Misc. matplotlib-related fixes

Checklist

• I have read the contribution guidelines.
• Unit tests have been added for any new or changed code, and the test suite passes. Note: Your request will likely not be merged without the appropriate tests.
• "closes #XXXX" is in the body of the MR description to link the related issue, if applicable.

• Matplotlib is a mandatory dependency nowadays, so do not guard against it not being there.
• Fix warning with newer matplotlib.
• Fix get_colors() where a list is erroneously used as a masked array.