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infernal: add osx-arm64 build #50997

Merged
merged 4 commits into from
Sep 27, 2024
Merged

infernal: add osx-arm64 build #50997

merged 4 commits into from
Sep 27, 2024

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mencian
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@mencian mencian commented Sep 26, 2024

Describe your pull request here


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Summary by CodeRabbit

  • New Features

    • Expanded runtime requirements to include libgomp for Linux and llvm-openmp for macOS.
    • Added support for the osx-arm64 platform.
  • Bug Fixes

    • Incremented build number from 2 to 3 for improved versioning.
  • Documentation

    • Improved formatting in the about section for consistency, including URLs and descriptions.
    • Updated description to clarify the functionality of Infernal.

@mencian mencian added the osx-arm64 Related to adding osx-arm64 support label Sep 26, 2024
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coderabbitai bot commented Sep 26, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request introduces updates to the infernal recipe, including modifications to the build script and the metadata file. Key changes involve the addition of environment variables in the build script to enhance the configuration process and the increment of the build number in the metadata. Runtime dependencies have been expanded to include libgomp and llvm-openmp, and formatting improvements have been made in the about section. Additionally, support for a new platform, osx-arm64, has been added.

Changes

Files Change Summary
recipes/infernal/build.sh - Added environment variables: M4, INCLUDE_PATH, LDFLAGS.
- Updated autoreconf command options.
- Modified ./configure command with CC and CFLAGS settings.
recipes/infernal/meta.yaml - Incremented build number from 2 to 3.
- Added runtime dependencies: libgomp for Linux, llvm-openmp for macOS.
- Reformatted about section with quotes for URLs and descriptions.
- Added osx-arm64 to extra.additional-platforms.

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between e10cfed and eada544.

📒 Files selected for processing (1)
  • recipes/infernal/meta.yaml (3 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
  • recipes/infernal/meta.yaml

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Actionable comments posted: 0

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

5-7: LGTM! Consider using $CC instead of hardcoding gcc.

The addition of these environment variables improves the build process by ensuring the correct tools and paths are used. This is particularly important for cross-compilation and consistent builds across different environments.

Consider using $CC instead of hardcoding gcc in the LDFLAGS export:

-export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -fuse-ld=`$CC -print-prog-name=ld`"

This change ensures that the correct linker is used, which is especially important for cross-compilation scenarios.


26-26: LGTM! Consider separating CFLAGS and LDFLAGS.

The changes to the configure command are good improvements. Explicitly setting CC and CFLAGS ensures consistent compilation across different environments.

Consider separating CFLAGS and LDFLAGS for better clarity:

-./configure --prefix="${PREFIX}" CC="${CC}" CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib" "${ARCH_OPTS}"
+./configure --prefix="${PREFIX}" CC="${CC}" CFLAGS="${CFLAGS} -O3" LDFLAGS="${LDFLAGS}" "${ARCH_OPTS}"

This separation makes it clearer which flags are for compilation and which are for linking.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between ef1cf96 and 7f7dca8.

📒 Files selected for processing (2)
  • recipes/infernal/build.sh (2 hunks)
  • recipes/infernal/meta.yaml (3 hunks)
🔇 Additional comments (7)
recipes/infernal/build.sh (2)

11-11: LGTM! Good improvement to the autoreconf command.

The change from autoreconf -i to autoreconf -if is a good improvement. The -f flag forces the update of auxiliary files, which can help prevent build issues caused by outdated files.


Line range hint 1-28: Overall, these changes improve the build process and cross-compilation support.

The modifications to this build script enhance its flexibility and robustness, particularly for cross-compilation scenarios. The addition of new environment variables, the update to the autoreconf command, and the changes to the configure command all contribute to a more consistent and reliable build process across different architectures, including the new osx-arm64 target.

These changes align well with the PR objectives and follow conda build best practices. The minor suggestions provided in the previous comments can further refine the script, but the current version is already a significant improvement.

recipes/infernal/meta.yaml (5)

13-13: LGTM: Build number increment is appropriate.

The build number has been correctly incremented from 2 to 3. This is the expected practice when modifying a package without changing its version, ensuring that the new build can be distinguished from the previous one.


47-54: LGTM: Improved formatting in the 'about' section.

The formatting changes in the 'about' section, including enclosing URLs and descriptions in quotes, enhance consistency and readability. These modifications align with best practices for YAML formatting.


