Source code for pimmslearn.cmd_interface.setup_diff_analysis_website

"""Console script to create or append index.rst for static website of differential analysis workflow."""

import argparse
import textwrap
from collections import defaultdict
from pathlib import Path




def split_nb_name(nb: str) -> list:
    return nb.split(".")[0].split("_")



INDEX_RST = textwrap.dedent("""\
    Differential Analysis Notebooks
    -------------------------------

    Inspect the notebooks associated with the differential analysis workflow.

    .. toctree::
        :maxdepth: 2
        :caption: Differential analysis (ANCOVA)

    {nb_1}

    .. toctree::
        :maxdepth: 2
        :caption: Compare ANCOVAs

    {nb_2}

    .. toctree::
        :maxdepth: 2
        :caption: Compare single differential analysis

    {nb_4}

    .. toctree::
        :maxdepth: 2
        :caption: Logistic regression models

    {nb_3}
    """)




def main():
    parser = argparse.ArgumentParser(
        description="Create or append index.rst for static website "
        "displaying differential analysis notebooks."
    )
    parser.add_argument(
        "--folder", "-f", type=str, help="Path to the folder", required=True
    )
    parser.add_argument(
        "--subfolder_comparision",
        "-sf_cp",
        type=str,
        help="Subfolder for comparison",
        required=True,
    )
    args = parser.parse_args()

    folder_experiment = args.folder

    folder_experiment = Path(folder_experiment)
    subfolder_comparison = Path(args.subfolder_comparision)
    nbs = [
        _f.relative_to(folder_experiment)
        for _f in subfolder_comparison.glob("**/*.ipynb")
        if _f.is_file()
    ]

    groups = defaultdict(list)
    for nb in nbs:
        _group = nb.name.split("_")[1]
        groups[_group].append(nb)
    groups = dict(groups)

    # Parse notebooks present in imputation workflow

    nb_1 = ""
    for nb in groups["1"]:
        nb_1 += " " * 4 + split_nb_name(nb.name)[-1] + f" <{nb.as_posix()}>\n"

    nb_2 = ""
    for nb in groups["2"]:
        nb_2 += " " * 4 + " ".join(nb.parent.name.split("_")) + f" <{nb.as_posix()}>\n"

    nb_3 = ""
    for nb in groups["3"]:
        nb_3 += " " * 4 + " ".join(nb.parent.name.split("_")) + f" <{nb.as_posix()}>\n"
    print(nb_3)

    nb_4 = groups["4"][0]
    nb_4 = " " * 4 + "Compare single features" + f" <{nb_4.as_posix()}>\n"

    index_rst = INDEX_RST.format(nb_1=nb_1, nb_2=nb_2, nb_3=nb_3, nb_4=nb_4)
    # append to index.rst
    with open(folder_experiment / "index.rst", "a") as f:
        f.write(index_rst)

    msg = f"""\
    The index.rst file has been created or extended in {folder_experiment}:
    ```bash
    {folder_experiment / 'index.rst'}
    ```
    """

    msg = textwrap.dedent(msg)
    print(msg)



if __name__ == "__main__":
    main()