setup.py

import os
import sys

from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize

import numpy as np
from path import Path


if sys.platform == 'darwin':
    os.environ['CC'] = '/Users/aaronschein/opt/anaconda3/bin/gcc'
    os.environ['CXX'] = '/Users/aaronschein/opt/anaconda3/bin/g++'

include_gsl_dir = '/usr/local/include/'
lib_gsl_dir = '/usr/local/lib/'


def get_pkgs_and_exts(dir='.'):
    """
    src/
        Makefile
        setup.py
        __init__.py
        base.pyx
        first_pkg/
            __init__.py
            core.pyx
            things/
            __init__.py
                foo.pyx
                foo.pxd
        second_pkg/
            __init__.py
            core.pyx

    get_pkgs_and_exts()
    >>> [...], [first_pkg, first_pkg.things, second_pkg]

    Inspired by:
    https://github.com/cython/cython/wiki/PackageHierarchy
    """
    pkgs = set()
    exts = list()
    for ext_path in Path(dir).walkfiles('*.pyx'):
        ext_name = ext_path.namebase

        subdirs = ext_path.splitall()[1:-1]
        if subdirs:
            pkg = '.'.join(subdirs)
            pkgs.add(pkg)
            ext_name = pkg + '.' + ext_name

        exts.append(make_extension(ext_name, ext_path))

    return list(pkgs), exts


def make_extension(ext_name, ext_path=None):
    if ext_path is None:
        ext_path = Path.joinpath(*ext_name.split('.')) + '.pyx'
    assert Path(ext_path).isfile()

    return Extension(name=ext_name,
                     sources=[ext_path],
                     include_dirs=[np.get_include(),
                                   include_gsl_dir],
                     library_dirs=[lib_gsl_dir],
                     libraries=['gsl'],
                     extra_compile_args=['-fopenmp'],
                     extra_link_args=['-fopenmp'])


pkgs, exts = get_pkgs_and_exts()


setup(name='apf',
      version='1.0',
      description='Allocative Poisson Factorization (APF) framework and examples.',
      author='Aaron Joseph Steriade Schein',
      packages=pkgs,
      ext_modules=cythonize(exts))