setup.py

from setuptools import setup
from setuptools.extension import Extension
from Cython.Build import cythonize
import numpy as np

print(np.get_include())

setup(
    name="funlib.segment",
    version="0.1",
    description="Tools to segment graphs and volumes.",
    url="https://github.com/funkelab/funlib.segment",
    author="Jan Funke",
    author_email="funkej@janelia.hhmi.org",
    license="MIT",
    packages=[
        "funlib.segment",
        "funlib.segment.graphs",
        "funlib.segment.graphs.impl",
        "funlib.segment.arrays",
        "funlib.segment.arrays.impl",
    ],
    ext_modules=cythonize(
        [
            Extension(
                "funlib.segment.arrays.impl.replace_values_inplace",
                sources=["funlib/segment/arrays/impl/replace_values_inplace.pyx"],
                extra_compile_args=["-O3"],
                include_dirs=[np.get_include()],
                language="c++",
            ),
            Extension(
                "funlib.segment.arrays.impl.find_components",
                sources=[
                    "funlib/segment/arrays/impl/find_components.pyx",
                    "funlib/segment/arrays/impl/find_components_impl.cpp",
                ],
                extra_compile_args=["-O3", "-std=c++11"],
                include_dirs=[np.get_include()],
                language="c++",
            ),
            Extension(
                "funlib.segment.graphs.impl.connected_components",
                sources=[
                    "funlib/segment/graphs/impl/connected_components.pyx",
                    "funlib/segment/graphs/impl/connected_components_impl.cpp",
                ],
                extra_compile_args=["-O3", "-std=c++11"],
                include_dirs=[np.get_include()],
                language="c++",
            ),
        ]
    ),
    install_requires=[
        "funlib.persistence>=0.1",
        "funlib.geometry>=0.2",
        "daisy>=1.0",
        "cython",
        "numpy",
        "scikit-image",
        "zarr",
    ],
)