setup.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import subprocess
import sys

# Version check prior to non-stdlib imports
if sys.version_info < (3, 5):
    sys.stderr.write(
        "ERROR: mapDamage requires Python v3.5 or above, but "
        "Python v%i.%i was used\n" % sys.version_info[:2]
    )
    sys.exit(1)


from setuptools import Extension, setup
from setuptools.command.build_py import build_py as SetuptoolsBuildPy

VERSION = "2.3.0a0"


class GitVersionBuild(SetuptoolsBuildPy):
    def run(self):
        if os.path.exists(".git"):
            try:
                commit = (
                    subprocess.check_output(("git", "rev-parse", "--short", "HEAD"))
                    .decode("utf-8")
                    .strip()
                )
            except (subprocess.CalledProcessError, OSError) as error:
                raise SystemExit("Could not determine mapDamage version: %s" % (error,))

            with open(os.path.join("mapdamage", "_version.py"), "w") as handle:
                handle.write("#!/usr/bin/env python\n")
                handle.write('__version__ = "{}-{}"\n'.format(VERSION, commit))

        super().run()


setup(
    cmdclass={"build_py": GitVersionBuild},
    name="mapdamage",
    version=VERSION,
    author="Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson",
    packages=["mapdamage"],
    package_data={"mapdamage": ["r/*.r", "r/stats/*.r", "tests/*"]},
    entry_points={"console_scripts": ["mapDamage=mapdamage.main:entry_point"]},
    url="https://github.com/ginolhac/mapDamage",
    license="LICENSE.txt",
    description="mapDamage tracks and quantifies DNA damage patterns in ancient DNA sequencing reads generated by Next-Generation Sequencing platforms",
    long_description=open("README.md").read(),
    long_description_content_type="text/markdown",
    python_requires=">=3.5",
    install_requires=["coloredlogs", "pysam"],
    ext_modules=[
        Extension(
            "mapdamage.seqtk",
            sources=["mapdamage/seqtk/seqtk.c"],
            libraries=["z"],
        )
    ],
)