I'm still trying to migrate scikit-learn to numpydoc master.
I'm having some trouble with this issue:
http://stackoverflow.com/questions/12206334/sphinx-autosummary-toctree-contains-reference-to-nonexisting-document-warnings

Apparently something goes wrong with when autosummary is called?
That didn't use to be the case.
I can't really do numpydoc_show_class_members = False because then there is no method table any more :(