I add them by hand to requirements.txt and I try to keep it as minimum as possible. Yes it makes it not 100% reproducible, but it forces me to think about each dependency and I can see in my git log why it was added.
It's funny how "pip help list" or "pip help freeze" works. :-) I found I can add --path .lib to list/freeze those. It's an extra step, but not too terrible.
