setup.py

# setup.py

import os
from setuptools import setup, find_packages

# Load version from version.py
version = {}
with open(os.path.join('vntyper', 'version.py')) as f:
    exec(f.read(), version)

# ===========================
# Installation Reference
# ===========================
# After installing vntyper, you need to download and set up the required reference files.
# Run the following command to perform the installation of references:
#
#     vntyper install-references --output-dir /path/to/install --config-path /path/to/config.json
#
# For detailed instructions, refer to the README.md or visit:
# https://github.com/hassansaei/vntyper#installation

setup(
    name="vntyper",
    version=version['__version__'],
    packages=find_packages(),
    include_package_data=True,  # Include package data as specified in MANIFEST.in or package_data
    install_requires=[
        "pandas>=2.2.0",
        "numpy>=2.0.2",
        "regex>=2024.7.24",
        "biopython>=1.84",
        "setuptools>=72.2.0",
    ],
    entry_points={
        "console_scripts": [
            "vntyper=vntyper.cli:main",
        ],
    },
    author="Hassan Saei, Bernt Popp",
    author_email="hassan.saei@inserm.fr, bernt.popp.md@gmail.com",
    description="VNtyper: A tool for genotyping MUC1-VNTR",
    long_description=open("README.md").read(),
    long_description_content_type="text/markdown",
    url="https://github.com/hassansaei/vntyper",
    classifiers=[
        "Programming Language :: Python :: 3",
        "License :: OSI Approved :: MIT License",
        "Operating System :: OS Independent",
    ],
    python_requires='>=3.9',
    extras_require={
        "dev": [
            "pytest",
            "black",
            "flake8",
        ],
    },
    package_data={
        'vntyper.scripts': ['kestrel_config.json', 'install_references_config.json'],  # Include kestrel_config.json and install_references_config.json
        'vntyper': [
            'config.json',  # Include config.json in the vntyper package
            'templates/report_template.html',  # Include report_template.html
            'templates/cohort_summary_template.html',  # Include cohort_summary_template.html
            'dependencies/kestrel/*.jar',  # Include all JAR files in dependencies/kestrel/
        ],
    },
)