setup.py

# -*- coding: utf-8 -*-
"""
package setup

@author: C Heiser
"""
import sys
import os
import io
import setuptools
from setuptools import setup


try:
    from numpy.distutils.core import Extension, setup
except ImportError:
    sys.exit(
        "install requires: 'numpy'."
        " use pip or easy_install."
        " \n  $ pip install numpy"
    )


f_compile_args = ["-ffixed-form", "-fdefault-real-8"]


def read(fname):
    with io.open(
        os.path.join(os.path.dirname(__file__), fname), encoding="utf-8"
    ) as _in:
        return _in.read()


def get_lib_dir(dylib):
    import subprocess
    from os.path import realpath, dirname

    p = subprocess.Popen(
        "gfortran -print-file-name={}".format(dylib),
        stdout=subprocess.PIPE,
        stderr=subprocess.PIPE,
        shell=True,
    )
    retcode = p.wait()
    if retcode != 0:
        raise Exception("Failed to find {}".format(dylib))

    libdir = dirname(realpath(p.communicate()[0].strip().decode("ascii")))

    return libdir


if sys.platform == "darwin":
    GFORTRAN_LIB = get_lib_dir("libgfortran.3.dylib")
    QUADMATH_LIB = get_lib_dir("libquadmath.0.dylib")
    ARGS = ["-Wl,-rpath,{}:{}".format(GFORTRAN_LIB, QUADMATH_LIB)]
    f_compile_args += ARGS
    library_dirs = [GFORTRAN_LIB, QUADMATH_LIB]
else:
    library_dirs = None


glmnet_lib = Extension(
    name="_glmnet",
    sources=["dropkick/_glmnet.pyf", "dropkick/src/glmnet/glmnet5.f90"],
    extra_f90_compile_args=f_compile_args,
    library_dirs=library_dirs,
)

if __name__ == "__main__":
    import versioneer

    with open("README.rst", "r") as fh:
        long_description = fh.read()

    setup(
        name="dropkick",
        version=versioneer.get_version(),
        cmdclass=versioneer.get_cmdclass(),
        description="Automated scRNA-seq filtering",
        long_description=long_description,
        author="Cody Heiser",
        author_email="codyheiser49@gmail.com",
        url="https://github.com/KenLauLab/dropkick",
        install_requires=read("requirements.txt").splitlines(),
        ext_modules=[glmnet_lib],
        packages=setuptools.find_packages(),
        classifiers=[
            "Programming Language :: Python :: 3",
            "Operating System :: OS Independent",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Topic :: Scientific/Engineering",
        ],
        python_requires=">=3.6",
        entry_points={
          "console_scripts": [
              "dropkick = dropkick.__main__:main"
          ]
      },
    )