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add Rust package guidelines #33

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@mbhall88 mbhall88 commented Sep 30, 2024

Relates to and addresses bioconda/bioconda-recipes#50800

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coderabbitai bot commented Sep 30, 2024

Walkthrough

The pull request introduces significant updates to the guidelines for creating and maintaining bioconda recipes. A new section on Rust packaging has been added, detailing the use of the Rust compiler, best practices for including licenses, and ensuring reproducibility in builds with specific Cargo flags. The C/C++ packaging section has been expanded to clarify the specification of build tools and compilers, including the use of compiler macros and examples for structuring the meta.yaml file. Additionally, the guidelines for testing dependencies have been refined to address tests that rely on runtime dependencies, recommending a separate run_test.sh file. The Java packaging section now includes instructions for adding wrapper scripts and using the openjdk package from conda-forge, moving away from the deprecated java-jdk package. The guidelines for R packages have been clarified to distinguish between CRAN and Bioconductor packages, with detailed instructions for using the conda skeleton cran method. Overall, the document has been enriched with new content and clarifications, enhancing its comprehensiveness for bioconda contributors.

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Files Change Summary
_sources/contributor/guidelines.rst.txt Added a new section on Rust packaging, including compiler usage and Cargo flags. Expanded C/C++ packaging section to clarify compiler macros and dependencies. Overall document structure refined for clarity.

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
_sources/contributor/guidelines.rst.txt (1)

486-559: Excellent addition of Rust packaging guidelines!

The new Rust section is a valuable addition to the guidelines. It provides comprehensive information on compiler specification, license handling, and recommended Cargo flags for reproducible builds. The typical Rust recipe example is particularly helpful.

One suggestion for improvement:

Consider adding a brief explanation of why the run_exports section is included in the example recipe. This would help contributors understand when and why they should use this feature in their Rust recipes.

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_sources/contributor/guidelines.rst.txt (3)

Line range hint 410-485: Improved C/C++ packaging guidelines: Great addition!

The expanded C/C++ section provides clearer guidance on specifying build tools and compilers in recipes. The explanation of the {{ compiler('c') }} and {{ compiler('cxx') }} macros, along with the distinction between build and host dependencies, will help contributors create more accurate and portable recipes.


Line range hint 735-753: Improved guidance on package testing: Approved!

The updates to the "Tests" section provide clearer guidelines on what constitutes an adequate test for a recipe. The emphasis on avoiding the inclusion of test data in the repository is particularly important for maintaining a lean codebase.


Line range hint 1-863: Well-structured and consistent document: Approved!

The updated guidelines maintain a consistent style and structure throughout. The new sections on Rust packaging and the expanded C/C++ section integrate seamlessly with the existing content, enhancing the overall value of the document for contributors.

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mbhall88 commented Oct 8, 2024

Don't mean to be impatient sorry, but would it be possible to get a review of this addition to the docs @bioconda/core? This is related to bioconda/bioconda-recipes#50800

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I made minor comments to make language consistent across flags; otherwise structurally this looks great. I don't know anything about rust though, so will probably need @johanneskoester to review for content.

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
_sources/contributor/guidelines.rst.txt (1)

486-559: Great addition of Rust packaging guidelines!

The new Rust section is comprehensive and well-structured, covering:

  • Compiler specification using {{ compiler('rust') }}
  • License handling with cargo-bundle-licenses
  • Recommended Cargo flags for reproducible builds
  • A detailed template for a typical Rust recipe

This addition will significantly improve the quality and consistency of Rust packages in bioconda.

One suggestion for improvement:

Consider adding a brief explanation of the run_exports section in the template, as it might not be familiar to all contributors.

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  • _sources/contributor/guidelines.rst.txt (2 hunks)
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🔇 Additional comments (2)
_sources/contributor/guidelines.rst.txt (2)

Line range hint 410-485: Excellent addition of C/C++ packaging guidelines!

The new C/C++ section provides crucial information for package maintainers, including:

  • Proper specification of build tools and compilers
  • Use of compiler macros (e.g., {{ compiler('c') }}, {{ compiler('cxx') }})
  • Distinction between build and host dependencies

This addition will greatly improve the consistency and correctness of C/C++ packages in bioconda.


Line range hint 1-559: Overall excellent updates to the guidelines document!

The changes made to this document significantly improve its comprehensiveness and usefulness for bioconda contributors. The additions of detailed C/C++ and Rust packaging guidelines are particularly valuable. The existing sections have been refined without introducing any inconsistencies.

These updates will greatly assist package maintainers in creating high-quality, consistent recipes across various programming languages and build systems.

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Ping @bioconda/rust

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@martin-g martin-g left a comment

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LGTM!

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