setup.py

from setuptools import setup, find_packages, Extension
import os

current_dir = os.path.abspath(os.path.dirname(__file__))
with open(os.path.join(current_dir, 'README.md'), encoding='utf-8') as f:
    long_description = f.read()

exec(open("nanovar/version.py").read())

setup(
    name='nanovar',
    version=__version__,
    packages=find_packages(),
    package_data={'nanovar.model': ['*.h5'],
                  'nanovar.gaps': ['*.bed'],
                  'nanovar.css': ['*.css'],
                  'nanovar.js': ['*.js'],
                  'nanovar.ref': ['*L1*']},
    include_package_data=True,
    ext_modules=[Extension('nanovar.nv_bam_parser', ['nanovar/nv_bam_parser.pyx'])],
    scripts=['nanovar/nanovar'],
    url='https://github.com/cytham/nanovar',
    download_url='https://github.com/cytham/nanovar/releases',
    license='gpl-3.0',
    author='Tham Cheng Yong',
    author_email='chengyong.tham@u.nus.edu',
    description='Structural variant caller using low-depth long reads',
    keywords=['nanovar', 'structural variant caller', 'sv', 'nanopore', 'long read', 'low coverage', 'low depth'],
    long_description=long_description,
    long_description_content_type="text/markdown",
    install_requires=['numpy>=1.17.3', 'scipy>=1.2.1', 'biopython>=1.82', 'pybedtools>=0.8.2', 'matplotlib>=2.2.3',
                      'tensorflow-cpu>=2.0.0, <=2.15.1', 'natsort>=6.2.0', 'progress>=1.4', 'pysam>=0.15.3', 'htmlark>=1.0.0', 'nanoinsight>=0.0.3'],
    python_requires='>=3.8',
    classifiers=[
        "Operating System :: POSIX :: Linux",
        "Programming Language :: Python :: 3.8",
        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
        "Topic :: Scientific/Engineering :: Bio-Informatics"
    ]
)