I'm packaging pywikibot for Arch Linux here: https://aur.archlinux.org/packages/python2-pywikibot-git/
Packing software for distribution means that install scripts might be run by a different person than the user. Install scripts are not the place for user config, and it's also bad practice to force ANY interactive configs at that stage.
Please don't run generate_user_files.py from setup.py. Find some way to do this at runtime.
Or, ideally, to behave sanely with no configs at all.
At the moment we are just providing a sample config for users to edit, and doing: sed -i /generate_user_files.py/Id setup.py