setup.py

# based on https://github.com/pypa/sampleproject
from codecs import open
from distutils.command.sdist import sdist as _sdist
from distutils.core import setup
from distutils.extension import Extension
from os import path

from setuptools import find_packages, setup

here = path.abspath(path.dirname(__file__))

try:
    from Cython.Distutils import build_ext
    from Cython.Build import cythonize
except ImportError:
    use_cython = False
else:
    use_cython = True

cmdclass = {}

if use_cython:
    ext_modules = cythonize("mergesvvcf/*pyx")
    cmdclass.update({"build_ext": build_ext})
else:
    ext_modules = [
        Extension("mergesvvcf.locations", ["mergesvvcf/locations.c"]),
        Extension("mergesvvcf.variantdict", ["mergesvvcf/variantdict.c"]),
        Extension("mergesvvcf.vcftobreakpoints", ["mergesvvcf/vcftobreakpoints.c"]),
    ]


class sdist(_sdist):
    def run(self):
        # Make sure the compiled Cython files in the distribution are up-to-date
        from Cython.Build import cythonize

        cythonize(["mergesvvcf/*.pyx"])
        _sdist.run(self)


cmdclass["sdist"] = sdist

# Get the long description from the relevant file
with open(path.join(here, "DESCRIPTION.md"), encoding="utf-8") as f:
    long_description = f.read()

setup(
    name="mergesvvcf",
    version="1.0.3",
    description="Merge SV VCF calls. Fork of https://github.com/ljdursi/mergevcf by Jonathan Dursi (Jonathan.Dursi@oicr.on.ca)",
    long_description=long_description,
    # The project's main homepage.
    url="https://github.com/papaemmelab/mergeSVvcf",
    # Author details
    author="Max Levine",
    author_email="levinem1@mskcc.org",
    # Choose your license
    license="GPL",
    classifiers=[
        #   5 - Production/Stable
        "Development Status :: 5 - Production/Stable",
        "Intended Audience :: Science/Research",
        "Topic :: Scientific/Engineering",
        "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
        "Programming Language :: Python :: 2",
        "Programming Language :: Python :: 3",
    ],
    keywords="merge sv vcfs",
    packages=find_packages(exclude=["contrib", "docs", "tests*"]),
    install_requires=["pysam>=0.15.2", "Cython>=0.29.7"],
    # ext_modules=[],
    test_suite="tests",
    extras_require={"dev": ["check-manifest"], "test": ["coverage"]},
    # If there are data files included in your packages that need to be
    # installed, specify them here.  If using Python 2.6 or less, then these
    # have to be included in MANIFEST.in as well.
    #    package_data={
    #        'sample': ['package_data.dat'],
    #    },
    entry_points={"console_scripts": ["mergesvvcf=mergesvvcf:main"]},
    ext_modules=ext_modules,
    cmdclass={"sdist": sdist},
)