Followup: I discovered/realized that, even though I was using cygwin's python, the windows python (Anaconda in my case) was still in my cygwin path, because the

Followup: I discovered/realized that, even though I was using cygwin's python, the windows python (Anaconda in my case) was still in my cygwin path, because the cygwin path has the windows path elements in it. You can see that if you run this, and see two pythons: which -a python I discovered this when I ran pip and ipython in cygwin, and they "worked," i.e. something ran, but not right. I put this at the end of my .bashrc to remove windows python from cygwin's path: export PATH=$(echo $PATH |sed -e "s/:[^:]*Anaconda[^:]*:/:/g" |sed -e "s/:[^:]*Anaconda[^:]*:/:/g") There were two anaconda directories in the path, and /g should have taken care of both, but my RE-fu is apparently lacking, so brute force. Cygwin has pitfalls.