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3257 - Add linkify version to fix bioconda dependencies #3260

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3257 - Add linkify version to fix bioconda dependencies #3260

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pmoris
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@pmoris pmoris commented Oct 29, 2024 •
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As described in issue: #3257

Also see PR against the bioconda recipe (as a temporary fix): bioconda/bioconda-recipes#51762

The bioconda version of nf-core tools produced errors when running commands that launched the trogon TUI. The reason was the missing package linkify,
which gets pulled in as a dependency of textual in the PyPi build, but not in the conda-forge recipe.
See https://github.com/Textualize/textual/blob/22770300252deb28d266fe4ed4766d6e2a2f5dd2/pyproject.toml#L44, https://github.com/conda-forge/textual-feedstock/blob/main/recipe/meta.yaml and #3257.

Unless the conda-forge recipe for textual gets fixed, the bioconda recipe fix might get lost when a new version is built against the PyPi version of nf-core. So I propose that we also explicitly specify linkify in the requirements.txt file.

Before this is merged, could someone please verify if the version pinning makes sense? As you can see in the bioconda PR, coderabbitai suggested pinning a specific version, but I think it got it the wrong way around.

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!
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@pmoris
Add linkify-py-it as explicit dependency
6d244d2 
The bioconda version of nf-core tools produced errors
when running commands that launched the trogon TUI.
The reason was the missing package linkify,
which gets pulled in as a dependency of textual in the PyPi
build, but not in the conda-forge recipe.
See https://github.com/Textualize/textual/blob/22770300252deb28d266fe4ed4766d6e2a2f5dd2/pyproject.toml#L44,
https://github.com/conda-forge/textual-feedstock/blob/main/recipe/meta.yaml
and nf-core#3257.
@pmoris
Pin linkify version
71c004f 
Code Rabbit AI suggestion:
The textual package version 0.71.0 depends on
markdown-it-py[linkify]>=2.1.0, which in turn
requires linkify-it-py>=2.0.0.

However, checking the actual dependencies of
markdown-it-py, it seems it wants linkify-it-py
to be >=1,<3.

See bioconda/bioconda-recipes#51762
@pmoris
Update changelog
3a80996
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pmoris commented Oct 29, 2024 •
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As mentioned in the issue, I also opened a PR against the conda-forge recipe for textual: conda-forge/textual-feedstock#150

If/when it gets added there, it would not strictly be necessary to add linkify-it-py to the nf-core requirements anymore. But for the time being this would fix problems with people installing it through bioconda at least.

@pmoris pmoris requested review from mirpedrol and mashehu and removed request for mirpedrol October 29, 2024 13:47
mirpedrol
mirpedrol approved these changes Oct 29, 2024
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LGTM, thanks!

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 75.51%. Comparing base (eb4c237) to head (3a80996).
Report is 9 commits behind head on dev.

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pmoris commented Oct 30, 2024

The conda-forge recipe update already got merged, so hopefully any future releases/builds should work.

That means that this PR can be closed without merging it, but the bioconda-recipe one should still be merged to fix the current version of the package.

@pmoris pmoris closed this Oct 30, 2024
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@mirpedrol mirpedrol mirpedrol approved these changes

@mashehu mashehu mashehu approved these changes

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