the pyside rc file, False to load the PyQt rc file :return the stylesheet string """ # Smart import of the rc file import qdarkstyle.pyqt5_style_rc # Load the stylesheet c...

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def connection_string_parser(uri: str) -> list: """ Parse Connection string to extract host and port. :param uri: full URI for redis connection in the form of host:port :returns: list of RedisConnection objects """ redis_connections = [] raw_connections = uri.sp...

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def replace(self, *args, **kargs): """ lst.replace(<field>,[<oldvalue>,]<newvalue>) lst.replace( (fld,[ov],nv),(fld,[ov,]nv),...) if ov is None, all values are replaced ex: lst.replace( IP.src, "192.168.1.1", "10.0.0.1" ) lst.replace( IP.ttl, 64 ) ...

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def run (self): """Handle keyboard interrupt and other errors.""" try: self.run_checked() except KeyboardInterrupt: thread.interrupt_main() except Exception: self.internal_error()

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def request(self, method, url_parts, headers=None, data=None): """ Method for making requests to the Optimizely API """ if method in self.ALLOWED_REQUESTS: # add request token header headers = headers or {} # test if Oauth token if self.token_type...

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def get_blobstore(layout): """Return Blobstore instance for a given storage layout Args: layout (StorageLayout): Target storage layout. """ if layout.is_s3: from wal_e.blobstore import s3 blobstore = s3 elif layout.is_wabs: from wal_e.blobstore import wabs blo...

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def is_valid_intensity_measure_types(self): """ If the IMTs and levels are extracted from the risk models, they must not be set directly. Moreover, if `intensity_measure_types_and_levels` is set directly, `intensity_measure_types` must not be set. """ if self.grou...

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def replace(text, old, new, count=None, strip=False): ''' Replace an ``old`` subset of ``text`` with ``new``. ``old`` type may be either a string or regular expression. If ``strip``, remove all leading/trailing whitespace. If ``count``, replace the specified number of occurence, other...

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def get_stats_str(list_=None, newlines=False, keys=None, exclude_keys=[], lbl=None, precision=None, axis=0, stat_dict=None, use_nan=False, align=False, use_median=False, **kwargs): """ Returns the string version of get_stats DEPRICATE in favor of ut.repr3(ut.get_stats(.....

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def equals(self, data): """Adds new `IN` or `=` condition depending on if a list or string was provided :param data: string or list of values :raise: - QueryTypeError: if `data` is of an unexpected type """ if isinstance(data, six.string_types): return s...

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def seq_len(self,L): """set the length of the uncompressed sequence. its inverse 'one_mutation' is frequently used as a general length scale. This can't be changed once it is set. Parameters ---------- L : int length of the sequence alignment """ ...

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def get_variable(self, variable_name, client=None): """API call: get a variable via a ``GET`` request. This will return None if the variable doesn't exist:: >>> from google.cloud import runtimeconfig >>> client = runtimeconfig.Client() >>> config = client.config('my-conf...

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def getRepositories(self): """Returns a list of repositories for this directory. """ if self.srcdir and not self.duplicate: return self.srcdir.get_all_rdirs() + self.repositories return self.repositories

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def replace(self, html): """Perform replacements on given HTML fragment.""" self.html = html text = html.text() positions = [] def perform_replacement(match): offset = sum(positions) start, stop = match.start() + offset, match.end() + offset ...

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31.740741

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def new_thing(self, name, **stats): """Create a new thing, located here, and return it.""" return self.character.new_thing( name, self.name, **stats )

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def audio(self, audio, sample_rate, name=None, subdir=''): """Summary audio to listen on web browser. Args: audio (:class:`numpy.ndarray` or :class:`cupy.ndarray` or \ :class:`chainer.Variable`): sampled wave array. sample_rate (int): sampling rate. n...

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def _extend_str(class_node, rvalue): """function to extend builtin str/unicode class""" code = dedent( """ class whatever(object): def join(self, iterable): return {rvalue} def replace(self, old, new, count=None): return {rvalue} def format(self, *args...

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32.909091

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def cleaned_date(day, keep_datetime=False): """ Return a "clean" date type. * keep a `date` unchanged * convert a datetime into a date, * convert any "duck date" type into a date using its `date()` method. """ if not isinstance(day, (date, datetime)): raise UnsupportedDateType( ...

