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Retrieve the parent in which this activity is defined. If this is a task on top level, it raises NotFounderror. :return: a :class:`Activity2` :raises NotFoundError: when it is a task in the top level of a project :raises APIError: when other error occurs Example ------...
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Gets BUFF score for interaction between two AMPAL objects
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Return version of the TR DWE.
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Build an object that can run ScienceTools application Parameters ---------- appname : str Name of the application (e.g., gtbin) dry_run : bool Print command but do not run it kwargs : arguments used to invoke the application Returns `GtApp.GtApp` object that will run the appl...
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Fetch data from NDS into a `StateVector`. Parameters ---------- channel : `str`, `~gwpy.detector.Channel` the name of the channel to read, or a `Channel` object. start : `~gwpy.time.LIGOTimeGPS`, `float`, `str` GPS start time of required data, any in...
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r""" Base method for dividing two factor sets. Division of two factor sets :math:`\frac{\vec\phi_1}{\vec\phi_2}` basically translates to union of all the factors present in :math:`\vec\phi_2` and :math:`\frac{1}{\phi_i}` of all the factors present in :math:`\vec\phi_2`. Parameters ---------- f...
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Read only input files for a GSSHA project into the database. Use this method to read a project when only pre-processing tasks need to be performed. Args: directory (str): Directory containing all GSSHA model files. This method assumes that all files are located in the same ...
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'del_token'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'token'}...
Delete an eauth token by name CLI Example: .. code-block:: shell salt-run auth.del_token 6556760736e4077daa601baec2b67c24
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List nodes, with all available information CLI Example: .. code-block:: bash salt-cloud -F
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Configures the host cache on the selected host. enabled Boolean flag specifying whether the host cache is enabled. datastore Name of the datastore that contains the host cache. Must be set if enabled is ``true``. swap_size_MiB Swap size in Mibibytes. Needs to be set if ena...
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'log_coroutine'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '8']}; {'id': '4', 'type': 'identifier', 'children': [...
Run a coroutine logging any exception raised. This routine will not block until the coroutine is finished nor will it return any result. It will just log if any exception is raised by the coroutine during operation. It is safe to call from both inside and outside the event loop. ...
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'abs'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'cl...
Returns a TensorFluent for the abs function. Args: x: The input fluent. Returns: A TensorFluent wrapping the abs function.
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Given a string representation of a hex file, this function copies it to the specified path thus causing the device mounted at that point to be flashed. If the hex_file is empty it will raise a ValueError. If the filename at the end of the path does not end in '.hex' it will raise a ValueError.
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Validates if path1 and path2 matches, ignoring any kwargs in the string. We need this to ensure we can match Swagger patterns like: /foo/{id} against the observed pyramid path /foo/1 :param path1: path of a url :type path1: string :param path2: path of a url :type path2: string...
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '13']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_group_by_equal_size'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children':...
Partition a list of objects evenly and by file size Files are placed according to largest file in the smallest bucket. If the file is larger than the given threshold, then it is placed in a new bucket by itself. :param obj_list: a list of dict-like objects with a 'size' property :param tot_groups: ...
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'notUnique'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'it...
Returns the elements in `iterable` that aren't unique; stops after it found `reportMax` non-unique elements. Examples: >>> list(notUnique([1,1,2,2,3,3])) [1, 2, 3] >>> list(notUnique([1,1,2,2,3,3], 1)) [1]
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Find a config item along a path; leading slash is optional and ignored.
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Wait for one or more waitable objects. This method waits until *count* elements from the sequence of waitable objects *objects* have become ready. If *count* is ``None`` (the default), then wait for all objects to become ready. What "ready" is means depends on the object type. A waitable object is a ...
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'boolean'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'flag'}; {...
Convert string in boolean
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Extracts relevant install history entries. Args: parser_mediator (ParserMediator): mediates interactions between parsers and other components, such as storage and dfvfs. top_level (dict[str, object]): plist top-level key.
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'start'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'i...
The main loop, run forever.
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Create or update a Media attached to a post. :param bulk_mode: If True, minimize db operations by bulk creating post objects :param api_media_attachment: the API data for the Media :return: the Media attachment object
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '__parse_namespace'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': ...
Parse the namespace from various sources
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Generates file-like objects from a list of filenames. Args: filenames: iterable of filenames Yields: each file as a :class:`TextIO` object
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This method is inserted into the inner cbpdn object, replacing its own ystep method, thereby providing a hook for applying the additional steps necessary for the AMS method.
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_list_getter'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self...
Return a function object suitable for the "get" side of a list property descriptor.
