I had to switch to the Qt4Agg backend for matplotlib to get the auto close of plotting windows to work correctly. This is a new "feature" on my mac running mohave that didn't exist in 10.12
The plot windows can be closed with a cntrl-d when Tk is used, but they shouldn't need that. There was a switch in ipython from using readline to prompt toolkit, which may be part of the issue.
I had to switch to the Qt4Agg backend for matplotlib to get the auto close of plotting windows to work correctly. This is a new "feature" on my mac running mohave that didn't exist in 10.12