gappa: add arm64 build

[mencian]

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Summary by CodeRabbit

• New Features
  • Updated package version to 0.8.5 with a new build number.
  • Added support for libgomp as a host requirement for Linux.
  • Introduced osx-arm64 as an additional platform.
  • Included a new DOI entry in the package identifiers.
• Bug Fixes
  • Ensured the gappa binary has the correct executable permissions during installation.

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request introduces modifications to the build.sh script and the meta.yaml file for the gappa package. The build.sh script now includes a command to set executable permissions for the gappa binary. The meta.yaml file updates the package version and build number, alters host dependencies for Linux and macOS, adds a license family, introduces a new platform, and includes a new DOI identifier.

Changes

File	Change Summary
recipes/gappa/build.sh	Added chmod 0755 bin/gappa to set executable permissions for the gappa binary before installation.
recipes/gappa/meta.yaml	Updated version from 0.8.5 to 0.8.5, incremented build number from 1 to 2, changed host dependency from llvm-openmp to libgomp for Linux, added libgomp for Linux in the run section, added license_family: GPL3, included osx-arm64 in additional platforms, and added DOI identifier.

Possibly related PRs

• recipe for pgrc #50973: Changes in build.sh for the pgrc recipe involve setting up the build environment and copying the binary to $PREFIX/bin, similar to the permission changes made in the gappa binary in the main PR.
• pgrc: add linux-aarch64 build #51009: The pgrc recipe updates include changes to the meta.yaml file that align with the updates made in the gappa recipe, particularly regarding the addition of libgomp for Linux, which is relevant to the changes in dependencies in the main PR.
• bambamc: add aarch64/arm64 builds #51067: The bambamc recipe's build.sh modifications include enhancements for building on ARM architectures, which is relevant to the changes made in the gappa recipe regarding executable permissions and architecture support.

Suggested labels

aarch64, osx-arm64

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 3c24058 and 46f84b7.

📒 Files selected for processing (2)

• recipes/gappa/build.sh (1 hunks)
• recipes/gappa/meta.yaml (4 hunks)

🔇 Additional comments (8)

recipes/gappa/build.sh (3)

Line range hint 1-13: Summary of review and next steps

The build script changes look good overall, with the addition of the chmod command improving permission consistency. However, there are two main points to address:

1. Verify if the explicit chmod command aligns with Bioconda's best practices.
2. Ensure proper support for ARM64 builds, as mentioned in the PR objectives.

Please run the provided verification scripts and make any necessary adjustments based on the results. If you need any assistance with implementing ARM64 support or have any questions about the Bioconda best practices, feel free to ask.

---

Line range hint 1-13: Verify ARM64 build support and cross-compilation configuration.

The current build script doesn't explicitly address the ARM64 build mentioned in the PR objectives. While the script may work for ARM64 if the underlying build system (make) supports it, it's important to ensure that cross-compilation is properly configured.

Consider the following points:

1. Verify that the Makefile or underlying build system supports ARM64 targets.
2. Ensure that any necessary ARM64-specific flags or configurations are set.
3. If cross-compilation is required, make sure the appropriate toolchain is used.

To check for ARM64 support and cross-compilation configuration, please run the following script:

#!/bin/bash
# Description: Check for ARM64 support in the gappa package

# Check Makefile for ARM64 or aarch64 references
echo "Checking Makefile for ARM64 support:"
rg --type make 'arm64|aarch64' recipes/gappa/Makefile

# Check for cross-compilation tools or flags in the recipe
echo "Checking meta.yaml for cross-compilation configuration:"
rg --type yaml 'cross-compilation|arm64|aarch64' recipes/gappa/meta.yaml

# Check if there are any ARM64-specific patches
echo "Checking for ARM64-specific patches:"
ls recipes/gappa/*arm64*.patch recipes/gappa/*aarch64*.patch 2>/dev/null || echo "No ARM64-specific patches found"

This script will help identify any explicit ARM64 support or cross-compilation configuration in the package. If these are not present, you may need to add appropriate configurations to ensure proper ARM64 builds.

---

11-11: Approve the addition of chmod, but verify alignment with Bioconda practices.

The addition of chmod 0755 bin/gappa ensures that the binary has the correct permissions (owner can read/write/execute, others can read/execute) before installation. This is generally a good practice to ensure consistency across different systems.

However, it would be beneficial to verify if this explicit permission setting is necessary and aligns with Bioconda's best practices for package installation scripts.

