tidk: add aarch64/arm64 builds

[martin-g]

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Summary by CodeRabbit

• New Features
  • Added support for additional platforms: linux-aarch64 and osx-arm64.
• Version Updates
  • Updated package version to 0.2.63.
  • Incremented build number from 0 to 1.

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request includes modifications to two files: build.sh and meta.yaml for the tidk package. The build.sh script's shebang line has been changed, and the set -xe command has been added, along with an update to the cargo install command to include the --no-track option. The meta.yaml file has been updated to reflect a new version number, an incremented build number, and the addition of support for two new platforms: linux-aarch64 and osx-arm64.

Changes

File	Change Summary
recipes/tidk/build.sh	Changed shebang from #!/bin/bash -e to #!/bin/bash, added set -xe, updated cargo install with --no-track.
recipes/tidk/meta.yaml	Version updated to "0.2.63", build number incremented to 1, added additional-platforms for linux-aarch64 and osx-arm64.

Possibly related PRs

• tracs: add aarch64/arm64 builds #50103: Updates meta.yaml for the tracs package to include support for linux-aarch64 and osx-arm64.
• tidk v0.2.62 #50836: Updates meta.yaml for the tidk package, including a version update and platform support additions.
• pgrc: add linux-aarch64 build #51009: Adds support for linux-aarch64 in the pgrc package.
• bambamc: add aarch64/arm64 builds #51067: Introduces linux-aarch64 builds for the bambamc package.
• pyslow5: add aarch64/arm64 builds #51105: Adds linux-aarch64 and osx-arm64 support in the pyslow5 package.
• metacache: add linux-aarch64 build #51106: Adds linux-aarch64 support for the metacache package.
• perl-convert-binary-c: add aarch64/arm64 build #51107: Introduces linux-aarch64 and osx-arm64 builds for the perl-convert-binary-c package.
• gxf2bed: add aarch64/arm64 builds #51120: Adds linux-aarch64 and osx-arm64 support for the gxf2bed package.
• longreadsum: add aarch64/arm64 builds #51121: Introduces linux-aarch64 and osx-arm64 builds for the longreadsum package.
• lighter: add aarch64/arm64 builds #51136: Adds linux-aarch64 and osx-arm64 support for the lighter package.

Suggested reviewers

• bgruening: Suggested reviewer for the changes made in this pull request.

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 625280e and d86b10c.

📒 Files selected for processing (2)

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

🔇 Additional comments (7)

recipes/tidk/build.sh (3)

1-1: LGTM: Shebang line modification improves flexibility.

The removal of the -e option from the shebang line is a good change. It allows for more granular control over error handling within the script. This modification is compensated by the addition of set -xe on line 3, which re-enables immediate exit on error along with verbose output.

---

3-3: Excellent addition: Enhanced debugging and error handling.

The addition of set -xe is a great improvement to the script. It serves two important purposes:

1. The -x option enables verbose output, printing each command before execution. This significantly aids in debugging and understanding the script's flow.
2. The -e option ensures the script exits immediately if any command fails, maintaining the strict error handling that was previously set in the shebang line.

This change will make the build process more transparent and easier to troubleshoot if issues arise.

---

6-6: Please clarify the use of --no-track option.

The addition of the --no-track option to the cargo install command is noteworthy. This option prevents Cargo from tracking which files are installed by this package. While this might be intentional, it's important to understand the reasoning behind this change and its potential implications for package management within the Bioconda ecosystem.

Could you please provide more context on:

1. Why was the --no-track option added?
2. How does this align with Bioconda's package management practices?
3. Are there any potential drawbacks or benefits to using this option in this context?

To help assess the impact of this change, let's check if other Rust-based recipes in Bioconda use this option:

This will help us understand if this is a common practice or a unique case for the tidk package.

✅ Verification successful

--no-track Option Usage Verified

The --no-track option is consistently used across multiple Rust-based recipes within the Bioconda repository, including recipes/tidk/build.sh. This confirms that its inclusion aligns with Bioconda's established package management practices.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Search for other Rust-based recipes using cargo install
rg --type sh 'cargo install' recipes

Length of output: 12192

recipes/tidk/meta.yaml (4)

8-10: Build number increment looks good

The build number has been correctly incremented to 1. The presence of the run_exports section is also good for maintaining ABI compatibility across minor version updates.

---

Line range hint 1-42: Overall changes look good

The changes in this PR are minimal and focused:

1. Version update to 0.2.63
2. Build number increment to 1
3. Addition of linux-aarch64 and osx-arm64 platforms

These changes align with the PR objectives and follow Bioconda guidelines. The rest of the recipe remains unchanged, which is appropriate as no other modifications seem necessary for the new platforms.

Please ensure that all verification steps mentioned in previous comments are completed successfully before merging this PR.

---

Line range hint 1-1: Verify version update and related changes

The version has been updated to "0.2.63". This change looks good, but please ensure that the source URL and SHA256 hash (lines 14-15) have also been updated to match this new version.

---

39-42: Additional platforms look good, verify build success

The addition of linux-aarch64 and osx-arm64 platforms is in line with the PR objectives. This change looks good and is correctly placed in the extra section.

To ensure that the package builds successfully on these new platforms, please verify the build logs or artifacts for linux-aarch64 and osx-arm64. You can use the following command to check if the builds were successful:

If the builds were successful, you should see output indicating that the packages were created for these platforms.

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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	tidk-0.2.63-h2e7e638_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	tidk-0.2.63-hd2a67f9_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	tidk-0.2.63-ha48a4ba_1.tar.bz2	repodata.json	CircleCI	show You may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/457b224a-d733-48b8-9cf0-525b545bcb97/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64	tidk-0.2.63-h7b3948c_1.tar.bz2	repodata.json	CircleCI	show You may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/3d4c46ad-8683-4d78-891f-c90e7bcd733b/artifacts/0/tmp/artifacts/packages <package name>

---

Docker image(s) built:

Package	Tag	CI	Install with docker
tidk	0.2.63--h2e7e638_1	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/tidk:0.2.63--h2e7e638_1.tar.gz | docker load

[martin-g]

mgrigorov in 🌐 euler-arm-22 in /tmp/tidk via 🅒 test123 took 9s 
❯ tar xvf tidk-0.2.63-h7b3948c_1.tar.bz2                                                                                                                                                                   (test123) 
info/files
info/test/run_test.sh
info/run_exports.json
info/recipe/build.sh
info/paths.json
info/hash_input.json
info/index.json
info/recipe/meta.yaml.template
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/git
bin/tidk

mgrigorov in 🌐 euler-arm-22 in /tmp/tidk via 🅒 test123 
❯ file bin/*                                                                                                                                                                                               (test123) 
bin/tidk: 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, not stripped

mgrigorov in 🌐 euler-arm-22 in /tmp/tidk via 🅒 test123 
❯ ./bin/tidk                                                                                                                                                                                               (test123) 
Warning! No clades found in the database. Run 'tidk build' to fetch the latest data.

A Telomere Identification Toolkit.

Usage: tidk [COMMAND]

Commands:
  build    Build the reference database of telomeric repeat sequences. This is required for the 'find' subcommand.
  find     Supply the name of a clade your organsim belongs to, and this submodule will find all telomeric repeat matches for that clade.
  explore  Use a range of kmer sizes to find potential telomeric repeats.
           One of either length, or minimum and maximum must be specified.
  search   Search the input genome with a specific telomeric repeat search string.
  plot     SVG plot of TSV generated from tidk search.
  help     Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

LGTM!

[martin-g]

@BiocondaBot please add label