setup.py

#!/usr/bin/env python

import os
import subprocess

from distutils.cmd import Command
from setuptools import setup
from setuptools.command.develop import develop
from setuptools.command.install import install


class InstallXcmsCommand(Command):
  """ Install XCMS using the Python developer tools """

  description = 'install XCMS'
  user_options = [
    ('xcms-install-dir=', None, 'R library/directory in which to install XCMS'),
  ]

  def initialize_options(self):
    self.xcms_install_dir = os.environ.get('XCMS_INSTALL_DIR')

  def finalize_options(self):
    if self.xcms_install_dir:
      assert os.path.isdir(self.xcms_install_dir), 'XCMS install path must be a valid directory'

  def run(self):
    xcms_install_args = []

    if self.xcms_install_dir:
      xcms_install_args = ['-l', self.xcms_install_dir]

    subprocess.check_call(['R', 'CMD', 'INSTALL'] + xcms_install_args + ['.'])


class InstallCommandWithXcms(install):
  def run(self):
    self.run_command('install_xcms')
    install.run(self)


class DevelopCommandWithXcms(develop):
  def run(self):
    self.run_command('install_xcms')
    develop.run(self)


setup(
  name='xcms',
  version='1.39.2+ginkgo2',

  description="Ginkgo Bioworks' forked extensions and fixes to XCMS",
  long_description=open('README.md', 'r').read(),
  url='https://bioconductor.org/packages/release/bioc/html/xcms.html',

  author='XCMS Team, Benjie Chen, Ginkgo Bioworks Test Devs',
  author_email='test-devs@ginkgobioworks.com',

  license='GPL-2.0',

  classifiers=[
    'Development Status :: 5 - Production/Stable',
    'Environment :: Console',
    'Environment :: Other Environment',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
    'Natural Language :: English',
    'Operating System :: OS Independent',
    'Programming Language :: Other',
    'Programming Language :: R',
    'Programming Language :: C++',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
    'Topic :: Scientific/Engineering :: Chemistry',
    'Topic :: Scientific/Engineering :: Information Analysis',
    'Topic :: Utilities',
  ],

  packages=[],
  include_package_data=True,

  cmdclass={
    'install_xcms': InstallXcmsCommand,
    'install': InstallCommandWithXcms,
    'develop': DevelopCommandWithXcms,
  },

  install_requires=[],
  zip_safe=False,

  extras_require={
    'release': [
      'bumpversion',
      'twine',
      'wheel',
    ],
  },
)