setup.py

#!/usr/bin/env python
# -*- encoding: utf-8 -*-
from __future__ import absolute_import
from __future__ import print_function

import io
from glob import glob
from os.path import basename
from os.path import dirname
from os.path import join
from os.path import splitext

from setuptools import find_packages
from setuptools import setup


def read(*names, **kwargs):
    with io.open(
        join(dirname(__file__), *names),
        encoding=kwargs.get('encoding', 'utf8')
    ) as fh:
        return fh.read()


setup(
    name='subclone-prism',
    version='1.0.1',
    license='MIT license',
    description='Methylation Pattern-based, Reference-free Inference of Subclonal Makeup',
    # long_description='%s\n%s' % (
    #     re.compile('^.. start-badges.*^.. end-badges', re.M | re.S).sub('', read('README.rst')),
    #     re.sub(':[a-z]+:`~?(.*?)`', r'``\1``', read('CHANGELOG.rst'))
    # ),
    long_description=read('README.md'),
    long_description_content_type='text/markdown',
    author='Dohoon Lee',
    author_email='dohlee.bioinfo@gmail.com',
    url='https://github.com/dohlee/prism',
    packages=find_packages('src'),
    package_dir={'': 'src'},
    py_modules=[splitext(basename(path))[0] for path in glob('src/*.py')],
    include_package_data=True,
    zip_safe=False,
    classifiers=[
        # complete classifier list: http://pypi.python.org/pypi?%3Aaction=list_classifiers
        'Development Status :: 5 - Production/Stable',
        'Intended Audience :: Developers',
        'License :: OSI Approved :: MIT License',
        'Operating System :: Unix',
        'Operating System :: POSIX',
        'Operating System :: Microsoft :: Windows',
        'Programming Language :: Python',
        # 'Programming Language :: Python :: 2.7',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.4',
        'Programming Language :: Python :: 3.5',
        'Programming Language :: Python :: 3.6',
        'Programming Language :: Python :: 3.7',
        'Programming Language :: Python :: Implementation :: CPython',
        'Programming Language :: Python :: Implementation :: PyPy',
        # uncomment if you test on these interpreters:
        # 'Programming Language :: Python :: Implementation :: IronPython',
        # 'Programming Language :: Python :: Implementation :: Jython',
        # 'Programming Language :: Python :: Implementation :: Stackless',
        'Topic :: Utilities',
    ],
    keywords=[
        # eg: 'keyword1', 'keyword2', 'keyword3',
    ],
    install_requires=[
        # eg: 'aspectlib==1.1.1', 'six>=1.7',
        'cycler>=0.10.0',
        'cleanlog>=0.1.4',
        'matplotlib>=3.0.2',
        'numpy>=1.15.0',
        'pybedtools>=0.7.10',
        'pysam>=0.15.0',
        'scipy>=1.0.1',
        'scikit-learn>=0.20.1',

    ],
    extras_require={
        # eg:
        #   'rst': ['docutils>=0.11'],
        #   ':python_version=="2.6"': ['argparse'],
    },
    entry_points={
        'console_scripts': [
            'prism = prism.cli:main',
        ]
    },
)