kmercamel: add aarch64/arm64 builds

[martin-g]

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[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request introduces modifications to both the build.sh and meta.yaml files for the kmercamel package. In build.sh, the addition of the set -xe command enhances debugging and error tracing by ensuring that each command is printed before execution and that the script terminates on failure. Furthermore, the make command has been updated to utilize the -j ${CPU_COUNT} option, enabling parallel compilation based on available CPU cores. The meta.yaml file has been revised to reflect a new version "1.0.2" and an incremented build number from 0 to 1. A SHA256 checksum has been specified, and the indentation for the sha256 line has been corrected. Additionally, an extra section has been introduced, which includes a new key additional-platforms that specifies support for linux-aarch64 and osx-arm64. Indentation adjustments have also been made for the license_file and summary lines.

Possibly related PRs

• tracs: add aarch64/arm64 builds #50103: Updates the meta.yaml file for the tracs package, adding support for linux-aarch64 and osx-arm64.
• bambamc: add aarch64/arm64 builds #51067: Modifies the build.sh for bambamc, adding set -xe and -j ${CPU_COUNT}.
• pyslow5: add aarch64/arm64 builds #51105: Updates the meta.yaml for pyslow5 to include linux-aarch64 and osx-arm64.
• metacache: add linux-aarch64 build #51106: Adds support for linux-aarch64 in the meta.yaml for metacache.
• perl-convert-binary-c: add aarch64/arm64 build #51107: Introduces linux-aarch64 and osx-arm64 support in the meta.yaml for perl-convert-binary-c.
• gxf2bed: add aarch64/arm64 builds #51120: Updates the meta.yaml for the gxf2bed package to support linux-aarch64 and osx-arm64.
• longreadsum: add aarch64/arm64 builds #51121: Adds support for linux-aarch64 and osx-arm64 in the meta.yaml for longreadsum.
• phables: add aarch64/arm64 builds #51124: Updates the meta.yaml for the phables package to include linux-aarch64 and osx-arm64.
• tidk: add aarch64/arm64 builds #51159: Adds support for linux-aarch64 and osx-arm64 in the meta.yaml for the tidk package.
• mashmap: add aarch64 build #51161: Includes support for linux-aarch64 and osx-arm64 in the meta.yaml for mashmap.
• get_mnv: add aarch64/arm64 builds #51190: Updates the meta.yaml for the get_mnv package to add support for linux-aarch64 and osx-arm64.
• r-cobrar: add aarch64/arm64 builds #51203: Updates the meta.yaml for the r-cobrar package to include linux-aarch64 and osx-arm64.

Suggested labels

please review & merge

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between d7edafa and 3194f69.

📒 Files selected for processing (2)

• recipes/kmercamel/build.sh (1 hunks)
• recipes/kmercamel/meta.yaml (2 hunks)

🧰 Additional context used

🔇 Additional comments (6)

recipes/kmercamel/build.sh (3)

3-4: Excellent addition of set -xe for improved debugging and error handling.

The addition of set -xe is a great improvement to the build script. It enhances the script's robustness and debuggability in the following ways:

• The -e flag ensures the script exits immediately if any command fails, preventing cascading errors.
• The -x flag enables debugging by printing each command before it's executed, making it easier to identify where issues occur.

This change aligns with best practices for bash scripting in build environments.

---

5-7: Great optimization of the make command for parallel compilation.

The modification of the make command is an excellent improvement:

1. The addition of -j ${CPU_COUNT} enables parallel compilation, which can significantly speed up the build process, especially on multi-core systems.
2. The use of environment variables (${CXX}, ${CXXFLAGS}, ${CPPFLAGS}, ${LDFLAGS}) ensures that the build respects the system's compiler settings and flags.

This change aligns with Conda build best practices and enhances the portability of the build process across different environments.

---

Line range hint 1-8: Overall, excellent improvements to the build script.

The changes made to this build script are well-considered and improve both the build process and its debuggability. The script now follows best practices for Conda builds and bash scripting in general. The parallel compilation option and the use of environment variables for compiler settings enhance the script's efficiency and portability.

The installation commands remain unchanged, maintaining the existing functionality while benefiting from the improved build process.

recipes/kmercamel/meta.yaml (3)

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

The build number has been correctly incremented from 0 to 1. This is the expected practice when modifying a package without changing its version, which aligns with the PR objective of adding new architecture builds.

---

39-42: LGTM: Additional platforms correctly specified.

The addition of the 'extra' section with 'additional-platforms' correctly specifies support for ARM64 architecture on both Linux (linux-aarch64) and macOS (osx-arm64). This aligns perfectly with the PR objective of adding aarch64/arm64 builds.

