setup.py

from __future__ import print_function
from setuptools import setup
from distutils.extension import Extension
import warnings
import os
import sys


use_cython = True

try:
    from Cython.Build import cythonize
except ImportError:
    use_cython = False
    warnings.warn("No cython found -- install will use pre-generated C files")


def create_ext_modules():
    """
    Build commands require preinstalled numpy to compile the c extensions. A global "import numpy"
    here would break tox and also if installed as a dependency from another python package.
    So we only require numpy for the cases where its header files are actually needed.
    """

    build_commands = (
        "build",
        "build_ext",
        "build_py",
        "build_clib",
        "build_scripts",
        "bdist_wheel",
        "bdist_rpm",
        "bdist_wininst",
        "bdist_msi",
        "bdist_mpkg",
        "build_sphinx",
    )

    ext_modules = []
    for command in build_commands:
        if command in sys.argv[1:]:
            try:
                import numpy
            except ImportError:
                raise Exception(
                    "please install numpy, need numpy header files to compile c extensions"
                )
            ext_modules = [
                Extension(
                    "imnet.process_strings_cy",
                    sources=["imnet/process_strings_cy.pyx"],
                    include_dirs=[numpy.get_include()],
                )
            ]
            if use_cython:
                print("Using cython")
                ext_modules = cythonize(ext_modules)

            break
    return ext_modules


currdir = os.getcwd()


setup(
    name="imnet",
    author="Rok Roskar",
    version="0.2.1",
    author_email="roskar@ethz.ch",
    url="http://github.com/rokroskar/imnet",
    package_dir={"imnet/": ""},
    packages=["imnet"],
    ext_modules=create_ext_modules(),
    scripts=["scripts/imnet-analyze"],
    install_requires=[
        "click",
        "findspark",
        "python-Levenshtein",
        "scipy",
        "networkx",
        "pandas",
        "cython",
    ],
    keywords=["pyspark", "genomics", "hpc", "bioinformatics"],
)