Update pggb to 0.7.0 #51436
Update pggb to 0.7.0 #51436
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces updates to the Possibly related PRs
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/pggb/meta.yaml (1 hunks)
🧰 Additional context used
🔇 Additional comments (4)
recipes/pggb/meta.yaml (4)
2-2: Version update looks good.The version has been correctly updated to 0.7.0, which aligns with the PR objective.
1-1: Unchanged sections appear correct.The following sections remain unchanged and appear to be correct for this version update:
- Package name and URL structure
- Build configuration (except for the changes we noted earlier)
- Test command
- About section (license, summary, etc.)
- Extra section (recipe maintainers)
These sections don't require modifications for the version update to 0.7.0.
Also applies to: 3-9, 11-12, 14-16, 18-20, 31-52
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-13: Build configuration changes.
A new line has been added to skip the build on macOS. This is a significant change that will affect users on that platform. Please confirm if this is intentional and if there's a specific reason for excluding macOS.
The build number has been reset to 0, which is the correct practice when updating to a new version.
To verify the impact of skipping macOS builds, you can run the following script:
#!/bin/bash # Description: Check for any macOS-specific code or dependencies # Search for macOS-specific conditionals or comments echo "Searching for macOS-specific code or comments:" rg --type yaml '(?i)macos|darwin|osx' # Check if any dependencies are macOS-specific echo "Checking for macOS-specific dependencies:" rg --type yaml 'osx'Also applies to: 17-17
10-10: SHA256 checksum updated.The SHA256 checksum has been updated, which is consistent with the version change. However, it's crucial to verify that this checksum is correct for the new version's tarball.
To verify the SHA256 checksum, you can run the following script:
| - wfmash ==0.14.0 | ||
| - seqwish ==0.7.11 | ||
| - smoothxg ==0.8.0 | ||
| - odgi ==0.9.0 | ||
| - gfaffix ==0.1.5b | ||
| - vg ==1.59.0 | ||
| - vcfbub ==0.1.1 | ||
| - vcflib ==1.0.10 | ||
| - multiqc ==1.22 | ||
| - python-igraph ==0.11.5 |
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💡 Codebase verification
Missing meta.yaml File in Tag v0.7.0.
The meta.yaml file was not found in the pggb repository at tag v0.7.0. This may indicate that the file has been moved, renamed, or removed in this version.
Please verify the location of the dependencies file or update the review comment to reflect the current structure of the repository.
🔗 Analysis chain
Significant changes in dependencies.
The requirements section has undergone substantial changes:
- New dependencies added: wfmash, seqwish, smoothxg, odgi, gfaffix, vg, vcfbub, vcflib, multiqc, and python-igraph.
- Some existing dependencies have been updated or removed.
These changes are likely necessary for the new version of pggb. However, please ensure that:
- All these dependencies are indeed required for version 0.7.0.
- The specified versions are compatible with each other and with pggb 0.7.0.
- There are no missing dependencies that pggb 0.7.0 might need.
To verify the dependencies, you can run the following script:
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Actionable comments posted: 2
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/pggb/meta.yaml (2 hunks)
🧰 Additional context used
🔇 Additional comments (5)
recipes/pggb/meta.yaml (5)
2-2: LGTM: Version update to 0.7.0The version update from 0.6.0 to 0.7.0 is consistent with the PR objective.
13-14: Build section changesThe build number reset to 0 is correct for the new version. However, please clarify the reason for skipping the build on macOS. Is there a known compatibility issue?
Line range hint
1-51: Overall review summaryThe update to pggb version 0.7.0 includes several significant changes:
- Version update from 0.6.0 to 0.7.0
- Updated SHA256 checksum
- Reset build number and added macOS skip condition
- Significant changes in dependencies
- Modified package summary
- Added skip-lints for
should_be_noarch_genericPlease address the following concerns:
- Verify the SHA256 checksum
- Clarify the reason for skipping macOS builds
- Confirm all dependency changes are necessary and compatible
- Revise the incomplete package summary
- Resolve the conflict between architecture-dependent and architecture-independent implications
Once these issues are addressed, the update should be ready for merging.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
10-10: Verify SHA256 checksumPlease ensure that the updated SHA256 checksum matches the source tarball for version 0.7.0.
To verify the SHA256 checksum, you can run the following command:
curl -sL https://github.com/pangenome/pggb/archive/refs/tags/v0.7.0.tar.gz | shasum -a 256Compare the output with the checksum in the recipe.
20-29: Verify changes in dependenciesSignificant changes have been made to the dependencies:
- New dependencies added: wfmash, seqwish, smoothxg, odgi, gfaffix, vg, vcfbub, vcflib, multiqc, and python-igraph.
- Some existing dependencies have been updated or removed.
Please confirm that:
- All these dependencies are required for version 0.7.0.
- The specified versions are compatible with each other and with pggb 0.7.0.
- There are no missing dependencies that pggb 0.7.0 might need.
To verify the dependencies, you can run the following script:
| @@ -40,8 +42,10 @@ about: | |||
| home: https://github.com/pangenome/pggb | |||
| license: MIT | |||
| license_file: LICENSE | |||
| summary: This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). | |||
| summary: PanGenome Graph Building pipeline renders | |||
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Incomplete package summary
The updated summary appears to be truncated and doesn't provide a clear description of the package's functionality. Please revise the summary to accurately and completely describe the purpose of the pggb package.
Consider reverting to the previous summary or providing a more comprehensive description:
summary: This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model).| skip-lints: | ||
| - should_be_noarch_generic |
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Clarify architecture requirements
The addition of should_be_noarch_generic to skip-lints suggests that the package should be architecture-independent. However, this conflicts with the earlier addition of skip: true # [osx], which implies the package is not compatible with macOS.
Please clarify:
- Is the package truly architecture-dependent? If so, remove the
should_be_noarch_genericskip-lint. - If the package is architecture-independent, remove the
skip: true # [osx]condition and keep the skip-lint.
Update
pggb: 0.6.0 → 0.7.0recipes/pggb(click to view/edit other files)@pangenomeThis pull request was automatically generated (see docs).