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'local'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'i...
Finds the current location of a container. Also unpacks the project if necessary. Returns: target: The path, where the container lies in the end.
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '__get_host'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'n...
Return public IP, private IP, or hostname for the libcloud 'node' object
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get primary gene name from XML node entry :param entry: XML node entry :return: str
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Find the most recent old settings to migrate. The input is the path to an unqualified settings file - e.g. /mnt/usbdrive/config/robotSettings.json This will return - None if the input is None (to support chaining from dict.get()) - The input if it exists, or - The file named normal_path-TIMEST...
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '14']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_api_version'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11']}; {'id': '4', 'type': 'identifier', 'children'...
Get the API version specified or resolve the latest version :return api version :rtype: float
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Generate the path to the icon for charms. @param charm_id The ID of the charm. @param channel Optional channel name. @return The url to the icon.
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Add a rule with a pattern that should apply to all keys. Any key not explicitly listed in an add_required or add_optional rule must match ONE OF the rules given in a call to key_rule(). So these rules are all OR'ed together. In this case you should pass a raw string specifying a regex ...
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Print coordinates V with corresponding atoms to stdout in XYZ format. Parameters ---------- atoms : list List of element types V : array (N,3) matrix of atomic coordinates title : string (optional) Title of molecule
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Creates a penalty satisfaction list Given a sampleSet and a bqm object, will create a binary list informing whether the penalties introduced during degree reduction are satisfied for each sample in sampleSet Args: response (:obj:`.SampleSet`): Samples corresponding to provided bqm bqm...
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Get a logging handle. As with ``setup_logging``, a stream handler is added to the log handle. Arguments: name (str): Name of the log handle. Default is ``None``.
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Write the alignment to file using Bio.AlignIO
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Extracts differences between lists. For debug purposes
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Return a tuple suitable for import into a database. Attributes field and extra field jsonified into strings. The order of fields is such that they can be supplied as arguments for the query defined in :attr:`gffutils.constants._INSERT`. If `encoding` is not None, then convert string fi...
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Returns the compact records for all sections in the specified project. Parameters ---------- project : {Id} The project to get sections from. [params] : {Object} Parameters for the request
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'Parse'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}...
Take the results and yield results that passed through the filters. The output of each filter is used as the input for successive filters. Args: raw_data: An iterable series of rdf values. Returns: A list of rdf values that matched all filters.
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '13', '19']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'join_paths'}; {'id': '3', 'type': 'parameters', 'children': ['4', '8']}; {'id': '4', 'type': 'typed_parameter', 'children': ['5...
Join `path` to every file name in `fnames`.
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_determine_rotated_logfile'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], ...
We suspect the logfile has been rotated, so try to guess what the rotated filename is, and return it.
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_build_command'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [...
Generate ``mkdocs build`` command to build the site. :param mkdocs_site_path: Path to the output directory for the site
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Load artifacts from all sources.
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '14']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'run_samtools'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '11']}; {'id': '4', 'type': 'identifier', 'ch...
Detect SNPs and indels with samtools mpileup and bcftools.
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Determine whether the schema already exists.
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Distribute the computations amongst the multiprocessing pools Parameters ---------- f : function Function to be distributed to the processors n : int The values in range(0,n) will be passed as arguments to the function f.
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'restore_default'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value...
Set the value of the given index row to its default :param index: :type index: :returns: :rtype: :raises:
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Get a specific resource attribte, by ID If type_id is Gspecified, only return the resource attributes within the type.
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'bool_env'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'key...
Parse an environment variable as a boolean switch `True` is returned if the variable value matches one of the following: - ``'1'`` - ``'y'`` - ``'yes'`` - ``'true'`` The match is case-insensitive (so ``'Yes'`` will match as `True`) Parameters ---------- key : `str` the na...
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Check if reana can start new workflows.
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Calculate the Pearson correlation coefficient of one position compared to another position. Returns ------- score : float Pearson correlation coefficient.
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Randomly morph a single character.
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Calls all necessary methods to build the Lambda Package
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Parse the string or bytes. Args: strict (bool): If True, errors will not be ignored Raises: :class:`ValueError` if the record is malformed.
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Check if our local latest sha matches the remote latest sha
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Guess the default python env to use.
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Serves a cross-domain policy which can allow other policies to exist on the same domain. Note that this view, if used, must be the master policy for the domain, and so must be served from the URL ``/crossdomain.xml`` on the domain: setting metapolicy information in other policy files is forbidden b...
