Update bakta to 1.10.0 #52112
Update bakta to 1.10.0 #52112
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📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe pull request involves an update to the Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/bakta/meta.yaml (2)
52-55: Consider enhancing test coverageWhile the import tests have been updated to include new dependencies, consider adding functional tests for the new
bakta_ioentry point and features provided by the new dependencies.Add a test command for the new entry point:
commands: - bakta --help + - bakta_io --help
1-44: Overall assessment of the version updateThe update from 1.9.4 to 1.10.0 includes:
- Appropriate version bumps for the package and dependencies
- New functionality (bakta_io)
- Extended Python version support
The changes appear well-structured and follow Bioconda's practices. However, please ensure:
- All dependency version updates are available in Bioconda
- The new Python version requirements don't break existing functionality
- The new entry point is properly tested
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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recipes/bakta/meta.yaml(1 hunks)
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🪛 yamllint
recipes/bakta/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/bakta/meta.yaml (4)
26-26: Review Python version requirement change
The Python version requirement has been increased from >=3.8, <3.11 to >=3.9, <3.12. This change:
- Drops support for Python 3.8
- Adds support for Python 3.11 and 3.12
#!/bin/bash
# Description: Check for potential compatibility issues with Python version change
# Search for Python version specific code or imports
rg -l 'python_version|sys.version_info|@python2|@python3' Also applies to: 29-29
20-20: Verify the new bakta_io entry point
A new entry point bakta_io has been added. Let's verify that the corresponding module and function exist.
#!/bin/bash
# Description: Verify the existence of the json_io module and main function
# Search for the json_io.py file and its main function
ast-grep --pattern 'def main():' | rg 'json_io.py'35-35: Verify compatibility of updated dependencies
Several dependencies have significant version updates:
- pyrodigal: >=3.1.0 → >=3.5.0
- pyhmmer: >=0.10.4 → >=0.10.15
- diamond: ==2.1.8 → >=2.1.10
- ncbi-amrfinderplus: >=3.11.26 → >=4.0.3
- New: pycirclize >=1.7.0
These changes warrant careful review of compatibility and potential breaking changes.
#!/bin/bash
# Description: Check for potential breaking changes in dependencies
# Check if these versions exist in bioconda
curl -s "https://conda.anaconda.org/bioconda/noarch/repodata.json" | jq -r '.packages | to_entries[] | select(.value.name == "pyrodigal" or .value.name == "pyhmmer" or .value.name == "diamond" or .value.name == "ncbi-amrfinderplus" or .value.name == "pycirclize") | "\(.value.name) \(.value.version)"'Also applies to: 40-40, 41-41, 43-43, 44-44
1-9: Verify SHA256 checksum of the source archive
Let's ensure the SHA256 checksum matches the source archive from GitHub.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
Update
bakta: 1.9.4 → 1.10.0recipes/bakta(click to view/edit other files)This pull request was automatically generated (see docs).