Hey, I am a little puzzled about the behavior of the pytest.yml. The current condition

run-tests

will always yield false (e.g. PR against dev), unless branch ref is main (https://github.com/nf-core/tools/blob/5ab6be3a893dcc5b76289c64ba91ef79939e70e5/.github/workflows/pytest.yml#L43). This condition is queried in the test job (https://github.com/nf-core/tools/blob/5ab6be3a893dcc5b76289c64ba91ef79939e70e5/.github/workflows/pytest.yml#L68), but seems to be ignored, but only for py14. For py10 no tests are run (see here for an example: (https://github.com/nf-core/tools/actions/runs/19102219542). Is there a magic that I don't see, or are there some unintended side effects that make this work?

we don't want to check PRs to dev with every python version, only the minimum. then for release we do both

exactly, the condition there will always be false unless the current branch on which the workflow runs is main. So also when you do a PR from dev to main, it will not activate both python versions. Not sure if that is intended. Yet, the workflow still runs for py3.14, although the if condition here https://github.com/nf-core/tools/blob/5ab6be3a893dcc5b76289c64ba91ef79939e70e5/.github/workflows/pytest.yml#L68 should be false.

actually i think the problem is that we overwrite the value in the different runs...

I think the if condition is wrong as well. It probably should be: if: ${{ needs.setup.outputs.run-tests == 'true' }}, as otherwise it will always be interpreted as a non zero value and therefore yield always true. Then the tests will be skipped as expected: https://github.com/nf-core/tools/actions/runs/19228940000

shouldn't we remove the pytest in any case?

Well, the general issue with the current workflow is that it does not work as intended. The outputs of a job get merged no matter how big the execution matrix. This explains why we also see that only 3.14 tests are run. It overwrites the setting for py3.10.

great detective work!