setup.py

from distutils.sysconfig import get_python_inc, get_config_var
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext as _build_ext
import os

include_dirs = [
    os.path.join(os.path.dirname(os.path.abspath(__file__)), "mala"),
    os.path.dirname(get_python_inc()),
    get_python_inc()
]

library_dirs = [
    os.path.join(os.path.dirname(os.path.abspath(__file__)), "mala"),
    get_config_var("LIBDIR")
]

class build_ext(_build_ext):
    def finalize_options(self):
        _build_ext.finalize_options(self)
        # Prevent numpy from thinking it is still in its setup process:
        __builtins__.__NUMPY_SETUP__ = False
        import numpy
        self.include_dirs.append(numpy.get_include())

setup(
        name='mala',
        version='0.2',
        description='Training and evaluation scripts for MALA (https://arxiv.org/abs/1709.02974).',
        url='https://github.com/funkey/mala',
        author='Jan Funke',
        author_email='jfunke@iri.upc.edu',
        license='MIT',
        cmdclass={
            'build_ext': build_ext
        },
        install_requires=['cython','numpy'],
        setup_requires=['cython','numpy'],
        packages=[
            'mala',
            'mala.losses',
            'mala.networks',
            'mala.gunpowder',
        ],
        ext_modules = [
            Extension(
                "mala.wrappers",
                ["mala/wrappers.pyx", "mala/emst.cpp", "mala/um_loss.cpp"],
                include_dirs=include_dirs,
                library_dirs=library_dirs,
                language='c++',
                extra_link_args=["-std=c++11", "-lmlpack"],
                extra_compile_args=["-std=c++11", "-w"])],
)