setup.py

from setuptools.command.test import test as TestCommand
from setuptools import setup
import os
import sys


class PyTest(TestCommand):
    user_args = [("pytest-args=", "a", "Arguments to pass to py.test")]

    def initialize_options(self):
        TestCommand.initialize_options(self)
        self.pytest_args = []

    def run_tests(self):
        import pytest

        errno = pytest.main(self.pytest_args)
        if errno:
            sys.exit(errno)
        else:
            errno = pytest.main(["--doctest-modules", "-Wignore"])
            sys.exit(errno)


def readme():
    path = os.path.dirname(__file__) if os.path.dirname(__file__) else "."
    with open(path + "/README.rst") as rst:
        return rst.read()


setup(
    name="bamnostic",
    version=open("version").read(),
    description="Pure Python, OS-agnostic Binary Alignment Map (BAM) random access and parsing tool",
    long_description=readme(),
    url="https://github.com/betteridiot/bamnostic/",
    author="Marcus D. Sherman",
    author_email="mdsherm@umich.edu",
    license="BSD 3-Clause",
    # setup_requires=['pytest-runner'],
    tests_require=["pytest"],
    cmdclass={"test": PyTest},
    packages=["bamnostic", "tests"],
    package_dir={"bamnostic": "./bamnostic", "tests": "./tests"},
    package_data={
        "bamnostic": [
            "data/*",
            "LICENSE",
            "CONTRIBUTING.md",
            "CODE_OF_CONDUCT.md",
            "version",
        ]
    },
    classifiers=[
        "Development Status :: 5 - Production/Stable",
        "Intended Audience :: Developers",
        "Intended Audience :: End Users/Desktop",
        "Intended Audience :: Science/Research",
        "Intended Audience :: Information Technology",
        "License :: OSI Approved :: BSD License",
        "Natural Language :: English",
        "Operating System :: Unix",
        "Operating System :: Microsoft :: Windows",
        "Operating System :: MacOS",
        "Programming Language :: Python :: 2.7",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.0",
        "Programming Language :: Python :: 3.1",
        "Programming Language :: Python :: 3.2",
        "Programming Language :: Python :: 3.3",
        "Programming Language :: Python :: 3.4",
        "Programming Language :: Python :: 3.5",
        "Programming Language :: Python :: 3.6",
        "Programming Language :: Python :: 3.7",
        "Programming Language :: Python :: 3.8",
        "Programming Language :: Python :: Implementation :: CPython",
        "Programming Language :: Python :: Implementation :: PyPy",
        "Topic :: Scientific/Engineering",
        "Topic :: Scientific/Engineering :: Information Analysis",
    ],
    keywords="BAM pysam genomics genetics struct",
    include_package_data=True,
    zip_safe=False,
)