setup.py

from setuptools import setup, find_packages
from setuptools.command.build_ext import build_ext
from setuptools.command.install import install
from distutils.command.build import build

from plip.basic import config

def install_pkg_via_pip(package):
    import sys
    import subprocess
    subprocess.check_call([sys.executable, '-m', 'pip', 'install', package])

def build_ob_py_bindings():
    """ Fix openbabel issue (https://github.com/openbabel/openbabel/issues/2408) manually
      - Download openbabel bindings from pypi
      - extract to a tmpdir
      - fix version in $tmpdir/openbabel-3.1.1.1/openbabel/__init__.py to have 2 dot version only
      - install the fixed version with setuptools/pip
      - cleanup the tmpdir
    """
    import requests
    import tarfile
    import tempfile
    import shutil
    import fileinput
    import subprocess
    import sys

    openbabel_pypi_url='https://files.pythonhosted.org/packages/9d/3f/f08f5d1422d74ed0e1e612870b343bfcc26313bdf9efec9165c3ea4b3ae2/openbabel-3.1.1.1.tar.gz'

    print (f"Downloading openbabel package from : {openbabel_pypi_url}")
    obtar=requests.get(openbabel_pypi_url)
    obtmpdir = tempfile.mkdtemp()
    obtmp = obtmpdir+'/openbabel-3.1.1.1.tar'
    open(obtmp,'wb').write(obtar.content)
    print(f"Saving openbabel tar.gz to {obtmpdir}")
    versfile = obtmpdir+'/openbabel-3.1.1.1/openbabel/__init__.py'

    with tarfile.open(obtmp,mode='r') as tf:
        tf.extractall(obtmpdir)

    print ('Fix versions: s/3.1.1.1/3.1.1/ to make StrictVersion() in openbabel\'s setup.py happy')
    print ('See https://github.com/openbabel/openbabel/issues/2408 for more details')
    with fileinput.input(files=versfile,inplace=True) as f:
        for line in f:
            op = line.replace('__version__ = "3.1.1.1"', '__version__ = "3.1.1"')
            print(op, end='')

    install_pkg_via_pip(obtmpdir+'/openbabel-3.1.1.1/')
    print (f"Cleanup tmpdir: {obtmpdir}")
    shutil.rmtree(obtmpdir)

class CustomBuild(build):
    """Ensure build_ext runs first in build command."""
    def run(self):
        self.run_command('build_ext')
        build.run(self)

class CustomInstall(install):
    """Ensure build_ext runs first in install command."""
    def run(self):
        self.run_command('build_ext')
        install.run(self)

class CustomBuildExt(build_ext):
    """ Check if openbabel bindings are installed || build them """
    def run(self):
        try: import openbabel
        except ModuleNotFoundError:
            try: import requests
            except ModuleNotFoundError:
                install_pkg_via_pip('requests')
            build_ob_py_bindings()
        return

setup(name='plip',
    version=config.__version__,
    description='PLIP - Fully automated protein-ligand interaction profiler',
    classifiers=[
        'Development Status :: 5 - Production/Stable',
        'Intended Audience :: Science/Research',
        'Natural Language :: English',
        'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
        'Programming Language :: Python :: 3.6',
        'Topic :: Scientific/Engineering :: Bio-Informatics'
        ],
    url='https://github.com/pharmai/plip',
    author='PharmAI GmbH',
    author_email='hello@pharm.ai',
    license='GPLv2',
    packages=find_packages(),
    scripts=['plip/plipcmd.py'],
    cmdclass={'build': CustomBuild, 'build_ext': CustomBuildExt, 'install': CustomInstall},
    install_requires=[
        'numpy',
        'lxml'
        ],
    entry_points={
        "console_scripts": [
            "plip = plip.plipcmd:main"
            ]
        },
    zip_safe=False)