I'm kind of reluctant to join this thread, but regarding scikit-learn and np.matrix I thought I'd just add some relevant links.  Here's the scikit-learn history page http://scikit-learn.org/stable/about.html, here's a 2011 scikit-learn thread about what to do about np.matrix http://osdir.com/ml/python-scikit-learn/2011-10/msg00212.html and here's a related sklearn github issue https://github.com/scikit-learn/scikit-learn/issues/392.  I haven't read these links in detail and I'm not trying to use them to make any argument regarding the PEP.