add gafpack #51389
add gafpack #51389
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces two new files in the Possibly related PRs
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🧰 Additional context used🪛 yamllint
🔇 Additional comments (8)
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/gafpack/build.sh (2)
6-6: Good debugging setup, consider conditional activation.Setting
RUST_BACKTRACE=1is excellent for debugging as it provides detailed error information if the Rust compilation or installation process fails.However, for production builds, this level of detail might not be necessary and could potentially expose sensitive information.
Consider making this setting conditional based on a debug flag or environment variable. For example:
if [ "${DEBUG:-}" = "1" ]; then export RUST_BACKTRACE=1 fiThis way, you can easily enable or disable detailed backtraces as needed.
7-7: Appropriate cargo install command, consider version specification.The
cargo installcommand is well-constructed with appropriate flags:
--verboseprovides detailed output, aiding in debugging.--path .correctly specifies the current directory as the package source.--root ${PREFIX}ensures installation in the conda-specified directory.--no-trackprevents cargo from tracking the installed package, which is correct for system-wide installations.The use of
${PREFIX}indicates this script is designed to work within conda's build system, which is excellent.Consider explicitly specifying the version to install. This can help ensure consistency across builds. You could add a
--versionflag or use an environment variable. For example:cargo install --verbose --path . --root ${PREFIX} --no-track --version ${VERSION}Where
${VERSION}could be set earlier in the script or passed as an environment variable from the meta.yaml file.
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- recipes/gafpack/build.sh (1 hunks)
- recipes/gafpack/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/gafpack/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (8)
recipes/gafpack/build.sh (2)
1-3: Excellent error handling and verbosity setup.The script begins with robust error handling and verbosity settings. The shebang
#!/bin/bash -euoensures that the script exits immediately if any command fails, treats unset variables as an error, and exits if any part of a pipeline fails. The additionalset -xefurther enhances this by enabling verbose output and causing the script to exit on the first error.These settings are crucial for build scripts as they help catch and diagnose issues early in the build process.
1-7: Overall, excellent build script with minor improvement opportunities.This build script is well-crafted for building a Rust package within the conda ecosystem. It demonstrates good practices in error handling, debugging setup, and use of conda-specific environment variables. The cargo install command is appropriately configured for this context.
The suggested improvements (conditional debug activation and explicit version specification) are minor and aimed at enhancing flexibility and reproducibility. These changes could make the script even more robust and easier to maintain in the long run.
Great job on creating a concise and effective build script!
recipes/gafpack/meta.yaml (6)
1-6: LGTM: Package and version information is correctly defined.The package name "gafpack" and version "0.1.0" are properly set using Jinja2 templating. This aligns with the PR objectives and follows best practices for conda recipe files.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-15: Build number is correct, but run_exports might be unnecessary.The build number is correctly set to 0 for the initial release. However, the
run_exportssection is uncommon for Rust packages and might not be necessary.Could you please clarify the need for the
run_exportssection? If it's not required, consider removing it. If it is needed, please provide a brief explanation of its purpose in this context.
17-19: LGTM: Build requirements are correctly specified.The Rust compiler is properly listed as the only build requirement, which is appropriate for a Rust project. The absence of runtime requirements is typical for statically linked Rust binaries.
25-31: LGTM: About section is comprehensive and accurate.The about section is well-defined with:
- Correct home and dev URLs pointing to the GitHub repository
- Proper license specification (MIT) with license file reference
- A concise summary that aligns with the PR objectives
This provides good metadata for the package.
33-38: LGTM: Extra information is correctly specified.The extra section properly includes:
- Additional supported platforms (linux-aarch64 and osx-arm64)
- The recipe maintainer (AndreaGuarracino), who is also the PR submitter
This information is valuable for package management and maintenance.
8-10: LGTM: Source information is correctly specified.The source URL and SHA256 checksum are properly defined. The URL is correctly constructed using Jinja2 templating to reference the package name and version.
To ensure the integrity of the source, please verify the SHA256 checksum independently. You can use the following command:
Compare the output with the checksum in the meta.yaml file.
recipes/gafpack/meta.yaml
Outdated
| test: | ||
| commands: | ||
| - gfainject --help |
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Verify test command and consider testing all binaries.
The test command checks the help output of gfainject, which seems inconsistent with the package name gafpack.
Please clarify:
- Is
gfainjectthe correct binary to test, or should it begafpack? - Are there other binaries installed by this package that should be tested?
Consider updating the test section to verify all installed binaries. For example:
test:
commands:
- gafpack --help
- gfainject --help # If this is indeed a part of the package
# Add tests for any other binaries installed by the package
gafpackis a tool to convert alignments to pangenome variation graphs to coverage maps (vectors). These vectors can be used together withodgi,pggb, andcosigtto perform pangenome-based genotyping.