Source code for lyscripts.data

"""Commands and functions for managing CSV data on patterns of lymphatic progression.

This contains helpful CLI commands that allow building quick and reproducible workflows
even when using language-agnostic tools like `Make`_ or `DVC`_.

Most of these commands can load `LyProX`_ style data from CSV files, but also from
the installed datasets provided by the `lydata`_ package and directly from the
associated `GitHub repository`_.

Another cool feature is the built-in mini web application that allows collecting nodal
involvement data interactively and in the same standardized format as we have published
in the past, both on `LyProX`_ and in our `GitHub repository`_. It can be launched by
running `lyscripts data collect` in the terminal. See the docs for the
:py:mod:`lyscripts.data.collect` submodule on more information.

.. _Make: https://www.gnu.org/software/make/
.. _DVC: https://dvc.org
.. _LyProX: https://lyprox.org
.. _lydata: https://lydata.readthedocs.io
.. _GitHub repository: https://github.com/lycosystem/lydata
"""

from pydantic_settings import BaseSettings, CliApp, CliSubCommand

from lyscripts.data import (  # noqa: F401
    collect,
    enhance,
    fetch,
    generate,
    join,
    lyproxify,
    split,
)

# Avoid conflict with built-in `filter` function
from lyscripts.data import filter as filter_




class DataCLI(BaseSettings):
    """Work with lymphatic progression data through this CLI."""

    collect: CliSubCommand[collect.CollectorCLI]
    lyproxify: CliSubCommand[lyproxify.LyproxifyCLI]
    join: CliSubCommand[join.JoinCLI]
    split: CliSubCommand[split.SplitCLI]
    fetch: CliSubCommand[fetch.FetchCLI]
    filter: CliSubCommand[filter_.FilterCLI]
    enhance: CliSubCommand[enhance.EnhanceCLI]
    generate: CliSubCommand[generate.GenerateCLI]



    def cli_cmd(self) -> None:
        """Run one of the ``data`` subcommands."""
        CliApp.run_subcommand(self)