CoverageWarning in tests

[jhlegarreta]

What happened?

Although code coverage is being reported through codecov, CIs are showing a warning about the coverage.

Previous versions of the package were not raising the warning, e.g.
https://github.com/nipreps/nifreeze/actions/runs/12872267299/job/35887373250#step:11:1030

Additionally, the coverage is not displayed in the CI log.

The addition of the Run notebooks task does not seem to be the culprit here, i.e.
https://github.com/nipreps/nifreeze/actions/runs/12875170186/job/35897165873#step:12:1029

What command did you use?

pytest --doctest-modules --cov nifreeze -n auto --cov-report xml --junitxml=test-results.xml -v src test

What version of the software are you running?

HEAD (happens with any recent version)

How are you running this software?

Local installation ("bare-metal")

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

/home/runner/work/nifreeze/nifreeze/.tox/py312/lib/python3.12/site-packages/coverage/inorout.py:524: CoverageWarning: Module nifreeze was previously imported, but not measured (module-not-measured)
    self.warn(msg, slug="module-not-measured")

Additional information / screenshots

According to the coverage docs:

Module XXX was previously imported, but not measured (module-not-measured)

You asked coverage.py to measure module XXX, but it had already been imported when coverage started. This meant coverage.py couldn’t monitor its execution.

Google shows multiple leads, e.g.
pytest-dev/pytest-cov#437
pytest-dev/pytest-cov#664
https://pytest-cov.readthedocs.io/en/latest/plugins.html#plugin-coverage

But unsure what the solution is here.