Update nf-core - Add missing linkify dependency #51762
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- recipes/nf-core/meta.yaml (1 hunks)
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recipes/nf-core/meta.yaml (1)
53-53: Implementation correctly addresses the reported TUI errors.
The addition of linkify-it-py as a runtime dependency aligns with the PR objectives and should resolve the TUI errors in the bioconda version of nf-core tools. The package's use of run_exports ensures API/ABI compatibility is maintained.
recipes/nf-core/meta.yaml
Outdated
| @@ -50,6 +50,7 @@ requirements: | |||
| - ruamel.yaml | |||
| - tabulate | |||
| - textual ==0.71.0 | |||
| - linkify-it-py | |||
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💡 Codebase verification
Add version constraint >=2.0.0 to linkify-it-py dependency
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. To ensure compatibility, please update the dependency line to:
- linkify-it-py >=2.0.0🔗 Analysis chain
Consider adding version constraints for linkify-it-py.
While adding the dependency is correct, it's recommended to specify version constraints to ensure compatibility with textual 0.71.0 and prevent potential future issues.
Let's verify the required version:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check textual's dependencies to determine the required linkify-it-py version
# Test: Search for linkify-it-py in textual's pyproject.toml or setup.py
rg -A 5 'linkify-it-py'
# Fallback: Check if there's a requirements.txt
fd -g 'requirements*.txt' -x cat {} \; | rg 'linkify-it-py'
Length of output: 321
Script:
#!/bin/bash
# Let's try to find any version constraints or usage of linkify-it-py in the codebase
# First, check if there's a pyproject.toml or setup.py
fd -g 'pyproject.toml|setup.py' -x cat {} \; | rg -i 'linkify|dependencies'
# Also check for any imports or direct usage
rg -l 'import.*linkify|from.*linkify'
# Let's also check if there are any version constraints in other meta.yaml files
fd -g 'meta.yaml' -x cat {} \; | rg -A 2 -B 2 'linkify-it-py'
Length of output: 279
Script:
#!/bin/bash
# Let's check the textual package's dependencies directly from PyPI
# Using curl to fetch the PyPI API data for textual version 0.71.0
curl -s https://pypi.org/pypi/textual/0.71.0/json | jq -r '.info.requires_dist[] | select(contains("linkify"))'
# Also check the latest version constraints from other packages that use linkify-it-py
curl -s https://pypi.org/pypi/linkify-it-py/json | jq -r '.info.version'
Length of output: 231
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A double check on this would be nice. I think coderabbitai got confused: Textual 0.71.0 (which nf-core pins) indeeds depends on However, it then suggests that I think pinning linkify to |
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/tools#3257.
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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.
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
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/tools#3257.
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