setup.py

from setuptools import setup, Extension
import sys
import os
import numpy


ext_modules = []
cmdclass = {}
if os.name != "nt":
    try:
        from Cython.Distutils import build_ext
        ext_modules += [
            Extension(
                "mirnylib.numutils_new",
                ["mirnylib/numutils_new.pyx"],
                language = "c++",
                include_dirs=[numpy.get_include()]),
        ]

        # On MacOS, use homebrew-installed LLVM OpenMP if the CC variable is set
        if sys.platform == 'darwin' and os.environ.get('CC', None) == 'clang-omp':
            opts = {
                'language': 'c++',
                'include_dirs': [numpy.get_include(), '/usr/local/include'],
                'library_dirs': ['/usr/local/lib'],
                'extra_compile_args': ["-march=native" , "-O3", "-ffast-math", "-fopenmp"],
                'extra_link_args': ["-march=native" , "-O3", "-ffast-math", "-liomp5"],
            }
        else:
            opts = {
                'language': 'c++',
                'include_dirs': [numpy.get_include()],
                'extra_compile_args': ["-march=native" , "-O3", "-ffast-math", "-fopenmp"],
                'extra_link_args': ["-march=native" , "-O3", "-ffast-math", "-lgomp"],
            }

        ext_modules += [
            Extension(
                "mirnylib.fastExtensions",
                ["mirnylib/fastExtensions/fastExtensionspy.pyx", "mirnylib/fastExtensions/fastExtensions.cpp"],
                **opts)
        ]

        cmdclass.update( {'build_ext': build_ext} )

    except ImportError:
        if not os.path.isfile('mirnylib/numutils_new.c'):
            raise RuntimeError("Cython is required to build extension modules for mirnylib.")
        ext_modules += [
            Extension(
                "mirnylib.numutils_new",
                ["mirnylib/numutils_new.c"],
                include_dirs=[numpy.get_include()]),
        ]


setup(
    name='mirnylib',
    url='https://bitbucket.org/mirnylab/mirnylib/',
    description=('Libraries, shared between different mirnylab projects.'),
    packages=['mirnylib',"mirnylib/h5dictUtils"],
    ext_modules=ext_modules,
    cmdclass=cmdclass,
    install_requires=[
        'biopython',
        'joblib>=0.6.3',
        'h5py',
    ],
    dependency_links=[
        'https://bitbucket.org/james_taylor/bx-python/get/tip.tar.bz2'
    ],
)