setup.py

import os, re, io

from setuptools import find_packages
from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize

import numpy

cmdclass = {}

def _read(*parts, **kwargs):
    filepath = os.path.join(os.path.dirname(__file__), *parts)
    encoding = kwargs.pop('encoding', 'utf-8')
    with io.open(filepath, encoding=encoding) as fh:
        text = fh.read()
    return text

def get_version():
    version = re.search(
        r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
        _read('polychrom', '__init__.py'),
        re.MULTILINE).group(1)
    return version

def get_long_description():
    return _read('README.md')


def get_requirements(path):
    content = _read(path)
    return [
        req
        for req in content.split("\n")
        if req != '' and not req.startswith('#')
    ]

cmdclass.update({"build_ext": build_ext})

ext_modules = cythonize(
    [
        Extension(
            "polychrom._polymer_math",
            ["polychrom/_polymer_math.pyx", "polychrom/__polymer_math.cpp"],
        )
    ]
)


setup(
    name="polychrom",
    author='Mirny Lab',
    author_email='espresso@mit.edu',
    version=get_version(),
    url="http://github.com/mirnylab/polychrom",
    description=("A library for polymer simulations and their analyses."),
    long_description=get_long_description(),
    long_description_content_type='text/markdown',
    keywords=['genomics', 'polymer', 'Hi-C', 'molecular dynamics', "chromosomes"],    
    ext_modules=ext_modules,
    cmdclass=cmdclass,
    packages=find_packages(),
    entry_points={
        'console_scripts': [
             'polychrom = polychrom.cli:cli',
        ]
    }    
)