setup.py

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

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

from setuptools import find_packages
from setuptools import setup, Extension

try:
    # Allow installing package without any Cython available. This
    # assumes you are going to include the .c files in your sdist.
    import Cython
except ImportError:
    Cython = None

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

#extensions = [
#  Extension("*", ["*.pyx"], include_dirs=[numpy.get_include()])
#]

# Enable code coverage for C code: we can't use CFLAGS=-coverage in tox.ini, since that may mess with compiling
# dependencies (e.g. numpy). Therefore we set SETUPPY_CFLAGS=-coverage in tox.ini and copy it to CFLAGS here (after
# deps have been safely installed).
if 'TOXENV' in os.environ and 'SETUPPY_CFLAGS' in os.environ:
    os.environ['CFLAGS'] = os.environ['SETUPPY_CFLAGS']

setup(
    name='scregseg',
    version='0.1.3',
    license='GPL-3.0',
    description='Single cell chromatin segmentation',
    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_content_type='text/x-rst',
    author='Wolfgang Kopp',
    author_email='wolfgang.kopp@mdc-berlin.de',
    url='https://github.com/BIMSBbioinfo/scregseg',
    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',
    ],
    project_urls={
        'Documentation': 'https://scregseg.readthedocs.io/',
        'Changelog': 'https://scregseg.readthedocs.io/en/latest/changelog.html',
        'Issue Tracker': 'https://github.com/wkopp/scregseg/issues',
    },
    keywords=[
        # eg: 'keyword1', 'keyword2', 'keyword3',
    ],
    python_requires='>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*',
    install_requires=[
        # eg: 'aspectlib==1.1.1', 'six>=1.7',
                'cython',
                'scikit-learn',
                'scipy',
                'numpy',
                'hmmlearn>=0.2.7',
                #'janggu',
                'pandas',
                'numba',
                'anndata',
                'scanpy',
                'pybedtools',
                'pysam',
                'matplotlib',
                'seaborn',
                'coolbox',
    ],
    extras_require={
        'janggu' : ['janggu', 'tensorflow==2.2', 'keras==2.4.3'],
        # eg:
        #   'rst': ['docutils>=0.11'],
        #   ':python_version=="2.6"': ['argparse'],
    },
    setup_requires=[
        'cython',
        'scikit-learn',
        'scipy',
        'numpy',
        'pandas'
    ] if Cython else [
        'scikit-learn',
        'scipy',
        'numpy',
        'pandas'
    ],
    ext_modules=[
        Extension(
            splitext(relpath(path, 'src').replace(os.sep, '.'))[0],
            sources=[path],
            include_dirs=[dirname(path), numpy.get_include()]
        )
        for root, _, _ in os.walk('src')
        for path in glob(join(root, '*.pyx' if Cython else '*.c'))
    ],
    entry_points={
        'console_scripts': [
            'scregseg = scregseg.cli:main',
        ]
    },
)