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Add GitHub Actions workflow #41

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merged 5 commits into from
Jan 22, 2025

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samuell
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@samuell samuell commented Dec 18, 2024

As a first attempt at addressing #39 , this PR adds a somewhat minimal GitHub Actions workflow that:

  • Runs a basic flake8 lint (warns mostly, only fails on critical issues)
  • Runs pytest which right now just contains of a test placeholder (to keep the PR small)
  • Runs the example workflows previously defined in .gitlab-ci.yml
  • [Edit 2024-12-20]: Run the example workflows previously defined in .gitlab-ci.yml via pytest, and checking that their generated abundancies are as expected.

It also adds a badge for the status of the tests, in README.md.

Worth noting:

  • The workflow uses Python 3.6.15, as 3.6 is specified as the lowest requirement in environment.yml, and since this is a bit of an old version, it requires the slightly older ubuntu-20.04 image. This could perhaps be updated later.
  • Right now the workflow is run on any push. One could limit this to only run on e.g. PRs towards master or similar.

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samuell commented Dec 18, 2024

I'm a little surprised why the CI doesn't show it's status here in the PR, but maybe that is because it is running on my forked repo (For this specific branch/PR here, and the latest run here) and not activated in this repo yet...

@samuell samuell force-pushed the add-github-actions-workflow branch from c4fc75c to 6eb78ec Compare December 20, 2024 14:55
"Staphylococcus aureus": 1.0 / 3,
"Salmonella enterica": 1.0 / 3,
"Enterococcus columbae": 1.0 / 3,
},
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I'm not completely sure here if it is expected that "Staphylococcus hominis" no longer shows up, and instead we get three equal parts of three other species, although the same forward strand file is used?

@kdc10 kdc10 merged commit 0734a77 into treangenlab:master Jan 22, 2025
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2 participants