setup.py

from setuptools import setup
import os
from pathlib import Path


def walk_and_add(d, pkg_files):
    folders = [
        "annotator_template",
        "base",
        "cli",
        "liftover",
        "module",
        "store",
        "system",
        "util",
        "webresult",
        "webstore",
        "websubmit",
    ]
    for root, _, files in os.walk(d):
        root_spl = root.split(os.sep)
        if len(root_spl) <= 1:
            continue
        root_f = root_spl[1]
        root_l = root_spl[-1]
        if root_f in folders and root_l != "__pycache__":
            root_files = [os.path.join("..", root, f) for f in files]
            pkg_files.extend(root_files)


this_directory = Path(__file__).parent
long_description = (this_directory / "README.rst").read_text()
oakvar_files = [
    "exampleinput",
    "oakvar.yml",
    "system.yml",
    "favicon.ico",
]
cravat_files = []
walk_and_add("oakvar", oakvar_files)
walk_and_add("cravat", cravat_files)
setup(
    name="oakvar",
    version="2.5.56",
    description="A genomic variant analysis platform",
    long_description=long_description,
    long_description_content_type="text/x-rst",
    url="https://github.com/rkimoakbioinformatics/oakvar",
    author="Ryangguk Kim",
    author_email="rkim@oakbioinformatics.com",
    license="",
    classifiers=[""],
    keywords="genomic variant analysis interpretation genome",
    project_urls={
        "Documentation": "https://oakvar.readthedocs.io",
        "Source": "https://github.com/rkimoakbioinformatics/oakvar",
        "Tracker": "https://github.com/rkimoakbioinformatics/oakvar/issues",
    },
    packages=["oakvar", "cravat"],
    py_modules=[],
    install_requires=[
        "requests",
        "requests-toolbelt",
        "pyliftover",
        "markdown",
        "aiohttp",
        "chardet>=3.0.4",
        "aiosqlite",
        "oyaml",
        "nest-asyncio",
        "psutil",
        "python-dateutil",
        "download",
        "gdown",
        "split-file-reader",
        "packaging",
        "Pillow",
        # below are module-specific. move them to module's yml.
        "mpmath",
        "twobitreader",
        # ok to delete the below?
        "intervaltree",
    ],
    python_requires=">=3.8",
    package_data={"oakvar": oakvar_files, "cravat": cravat_files},
    data_files=[],
    scripts=[],
    entry_points={
        "console_scripts": ["ov=oakvar.__main__:main", "oc=oakvar.__main__:main"]
    },
)