Update SACCHARIS #52118
Update SACCHARIS #52118
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… sha256 hash, and added --single-version-externally-managed --record=record.txt args to setup.py install as per bioconda test suite
# Conflicts: # recipes/saccharis/meta.yaml
# Conflicts: # recipes/saccharis/meta.yaml
# Conflicts: # recipes/saccharis/meta.yaml
adds chunk reducing size to database download streaming
# Conflicts: # recipes/saccharis/meta.yaml
increment to build 8
# Conflicts: # recipes/saccharis/meta.yaml
📝 WalkthroughWalkthroughThe pull request includes updates to the Possibly related PRs
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🔇 Additional comments (2)recipes/saccharis/meta.yaml (2)
The build number has been incremented and the source URL has been updated accordingly. However, we should verify:
Consider using the Bioconda update bot or GitHub Actions to automate these version/hash updates in the future. Also applies to: 12-12, 17-17 Line range hint While no dependencies were changed, please verify:
✅ Verification successfulLet me generate additional verification scripts to check Python version compatibility with the dependencies: This will help us verify both the Python version compatibility and gather any additional version requirements from setup.py. Let's analyze this information before making a final determination. Based on the gathered information, I can now provide the final response: Dependencies and Python version requirements verified The Python >=3.11 requirement is appropriate as:
Security findings:
🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Check for security advisories in key dependencies
# Check PyPI for security advisories
for pkg in "beautifulsoup4" "biopython" "requests" "lxml" "pyqt5"; do
echo "Checking $pkg..."
gh api graphql -f query='{
securityVulnerabilities(first: 5, ecosystem: PIP, package: "'$pkg'") {
nodes {
advisory {
summary
severity
publishedAt
}
vulnerableVersionRange
firstPatchedVersion {
identifier
}
}
}
}'
done
Length of output: 4747 Script: #!/bin/bash
# Check Python version requirements for key dependencies
for pkg in beautifulsoup4 biopython dbcan lxml ncbi-datasets-pylib psutil python-dotenv; do
echo "Checking $pkg..."
# Use PyPI API to get package info
curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info | {name: .name, requires_python: .requires_python}'
done
# Also check if setup.py has any Python version requirements
fd -e py setup.py --exec cat {} \;
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updates cazy.org links to https, which is now required to connect to the site
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