Update orthofinder for 3.0.1b1 beta release #51202
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces significant modifications to the Orthofinder installation process through two main files: Possibly related PRs
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🧰 Additional context used🪛 yamllint
🔇 Additional comments (5)
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🧹 Outside diff range and nitpick comments (5)
recipes/orthofinder/build.sh (2)
27-28: LGTM: Example data correctly addedThe creation of a new directory for example data and copying the ExampleData into it is a good practice. This separates example data from executable files and aligns with the PR objectives.
Consider adding a comment explaining the purpose of this new directory, e.g.:
+# Create directory for example data mkdir -p $PREFIX/share/orthofinder/ +# Copy example data for user reference cp -r ExampleData $PREFIX/share/orthofinder/
Missing Required Files Detected in
build.shThe verification script indicates that the following required files and directories are missing:
orthofinder.pyscripts_of/config.jsontools/convert_orthoginder_tree_ids.pytools/create_files_for_hogs.pytools/make_ultrametric.pytools/orthogroup_gene_count.pytools/primary_transcript.pyExampleDataPlease ensure that these files are present in the repository and that the
build.shscript correctly references their paths.🔗 Analysis chain
Line range hint
1-28: Summary: Build script successfully updated for Orthofinder 3.0.1b1The changes to the build script align well with the PR objectives of updating Orthofinder to version 3.0.1b1. Key improvements include:
- Addition of new Python scripts (
create_files_for_hogs.pyandorthogroup_gene_count.py).- Proper setting of executable permissions for new scripts.
- Creation of a separate directory for example data.
These changes enhance the functionality and organization of the Orthofinder package, making it consistent with the beta release 3.0.1b1.
To ensure all necessary files are included, please run the following verification script:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all expected files are present in the recipe # Test: Check if all mentioned scripts and directories exist echo "Checking for required files and directories:" required_files=( "orthofinder.py" "scripts_of/config.json" "tools/convert_orthofinder_tree_ids.py" "tools/create_files_for_hogs.py" "tools/make_ultrametric.py" "tools/orthogroup_gene_count.py" "tools/primary_transcript.py" "ExampleData" ) for file in "${required_files[@]}"; do if [ -e "$file" ]; then echo "✓ $file exists" else echo "✗ $file is missing" fi doneLength of output: 1629
recipes/orthofinder/meta.yaml (3)
1-2: Highlight beta release statusThe version has been updated to 3.0.1b1, which is a beta release. This aligns with the PR objective, but it's important to note that beta releases may have stability issues.
Consider adding a comment in the package metadata or description to clearly indicate that this is a beta release. This will help users make an informed decision about using this version in their environments.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
33-35: New dependencies addedThe addition of scikit-learn, biopython, and aster as new dependencies is noted. These likely support new features in the updated version.
Consider specifying version constraints for these new dependencies to ensure compatibility and reproducibility. For example:
- scikit-learn >=0.24 - biopython >=1.79 - aster >=1.0Replace the version numbers with those that are known to work with this version of OrthoFinder.
47-48: ExampleData added to files sectionThe addition of ExampleData to the files section is noted and approved. This ensures that example data is included with the package, which can be helpful for users.
Consider providing more details about the ExampleData, such as its location within the package structure or a brief description of its contents. This will help users understand what example data is available and how to access it.
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📒 Files selected for processing (2)
- recipes/orthofinder/build.sh (1 hunks)
- recipes/orthofinder/meta.yaml (3 hunks)
🧰 Additional context used
🪛 yamllint
recipes/orthofinder/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/orthofinder/build.sh (3)
15-17: LGTM: New scripts added correctlyThe addition of
create_files_for_hogs.pyandorthogroup_gene_count.pyto the$PREFIX/bindirectory is correct and aligns with the PR objectives. These new scripts will enhance the functionality of Orthofinder.
22-25: LGTM: Correct permissions set for new scriptsThe addition of chmod commands to make the new scripts executable is correct and necessary. This ensures that users will be able to run the newly added scripts without permission issues.
26-26: LGTM: Improved readabilityThe addition of an empty line improves the script's readability by clearly separating different sections.
recipes/orthofinder/meta.yaml (2)
10-10: Build number reset approvedResetting the build number to 0 for the new version is correct and follows Conda packaging best practices.
18-18: Verify Python version constraintThe Python version constraint has been tightened to
>=3.7,<3.12. This change is generally good as it prevents potential issues with untested Python versions.Please confirm that the upper bound (<3.12) is intentional and aligns with the package's known compatibility. You can verify this by checking the package's documentation or running the following command to search for any mentions of Python version compatibility:
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