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Merged
merged 119 commits into from
Apr 16, 2025
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JulianFlesch
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@JulianFlesch JulianFlesch commented Mar 18, 2025

This is a DRAFT.

This PR adds functionality to list and search the nf-core/test-datasets github repository via a new subcommand test-datasets. Closes #3487 where this feature was requested.

Changes:

  • Adds new subcommands: test-datasets search, test-datasets list, test-datasets list-branches
  • Adds new test-datasets folder with command and utility functions

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

Julian Flesch added 29 commits March 13, 2025 14:20
@JulianFlesch JulianFlesch marked this pull request as draft March 18, 2025 08:04
@jfy133
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jfy133 commented Mar 31, 2025

I'm on the fence on this one. Usually I also prefer plain text output because it is just easier to pipe, but rich is used a lot in nf-core, right?
How about another flag -t, --plain-text to print plain text output instead of a rich table? Or we could always default to plain text, if -u or -g is given.

Latter is probably best I think, as makes me and you happy but default sticks with the typical nf-core convention

@JulianFlesch
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Oh and one more general question: Whats our stance on type hints @mirpedrol ? Should I add them?
Their use across nf-core seemed a bit inconsistent to me, at first. But now I see them more and more :D

@mirpedrol
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We are slowly adopting them when we add new code or modify old code, so yes, you should add them 😄

@JulianFlesch JulianFlesch changed the title [Draft] Feature/test datasets Feature/test datasets Apr 2, 2025
@JulianFlesch JulianFlesch marked this pull request as ready for review April 14, 2025 18:25
@JulianFlesch
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Could you have another look at your previous review @mirpedrol ?

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Just a couple of last small suggestions, otherwise LGTM! very nice 🙂

@JulianFlesch JulianFlesch merged commit 8571adb into nf-core:dev Apr 16, 2025
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4 participants