Add fastplong #51498
Add fastplong #51498
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fastplong is a tool for ultra-fast preprocessing and quality control for long-read sequencing data
📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces two main components for the Second, a new metadata file Possibly related PRs
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (3)
recipes/fastplong/build.sh (1)
1-6: Overall LGTM with minor enhancement suggestions.The build script is well-structured and follows good practices for a Conda build script. It covers the essential steps of setting up the environment, building, and installing the package.
To further enhance the script, consider:
- Adding error checking after critical steps (e.g., after
make).- Including more verbose logging for better traceability.
- Potentially adding a cleanup step if temporary files are created during the build process.
Would you like assistance in implementing these enhancements?
recipes/fastplong/meta.yaml (2)
16-26: Consider pinning dependency versions.The build, host, and run requirements look appropriate for the package. However, consider pinning the versions of
isa-landlibdeflateto ensure reproducibility and prevent potential compatibility issues in the future.Example:
host: - isa-l >=2.30.0,<3 - libdeflate >=1.7,<2 run: - isa-l >=2.30.0,<3 - libdeflate >=1.7,<2Please adjust the version numbers according to the specific requirements of fastplong.
28-30: Consider adding more comprehensive test commands.The current test command
fastplong --helpis a good basic check. However, consider adding more comprehensive tests to ensure the functionality of the package. For example:
- Check if the version matches the expected version:
- fastplong --version | grep {{ version }}- Test a basic functionality of the tool (if possible with a small sample file):
- fastplong -i sample.fastq -o output.fastqThese additional tests would provide more confidence in the package's correct installation and basic functionality.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/fastplong/build.sh (1 hunks)
- recipes/fastplong/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/fastplong/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (7)
recipes/fastplong/build.sh (2)
1-3: LGTM! Robust error handling and verbosity settings.The script starts with appropriate shell options that enhance error handling and debugging:
-x: Prints commands as they are executed, aiding in debugging.-e: Exits immediately if a command fails, preventing cascading errors.-u: Treats unset variables as an error, catching potential oversights.-o pipefail: Ensures pipeline failures are not masked.The creation of the binary directory using
$PREFIXaligns with Conda build conventions.
5-5: LGTM! Efficient parallel build with correct path settings.The
makecommand is well-constructed:
- Uses
${CPU_COUNT}for parallel jobs, optimizing build performance.- Correctly sets
INCLUDE_DIRSandLIBRARY_DIRSto use Conda environment paths.Could you confirm that the default make target (i.e., not specifying a target) is intentional and builds all necessary components? If a specific target is required, consider updating the command accordingly.
recipes/fastplong/meta.yaml (5)
1-5: LGTM: Version and package name are correctly defined.The version is set using a Jinja2 variable, which is a good practice for maintainability. The package name and version match the information provided in the PR objectives.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
7-9: LGTM: Source URL and checksum are correctly specified.The source URL is correctly formatted using the version variable, and a SHA256 checksum is provided for integrity verification. This aligns with best practices for Conda recipes.
32-35: LGTM: Additional platforms are correctly specified.The inclusion of linux-aarch64 and osx-arm64 as additional platforms is good for broader compatibility. This aligns with the information provided in the PR summary.
37-42: LGTM: About section is comprehensive and accurate.The about section provides all necessary information:
- The home URL points to the correct GitHub repository.
- License information is complete, including the license family and file.
- The summary clearly describes the package's purpose for long-read sequencing data preprocessing and quality control.
This information aligns with the PR objectives and provides good metadata for the package.
1-1: Note on yamllint warning: False positiveThe yamllint tool reports a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' is part of a valid Jinja2 template syntax commonly used in Conda recipes. The syntax is correct for a meta.yaml file, and no changes are needed.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
| mkdir -p $PREFIX/bin | ||
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| make -j ${CPU_COUNT} INCLUDE_DIRS="$PREFIX/include" LIBRARY_DIRS="$PREFIX/lib" | ||
| make install |
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Consider specifying installation prefix.
