setup.py

import codecs
import os
import re
from setuptools.extension import Extension
from setuptools import setup

here = os.path.abspath(os.path.dirname(__file__))


def read(*parts):
    with codecs.open(os.path.join(here, *parts), "r") as fp:
        return fp.read()


def find_version(*file_paths):
    version_file = read(*file_paths)
    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", version_file, re.M)
    if version_match:
        return version_match.group(1)
    raise RuntimeError("Unable to find version string.")


# Add $CONDA_PREFIX/{lib,include} if we are in a Conda environment
try:
    libdir = os.environ["CONDA_PREFIX"]
except:
    libdir = "."

# List requirement from `requirements.txt`
requirements = open("requirements.txt").read().splitlines()

# Use the C implementation of VBGMM from https://github.com/BinPro/CONCOCT/
module1 = Extension(
    name="vbgmm",
    library_dirs=[libdir + "/lib", libdir + "/include"],
    runtime_library_dirs=[libdir + "/lib", libdir + "/include"],
    libraries=["pthread", "gsl", "gslcblas"],
    include_dirs=["c-concoct"],
    sources=["c-concoct/vbgmmmodule.c"],
    define_macros=[
        ("N_RTHREADS", os.getenv("N_RTHREADS") or str(min(64, os.cpu_count())))
    ],
)

setup(
    name="fennec",
    version=find_version("fennec", "__init__.py"),
    description="DNA sequence modeling for machine learning",
    url="https://github.com/keuv-grvl/fennec",
    author="Kévin Gravouil",
    author_email="kevin.gravouil@uca.fr",
    license="MIT",
    packages=["fennec"],
    ext_modules=[module1],
    install_requires=requirements,
    # see: https://pypi.python.org/pypi?%3Aaction = list_classifiers
    classifiers=[
        "Development Status :: 2 - Pre-Alpha",
        "Operating System :: POSIX :: Linux",
        "Programming Language :: Python :: 3",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Intended Audience :: Science/Research",
    ],
    include_package_data=True,
)