setup.py

import sys
from setuptools import setup, find_packages, Command
#import versioneer

short_description = "The GREAT 3D package for multi-3D (epi)genomics.".split("\n")[0]

# from https://github.com/pytest-dev/pytest-runner#conditional-requirement
needs_pytest = {'pytest', 'test', 'ptr'}.intersection(sys.argv)
pytest_runner = ['pytest-runner'] if needs_pytest else []

try:
    with open("README.md", "r") as handle:
        long_description = handle.read()
except:
    long_description = None

class CleanCommand(Command):
    """Custom clean command to tidy up the project root."""
    user_options = []
    def initialize_options(self):
        pass
    def finalize_options(self):
        pass
    def run(self):
        os.system('rm -vrf ./__pycache__ ./build ./dist ./*.pyc ./*.pyo ./*.tgz ./*.egg-info')

setup(
    # Self-descriptive entries which should always be present
    name='great_3d',
    author='Costas Bouyioukos',
    author_email='costas.bouyioukos@u-paris.fr',
    description=short_description,
    long_description=long_description,
    long_description_content_type="text/markdown",
    #version=versioneer.get_version(),  # BROKEN on setuptools update
    #cmdclass=versioneer.get_cmdclass(),
    # Should make clean work with something like the following:
    #cmdclass={'clean': CleanCommand,},  FIXME classes with the versioneer command
    license='LGPLv3',
    # Which Python importable modules should be included when your package is installed
    # Handled automatically by setuptools. Use 'exclude' to prevent some specific
    # subpackage(s) from being added, if needed
    packages=find_packages(),
    # Optional include package data to ship with your package
    # Customize MANIFEST.in if the general case does not suit your needs
    # Comment out this line to prevent the files from being packaged with your software
    include_package_data=True,  # FIXME Add a data package
    scripts=["great3D"],
    # Allows `setup.py test` to work correctly with pytest
    setup_requires=[] + pytest_runner,
    # Additional entries you may want simply uncomment the lines you want and fill in the data
    # url='http://www.my_package.com',  # Website
    # install_requires=[],              # Required packages, pulls from pip if needed; do not use for Conda deployment
    # platforms=['Linux',
    #            'Mac OS-X',
    #            'Unix',
    #            'Windows'],            # Valid platforms your code works on, adjust to your flavor
    python_requires=">=3.6",          # Python version restrictions
    classifiers=[
        "Programming Language :: Python :: 3",
        "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
        "Operating System :: OS Independent",
        "Environment :: Console",
        "Development Status :: 3 - Alpha",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
    ],
    # Manual control if final package is compressible or not, set False to prevent the .egg from being made
    zip_safe = False,
)