setup.py

# compiling the .pyx module
import numpy as np
from distutils.core import setup
from Cython.Build import cythonize

# key-value pairs that tell disutils the name
# of the application and which extensions it
# needs to build
# 1. for the cython modules, we're using glob patterns
# e.g. '*.pyx' for every .pyx file or simply pass in
# a list of the filename.pyx
# 2. include_dirs, makes sure we can compile against numpy
# Extension modules that need to compile against NumPy should use this
# function to locate the appropriate include directory
# http://nullege.com/codes/search/numpy.get_include
setup(
    name = 'Hello',
    ext_modules = cythonize(['helloworld.pyx', 'pairwise1.pyx', 'pairwise2.pyx']),
    include_dirs = [np.get_include()]
)

# after that run
# python setup.py build_ext --inplace
# in the command line, and we can import it like
# normal python modules