setup.py

# -*- coding: utf-8 -*-
from setuptools import setup, Extension, find_packages
import setuptools_scm


DISTNAME = 'scikit-allel'

PACKAGE_NAME = 'allel'

DESCRIPTION = 'A Python package for exploring and analysing genetic ' \
              'variation data.'

with open('README.rst') as f:
    LONG_DESCRIPTION = f.read()

MAINTAINER = 'Alistair Miles'

MAINTAINER_EMAIL = 'alimanfoo@googlemail.com'

URL = 'https://github.com/cggh/scikit-allel'

DOWNLOAD_URL = 'http://pypi.python.org/pypi/scikit-allel'

LICENSE = 'MIT'

INSTALL_REQUIRES = ['numpy', 'dask[array]']

# full installation with all optional dependencies
EXTRAS_REQUIRE = {'full': ['scipy', 'matplotlib', 'seaborn', 'pandas', 'scikit-learn',
                           'h5py', 'numexpr', 'zarr', 'hmmlearn', 'pomegranate', 'nose']}

CLASSIFIERS = [
    'Development Status :: 4 - Beta',
    'License :: OSI Approved :: MIT License',
    'Intended Audience :: Developers',
    'Intended Audience :: Science/Research',
    'Programming Language :: Python',
    'Topic :: Software Development :: Libraries :: Python Modules',
    'Topic :: Scientific/Engineering',
    'Operating System :: Microsoft :: Windows',
    'Operating System :: POSIX',
    'Operating System :: Unix',
    'Operating System :: MacOS',
    'Programming Language :: Python :: 3',
    'Programming Language :: Python :: 3.8',
    'Programming Language :: Python :: 3.9',
    'Programming Language :: Python :: 3.10',
]


# noinspection PyUnresolvedReferences
def setup_extensions(metadata):
    try:
        print('[scikit-allel] setup extensions with cython')
        from Cython.Build import cythonize
        import numpy
        ext_modules = cythonize([
            Extension('allel.opt.model',
                      sources=['allel/opt/model.pyx'],
                      include_dirs=[numpy.get_include()],
                      ),
            Extension('allel.opt.stats',
                      sources=['allel/opt/stats.pyx'],
                      include_dirs=[numpy.get_include()],
                      ),
            Extension('allel.opt.io_vcf_read',
                      sources=['allel/opt/io_vcf_read.pyx'],
                      include_dirs=[numpy.get_include()],
                      ),
        ])
        metadata['ext_modules'] = ext_modules
    except ImportError:
        print('[scikit-allel] cython not available, not including extensions')


def setup_package():

    metadata = dict(
        name=DISTNAME,
        maintainer=MAINTAINER,
        maintainer_email=MAINTAINER_EMAIL,
        description=DESCRIPTION,
        long_description=LONG_DESCRIPTION,
        license=LICENSE,
        url=URL,
        download_url=DOWNLOAD_URL,
        package_dir={'': '.'},
        packages=find_packages(),
        package_data={'allel.test': ['data/*']},
        classifiers=CLASSIFIERS,
        install_requires=INSTALL_REQUIRES,
        extras_require=EXTRAS_REQUIRE,
        zip_safe=False,
    )
    setup_extensions(metadata)
    setup(**metadata)


if __name__ == '__main__':
    setup_package()