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One option for whitelisting files would be to subclass doctest.DocTestParser and pass an instance as the parser argument to doctest.DocFileSuite:
http://docs.python.org/dev/library/doctest.html#doctest.DocFileSuite
The custom parser could look for the per-file marker before falling back to the usual parsing logic. This would give us the functionality we need without having to make changes to doctest.