setup.py

from distutils.core import setup
from Cython.Build import cythonize
import subprocess
from glob import glob
from os import path
import sys

def pkgconfig(*packages, **kw):
    flag_map = {'-I': 'include_dirs', '-L': 'library_dirs', '-l': 'libraries'}
    for token in subprocess.check_output(["pkg-config", "--libs", "--cflags"] + list(packages)).strip().split(" "):
        kw.setdefault(flag_map.get(token[:2]), []).append(token[2:])
    return kw

#Cython build logic
cython_subdirs = [ "src/nest", "src/util" ]
cython_pyx = [pyxfile for d in cython_subdirs for pyxfile in glob(path.join(d, "*.pyx"))]
cython_modules= cythonize(cython_pyx)
for m in cython_modules:
	if sys.platform=="darwin":
		m.extra_compile_args = ["-stdlib=libstdc++","-mmacosx-version-min=10.6"]
		m.extra_link_args = ["-stdlib=libstdc++","-mmacosx-version-min=10.6"]

include_dirs = pkgconfig("eigen3")["include_dirs"] + ["/usr/include/c++/4.2.1","src"]

setup(ext_modules = cython_modules,
      include_dirs=include_dirs,
	)

# #!/usr/bin/env python
# from ez_setup import use_setuptools
# use_setuptools()

# from setuptools import setup, find_packages, Extension

# from Cython.Distutils import build_ext
# from Cython.Build import cythonize

# from os import path
# from glob import glob
# import subprocess

# #Cython extensions can be built in the standard fashion via distribute
# #but files including numpy headers must have numpy include path specified.
# import numpy

# #Versioning logic
# def get_git_version():
#     """Get current version tag via call to git describe.

#     Version tags are of the format:
#         v<major>.<minor>.<patch>
#     """
#     return "0.0.0"
#     version_string = subprocess.check_output(["git", "describe", "--match", "v*"])
#     return version_string.strip().lstrip("v")

# #Cython build logic
# cython_subdirs = [
#     "src",
# ]

# cython_modules= cythonize([pyxfile for d in cython_subdirs for pyxfile in glob(path.join(d, "*.pyx"))])

# for r in cython_modules:
#     r.extra_compile_args=["-fopenmp"]
#     r.extra_link_args=["-fopenmp"]

# def pkgconfig(*packages, **kw):
#     flag_map = {'-I': 'include_dirs', '-L': 'library_dirs', '-l': 'libraries'}
#     for token in subprocess.check_output(["pkg-config", "--libs", "--cflags"] + list(packages)).strip().split(" "):
#         kw.setdefault(flag_map.get(token[:2]), []).append(token[2:])
#     return kw

# include_dirs = [numpy.get_include(), path.abspath("."), path.abspath("src")] + pkgconfig("eigen3")["include_dirs"]

# setup(
#         name="Scheme",
#         description="PyRosetta modules for Scheme.",
#         author="Will Sheffler",
#         author_email="willsheffler@gmail.com",
#         url="https://github.com/willsheffler/scheme",
#         version=get_git_version(),
#         provides=["scheme"],
#         # packages=find_packages(where="scheme"),
#         install_requires=[
#             "numpy>=1.7",
#             "numexpr>=2.0",
#             "pandas>=0.12",
#             "scipy>=0.13",
#             "biopython",
#             "tables>=3.0.0",
#             "posix_ipc>=0.9.8",
#             "fastcluster",
#             "lockfile",
#             "futures",
#             "ipython>=1.0.0",
#             "ipython_glmol",
#             "pyrosetta>=3.4.20140216004611",
#             "Jinja2",
#             "SQLAlchemy>=0.9.4",
#             "MySQL-python>=1.2.5",
#             "bz2file",
#             "toolz",
#             "decorator"
#         ],
#         setup_requires=[
#             "Cython>=0.18",
#         ],
#         tests_require=[
#             "nose",
#             "nose-html",
#             "coverage",
#             "nose-progressive"
#         ],
#         test_suite = "nose.collector",
#         cmdclass = {'build_ext': build_ext},
#         #Extra options to cythonize are *not* the same 'Extension'
#         #See Cython.Compiler.Main.CompilationOptions for details
#         #
#         #In particular, include_dirs must be specified in setup
#         #   as opposed to Extension if globs are used.
#         include_dirs=include_dirs,
#         ext_modules = cython_modules
#         # entry_points = {
#         #         "console_scripts" : [
#         #             "close_structure_chainbreaks=interface_fragment_matching.apps.close_structure_chainbreaks:main"
#         #             ],
#         #         },
#         )