setup.py

# -*- coding: utf-8 -*-

from setuptools import setup, find_packages
import re
import subprocess

def get_git_revision_hash():
    return subprocess.check_output(['git', 'rev-parse', 'HEAD']).decode('utf-8')

def get_git_revision_short_hash():
    return subprocess.check_output(['git', 'rev-parse', '--short', 'HEAD'])

with open('README.md', 'r') as fp:
    readme = fp.read()

pkgs = find_packages('src', exclude=['data'])
print('found these packages:', pkgs)

schema_dir = 'schema'

# reqs_re = re.compile("[<=>]+")
# with open('requirements.txt', 'r') as fp:
#     reqs = [reqs_re.split(x.strip())[0] for x in fp.readlines()]

reqs = [
    'numpy',
    'scipy',
    'scikit-learn',
    'torch_optimizer',
    #'scikit-bio',
    'hdmf',
    'wandb',
]

print(reqs)

setup_args = {
    'version': '0.0.1',
    'name': 'deep-taxon',
    'description': 'A package for Exabiome code. Built from revisions ' + get_git_revision_hash(),
    'long_description': readme,
    'long_description_content_type': 'text/x-rst; charset=UTF-8',
    'author': 'Andrew Tritt',
    'author_email': 'ajtritt@lbl.gov',
    'url': 'http://github.com/exabiome/deep-taxon',
    'license': "BSD",
    'install_requires': reqs,
    'packages': pkgs,
    'package_dir': {'': 'src'},
    'package_data': {'deep_taxon.sequence': ["%s/*.yaml" % schema_dir, "%s/*.json" % schema_dir]},
    'classifiers': [
        "Programming Language :: Python",
        "Programming Language :: Python :: 3.5",
        "Programming Language :: Python :: 3.6",
        "Programming Language :: Python :: 3.7",
        "License :: OSI Approved :: BSD License",
        "Development Status :: 2 - Pre-Alpha",
        "Intended Audience :: Developers",
        "Intended Audience :: Science/Research",
        "Operating System :: Microsoft :: Windows",
        "Operating System :: MacOS",
        "Operating System :: Unix",
        "Topic :: Scientific/Engineering :: Medical Science Apps."
    ],
    #'scripts': ['bin/deep-taxon',],

    'entry_points': {
        'console_scripts': [
            'deep-taxon = deep_taxon:main',
        ],
    },
    'keywords': 'python '
                'HDF '
                'HDF5 '
                'cross-platform '
                'open-data '
                'data-format '
                'open-source '
                'open-science '
                'reproducible-research ',
    'zip_safe': False
}

if __name__ == '__main__':
    setup(**setup_args)