Line range hint 1-62: Summary of changes and recommendations

The changes to the meta.yaml file for the Infernal package are generally well-implemented and align with the PR objectives. Key points:

  1. The build number increment is appropriate.
  2. The addition of OpenMP dependencies suggests potential performance improvements.
  3. Formatting changes in the 'about' section enhance readability.
  4. Support for the osx-arm64 platform has been added.

To ensure these changes are fully supported and don't introduce any issues, please:

  1. Verify the usage and impact of the new OpenMP dependencies.
  2. Confirm that necessary build configurations and considerations for the osx-arm64 platform are in place.

Once these verifications are complete and any necessary adjustments are made, this PR should be ready for merging.


29-31: Verify the impact of new OpenMP dependencies.

The addition of libgomp for Linux and llvm-openmp for macOS as runtime dependencies is appropriate. This suggests that the package now utilizes OpenMP for parallel processing, which could potentially improve performance.

To ensure these changes don't introduce any issues, please run the following verification script:

This script will help verify that OpenMP is indeed used in the package and that the addition of these dependencies is justified.


59-59: Verify build configurations for osx-arm64 platform.

The addition of 'osx-arm64' to the 'additional-platforms' list is appropriate and aligns with the PR objective. This extends support to Apple Silicon (M1/M2) Macs.

To ensure proper support for this new platform, please run the following verification script:

This script will help verify that necessary configurations and considerations for the osx-arm64 platform are in place.

✅ Verification successful

osx-arm64 build configurations are properly integrated.

The addition of 'osx-arm64' to the 'additional-platforms' list aligns with existing ARM64 configurations in the build scripts, ensuring support for Apple Silicon (M1/M2) Macs.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify build configurations for osx-arm64 platform

# Test 1: Check if there are any osx-arm64 specific configurations in the build script
echo "Checking for osx-arm64 specific configurations in build.sh:"
rg -i 'osx-arm64|darwin-arm64' build.sh

# Test 2: Check if there are any conditional compilation flags for ARM architecture
echo "Checking for ARM-specific compilation flags:"
rg -i 'arm|aarch64' build.sh

# Test 3: Check if there are any mentions of cross-compilation or ARM64 support in documentation
echo "Checking for ARM64 support mentions in documentation:"
rg -i 'arm64|apple\s+silicon|m1|m2' --type md

Length of output: 840


Script:

#!/bin/bash
# Description: Search for build configuration files mentioning osx-arm64 or ARM architectures

echo "Searching for build configuration files related to osx-arm64 or ARM64 support:"

# Search common build scripts and configuration files
rg -i 'osx-arm64|darwin-arm64|arm64|apple\s+silicon|m1|m2' --type make,cmake,sh,py,js,ts,bat,ps1,CMakeLists.txt

Length of output: 350


Script:

#!/bin/bash
# Description: Search for build configuration files mentioning osx-arm64 or ARM architectures

echo "Searching for build configuration files related to osx-arm64 or ARM64 support:"

# Correctly specifying multiple file types by using separate --type flags
rg -i 'osx-arm64|darwin-arm64|arm64|apple\s+silicon|m1|m2' --type make --type cmake --type sh --type py --type js --type ts --type bat --type ps1 --type txt

Length of output: 353


Script:

#!/bin/bash
# Description: Search for build configuration files mentioning osx-arm64 or ARM architectures

echo "Searching for build configuration files related to osx-arm64 or ARM64 support:"

# Correctly specifying multiple file types by using separate --type flags, excluding unsupported 'bat'
rg -i 'osx-arm64|darwin-arm64|arm64|apple\s+silicon|m1|m2' --type make --type cmake --type sh --type py --type js --type ts --type ps1 --type txt

Length of output: 342


Script:

#!/bin/bash
# Description: Search for build configuration files mentioning osx-arm64 or ARM architectures

echo "Searching for build configuration files related to osx-arm64 or ARM64 support:"

# Correctly specifying multiple file types by using separate --type flags, excluding unsupported 'bat' and 'ps1'
rg -i 'osx-arm64|darwin-arm64|arm64|apple\s+silicon|m1|m2' --type make --type cmake --type sh --type py --type js --type ts --type txt

Length of output: 34711

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No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped.

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No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped.

@BiocondaBot
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No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped.

@BiocondaBot
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No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped.

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