setup.py

import os
import shutil
from setuptools import setup, find_packages


def get_version():
    with open(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'sphae', 'sphae.VERSION')) as f:
        return f.readline().strip()

def get_description():
    with open("README.md", "r") as fh:
        long_description = fh.read()
    return long_description

def get_requirements():
    reqs = []
    with open('requirements.txt', 'r') as f:
        for l in f:
            reqs.append(l.strip())
    return reqs

def get_data_files():
    data_files = [(".", ["README.md"])]
    return data_files

CLASSIFIERS = [
    "Environment :: Console",
    "Environment :: MacOS X",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Natural Language :: English",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

def main():
    setup(
        name='sphae',
        description="Assembling pure culture phages from both Illumina and Nanopore sequencing technology",
        long_description=get_description(),
        long_description_content_type="text/markdown",
        version=get_version(),
        author="Bhavya Papudeshi",
        author_email="npbhavya13@gmail.com",
        platforms='any',
        keywords="phage 'phage therapy' bioinformatics microbiology bacteria genome genomics",
        data_files=get_data_files(),
        license='The MIT License (MIT)',
        url='https://github.com/linsalrob/sphae',
        packages=find_packages(),
        include_package_data=True,
        classifiers=CLASSIFIERS,
        install_requires=[
            "snaketool-utils>=0.0.4",
            "snakemake>=8.11.6",
            "pyyaml>=6.0",
            "Click==8.1.3",
            "metasnek>=0.0.4",
            "attrmap>=0.0.7",
            "biopython>=1.8.1",
            "pandas",
            "snakemake-executor-plugin-slurm>=0.5.1",
        ],
        entry_points={
            'console_scripts': [
                'sphae=sphae.__main__:main'
            ]
        },
    )

if __name__ == "__main__":
    main()