Add complete docstrings for all functions and classes in MAIA (numpy format) and helpers for MAIA_scripts

[SimoneBendazzoli93]

Summary

Add comprehensive docstrings to all functions and classes in the MAIA package using the numpy docstring format. Also, update helper scripts in MAIA_scripts to include detailed argument parser sections and usage examples following the provided template.

Details

• Review all functions and classes in the core MAIA package and ensure each has a complete docstring in numpy format, detailing parameters, return types, exceptions, and example usage where relevant.
• For scripts in MAIA_scripts, add (or update) the argument parser docstring and usage section using the following template:

version = MAIA.__version__

TIMESTAMP = "{:%Y-%m-%d_%H-%M-%S}".format(datetime.datetime.now())

DESC = dedent(
    """
  DESCRIPTION
    """  # noqa: E501
)
EPILOG = dedent(
    """
    Example call:
    ::
        {filename} --ARGUMENTS
    """.format(  # noqa: E501
        filename=Path(__file__).stem
    )
)

def get_arg_parser():
    pars = ArgumentParser(description=DESC, epilog=EPILOG, formatter_class=RawTextHelpFormatter)
    <ARGUMENTS>
    pars.add_argument("-v", "--version", action="version", version="%(prog)s " + version)
    return pars

def main():
    arg_parser = get_arg_parser()
    args = arg_parser.parse_args()

• Replace <ARGUMENTS> with the full specification for each script, and ensure all arguments are documented.

Acceptance Criteria

• Every function and class in MAIA has a numpy-style docstring.
• Every script in MAIA_scripts uses the provided docstring and usage template, with a comprehensive description and example call.

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Labels: documentation, enhancement
Type: Task