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parsnp: add aarch64/arm64 builds #51064

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@martin-g martin-g commented Oct 1, 2024

Describe your pull request here


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Summary by CodeRabbit

  • New Features

    • Enhanced build script for improved functionality and robustness.
    • Added support for additional platforms: linux-aarch64 and osx-arm64.
  • Bug Fixes

    • Updated build process to ensure necessary directories are created and cleaned up after installation.
  • Documentation

    • Version updated in the meta.yaml file to reflect changes.
    • Updated dependency for Linux from openmp to libgomp.

@martin-g martin-g added aarch64 Related to adding linux-aarch64 support osx-arm64 Related to adding osx-arm64 support labels Oct 1, 2024
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📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request introduces modifications to the build.sh script and the meta.yaml file for the parsnp package. The build.sh script enhancements include improved error handling, directory structure management, and consistent compilation flags across platforms. The meta.yaml file reflects a version number increment and the addition of new platforms in the extra section, while maintaining existing requirements and documentation links.

Changes

File Change Summary
recipes/parsnp/build.sh Added set -xe for debugging; created $PREFIX/bin directory structure; updated CXXFLAGS for muscle; used ${CPU_COUNT} for parallel builds; cleaned up post-installation files; copied necessary application files to $PREFIX/bin.
recipes/parsnp/meta.yaml Updated build number from 0 to 1; adjusted source URL; changed Linux dependency from openmp to libgomp; added platforms linux-aarch64 and osx-arm64 in the extra section.

Possibly related PRs

  • pgrc: add linux-aarch64 build #51009: The changes in the main PR regarding the build.sh script and the use of ${CPU_COUNT} for parallel builds are relevant to the modifications made in the build.sh of the pgrc package, which also involves setting up a build environment and optimizing the build process.
  • recipe for pgrc #50973: The build.sh script for pgrc introduces a similar structure for creating a binary directory under $PREFIX/bin, which aligns with the changes made in the main PR to ensure proper directory creation for the parsnp application.

Suggested reviewers

  • apeltzer

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📥 Commits

Files that changed from the base of the PR and between 8cbcafe and b7c9d65.

📒 Files selected for processing (2)
  • recipes/parsnp/build.sh (3 hunks)
  • recipes/parsnp/meta.yaml (3 hunks)
🚧 Files skipped from review as they are similar to previous changes (2)
  • recipes/parsnp/build.sh
  • recipes/parsnp/meta.yaml

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (2)
recipes/parsnp/build.sh (2)

18-18: Improved build efficiency with parallel compilation.

Using ${CPU_COUNT} for parallel builds is an excellent optimization. This change can significantly speed up the compilation process on multi-core systems.

Consider adding a fallback in case ${CPU_COUNT} is not set:

-make -j ${CPU_COUNT}
+make -j ${CPU_COUNT:-1}

This ensures the build works even if ${CPU_COUNT} is not defined, defaulting to a single core.


29-29: Consistent parallel build optimization for main application.

Excellent addition of parallel compilation for the main application build, consistent with the muscle library build optimization.

As suggested earlier, consider adding a fallback for ${CPU_COUNT}:

-make -j ${CPU_COUNT} LDADD="$LDADD -lMUSCLE-3.7"
+make -j ${CPU_COUNT:-1} LDADD="$LDADD -lMUSCLE-3.7"

This ensures the build works even if ${CPU_COUNT} is not defined, defaulting to a single core.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 8fc154f and 8cbcafe.

📒 Files selected for processing (2)
  • recipes/parsnp/build.sh (3 hunks)
  • recipes/parsnp/meta.yaml (2 hunks)
🔇 Additional comments (6)
recipes/parsnp/build.sh (3)

3-4: Improved script robustness and debugging.

The addition of set -xe is a good practice. It enables command echoing (-x) for easier debugging and ensures the script exits immediately if any command fails (-e), preventing cascading errors.


Line range hint 35-43: Comprehensive file installation.

Good job ensuring all necessary files are copied to the installation directory. This includes the main executable, Python scripts, and additional resources.

The creation of a $PREFIX/bin/bin directory is unusual. Please verify if this structure is intentional and required for the package to function correctly. Run the following script to check the final directory structure:

Review the output to ensure the directory structure is correct and all files are in their intended locations.


Line range hint 31-33: Cleanup of build artifacts.

Good practice to remove unnecessary directories after installation, helping to keep the package size minimal.

Please verify that removing these directories doesn't impact the package functionality. Run the following script to check for any remaining references to these directories:

If the script returns any results, we may need to adjust the cleanup or update other parts of the package.

✅ Verification successful

Cleanup Verification Successful

The removal of the directories muscle/libMUSCLE, muscle/autom4te.cache, and muscle/m4 does not impact the package functionality.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for any remaining references to removed directories

# Test: Search for references to removed directories
rg -i 'muscle/libMUSCLE|muscle/autom4te.cache|muscle/m4' --type sh --type yaml

Length of output: 219

recipes/parsnp/meta.yaml (3)

12-12: LGTM: Build number increment is correct.

Incrementing the build number from 0 to 1 is appropriate when making changes to the package without altering the version. This change aligns with the PR objective of adding new architecture builds.


Line range hint 1-48: Verify architecture-specific requirements for new platforms.

The package version, source URL, and general requirements appear correct. However, given the addition of 'linux-aarch64' and 'osx-arm64' platforms, it's important to verify if any architecture-specific requirements or build flags are needed.

Could you confirm if any additional requirements or build flags are necessary for the 'linux-aarch64' and 'osx-arm64' architectures? This might include architecture-specific compiler flags or dependencies.

To assist in this verification, let's check for any existing architecture-specific patterns in the recipe:

#!/bin/bash
# Description: Check for architecture-specific patterns in the recipe

# Test: Search for architecture-specific selectors or flags
rg --type yaml '\[aarch64\]|\[arm64\]|\[osx-arm64\]' recipes/parsnp/meta.yaml

50-53: Clarification needed on 'additional-platforms' usage.

The addition of 'linux-aarch64' and 'osx-arm64' platforms aligns with the PR objective. However, 'additional-platforms' is not a standard Conda recipe field.

Could you clarify the purpose and effect of using 'additional-platforms' in the 'extra' section? Is this a Bioconda-specific feature?

To verify if this is a common practice in Bioconda recipes, let's run the following script:

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
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