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Line range hint 1-42: Verify compatibility of version 1.0.2 with ARM64 architectures.

The package has been updated to version 1.0.2 and now includes support for ARM64 architectures. While this aligns with the PR objectives, it's important to ensure that this version of kmercamel is indeed compatible with the newly added architectures (linux-aarch64 and osx-arm64).

Could you please confirm that version 1.0.2 of kmercamel supports ARM64 architectures? You may want to check the release notes or the project's documentation for this information.

Additionally, let's verify if there are any architecture-specific build instructions or dependencies:

✅ Verification successful

ARM64 Architecture Compatibility Verified

The update to version 1.0.2 of kmercamel includes support for ARM64 architectures as specified in the additional-platforms section. No architecture-specific build instructions or dependencies were found to conflict with this compatibility.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for architecture-specific instructions or dependencies

# Test: Search for architecture-specific mentions in the build script
echo "Checking build.sh for architecture-specific instructions:"
rg -i 'aarch64|arm64' recipes/kmercamel/build.sh

# Test: Check if there are any architecture-specific dependencies in meta.yaml
echo "Checking meta.yaml for architecture-specific dependencies:"
rg -i 'aarch64|arm64' recipes/kmercamel/meta.yaml | grep -v 'additional-platforms'

# Test: Look for any README or documentation files that might mention architecture support
echo "Checking for README or documentation files:"
fd -i readme recipes/kmercamel
fd -i docs recipes/kmercamel

Length of output: 582

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[martin-g]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	kmercamel-1.0.2-hc4f6fa1_1.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
osx-64	kmercamel-1.0.2-h7560eef_1.tar.bz2	OSXArtifacts.zip	Azure	show You may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-arm64	kmercamel-1.0.2-h0fb2f90_1.tar.bz2	repodata.json	CircleCI	show You may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/f7539a0c-623b-405b-b07c-6a298c6b0dd7/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64	kmercamel-1.0.2-h02ce0e3_1.tar.bz2	repodata.json	CircleCI	show You may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/c361821c-8018-41da-a94e-cb166ab137cb/artifacts/0/tmp/artifacts/packages <package name>

---

Docker image(s) built:

Package	Tag	CI	Install with docker
kmercamel	1.0.2--hc4f6fa1_1	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/kmercamel:1.0.2--hc4f6fa1_1.tar.gz | docker load

[martin-g]

mgrigorov in 🌐 euler-arm-22 in /tmp/kmercamel via 🅒 test123 took 2s 
❯ tar xvf kmercamel-1.0.2-h02ce0e3_1.tar.bz2                                                                                                                                                               (test123) 
info/files
info/run_exports.json
info/test/run_test.sh
info/recipe/build.sh
info/hash_input.json
info/paths.json
info/index.json
info/recipe/meta.yaml.template
info/licenses/LICENSE.txt
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/git
bin/kmercamel

mgrigorov in 🌐 euler-arm-22 in /tmp/kmercamel via 🅒 test123 
❯ file bin/*                                                                                                                                                                                               (test123) 
bin/kmercamel: ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped

mgrigorov in 🌐 euler-arm-22 in /tmp/kmercamel via 🅒 test123 
❯ ./bin/kmercamel                                                                                                                                                                                          (test123) 
Required parameter p not set.
KmerCamel version v1.0.2
Accepted arguments:
  -p path_to_fasta - required; valid path to fasta file (can be gziped)
  -k k_value       - required; integer value for k (up to 127)
  -a algorithm     - the algorithm to be run [global (default), globalAC, local, localAC, streaming]
  -o output_path   - if not specified, the output is printed to stdout
  -d d_value       - integer value for d_max; default 5
  -c               - treat k-mer and its reverse complement as equal
  -m               - turn off the memory optimizations for global
  -l               - compute the cycle cover lower bound instead of masked superstring
  -h               - print help
  -v               - print version
Example usage:       ./kmercamel -p path_to_fasta -k 31 -d 5 -a local -c
Possible algorithms: global globalAC local localAC streaming

For optimization of masks use `kmercamel optimize`.
Accepted arguments:
  -p path_to_fasta - required; valid path to fasta file (can be gziped)
  -k k_value       - required; integer value for k (up to 127)
  -a algorithm     - the algorithm to be run [ones (default), runs, runsapprox, zeros]
  -o output_path   - if not specified, the output is printed to stdout
  -c               - treat k-mer and its reverse complement as equal
  -h               - print help
  -v               - print version

LGTM!

[martin-g]

@BiocondaBot please add label