To ensure this change aligns with Bioconda's practices, please run the following script:

This script will help us understand if setting explicit permissions is common in Bioconda recipes and if gappa had any permission-related issues in the past.

✅ Verification successful

Approve the addition of chmod 0755 to ensure the gappa binary has correct execution permissions.
No existing Bioconda recipes utilize chmod in their build scripts, and no prior permission-related issues were found for gappa. This addition enhances installation reliability and consistency across different systems.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if other Bioconda recipes use chmod in their build scripts

# Search for chmod usage in other build.sh files
echo "Checking for chmod usage in other Bioconda build scripts:"
rg --type sh 'chmod.*bin/' recipes/*/build.sh

# Check if gappa previously had any permission-related issues
echo "Checking for any previous permission-related issues with gappa:"
rg --type yaml 'gappa.*permission' .github/workflows/*.yaml .circleci/config.yml

Length of output: 656

recipes/gappa/meta.yaml (5)

6-6: LGTM: Build number increment is appropriate.

The build number has been correctly incremented from 1 to 2. This is the expected practice when making changes to a package configuration without changing its version.

---

24-24: LGTM: Consistent run requirements added for Linux.

The addition of 'libgomp' as a run requirement for Linux mirrors the changes made to the host requirements. This ensures consistency between build-time and runtime environments, which is a good practice.

---

34-34: LGTM: License family added for clarity.

The addition of 'license_family: GPL3' provides more specific information about the license type. This is consistent with the existing GPL-3.0-only license and helps clarify the licensing terms for users and package managers.

---

48-48: LGTM: ARM64 support added and new identifier included. Verify ARM64 build.

The addition of 'osx-arm64' to the list of additional platforms indicates support for ARM-based Mac systems. This is a positive enhancement that broadens the package's compatibility. The new DOI identifier adds valuable information about related research.

To ensure the ARM64 support is fully implemented:

1. Verify that the package builds successfully on ARM64 Mac systems.
2. Test the resulting binary on an ARM64 Mac to confirm functionality.

You can use the following script to check for any ARM64-specific build configurations:

#!/bin/bash
# Description: Check for ARM64-specific build configurations

# Search for ARM64-related flags or conditions in build files
echo "Searching for ARM64-related configurations in build files:"
rg -i 'arm64|aarch64' --type make --type cmake

Also applies to: 52-52

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20-21: LGTM: Platform-specific OpenMP libraries added. Verify cross-platform compatibility.

The addition of 'libgomp' for Linux and retention of 'llvm-openmp' for macOS is a good practice for platform-specific optimization. This change likely addresses compiler differences between the two platforms.

To ensure this change doesn't introduce any cross-platform issues, please verify:

1. The package builds successfully on both Linux and macOS platforms.
2. The resulting binaries work as expected on their respective platforms.

You can use the following script to check for any OpenMP-related build flags or compiler options:

✅ Verification successful

LGTM: Platform-specific OpenMP libraries added without introducing cross-platform issues.

The addition of 'libgomp' for Linux and the retention of 'llvm-openmp' for macOS are consistent with the project's extensive use of OpenMP for parallel processing. This ensures that the package maintains optimal performance across both platforms without introducing compatibility issues.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for OpenMP-related build flags or compiler options

# Search for OpenMP-related flags in build files
echo "Searching for OpenMP-related flags in build files:"
rg -i 'openmp|gomp' --type make --type cmake

Length of output: 175

---

Script:

#!/bin/bash
# Description: Check for OpenMP-related build flags or compiler options

# Search for OpenMP-related flags in build files
echo "Searching for OpenMP-related flags in build files:"
rg -i 'openmp|gomp' --type make --type cmake

Length of output: 157

---

Script:

#!/bin/bash
# Description: Comprehensive check for OpenMP-related build flags or compiler options across various build files

# Search for OpenMP-related flags in common build configuration files
echo "Searching for OpenMP-related flags in make, cmake, Dockerfile, and setup.py files:"
rg -i 'openmp|gomp' --type make --type cmake --type Dockerfile --type py

Length of output: 284

---

Script:

#!/bin/bash
# Description: Comprehensive check for OpenMP-related build flags or compiler options across various build files

echo "Searching for OpenMP-related flags in build configuration files: Makefile, CMakeLists.txt, Dockerfile, setup.py"

# Find relevant build files and search for OpenMP-related flags
fd -e makefile -e Makefile -e CMakeLists.txt -e Dockerfile -e setup.py . | xargs rg -i 'openmp|gomp'

Length of output: 131308

---

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