For the long answer to your question, see https://github.com/matplotlib/matplotlib/pull/4779 (which I really need to finish and get merged). In short, to have both an interactive prompt and a window you need to have an 'input hook' installed to time-share between the GUI event loop an the prompt event loop. It sounds like you change a bunch of things at once (gtk2 -> gtk3 + matplotlib version bumps), did you also change IPython versions? If so, you will need to use their input hook mechanism explicitly (`%matplotlib gtk3` should do the trick) as they moved from readline -> ptprompt so the input hooks the GUI libraries ship no longer work.
It may also be worth checking the value of `mpl.get_backend()` to make sure pyplot as not defaulted to another GUI framework (ex Qt5) and you have 2 GUI frameworks in the same process conflicting with each other!
Recently I upgraded to from matplotlib 1.4.3 + gtk2 to matplotlib 2.2.2 + gtk3 and I have a problems with porting my old code.
I'm using matplotlib in Gtk window with typical:
win = Gtk.window()
vbox = Gtk.Box(...)
fig = pylab.figure()
canvas = FigureCanvas(fig)
toolbar = NavigationToolbar(canvas, fig)
axis = fig.add_axes(...)
After this code I have a valid window on screen however it does not reacts on mouse clicks (zooming etc.) until calling Gtk.main_iteration() in loop or Gtk.main(). I can understand why, however it was working differently with old matplotlib and gtk2 (window was responsive all time).
The rest of my code is a python "Text User Interface" application (controlled by commands typed to terminal), the window is only for showing the results (animated waveform). Now I would like to keep the application as it is, but also to have responsive matplotlib window, without calling Gtk.main(). Is it possible? If yes, then how to do this?
Sorry for the long mail - I have no idea how to describe the problem shortly and all examples I found always have Gtk.main() called so they are in fact full GTK programs. I want a simple text program with matplotlib window as a "result showing" addition only.