The make install command is used to install the built files, which is standard practice. However, to ensure that files are installed within the Conda environment, it's recommended to specify the installation prefix.
Consider updating the install command to:
-make install
+make install PREFIX=$PREFIXThis change ensures that all files are installed in the correct location within the Conda environment.
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| make install | |
| make install PREFIX=$PREFIX |
recipes/fastplong/meta.yaml
Outdated
| build: | ||
| number: 5 | ||
| run_exports: | ||
| - {{ pin_subpackage("fastplong", max_pin="x.x") }} |
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💡 Codebase verification
Reset build number to 0 and LGTM on run_exports.
The build number is currently set to 5. Since there are no previous versions of fastplong in the repository, it should be reset to 0 for the initial release.
The run_exports section is correctly implemented, ensuring proper dependency management as per the PR objectives.
🔗 Analysis chain
Verify the build number and LGTM on run_exports.
The build number is set to 5, which seems high for a new package version (0.2.0). Could you please verify if this is intentional or if it should be reset to 0 for the initial release?
The run_exports section is correctly implemented, which will help prevent downstream recipe expectation violations as suggested in the PR objectives.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if there are previous versions of fastplong in the repository
# Test: Search for previous versions of fastplong. Expect: No previous versions if this is a new package.
fd -t f 'meta.yaml' recipes/fastplong | xargs grep 'version:'
Length of output: 84
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/fastplong/meta.yaml (1)
28-30: LGTM: Basic test is present. Consider adding more comprehensive tests.The current test command (
fastplong --help) serves as a basic smoke test to ensure the package is installed and can be executed. However, consider adding more comprehensive tests to verify the functionality of key features of fastplong.Would you like assistance in generating additional test commands?
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/fastplong/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/fastplong/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/fastplong/meta.yaml (6)
1-5: LGTM: Package and version are correctly defined.The package name and version are properly set. The use of Jinja2 templating for the version is a good practice for maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
7-9: LGTM: Source URL and checksum are properly defined.The source URL is correctly formatted and uses the version variable. The SHA256 checksum is provided, which is crucial for package integrity verification.
11-14: LGTM: Build section is correctly configured.The build number is correctly set to 0 for the initial release, addressing the previous review comment. The run_exports section is properly implemented, which will help prevent downstream recipe expectation violations as suggested in the PR objectives.
37-42: LGTM: About section is comprehensive and well-defined.The about section contains all necessary metadata, including the home URL, license information, and a clear summary of the package's functionality. The specification of the license file is important for compliance.
16-26: LGTM: Requirements are well-defined. Consider verifying dependencies.The build, host, and run requirements are appropriately defined. The build requirements are suitable for a C/C++ project. However, it might be worth double-checking if isa-l and libdeflate are the only runtime dependencies required by fastplong.
32-35: LGTM: Additional platforms specified. Verify actual support.The inclusion of additional platforms (linux-aarch64 and osx-arm64) is good for broader compatibility. However, it's important to verify that fastplong actually supports these platforms.
✅ Verification successful
LGTM: Additional platforms appear appropriate, but verification recommended.
The inclusion of linux-aarch64 and osx-arm64 as additional platforms for fastplong seems appropriate based on the available information. The meta.yaml file explicitly lists these platforms, and the build process appears to be generic without architecture-specific instructions. This suggests that the software may be compatible with these architectures.
However, to ensure full compatibility and functionality, it would be advisable for the package maintainer or users to verify that fastplong works correctly on these platforms through testing.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for platform-specific code or build instructions # Test: Search for any platform-specific code or build instructions rg -i 'aarch64|arm64'Length of output: 447893
Script:
#!/bin/bash # Search for fastplong-specific files and architecture mentions echo "Searching for fastplong-specific files:" fd fastplong echo -e "\nChecking fastplong files for architecture-specific code:" rg -i 'aarch64|arm64' $(fd fastplong) echo -e "\nChecking build.sh for architecture-specific instructions:" cat recipes/fastplong/build.shLength of output: 713
fastplong is a tool for ultra-fast preprocessing and quality control for long-read sequencing data
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