setup.py

from setuptools import setup, find_packages
from distutils.core import Extension
import os


os.environ["CC"] = "g++"

setup(
    name='amq',
    version='0.2.1',
    packages=find_packages(),
    include_package_data=True,
    dependency_links=[
        "git+git://github.com/grayfall/scikit-bio@fastunifrac#egg=scikit-bio-0.5.1.dev0"
    ],
    install_requires=[
        'numpy>=1.11.0',
        'scipy>=0.17.0',
        'scikit-bio==0.5.1.dev0',
        'click>=6.6',
        'biopython>=1.66',
        'joblib>=0.9.4',
        'multiprocess>=0.70.4',
        'Comparable>=1.0',
        'bunch>=1.0.1',
        'pandas==0.19.2',
        'scikit-learn>=0.17.1',
        'codeclimate-test-reporter>=0.1.2',
        'colorama==0.3.7',
        'biom-format==2.1.6',
        'h5py'
    ],
    entry_points='''
        [console_scripts]
        amq=amquery.cli:cli
        amquery=amquery.cli:cli
    ''',
    ext_modules=[Extension('amquery.core.preprocessing.kmer_counter.lexrank.lexrank',
                           sources=['amquery/core/preprocessing/kmer_counter/lexrank/lexrank.cpp'],
                           extra_compile_args=['-std=c++11'],
                           ),
                 Extension('amquery.core.distance.metrics.jsd',
                           sources=['amquery/core/distance/metrics/jsd.cpp'],
                           extra_compile_args=['-std=c++11'],
                           )
                 ],
)