Add mzspeclib #52187
Add mzspeclib #52187
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/mzspeclib/meta.yaml (1)
34-42: Consider adding more comprehensive testsWhile the basic tests are good, consider adding:
- Test with example data files
- Validation of key functionality
- Output format checks
Would you like help adding more comprehensive test cases?
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recipes/mzspeclib/meta.yaml(1 hunks)
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🪛 yamllint
recipes/mzspeclib/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/mzspeclib/meta.yaml (4)
12-20: LGTM! Build configuration follows best practices
The build section correctly:
- Specifies noarch: python for architecture independence
- Includes run_exports for proper version pinning
- Defines the CLI entry point
43-50: Verify package relevance to Bioconda
The package appears to be related to the HUPO-PSI (Proteomics Standards Initiative) spectral library format, which is relevant to bioinformatics. However, let's verify its biological science focus as mentioned in the PR objectives.
✅ Verification successful
Package is highly relevant to Bioconda
The package is definitely appropriate for Bioconda as it implements a standardized format for mass spectrometry spectral libraries, which is a crucial component in proteomics research and bioinformatics:
- It's developed by HUPO-PSI (Proteomics Standards Initiative), a recognized authority in proteomics standards
- Handles spectral libraries used in proteomics data analysis and mass spectrometry
- Integrates with major proteomics resources like PeptideAtlas, PRIDE, GPMDB, and NIST
- Serves bioinformatics tools that perform spectral library searching in proteomics
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#!/bin/bash
# Check package description and documentation
curl -s https://raw.githubusercontent.com/HUPO-PSI/mzSpecLib/master/README.md
Length of output: 4328
9-10: Verify PyPI package checksum
28-32: Consider adding version constraints for dependencies
While some dependencies have version constraints (psims, pyteomics), others (sqlalchemy, click, mzpaf) don't. This could lead to compatibility issues.
Consider adding version constraints based on the minimum tested versions.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/mzspeclib/meta.yaml (1)
34-41: Consider adding more comprehensive tests.While the current tests verify basic functionality, consider adding:
- Tests for key package functionalities
- Version check command
- Basic data processing test if applicable
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📒 Files selected for processing (1)
recipes/mzspeclib/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/mzspeclib/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/mzspeclib/meta.yaml (6)
1-7: LGTM!
The package metadata section follows conda packaging best practices using Jinja2 variables.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: Verify the SHA256 checksum against the PyPI package.
Please ensure that the SHA256 checksum matches the one from the official PyPI package.
12-20: LGTM!
The build configuration is well-structured:
- Correctly specifies the CLI entry point
- Uses noarch: python for architecture independence
- Properly implements run_exports for dependency pinning
21-32: Consider adding version constraints for dependencies.
While most dependencies have version constraints, mzpaf, sqlalchemy, and click don't have any version bounds specified. Consider adding upper bounds to prevent potential compatibility issues with future versions.
43-50: LGTM!
The about section provides comprehensive package information with appropriate license and documentation links.
52-54: LGTM!
The maintainer section is properly configured.
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@bioconda-bot please add label |
This PR adds mzSpecLib.
This PR depends on #52166
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