setup.py

from setuptools import setup, find_packages
# If you have .pyx things to cythonize
from distutils.extension import Extension
from Cython.Build import cythonize
from pysam import get_include as pysam_get_include

name = "bam25prime"
__version__ = "0.1"

# https://github.com/cython/cython/blob/master/docs/src/reference/compilation.rst#configuring-the-c-build
extensions = [
    Extension(
        "bam25prime.libbam25prime", ["bam25prime/libbam25prime.pyx"],
        include_dirs=pysam_get_include()),
    ]

setup(
    name=name,
    version=__version__,
    description="Library providing utilities to collapse aligned segments"
                "in a bam file to their 5-prime end.",
    author="Blaise Li",
    author_email="blaise.li@normalesup.org",
    license="MIT",
    packages=find_packages(),
    scripts=["bin/%s" % name],
    ext_modules = cythonize(extensions),
    #ext_modules = cythonize("bam25prime/libbam25prime.pyx", include_path=pysam_get_include()),
    install_requires=["pysam", "pybedtools"])
# If you have .pyx things to cythonize
    #ext_modules = cythonize("libsmallrna/libsmallrna.pyx"),
    #install_requires=["cytoolz"],
    #zip_safe=False)