Update el_gato to 1.20.0 #51051
Update el_gato to 1.20.0 #51051
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces updates to the Changes
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@mencian Thanks for tidying up the recipe. The build is now failing because the database files that were being copied in the build.sh script aren't found. Are you able to offer any guidance here on how to fix this issue? Is the |
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It looks to me that the DB files were created by https://github.com/bioconda/bioconda-recipes/pull/51051/files#diff-23e0b91a3b7cd25eeb68639a967975077fa68686b822522cc35970d2fed9b2dcL3 |
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Yes, I saw the changes you made. However, the build now fails saying it is unable to find one of the files which should have been copied. It seems to be looking in the wrong location now:
That file should be in /opt/conda/conda-bld/el_gato.../bin/db/ Before your changes, the build failed with |
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Actionable comments posted: 1
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- recipes/el_gato/meta.yaml (3 hunks)
🔇 Additional comments (5)
recipes/el_gato/meta.yaml (5)
2-3: Version and hash update looks good.The version has been correctly updated to 1.20.0, and the corresponding SHA256 hash has been updated. This is consistent with the PR objectives.
22-22: Run exports update is appropriate.The change in
max_pinfrom 'x.x' to 'x' allows for more flexible version compatibility, which is consistent with common practices for Python packages.
49-49: Summary update is a minor improvement.The addition of a period at the end of the summary is a small but welcome grammatical improvement.
37-38: New dependencies added appropriately.The addition of
coloramafor Linux andimportlib-metadatafor Python <= 3.8 addresses specific requirements for different environments. The conditions are correctly specified.To ensure these dependencies are correctly utilized in the package, please run the following script:
#!/bin/bash # Description: Verify the usage of new dependencies in the package # Test: Check for imports or usage of colorama and importlib-metadata rg -i 'import\s+(colorama|importlib[-_]metadata)' --type python rg -i '(colorama|importlib[-_]metadata)\..' --type python
50-51: New URL additions are valuable.The addition of
dev_urlanddoc_urlprovides important links to development and documentation resources. The URLs are correctly formatted and use appropriate variables.To ensure these URLs are correct and accessible, please run the following script:
recipes/el_gato/meta.yaml
Outdated
| noarch: python | ||
| script: | ||
| - {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir | ||
| - mkdir -p $PREFIX/bin/db | ||
| - cp el_gato/db/* $PREFIX/bin/db/ |
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💡 Codebase verification
Issue with $PREFIX usage: Environment variable is not set.
The $PREFIX environment variable is not set, causing the script to attempt copying database files to /bin/db/, which does not exist.
Please ensure that $PREFIX is correctly set before running the build script.
🔗 Analysis chain
Build configuration update looks good, but verify $PREFIX usage.
The change to noarch: python is appropriate for a Python package. The new build script correctly installs the package using pip and copies the database files.
However, based on the PR comments, there might be an issue with the $PREFIX usage.
Please verify the correct path for database files using the following script:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the correct path for database files
# Test: Check if the database files are correctly copied to the expected location
fd -t f . "$PREFIX/bin/db"
Length of output: 281
Script:
#!/bin/bash
# Description: Verify the correct path for database files
# Test: Check if the database directory exists and list its contents
if [ -d "$PREFIX/bin/db" ]; then
echo "Contents of $PREFIX/bin/db:"
ls -la "$PREFIX/bin/db/"
else
echo "Error: Directory $PREFIX/bin/db does not exist."
exit 1
fi
Length of output: 120
Script:
#!/bin/bash
# Description: Print the value of $PREFIX
echo "PREFIX is set to: $PREFIX"
Length of output: 46
Update
el_gato: 1.19.0 → 1.20.0recipes/el_gato(click to view/edit other files)@appliedbinfThis pull request was automatically generated (see docs).