Update polap recipe #52142
Update polap recipe #52142
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📝 WalkthroughWalkthroughThe pull request includes modifications to the Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/polap/build.sh (1)
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1-85: Consider updating documentation and test coverageWith the addition of multiple new scripts for mtDNA and plastid analysis, please ensure:
- Documentation is updated to reflect new functionality
- Test cases exist for new scripts
- Usage examples are provided for new analysis workflows
This will help users understand how to properly utilize the new features in version 0.3.7.2.
Would you like help in generating:
- Documentation templates for new scripts?
- Example test cases?
- Usage examples for the new analysis workflows?
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📒 Files selected for processing (2)
recipes/polap/build.sh(4 hunks)recipes/polap/meta.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/polap/meta.yaml
🔇 Additional comments (3)
recipes/polap/build.sh (3)
45-45: Verify Python dependencies for mtDNA cycle detection
The new Python script run-polap-py-mtdna-find-cycle-with-node-revisits.py likely requires specific Python packages for graph analysis. Ensure these dependencies are properly declared in the recipe's meta.yaml.
#!/bin/bash
# Check for Python imports in the new script
echo "Python imports in new script:"
grep -E "^import |^from .* import" src/run-polap-py-mtdna-find-cycle-with-node-revisits.py
# Check if these imports are covered in conda environment files
echo -e "\nDependencies in conda environment files:"
grep -E "python|networkx|numpy|pandas" src/polap-conda-environment*.yaml53-62: Verify consistency between depth range analysis scripts
Multiple scripts related to depth range analysis have been added or modified:
- New:
run-polap-r-contig2edge.R - New:
run-polap-r-determine-depth-range_6.R - Restored:
run-polap-r-determine-depth-range.R
Please ensure these scripts maintain consistent functionality and don't have overlapping responsibilities.
#!/bin/bash
# Compare the main functions across depth range analysis scripts
echo "Analyzing depth range scripts for function definitions:"
for file in src/run-polap-r-determine-depth-range*.R; do
echo "=== $file ==="
grep -A 2 "function" "$file"
done15-16: Verify executable permissions for new package scripts
The new package scripts (polap-package-common.sh and polap-package-mtcontigs.sh) should be executable. While the build script sets permissions for polap and polap.sh, other scripts might need similar treatment.
Update polap recipe to v0.3.7.2