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Takes two lists of 3 x-y points each, and calculates the matrix representing the transformation from one space to the other. The 3x3 matrix returned by this method represents the 2-D transformation matrix from the actual point to the expected point. Example: If the expected points are: ...
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Shortcut only one at a time will work...
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Returns a list of ``Voice`` supported for synthesis. Example: >>> from google.cloud import texttospeech_v1beta1 >>> >>> client = texttospeech_v1beta1.TextToSpeechClient() >>> >>> response = client.list_voices() Args: language_code...
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Fill multiple paragraphs of text, returning a new string. Reformat multiple paragraphs in 'text' to fit in lines of no more than 'width' columns, and return a new string containing the entire wrapped text. As with wrap(), tabs are expanded and other whitespace characters converted to space. See Parag...
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Sort keys of unordered_dict and store in OrderedDict.
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List Reserved Capacities
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return 3-tuple of version info or None :return: (str, str, str)
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Runs the linter and tests :return: A bool - if the linter and tests ran successfully
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Show the set of IPs seen in Flow Log records.
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Gets movielens datasets Parameters --------- variant : string Which version of the movielens dataset to download. Should be one of '20m', '10m', '1m' or '100k'. Returns ------- movies : ndarray An array of the movie titles. ratings : csr_matrix A sparse matr...
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Shift bits by n to the left in place. Return self.
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Concrete message delivery.
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Create a struct of vectors. Parameters ---------- vec_of_structs : WeldObject Encoding a vector of structs. weld_types : list of WeldType The Weld types of the arrays in the same order. Returns ------- WeldObject Representation of this computation.
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A custom context processor which allows injection of additional context variables.
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Write vaultlocker configuration to disk and install alternative :param context: Dict of data from vault-kv relation :ptype: context: dict :param priority: Priority of alternative configuration :ptype: priority: int
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Mark as 'enriched' or 'purified'.
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Convert the set to a list of 64 bools.
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Returns a list of tuples with all known arguments for the given service- and action-name combination. The tuples contain the argument-name, direction and data_type.
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Returns a list of changes to represent the diff between old and new value. Returns: list: [string] representation of the change (if any) between old and new value
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Starts executing the method at the specified interval. Args: interval_s: The amount of time between executions of the method. Returns: False if the interval was already running.
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Memorizes an alias for an import or an imported item
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Extract largest connected set in mesh. Can be used to reduce residues obtained when generating an isosurface. Works only if residues are not connected (share at least one point with) the main component of the image. Parameters ---------- inplace : bool, optional ...
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Default sorting of GOEA results stored in namedtuples.
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Close the underlying connection.
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\ Fit and classify data efficiently. :param data: sparse input matrix (ideal dtype is `numpy.float32`) :type data: :class:`scipy.sparse.csr_matrix` :param labels: the labels associated with data :type labels: iterable :param unkown: the label to attribute if no label is ...
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Compute and IDLE PC value for an image :param compute_id: ID of the compute where the idlepc operation need to run :param platform: Platform type :param image: Image to use :param ram: amount of RAM to use
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Behold analysis procedure.
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Hungarian reordering. Assume A and B are coordinates for atoms of SAME type only
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Ensure we have benchmark data for `symbol` from `first_date` to `last_date` Parameters ---------- symbol : str The symbol for the benchmark to load. first_date : pd.Timestamp First required date for the cache. last_date : pd.Timestamp Last required date for the cache. no...
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Add given chars to char set
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return a list of keys of idfobjects that hve 'None Name' fields
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Load the csv of LINCS protein metadata into a dict. Produces a dict keyed by HMS LINCS protein ids, with the metadata contained in a dict of row values keyed by the column headers extracted from the csv.
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Prepare a delly-specific exclude file eliminating chromosomes. Delly wants excluded chromosomes listed as just the chromosome, with no coordinates.
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Get the requested regions.
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Yield an infinite series of values according to Howard and Ruder's "slanted triangular learning rate" schedule.
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Return the variables pickled pickled into `filename` with `saveVars` as a dict.
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Gets the top box office earning movies from the API. Sorted by most recent weekend gross ticket sales. Args: limit (optional): limits the number of movies returned, default=10 country (optional): localized data for selected country, default="us" Returns: A dict...
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Eradicate a destroyed pgroup. :param pgroup: Name of pgroup to be eradicated. :type pgroup: str :param \*\*kwargs: See the REST API Guide on your array for the documentation on the request: **DELETE pgroup/:pgroup** :type \*\*kwargs:...
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Runs the CLI, reading from sys.stdin by default
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Reads a complex fault geometry node and returns an
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Format log records to produce colored messages. :param record: log record :return: log message