Pegas #49759
Pegas #49759
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Actionable comments posted: 4
🧹 Outside diff range and nitpick comments (2)
recipes/pegas/meta.yaml (2)
39-48: LGTM: Comprehensive metadata provided.The about section is well-structured and provides all necessary information. The use of GPL-2.0 license is appropriate for an open-source project.
Consider expanding the description slightly to provide more context about the specific use cases or advantages of PeGAS. For example:
description: | PeGAS is a Snakemake pipeline for protein engineering and analysis. It automates the process of protein design and analysis using various bioinformatics tools. PeGAS streamlines workflows for tasks such as [specific examples of tasks], making it easier for researchers to [specific benefits or outcomes].This expanded description would give potential users a clearer idea of how PeGAS could benefit their work.
50-52: LGTM: Maintainer information provided.The extra section correctly lists the recipe maintainer. This is important for package management and communication.
Consider adding more maintainers if there are other contributors who are actively involved in maintaining this package. This can help ensure continued support and maintenance of the package. If appropriate, you could update the section like this:
extra: recipe-maintainers: - liviurotiul - other_contributorThis is optional and depends on your project's structure and contributors.
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📒 Files selected for processing (1)
- recipes/pegas/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/pegas/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/pegas/meta.yaml (2)
1-6: LGTM: Package name and version are well-defined.The use of Jinja2 variables for the package name and version is a good practice. The version number follows semantic versioning, which is recommended for package management.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-2: Note: Ignore the yamllint error for Jinja2 syntax.The static analysis tool yamllint reported a syntax error for the '%' character at the beginning of the file. This is a false positive. The '%' is part of the Jinja2 template syntax, which is valid and commonly used in Conda recipe files. You can safely ignore this warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
recipes/pegas/meta.yaml
Outdated
| source: | ||
| git_url: https://github.com/liviurotiul/PeGAS.git | ||
| git_branch: main |
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🛠️ Refactor suggestion
Consider using a specific tag or commit hash for the source.
While using the main branch works, it's generally recommended to pin the source to a specific tag or commit hash for better reproducibility. This ensures that the package is built from a known, stable version of the source code.
Consider updating the source section as follows:
source:
git_url: https://github.com/liviurotiul/PeGAS.git
git_rev: v{{ version }} # Assuming tags are in the format v0.2.13This change assumes that the repository uses tags for releases. If not, you could use a specific commit hash instead.
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Actionable comments posted: 3
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📒 Files selected for processing (1)
- recipes/pegas/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/pegas/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/pegas/meta.yaml (4)
1-10: LGTM! Package and source sections are well-defined.The package name and version are correctly defined using Jinja2 variables, and the source URL properly incorporates the version tag. The inclusion of a SHA256 checksum ensures integrity verification.
Note: The yamllint error
syntax error: found character '%' that cannot start any tokencan be safely ignored as it's a false positive due to the use of Jinja2 templating, which is standard in Conda recipes.🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
39-49: LGTM! Comprehensive metadata provided.The about section is well-structured and provides all necessary information, including:
- Home URL
- License details (GPL-2.0)
- Summary and description of the package
- Documentation and issue tracking links
This level of detail is excellent for users and maintainers alike.
51-53: LGTM! Maintainer information correctly provided.The extra section properly lists the recipe maintainer, which is essential for package management and communication within the Bioconda community.
1-53: Thank you for your contribution to Bioconda!Your
meta.yamlrecipe for thepegaspackage is well-structured and provides a good foundation. Here's a summary of the suggested improvements:
- Remove the unnecessary
run_exportssection in the build configuration.- Consider relaxing version constraints in the run requirements for better compatibility.
- Enhance the test section with more comprehensive tests to validate package functionality.
These adjustments will help improve the recipe's flexibility and reliability. Great job on your first open-source contribution! If you have any questions about the suggested changes, please don't hesitate to ask.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
| test: | ||
| commands: | ||
| - {{ name }} --help |
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🛠️ Refactor suggestion
Enhance test coverage for better package validation.
While running the help command is a good basic test to ensure the package is installed correctly, it doesn't verify the package's functionality.
Consider adding more comprehensive tests, such as:
- Running a simple analysis with sample data.
- Importing and testing key functions or classes.
- Verifying the presence of important files or directories.
For example:
test:
commands:
- {{ name }} --help
- {{ name }} --version
- python -c "from pegas import some_key_function; assert some_key_function() == expected_output"
files:
- path/to/test/data/sample.fastqThese additional tests would provide more confidence in the package's functionality after installation. Please adjust the suggested tests according to your package's specific features and requirements.
recipes/pegas/meta.yaml
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| build: | ||
| number: 0 | ||
| noarch: python | ||
| script: "{{ PYTHON }} -m pip install ." | ||
| run_exports: | ||
| - {{ pin_subpackage(name, max_pin="x") }} |
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🛠️ Refactor suggestion
Remove unnecessary run_exports section.
The build configuration looks good overall, but as mentioned in a previous comment, the run_exports section is typically not necessary for pure Python packages. This section is more commonly used for compiled libraries to ensure ABI compatibility.
Consider removing the run_exports section:
build:
number: 0
noarch: python
script: "{{ PYTHON }} -m pip install ."
- run_exports:
- - {{ pin_subpackage(name, max_pin="x") }}This simplification aligns better with typical Python package recipes in Conda-Forge and Bioconda.
📝 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.
| build: | |
| number: 0 | |
| noarch: python | |
| script: "{{ PYTHON }} -m pip install ." | |
| run_exports: | |
| - {{ pin_subpackage(name, max_pin="x") }} | |
| build: | |
| number: 0 | |
| noarch: python | |
| script: "{{ PYTHON }} -m pip install ." |
|
@antunderwood @pontus @brentp @ryanraaum |
recipes/pegas/meta.yaml
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| about: | ||
| home: https://github.com/liviurotiul/PeGAS | ||
| license: GPL-2.0 |
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Please use id from https://spdx.org/licenses/
You just need to mark your PRs with |
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@BiocondaBot please add label |
PR for an NGS bacteria analysis pipeline called "pegas".
This is my first attempt at an open source contribution so please be patient. :)