setup.py

import sys
import platform
from distutils.ccompiler import new_compiler
from distutils.sysconfig import customize_compiler
from setuptools import setup
from setuptools.extension import Extension
from subprocess import getoutput


# Check python version
if sys.version_info[:2] < (3, 8):
    raise RuntimeError("Python version >= 3.8 required.")

# The recommendation
# (https://cython.readthedocs.io/en/latest/src/userguide/source_files_and_compilation.html#distributing-cython-modules)
# is to distribute Cython compiled source files with the package. This is why
# the Cython compilation step is disabled by default here.
USE_CYTHON = False
ext = '.pyx' if USE_CYTHON else '.cpp'
language = "c++"
includedirs = []
cpp_extra_link_args = []

# These default compile flags mimic the flags used in the Zeo++/Voro++ Makefile
cpp_extra_compile_args = [
    "-Wall",
    "-ansi",
    "-pedantic",
    "-O3",
]

def using_clang():
    """Will we be using a clang compiler?
    """
    compiler = new_compiler()
    customize_compiler(compiler)
    compiler_ver = getoutput("{0} -v".format(compiler.compiler[0]))
    return "clang" in compiler_ver

# Needed to specify C++ runtime library on OSX. This solution is replicated
# from the setup.py of mdanalysis
if platform.system() == "Darwin" and using_clang():
    cpp_extra_compile_args.append("-stdlib=libc++")
    cpp_extra_compile_args.append("-mmacosx-version-min=10.9")
    cpp_extra_link_args.append("-stdlib=libc++")
    cpp_extra_link_args.append("-mmacosx-version-min=10.7")

extensions = [
    Extension(
        "pyzeo.extension", 
        sources=[
            'src/pyzeo/extension'+ext,
            'src/area_and_volume.cc',
            'src/channel.cc',
            'src/cluster.cc',
            'src/cycle.cc',
            'src/grid.cc',
            'src/geometry.cc',
            'src/graphstorage.cc',
            'src/voro++/src/voro++.cc',
            'src/net.cc',
            'src/networkaccessibility.cc',
            'src/networkanalysis.cc',
            'src/networkstorage.cc',
            'src/networkinfo.cc',
            'src/network.cc',
            'src/networkio.cc', 
            'src/material.cc',
            'src/mindist.cc',
            'src/OMS.cc',
            'src/psd.cc',
            'src/sphere_approx.cc',
            'src/string_additions.cc',
            'src/symbcalc.cc',
            'src/symmetry.cc',
            'src/ray.cc',
            'src/rmsd.cc',
            'src/voronoicell.cc',
            'src/v_network.cc',
        ],
        include_dirs=includedirs,
        extra_compile_args=cpp_extra_compile_args,
        extra_link_args=cpp_extra_link_args,
        language=language
    )
]

if USE_CYTHON:
    from Cython.Build import cythonize
    extensions = cythonize(extensions)

if __name__ == "__main__":
    setup(ext_modules=extensions)