Original comment byDaniel Hahler (Bitbucket: blueyed, GitHub: blueyed)
This warnings causes test failures for me when I am capturing output, and pytest-cov triggers the run for subprocess.call being used in the test.
The warning ("'Coverage.py warning: --include is ignored because --source is set (include-ignored)'") is being captured by pytest's capfd then, and is not expected to be there for the test(s).
What I was forgetting was that there's no need to connect the run and report settings together. Report inclusion and omission will default to the run settings by virtue of the data that the run phase collected. Thanks! :)