setup.py

#!/usr/bin/env python3

from setuptools import setup, find_namespace_packages
from src.molgenis.capice import __version__

with open('README.md', 'r', encoding='utf-8') as fh:
    long_description = fh.read()

setup(
    name='capice',
    version=__version__,
    packages=find_namespace_packages('src', exclude=['tests', 'scripts']),
    package_dir={"": "src"},
    url='https://capice.molgeniscloud.org/',
    license='LGPL-3.0',
    author='Shuang Li, Robert Sietsma and Molgenis',
    author_email='support@molgenis.org',
    description='Consequence Agnostic Pathogenicity Interpretation of '
                'Clinical Exoma variations. State of the art machine learning '
                'to predict SNVs and InDels pathogenicity.',
    long_description=long_description,
    long_description_content_type='text/markdown',
    classifiers=[
        'Development Status :: 4 - Beta',
        'License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)',
        'Programming Language :: Python :: 3.10'
    ],
    python_requires='>=3.10',
    install_requires=[
        'numpy==1.26.4',
        'pandas==1.5.3',
        'scipy==1.14.1',
        'scikit-learn==1.5.2',
        'xgboost==1.7.6'
    ],
    extras_require={
        'test': [
            'pytest',  # pytest
            'coverage',  # coverage run -m pytest --junitxml=results.xml && coverage html
            'mypy',  # mypy --ignore-missing-imports src/
            'flake8',  # flake8 src/ tests/
            'flake8-import-order'
        ]
    },
    entry_points={
        'console_scripts': [
            'capice = molgenis.capice.capice:main'
        ]
    }

)