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I am trying to get a good setup to do scientific python on windows 7. To be complete, I am using Anaconda for Python package management, and emacs 25.2 (the native windows build from GNU, not the cygwin build). My goal is to use elpy, with ipython as the Python shell. The problem is figure windows.

I have found some similar issues reported before, but the solutions don't work for me. In particular, my init.el has (elpy-enable) and (elpy-use-ipython).

So elpy and ipython work fine, until I do figure(1). I get a figure window, control is back at the ipython prompt, but the figure window says "not responding." And if I plot something it doesn't appear. Various attempts to use ion() and show() haven't worked.

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I recommend using emacs64 for Windows, which is compiled to support many types of images and will you allow to plot figures for instance in jupyter in your Emacs buffer. Repo: https://github.com/m-parashar/emax64
I'm still trying to figure out the shell part... I've relied a lot on the EmacsWiki for configuration (elpy, etc): https://www.emacswiki.org/emacs/PythonProgrammingInEmacs. I'm using the jupyter prompt as a shell, but it's kind of slow, and I can't get the auto-completion to work in the shell (but it does in python files). Let me know if you're able to figure that one out!

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