First let me say thanks for providing such an amazing tool, really makes a huge difference for code health.
I'm using pytest-cov, but it doesn't parse the .coveragerc so I believe it's a coverage bug. Basically if you provide an
omit option in [run] and [report] the last in the file wins.
This is because both store their value in
_omit, as you can see here. I'm not sure how to fix it though, as I just started to read through the source.