Bug report

When I try to use the jupyter notebook %matplotlib notebook magic command on Linux (as the first command executed in the notebook), I get this warning:

Warning: Cannot change to a different GUI toolkit: notebook. Using qt instead.

Plots then appear a separate qt window, outside the browser. The %matplotlib inline command does work.

This occurs in freshly-opened jupyter notebooks, with a fresh kernel.

• Operating system: Ubuntu 16.04/18.04
• Matplotlib version: 2.1.1
• Python version: 3.6.3
• jupyter (1.0.0)
• jupyter-client (5.2.3)
• jupyter-console (5.2.0)
• jupyter-core (4.4.0)
• notebook (5.5.0)

LSST miniconda:
https://github.com/lsst/lsstsw/blob/master/etc/conda3_packages-linux-64.txt

I've since upgraded matplotlib and jupyter to attempt to remedy this, but upgrading didn't change the error.