setup.py

from setuptools import setup, Extension
import os
import glob
import sys
import subprocess
import pkg_resources

if sys.version_info.major == 2 and sys.version_info.minor != 7:
    sys.stderr.write("ERROR: cyvcf2 is only for python 2.7 or greater you are running %d.%d\n", (sys.version_info.major, sys.version_info.minor))
    sys.exit(1)


def get_version():
    """Get the version info from the mpld3 package without importing it"""
    import ast

    with open(os.path.join("cyvcf2", "__init__.py"), "r") as init_file:
      module = ast.parse(init_file.read())

    version = (ast.literal_eval(node.value) for node in ast.walk(module)
         if isinstance(node, ast.Assign)
         and node.targets[0].id == "__version__")
    try:
      return next(version)
    except StopIteration:
          raise ValueError("version could not be located")


# Temporarily install dependencies required by setup.py before trying to import them.
# From https://bitbucket.org/dholth/setup-requires

sys.path[0:0] = ['setup-requires']
pkg_resources.working_set.add_entry('setup-requires')


def missing_requirements(specifiers):
    for specifier in specifiers:
        try:
            pkg_resources.require(specifier)
        except pkg_resources.DistributionNotFound:
            yield specifier


def install_requirements(specifiers):
    to_install = list(specifiers)
    if to_install:
        cmd = [sys.executable, "-m", "pip", "install",
            "-t", "setup-requires"] + to_install
        subprocess.call(cmd)


requires = ['cython', 'numpy', 'coloredlogs', 'click']
install_requirements(missing_requirements(requires))


excludes = ['irods', 'plugin']

sources = [x for x in glob.glob('htslib/*.c') if not any(e in x for e in excludes)] + glob.glob('htslib/cram/*.c')
# these have main()'s
sources = [x for x in sources if not x.endswith(('htsfile.c', 'tabix.c', 'bgzip.c'))]
sources.append('cyvcf2/helpers.c')

import numpy as np
import platform
from Cython.Distutils import build_ext

cmdclass = {'build_ext': build_ext}
extension = [Extension("cyvcf2.cyvcf2",
                        ["cyvcf2/cyvcf2.pyx"] + sources,
                        libraries=['z', 'bz2', 'lzma', 'curl', 'ssl'] + (['crypt'] if platform.system() != 'Darwin' else []),
                        include_dirs=['htslib', 'cyvcf2', np.get_include()])]


setup(
    name="cyvcf2",
    description="fast vcf parsing with cython + htslib",
    long_description_content_type="text/markdown",
    url="https://github.com/brentp/cyvcf2/",
    long_description=open("README.md").read(),
    license="MIT",
    author="Brent Pedersen",
    author_email="bpederse@gmail.com",
    version=get_version(),
    cmdclass=cmdclass,
    ext_modules=extension,
    packages=['cyvcf2', 'cyvcf2.tests'],
    entry_points=dict(
        console_scripts=[
            'cyvcf2 = cyvcf2.__main__:cli',
        ],
    ),
    test_suite='nose.collector',
    tests_require='nose',
    install_requires=['numpy'],
    include_package_data=True,
    zip_safe=False,
)