setup.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
from pathlib import Path
from setuptools import setup, find_packages
# add for remove error with pip install -e . with pyproject.toml
import site
import sys

site.ENABLE_USER_SITE = "--user" in sys.argv[1:]

NAME = 'culebrONT'
URL = 'https://github.com/SouthGreenPlatform/culebrONT'
CURRENT_PATH = Path(__file__).resolve().parent
VERSION = CURRENT_PATH.joinpath("culebrONT", "VERSION").open('r').readline().strip()

__doc__ = """CulebrONT is an open-source, scalable, modular and traceable Snakemake pipeline, able to launch multiple
assembly tools in parallel, giving you the possibility of circularise, polish, and correct assemblies, checking quality.
CulebrONT can help to choose the best assembly between all possibilities. """


def main():
    setup(
        # Project information
        name=NAME,
        version=VERSION,
        url=URL,
        project_urls={
            'Bug Tracker': f'{URL}/issues',
            'Documentation': f'https://{NAME}-pipeline.readthedocs.io/en/latest/',
            'Source Code': URL
        },
        download_url=f'{URL}/archive/{VERSION}.tar.gz',
        author='''Julie Orjuela (IRD),
                   Aurore Comte (IRD),
                   Sebastien Ravel (CIRAD),
                   Florian Charriat (INRAE),
                   Bao Tram Vi (IRD),
                   François Sabot (IRD)
                   Sebastien Cunnac (IRD)''',
        author_email='sebastien.ravel@cirad.fr',
        description=__doc__.replace("\n", ""),
        long_description=CURRENT_PATH.joinpath('README.rst').open('r', encoding='utf-8').read(),
        long_description_content_type='text/x-rst',
        license='GPLv3',

        # docs compilation utils
        command_options={
            'build_sphinx': {
                'project': ('setup.py', NAME),
                'version': ('setup.py', VERSION),
                'release': ('setup.py', VERSION),
                'source_dir': ('setup.py', CURRENT_PATH.joinpath('docs', 'source').as_posix()),
                'build_dir': ('setup.py', CURRENT_PATH.joinpath('docs', 'build').as_posix()),
            }},

        # Package information
        packages=find_packages(),
        include_package_data=True,
        use_scm_version={
            "version_scheme": 'release-branch-semver',
            'local_scheme': "node-and-date",
            'normalize': True,
            "root": ".",
            "relative_to": __file__,
            "fallback_version": VERSION,
            "write_to": 'culebrONT/_version.py',
        },
        setup_requires=['setuptools_scm'],
        python_requires='>=3.6',
        install_requires=[
            'PyYAML',
            'pandas',
            'matplotlib',
            'tabulate',
            'rpy2',
            'ipython',
            'biopython',
            'pysam',
            'numpy',
            'argparse',
            'snakemake',
            'tqdm',
            'click>=8.0.3',
            'cookiecutter',
            'docutils < 0.18'
        ],
        extras_require={
            'docs': ['sphinx_copybutton',
                     'sphinx_rtd_theme',
                     'sphinx_click'],
            'dev': ['tox'],
        },
        entry_points={
            f'{NAME}': [f'{NAME} = __init__'],
            'console_scripts': [f'{NAME} = {NAME}.main:main']},

        # Pypi information
        platforms=['unix', 'linux'],
        keywords=[
            'snakemake',
            'assembly',
            'workflow'
        ],
        classifiers=[
            'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
            'License :: CeCILL-C Free Software License Agreement (CECILL-C)',
            'License :: Free for non-commercial use',
            'Development Status :: 5 - Production/Stable',
            'Intended Audience :: Developers',
            'Intended Audience :: End Users/Desktop',
            'Operating System :: POSIX :: Linux',
            'Programming Language :: Python :: 3.6',
            'Programming Language :: Python :: 3.7',
            'Programming Language :: Python :: 3.8',
            'Programming Language :: Python :: 3.9',
            'Programming Language :: R',
            'Natural Language :: English',
            'Topic :: Scientific/Engineering',
            'Topic :: Scientific/Engineering :: Bio-Informatics',
            'Topic :: Software Development :: Assemblers'
        ],
        options={
            'bdist_wheel': {'universal': True}
        },
        zip_safe=True,  # Don't install the lib as an .egg zipfile
    )


if __name__ == '__main__':
    main()