Update kleborate v3 #51156
Update kleborate v3 #51156
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request includes the deletion of the Changes
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Actionable comments posted: 1
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (3)
- recipes/kleborate/build.sh (0 hunks)
- recipes/kleborate/fix_get_kaptive_path.patch (0 hunks)
- recipes/kleborate/meta.yaml (1 hunks)
💤 Files with no reviewable changes (2)
- recipes/kleborate/build.sh
- recipes/kleborate/fix_get_kaptive_path.patch
🧰 Additional context used
🪛 yamllint
recipes/kleborate/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/kleborate/meta.yaml (6)
11-20: LGTM! Build section updated with appropriate configurations.The build section has been updated with correct entry points, build script, and run_exports directive. These changes ensure proper installation and version pinning for downstream dependencies.
35-41: LGTM! Test section updated with appropriate checks.The test section has been improved with the addition of an imports test and updated command-line tests. These changes ensure that the package is installed correctly and its CLI functions as expected.
52-59: LGTM! Extra metadata added to enhance package information.The extra section has been populated with valuable metadata, including recipe maintainers and identifiers. This information enhances the discoverability and credibility of the package.
1-2: Ignore yamllint warning about '%' character.The yamllint tool reports a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' is part of the Jinja2 templating syntax used in Conda recipes. The current syntax is correct and should not be changed.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
43-50: LGTM! About section updated with comprehensive information.The about section has been updated with more detailed and accurate information, including new URLs and a more specific license identifier.
Please verify that the LICENSE file in the package repository matches the specified GPL-3.0-or-later license:
✅ Verification successful
LGTM! LICENSE file matches the specified GPL-3.0-or-later license.
The LICENSE file begins with the GNU General Public License Version 3, ensuring compliance with the specified license.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check the content of the LICENSE file curl -sL "https://raw.githubusercontent.com/klebgenomics/Kleborate/main/LICENSE" | head -n 5Length of output: 107
Script:
#!/bin/bash # Correctly check the content of the LICENSE file curl -sL "https://raw.githubusercontent.com/klebgenomics/Kleborate/main/LICENSE" | head -n 5Length of output: 318
1-10: LGTM! Package metadata and source updated correctly.The package name, version, source URL, and SHA256 checksum have been updated appropriately. The change from GitHub to PyPI as the source is a good practice for Python packages.
To ensure the integrity of the package, please verify the SHA256 checksum:
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
recipes/kleborate/meta.yaml
Outdated
| requirements: | ||
| host: | ||
| - python >=3.7 | ||
| - biopython >=1.73,<1.78 | ||
| - kaptive | ||
| - blast >=2.2.31 | ||
| - mash | ||
| - pip | ||
| - python >=3.9 | ||
| run: | ||
| - python >=3.7 | ||
| - biopython >=1.73,<1.78 | ||
| - kaptive | ||
| - blast >=2.2.31 | ||
| - python >=3.9 | ||
| - biopython >=1.83 | ||
| - numpy >=1.22 | ||
| - dna_features_viewer | ||
| - minimap2 | ||
| - mash | ||
| - kaptive |
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💡 Codebase verification
Dependencies Updated Without Documentation
The dependency changes in recipes/kleborate/meta.yaml are not documented in the project's changelog or release notes. Please update the documentation to reflect these updates for version 3.1.0.
🔗 Analysis chain
LGTM! Dependencies updated, but please verify documentation.
The requirements have been updated appropriately with new minimum versions and additional dependencies. These changes likely support new features in Kleborate 3.1.0.
Please ensure that these dependency changes are documented in the package's changelog or release notes. You can verify this by checking the project's documentation:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check for changelog or release notes
curl -sL "https://raw.githubusercontent.com/klebgenomics/Kleborate/main/CHANGELOG.md" | grep -i "3.1.0" -A 10
Length of output: 107
Script:
#!/bin/bash
# Check GitHub releases for version 3.1.0
curl -s "https://api.github.com/repos/klebgenomics/Kleborate/releases" | jq -r '.[] | select(.tag_name == "v3.1.0") | .name, .body'
Length of output: 131
Script:
#!/bin/bash
# Search for version 3.1.0 in the entire codebase
rg "3\.1\.0" --context 3
Length of output: 47423
Describe your pull request here
Updated kleborate v3.0.9 to v3.1.0
Updated SHA256
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New Features
numpy,dna_features_viewer, andminimap2.Bug Fixes
Documentation