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nf-core / tools

Python package with helper tools for the nf-core community.
https://nf-co.re
MIT License
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3257 - Add linkify version to fix bioconda dependencies #3260

Open pmoris opened 21 hours ago

pmoris commented 21 hours ago

As described in issue: https://github.com/nf-core/tools/issues/3257

Also see PR against the bioconda recipe (as a temporary fix): https://github.com/bioconda/bioconda-recipes/pull/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 https://github.com/nf-core/tools/issues/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

pmoris commented 19 hours ago

As mentioned in the issue, I also opened a PR against the conda-forge recipe for textual: https://github.com/conda-forge/textual-feedstock/pull/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.

codecov[bot] commented 19 hours ago

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