Update nf-core - Add missing linkify dependency

pmoris commented 2 days ago

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.

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📝 Walkthrough

## Walkthrough The pull request modifies the `meta.yaml` file for the `nf-core` package by updating the build number from `0` to `1`. Additionally, it introduces a new dependency, `linkify-it-py`, to the `run` requirements section, specifying a version constraint of `>=1,<3`. No other changes to the structure, logic, or error handling of the file are present in this diff. ## Possibly related PRs - **#51249**: This PR updates the `meta.yaml` file for the `nf-core` package, which is directly related to the main PR that also modifies the `meta.yaml` file for the same package by updating the build number and adding a new dependency. - **#51272**: This PR continues the updates for the `nf-core` package, incrementing the version and adding a new dependency, which aligns with the changes made in the main PR regarding dependency management. - **#51333**: This PR further updates the `nf-core` package, indicating ongoing modifications to the `meta.yaml` file, which is relevant to the changes made in the main PR. ## Suggested labels `please review & merge` ## Suggested reviewers - martin-g - adamhospital

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pmoris commented 2 days ago

A double check on this would be nice. I think coderabbitai got confused:

Textual 0.71.0 (which nf-core pins) indeeds depends on markdown-it-py[linkify]>=2.1.0:

└─▶ curl -s https://pypi.org/pypi/textual/0.71.0/json | jq -r '.info.requires_dist[] | select(contains("linkify"))'
markdown-it-py[linkify,plugins]>=2.1.0

However, it then suggests that markdown-it-py>=2.1.0 depends on linkify-it-py>=2.0.0, which doesn't seem to be the case:

└─▶ curl -s https://pypi.org/pypi/markdown-it-py/2.1.0/json | jq -r '.info.requires_dist[] | select(contains("linkify"))'
linkify-it-py~=1.0 ; extra == "linkify"

└─▶ curl -s https://pypi.org/pypi/markdown-it-py/3.0.0/json | jq -r '.info.requires_dist[] | select(contains("linkify"))'
linkify-it-py>=1,<3 ; extra == "linkify"

I think pinning linkify to >=1<3 instead is the right call here?

bioconda / bioconda-recipes