Can you reproduce this not in spyder (either in plain python or ipython prompts)? Are there any other tracking issues for this on other projects?

attn @anntzer @ccordoba12

No other projects are currently tracking this issue. In the WinPython project, I gave this issue as the reason why I continue to need PyQt4 for now.

I tried to execute in plain python and by configuring Spyder's run settings to execute in an external System terminal. In both cases, tkinter is used as the backend instead of Qt, and only one figure window displays at a time (I have to close one figure window to see the next, and I can't go back). matplotlib's figure edit menu is totally different with tkinter. I don't see the same problem with tkinter, but then tkinter is not usable for me since I can't navigate between multiple figure windows. Qt plots support many more features that I depend on.

How do I get matplotlib to use the Qt backend and support multiple simultaneous figure windows when using plain python? WinPython has a convenient Command Prompt that sets up the PATH environment variable for me. Or is this problem tied to Spyder because it depends on Spyder plot support functions?

I cannot reproduce the issue with python 3.5.2, matplotlib 1.5.3, pyqt 5.6.0, spyder 3.0.2 (all from conda). The script I tried is

import matplotlib as mpl; mpl.use("qt5agg")
from matplotlib import pyplot as plt

fig, ax = plt.subplots()
mng = plt.get_current_fig_manager()
mng.window.showMinimized()

fig, ax = plt.subplots()
mng = plt.get_current_fig_manager()
mng.window.showMinimized()

plt.show()

@hiccup7 See http://matplotlib.org/faq/usage_faq.html#what-is-a-backend for all of the ways to change the backend.

You will need to call plt.ion() or make the figures before calling show to not block the command prompt when the figures are up in either plain python or IPython (in the case of IPython you can also use %matplotlib).

I have not yet had time to reproduce the problem outside Spyder or produce a simple example script. Today, however, I reproduced the problem using the latest versions in WinPython 3.5.3.0Qt5:

• Python 3.5.3, Spyder 3.1.2, matplotlib 2.0.0, Qt 5.7.1, PyQt5 5.7.1

Again, I worked around the problem by reverting Qt:

• Python 3.5.3, Spyder 3.1.2, matplotlib 2.0.0, Qt 4.8.7, PyQt4 4.11.4

This seems to be a Windows problem (I can't reproduce it on Linux). I'll take a look at it.

@hiccup7, does this problem appear on Spyder IPython console? Or just the Python one?

I have not tried the Spyder IPython console. I always use the Spyder Python console.

Could you try in the IPython one, please? I'm sorry to say it but we're about to remove the Python console in the coming months because it has a lot of very, very hard to fix bugs.

I tried the Spyder IPython console. By default, this creates in-line plots within the console. I strongly prefer a separate window for each plot, and the Python console provides this. I need to selectively expand plots to full screen and choose among existing plot windows to view them side-by-side for comparison of processing algorithms. This is just like the visualizations I do in MATLAB.

I found this: http://stackoverflow.com/questions/14261903/how-can-i-open-the-interactive-matplotlib-window-in-ipython-notebook
Using my latest configuration that reproduces the problem (Python 3.5.3, Spyder 3.1.2, matplotlib 2.0.0, Qt 5.7.1, PyQt5 5.7.1), I entered in the IPython console %matplotlib qt. It threw ImportError: No module name 'PyQt4'.
I entered in the IPython console %matplotlib notebook before I ran my Python script, and this correctly produced separate windows for each plot. However, I can't interact with the plots or even view plot figures other than the last one generated. Every time I click on the last figure window, I get a Windows error beep, just like the problem I stated in the opening post.

In my latest working configuration (Python 3.5.3, Spyder 3.1.2, matplotlib 2.0.0, Qt 4.8.7, PyQt4 4.11.4), if I change the Run Settings to "Execute in current Python or IPython console" and then click (move focus) to an IPython console, Spyder crashes.

I resolved this issue by configuring Spyder to run scripts in IPython, and for Spyder's IPython backend to Automatic (instead of Inline). Thanks @ccordoba12 for suggesting IPython!