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Consider reducing test dataset sizes #63

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widdowquinn opened this issue Aug 19, 2024 · 3 comments · Fixed by #87
Closed

Consider reducing test dataset sizes #63

widdowquinn opened this issue Aug 19, 2024 · 3 comments · Fixed by #87
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testing Related to `pyani-plus` tests

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@widdowquinn
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Summary:

In the old pyani we used Blochmannia genome example datasets (among other things), and moving to pyani-plus gives us an opportunity to update our choices to reduce test run time and target particular known (prior) issues.

For example, we could introduce Donovan Parks' virus sequences (widdowquinn/pyani#340), which would allow us to simultaneously reduce input test dataset size and confirm that our fixes for the coverage problem continue to work (and validate ANIm/other tests).

@widdowquinn widdowquinn added the testing Related to `pyani-plus` tests label Aug 19, 2024
@widdowquinn
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We may want to consider dividing tests of datasets into groups (e.g. "fast" and "slow"; "viral", "bacterial", "linear genomes") etc. and running these on different schedules. For example:

  • "fast" tests would run in CI on a push
  • "slow" tests would run in CI on a PR merge
  • "complete" tests might run monthly on CI/locally when being particularly paranoid about a change.

@peterjc
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peterjc commented Aug 19, 2024

See e.g. https://docs.pytest.org/en/7.1.x/example/markers.html#registering-markers which uses marking some tests as "slow" for example.

@widdowquinn
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This would help avoid the current duplicate push and pull-request GH Action runs we have at the moment. Running the "fast" tests only on push and the "slow"/"complete" tests on pull-request would be a useful, meaningful separation of the two activities.

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testing Related to `pyani-plus` tests
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