setup.py

from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext as build_ext_orig
import os
import pathlib

## From https://stackoverflow.com/questions/42585210/extending-setuptools-extension-to-use-cmake-in-setup-py ##
class CMakeExtension(Extension):

    def __init__(self, name):
        # don't invoke the original build_ext for this special extension
        super().__init__(name, sources=[])


class build_ext(build_ext_orig):

    def run(self):
        for ext in self.extensions:
            self.build_cmake(ext)
        super().run()

    def build_cmake(self, ext):
        cwd = pathlib.Path().absolute()

        # these dirs will be created in build_py, so if you don't have
        # any python sources to bundle, the dirs will be missing
        build_temp = pathlib.Path(self.build_temp)
        build_temp.mkdir(parents=True, exist_ok=True)
        extdir = pathlib.Path(self.get_ext_fullpath(ext.name))
        extdir.parent.mkdir(parents=True, exist_ok=True)

        # example of cmake args
        config = 'Debug' if self.debug else 'Release'
        cmake_args = [
            '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_%s=%s' % (config.upper(), str(extdir.parent.absolute())),
            '-DCMAKE_BUILD_TYPE=%s' % config
        ]

        # example of build args
        build_args = [
            '--config', config
        ]

        os.chdir(str(build_temp))
        self.spawn(['cmake', str(cwd)] + cmake_args)
        if not self.dry_run:
            self.spawn(['cmake', '--build', '.'] + build_args)
        # Troubleshooting: if fail on line above then delete all possible 
        # temporary CMake files including "CMakeCache.txt" in top level dir.
        os.chdir(str(cwd))

## End from https://stackoverflow.com/questions/42585210/extending-setuptools-extension-to-use-cmake-in-setup-py ##

# Not put in the setup, but these are the minimum packages
# you should have to use everytihng in the repo.
install_requires=[
        'pytorch',
        'torch-geometric',
        'torch-scatter',
        'torch-sparse'
        'pytorch-lightning',
        'dotmap',
        'seaborn',
        'numpy',
        'matplotlib'
    ]

setup(
    name='automate',
    version='1.0.1',
    author='Ben Jones',
    author_email='benjones@cs.washington.edu',
    url='',
    description='',
    license='MIT',
    python_requires='>=3.6',
    ext_modules=[CMakeExtension('automate_cpp')],
    cmdclass={
        'build_ext': build_ext
    },
    packages=find_packages()
)