Well I think I found the culprit. I knew it must be something simple. And it was. Our pydisutils.cfg had both an index-url and find_links, both with the same simple url. When I removed the find_links, all the time sinks went away. What did take 3hr is now back to 24min. /facepalm
fwiw, this is just a python setup.py test, and uses tox virtualenv setuptools. I also thought that setuptools just used pip, but now I see it's actually easy-install, which I didn't realize was a different thing from pip. Good luck on https://github.com/pypa/setuptools/issues/917
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