Adding msa4u #51864
Adding msa4u #51864
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@BiocondaBot please update |
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I encountered an error updating your PR branch. You can report this to bioconda/core if you'd like. |
Clean up dependencies
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/msa4u/meta.yaml (1)
29-33: Consider adding more comprehensive tests.While the current tests check basic functionality, consider adding more test commands to verify key features.
Consider adding these additional tests:
commands: - msa4u --help + - msa4u --version + - python -c "import msa4u; assert msa4u.__version__ == '0.4.0'"
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/msa4u/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/msa4u/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/msa4u/meta.yaml (4)
1-6: LGTM! Package metadata follows conda-forge standards.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-39: Overall recipe structure is good with minor improvements needed.
The recipe follows conda-forge standards and is appropriate for Bioconda as it's a bioinformatics tool. The suggested improvements (dependency constraints, additional tests, license consideration) will enhance reliability and maintainability, but the current implementation is functional.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-17: Consider adjusting the run_exports pin.
The current pin x.x might be too strict for a pure Python package. Unless this package has C extensions or strict version requirements, consider using x.x.x instead.
Consider updating the pin:
- - {{ pin_subpackage("msa4u", max_pin="x.x") }}
+ - {{ pin_subpackage("msa4u", max_pin="x.x.x") }}8-10: Verify package availability and checksum.
The source configuration looks correct, but let's verify the package existence and integrity.
recipes/msa4u/meta.yaml
Outdated
| about: | ||
| home: https://art-egorov.github.io/msa4u/ | ||
| summary: "A simple visualisation tool for Multiple Sequence Alignment." | ||
| license: WTFPL | ||
| license_file: LICENSE |
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💡 Codebase verification
Consider using a more appropriate license for scientific software
The verification confirms that the package indeed uses the WTFPL license. For scientific software that may be used in academic or research contexts, this license choice raises concerns:
- Lacks explicit terms for attribution and citation requirements
- No clear statements about warranties and liability
- May not meet institutional requirements for software usage
- Could potentially limit adoption in professional/academic environments
Recommended alternatives:
- MIT License: Simple, permissive, with clear liability disclaimers
- BSD License: Well-recognized in academic communities
- Apache 2.0: Comprehensive coverage of patents and contributions
🔗 Analysis chain
Review license choice for scientific software.
The WTFPL license might not be the most appropriate choice for scientific software as it lacks explicit terms for attribution, warranties, and liability. Consider suggesting a more standard license like MIT, BSD, or Apache 2.0.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check upstream license
# Expected: Should show actual license content from the source
# Test: Look for LICENSE file content in the package
curl -sL "https://raw.githubusercontent.com/art-egorov/msa4u/main/LICENSE"
Length of output: 557
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@BiocondaBot please add label |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/msa4u/meta.yaml (2)
12-17: Consider relaxing version pinning and enabling build isolation.
- The
x.xpin inrun_exportsmight be too restrictive for a visualization tool. Consider usingxinstead unless there are known API breaking changes between minor versions.- Building without isolation (
--no-build-isolation) could lead to reproducibility issues.build: run_exports: - - {{ pin_subpackage("msa4u", max_pin="x.x") }} + - {{ pin_subpackage("msa4u", max_pin="x") }} - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vv --no-deps
1-40: Overall assessment: Recipe structure is good with minor improvements needed.The recipe is well-structured and appropriate for Bioconda. Key points to address:
- Verify the 'configs' package requirement
- Consider enabling build isolation
- Consider relaxing version pinning in run_exports
The package fits Bioconda's scope as it's a biological sequence alignment visualization tool.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/msa4u/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/msa4u/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/msa4u/meta.yaml (4)
1-6: LGTM! Package metadata is well-structured.
The package name and version are correctly templated using Jinja2, following conda-forge best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
30-34: LGTM! Test section includes both import and CLI verification.
The tests appropriately verify both the Python package installation and CLI functionality.
28-28: Verify the 'configs' package requirement.
The 'configs' package is not a common Python package name. Please verify:
- Is this the correct package name?
- Is it available on conda-forge or bioconda?
#!/bin/bash
# Description: Check if configs package exists in conda channels
# Expected: Should find the package in conda-forge or bioconda
# Test: Search for configs package in conda channels
conda search configs -c conda-forge -c bioconda --info8-10: Verify package source availability and integrity.
The source URL and checksum need verification to ensure the package can be downloaded successfully.
✅ Verification successful
Package source and checksum verified successfully
The PyPI package source is available and the SHA256 checksum matches exactly with the one specified in the recipe. The package can be downloaded from PyPI and its integrity is verified.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify package source availability and checksum
# Expected: Should be able to download the package and verify its checksum
# Test: Download the package and verify checksum
curl -sL "https://pypi.org/packages/source/m/msa4u/msa4u-0.4.0.tar.gz" | sha256sum
Length of output: 223
Script:
#!/bin/bash
# Let's verify the package source using a different approach
# First, let's check if the package exists on PyPI
curl -sI "https://pypi.org/pypi/msa4u/0.4.0/json" | head -n 1
# Then let's get the actual download URL and checksum from PyPI
curl -s "https://pypi.org/pypi/msa4u/0.4.0/json" | jq -r '.urls[] | select(.packagetype=="sdist") | "\(.url)\n\(.digests.sha256)"'
Length of output: 396
recipes/msa4u/meta.yaml
Outdated
| about: | ||
| home: https://art-egorov.github.io/msa4u/ |
There was a problem hiding this comment.
💡 Codebase verification
Homepage URL is not accessible
The specified homepage URL (https://art-egorov.github.io/msa4u/) returns a 404 error, indicating that the documentation site is not available. Please:
- Update the homepage URL in
recipes/msa4u/meta.yamlto point to a valid, accessible documentation site - Consider using the GitHub repository URL as a fallback if a dedicated documentation site is not yet published
🔗 Analysis chain
Verify homepage accessibility.
Let's ensure the documentation homepage is accessible and contains relevant information.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if the homepage is accessible
# Expected: Should return a successful status code
# Test: Check homepage availability
curl -sL -w "%{http_code}" "https://art-egorov.github.io/msa4u/" -o /dev/null
Length of output: 81
Describe your pull request here
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
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If not already present in the meta.yaml, make sure to specify
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