from setuptools import setup, find_packages
from setuptools.extension import Extension
from Cython.Build import cythonize
extensions = [Extension('myPackage.myModule', ['myPackage/myModule.pyx'],
    include_dirs=['/some/path/to/include/'], libraries=['fftw3', 'fftw3f',
    'fftw3l', 'fftw3_threads', 'fftw3f_threads', 'fftw3l_threads'],
    library_dirs=['/some/path/to/include/'])]
Using setuptools to create a cython package calling an external C library