setup.py

import os
from setuptools import find_packages, setup, Extension
from distutils.sysconfig import get_python_inc

import numpy as np
from Cython.Build import cythonize

# libraries
py_path = get_python_inc().split("/")
libs = ["mkl_rt"]

lib_dirs = ["/".join(py_path[:-2] + ["lib"]), np.get_include()]
include_dirs = ["/".join(py_path[:-1]), np.get_include()]

# compiler option
os.environ["CC"] = "gcc"
os.environ["CXX"] = "g++"
flags = ["-O3", "-fopenmp", "-xhost"]

# description
with open("README.md", "r") as f:
    long_description = f.read()

# C-extensions
c_extensions = [
    Extension(
        name="fastrna.utils",
        sources=["fastrna/utils.pyx"],
        extra_compile_args=flags,
        extra_link_args=flags,
    ),
    Extension(
        name="fastrna.mkl_funcs",
        sources=["fastrna/mkl_funcs.pyx"],
        include_dirs=include_dirs,
        libraries=libs,
        library_dirs=lib_dirs,
        extra_compile_args=flags,
        extra_link_args=flags,
    ),
    Extension(
        name="fastrna.core",
        sources=["fastrna/core.pyx"],
        include_dirs=include_dirs,
        libraries=libs,
        library_dirs=lib_dirs,
        extra_compile_args=flags,
        extra_link_args=flags,
        cython_directives={"embedsignature": True},
    ),
]

setup(
    name="FastRNA",
    version="0.1.0",
    packages=find_packages(),
    author="Hanbin Lee",
    author_email="hanbin973@gmail.com",
    description="FastRNA for scalable scRNA-seq analysis",
    long_description=long_description,
    long_description_content_type="text/markdown",
    url="https://github.com/hanbin973/FastRNA",
    ext_modules=cythonize(c_extensions),
    include_dirs=np.get_include(),
    install_requires=[
        "numpy",
        "scipy",
        "mkl",
        "Cython",
    ],
)