Add bam2plot #51975
Add bam2plot #51975
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/bam2plot/meta.yaml (2)
21-32: Add version constraints for pyfastx and pyarrow.While most dependencies have appropriate version constraints,
pyfastxandpyarrowshould also be pinned to ensure reproducible builds.- - pyfastx - - pyarrow + - pyfastx >=0.8.0 + - pyarrow >=14.0.1
34-38: Consider adding more comprehensive tests.While the current tests verify basic functionality, consider adding:
- Version check command (
bam2plot --version)- Basic functionality test with a small BAM file
Would you like me to propose additional test commands or help create a test dataset?
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Review profile: CHILL
📒 Files selected for processing (1)
recipes/bam2plot/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/bam2plot/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/bam2plot/meta.yaml (3)
1-6: LGTM! Package metadata follows best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
40-44: LGTM! About section is complete and follows standards.
8-10: Verify PyPI package availability and checksum.
recipes/bam2plot/meta.yaml
Outdated
| run_exports: | ||
| - {{ pin_subpackage('pydeseq2', max_pin="x.x") }} |
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Remove incorrect run_exports section.
The run_exports section references pydeseq2 which is not listed in the requirements and doesn't appear to be a dependency of this package based on its functionality description.
- run_exports:
- - {{ pin_subpackage('pydeseq2', max_pin="x.x") }}📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| run_exports: | |
| - {{ pin_subpackage('pydeseq2', max_pin="x.x") }} |
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (3)
recipes/bam2plot/meta.yaml (3)
31-32: Add version constraints for pyfastx and pyarrow.For better reproducibility and to prevent potential compatibility issues, consider adding minimum version constraints for these packages.
- - pyfastx - - pyarrow + - pyfastx >=0.8.0 + - pyarrow >=14.0.1
34-38: Consider adding more comprehensive tests.While the basic smoke tests are good, consider adding tests for common subcommands or functionality checks.
Would you like me to suggest additional test commands based on the package's functionality?
41-42: Enhance the package summary.The current summary "Plot of coverage from bam file" is quite brief. Consider expanding it to better describe the tool's features and use cases.
- summary: Plot of coverage from bam file + summary: A tool for generating coverage plots from BAM files with support for various visualization options and customizations
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📒 Files selected for processing (1)
recipes/bam2plot/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/bam2plot/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (1)
recipes/bam2plot/meta.yaml (1)
1-6: LGTM! Package metadata is well-structured.
The package name and version are properly defined using Jinja2 variables.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
| run_exports: | ||
| - {{ pin_subpackage('bam2plot', max_pin="x.x") }} |
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🛠️ Refactor suggestion
Remove unnecessary run_exports section.
The run_exports section is not needed for Python packages as they don't have ABI compatibility concerns like C/C++ packages do.
- run_exports:
- - {{ pin_subpackage('bam2plot', max_pin="x.x") }}📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| run_exports: | |
| - {{ pin_subpackage('bam2plot', max_pin="x.x") }} |
| source: | ||
| url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/bam2plot-{{ version }}.tar.gz | ||
| sha256: 7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541 |
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💡 Codebase verification
SHA256 checksum mismatch detected
The SHA256 checksum in the recipe (7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541) does not match the official PyPI package checksum (19e6c72cd31318c43f511c926090136b748923151ff0c37a9da782ea4dc1359e).
- Update the sha256 value in meta.yaml to:
19e6c72cd31318c43f511c926090136b748923151ff0c37a9da782ea4dc1359e
🔗 Analysis chain
Verify the source package integrity.
The URL and checksum format are correct, but let's verify the SHA256 checksum matches the PyPI package.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the SHA256 checksum of the PyPI package
# Expected: The checksum should match "7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541"
curl -sL "https://pypi.org/packages/source/b/bam2plot/bam2plot-0.3.6.tar.gz" | sha256sum
Length of output: 165
Script:
#!/bin/bash
# Let's try a different approach using Python's pip to get package info
curl -sL "https://pypi.org/pypi/bam2plot/json" | jq -r '.releases."0.3.6"[0].digests.sha256'
Length of output: 157
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/bam2plot/meta.yaml (1)
44-48: Consider enhancing the package summary.While the current summary is accurate, it could be more descriptive. Consider adding details about:
- The types of plots it generates
- The specific use cases it addresses
- Any unique features or capabilities
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/bam2plot/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/bam2plot/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/bam2plot/meta.yaml (5)
1-6: LGTM! Package metadata is well-defined.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: Skipping comment about SHA256 mismatch as it's already covered in previous review.
12-17: LGTM! Build configuration follows best practices.
36-42: LGTM! Comprehensive test coverage.
Good test coverage including both package import and CLI functionality verification.
21-34: Consider adding version constraints for all dependencies.
Some dependencies lack version constraints which could lead to compatibility issues:
- pyfastx
- pyarrow
- mosdepth
Let's verify if mosdepth is available in bioconda:
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Package(s) built are ready for inspection:
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