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def parse_cmd_arguments(): """Parse command line arguments.""" parser = argparse.ArgumentParser() parser.add_argument('file', type=str, help='Filename to be staticfied') parser.add_argument('--static-endpoint', help='Static endpoint which is "static" by de...

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47.368421

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def add_aggregated_lv_components(network, components): """ Aggregates LV load and generation at LV stations Use this function if you aim for MV calculation only. The according DataFrames of `components` are extended by load and generators representing these aggregated respecting the technology type...

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38.851852

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def slice(self, who): "return the slice entry (in a bed6 format), AS IS in the chain header" assert who in ('t', 'q'), "who should be 't' or 'q'" if who == 't': return (self.tName, self.tStart, self.tEnd, self.id, self.score, self.tStrand) else: return (self.qNa...

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41.555556

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def skewvT(self,R,romberg=False,nsigma=None,phi=0.): """ NAME: skewvT PURPOSE: calculate skew in vT at R by marginalizing over velocity INPUT: R - radius at which to calculate <vR> (can be Quantity) OPTIONAL INPUT: nsigma - numbe...

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24.853659

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def get_id_for_extra_dim_type(type_str): """ Returns the index of the type as defined in the LAS Specification Parameters ---------- type_str: str Returns ------- int index of the type """ try: return _type_to_extra_dim_id_style_1[type_str] except KeyError: ...

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22.3

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def from_scene_coords(self, x=0, y=0): """Converts x, y given in the scene coordinates to sprite's local ones coordinates""" matrix = self.get_matrix() matrix.invert() return matrix.transform_point(x, y)

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39.666667

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def is_obtuse(p1, v, p2): '''Determine whether the angle, p1 - v - p2 is obtuse p1 - N x 2 array of coordinates of first point on edge v - N x 2 array of vertex coordinates p2 - N x 2 array of coordinates of second point on edge returns vector of booleans ''' p1x = p1[:,1] p1y ...

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24.75

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def _format_output(selected_number, raw_data): """Format data to get a readable output""" tmp_data = {} data = collections.defaultdict(lambda: 0) balance = raw_data.pop('balance') for number in raw_data.keys(): tmp_data = dict([(k, int(v) if v is not None else "No limit") ...

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33

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def to_html(self): """Render a Table MessageElement as html. :returns: The html representation of the Table MessageElement :rtype: basestring """ table = '<table%s>\n' % self.html_attributes() if self.caption is not None: if isinstance(self.caption, MessageEl...

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34.16

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def parse_package(package_string, arch_included=True): """Parse an RPM version string to get name, version, and arch Splits most (all tested) RPM version strings into name, epoch, version, release, and architecture. Epoch (also called serial) is an optional component of RPM versioning and is also optio...

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41.390244

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def _convert(self, args): '''convert '(1,1)' to 'B2' and 'B2' to '(1,1)' auto-recongnize''' if args.find(",") > -1: b, a = args.replace("(", "").replace(")", "").split(",") a = chr(int(a)+65)#chr(65) is "A" and ord("A") is 65 b = str(int(b)+1) return a+b ...

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def scroll_to(self, line): """ Scroll the abstract canvas to make a specific line. :param line: The line to scroll to. """ self._buffer.scroll(line - self._start_line) self._start_line = line

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29.125

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def create_folder(self, name, parent_folder_id=0): """Create a folder If the folder exists, a BoxError will be raised. Args: folder_id (int): Name of the folder. parent_folder_id (int): ID of the folder where to create the new one. Returns: dict. R...

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31.913043

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def condense_otus(otuF, nuniqueF): """ Traverse the input otu-sequence file, collect the non-unique OTU IDs and file the sequences associated with then under the unique OTU ID as defined by the input matrix. :@type otuF: file :@param otuF: The output file from QIIME's pick_otus.py :@type nu...

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30.236842

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def get_distribution(cls, ctx, name=None, recipes=[], ndk_api=None, force_build=False, extra_dist_dirs=[], require_perfect_match=False, allow_replace_dist=True): '''Takes information abou...

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38.426087

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def remove_other_cflags(self, flags, target_name=None, configuration_name=None): """ Removes the given flags from the OTHER_CFLAGS section of the target on the configurations :param flags: A string or array of strings. If none, removes all values from the flag. :param target_name: Target...

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70.555556

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