Update quast to 5.3.0 #52028
Update quast to 5.3.0 #52028
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request updates the Suggested reviewers
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🧰 Additional context used🪛 yamllintrecipes/quast/meta.yaml[error] 1-1: syntax error: found character '%' that cannot start any token (syntax) 🔇 Additional comments (3)recipes/quast/meta.yaml (3)
The version update looks correct, but let's verify the SHA256 hash matches the source files. 🧰 Tools🪛 yamllint[error] 1-1: syntax error: found character '%' that cannot start any token (syntax)
The build number reset to 0 is correct for a version update. However, the addition of
Please confirm this change is intentional and aligns with the package's compatibility guarantees. ✅ Verification successfulLet me try another search strategy to find reverse dependencies. This should help us:
Let me try one final search to check for any direct dependencies on quast. This will help us:
The addition of run_exports is appropriate and well-configured The search results show that quast is a direct dependency for several bioconda packages (saspector, proksee, metawrap-mg, hapsolo, datma, bacpage, asqcan, aquamis). The addition of run_exports with
🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Check if other bioconda packages depend on quast
# Expected: List of dependent packages that might be affected
echo "Checking for reverse dependencies..."
rg -l "quast" --type yaml | while read -r file; do
if [[ "$file" != "recipes/quast/meta.yaml" ]]; then
echo "Found potential dependency in: $file"
grep -A 5 -B 5 "quast" "$file"
fi
done
Length of output: 895 Script: #!/bin/bash
# Search for quast in requirements sections of meta.yaml files
echo "Searching for quast dependencies in meta.yaml files..."
rg -U "requirements:[\s\S]*?(?:build|host|run):\s*(?:-\s*quast|\s*quast)" --type yaml
# Also check if there are any existing run_exports in other bioconda packages
echo -e "\nChecking for existing run_exports patterns in bioconda..."
rg -U "run_exports:[\s\S]*?pin_subpackage.*quast" --type yaml
Length of output: 636 Script: #!/bin/bash
# Search specifically for quast as a dependency in requirements sections
echo "Searching for direct quast dependencies..."
rg -U "requirements:[\s\S]+?(?:host:|build:|run:)(?:\s*-[^\n]*\n)*?\s*-\s+quast\b" --type yaml
# Also get the content of quast's meta.yaml for version info
echo -e "\nChecking quast's meta.yaml..."
cat recipes/quast/meta.yaml
Length of output: 8796 Line range hint The dependencies remain unchanged from the previous version. Please verify that:
✅ Verification successfulLet me try another verification strategy to check for dependency changes by examining the installation requirements and documentation. Let me try one final verification by checking the source code for any new tool dependencies or version requirements. Based on the verification results, I can now provide a final response: Dependencies are appropriate for version 5.3.0 The verification confirms that:
🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Check for changes in dependencies between versions
# Expected: No significant changes in dependency requirements
# Check release notes or changelog for dependency changes
echo "Checking for CHANGELOG or release notes..."
curl -sL "https://raw.githubusercontent.com/ablab/quast/quast_5.3.0/CHANGELOG" || \
curl -sL "https://raw.githubusercontent.com/ablab/quast/quast_5.3.0/ChangeLog"
# Check setup.py for Python dependencies
echo "Checking setup.py for Python dependencies..."
curl -sL "https://raw.githubusercontent.com/ablab/quast/quast_5.3.0/setup.py" | \
grep -A 10 "install_requires"
Length of output: 895 Script: #!/bin/bash
# Check installation requirements from README and docs
echo "Checking README for requirements..."
curl -sL "https://raw.githubusercontent.com/ablab/quast/quast_5.3.0/README.md" | grep -A 20 "Requirements\|Dependencies"
echo -e "\nChecking docs for requirements..."
curl -sL "https://raw.githubusercontent.com/ablab/quast/quast_5.3.0/manual.html" | grep -A 20 "Requirements\|Dependencies"
# Check requirements.txt if it exists
echo -e "\nChecking requirements.txt..."
curl -sL "https://raw.githubusercontent.com/ablab/quast/quast_5.3.0/requirements.txt"
# Check previous version's setup.py for comparison
echo -e "\nChecking previous version setup.py..."
curl -sL "https://raw.githubusercontent.com/ablab/quast/quast_5.2.0/setup.py" | grep -A 10 "install_requires"
Length of output: 1155 Script: #!/bin/bash
# Check for tool version requirements in source files
echo "Checking tool requirements in source..."
curl -sL "https://raw.githubusercontent.com/ablab/quast/quast_5.3.0/quast_libs/qconfig.py" | grep -A 5 "min\|version\|require"
# Check install scripts for dependencies
echo -e "\nChecking install scripts..."
curl -sL "https://raw.githubusercontent.com/ablab/quast/quast_5.3.0/install.sh" | grep -B 2 -A 2 "install\|depend"
# Check main script for tool invocations
echo -e "\nChecking main script for tools..."
curl -sL "https://raw.githubusercontent.com/ablab/quast/quast_5.3.0/quast.py" | grep -B 1 -A 1 "subprocess.call\|check_output"
Length of output: 13036 🧰 Tools🪛 yamllint[error] 1-1: syntax error: found character '%' that cannot start any token (syntax) Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
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Update
quast: 5.2.0 → 5.3.0recipes/quast(click to view/edit other files)https://sourceforge.net/projects/quast/files/
@ablabThis pull request was automatically generated (see docs).