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Although the interface has improved, I'm still not sure it's possible to do this without some hackery. They do have a main() function now, but it still doesn't accept arguments. This is possibly because it depends on pep8 and pyflakes and they might not offer great interfaces either.
I would guess the only way to do it without subprocess would be to manually override sys.argv, which has trouble written all over it. Since the current subprocess approach does work, I'm going to put this on the shelf for a while.
Flake8 now offers a much-improved interface and it shouldn't be necessary to subprocess for it anymore.
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