Add KmerCamel #51245
Add KmerCamel #51245
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📝 Walkthrough📝 WalkthroughWalkthroughThe changes introduced in this pull request include the addition of two new files in the The The Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (5)
recipes/kmercamel/build.sh (2)
3-3: Consider quoting variable expansions in the make command.The make command correctly uses environment variables for compiler settings, which is good practice. However, to handle potential spaces in the variable values, consider quoting the expansions:
-make CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" +make CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}"This change ensures that spaces in any of the variables don't cause unexpected behavior.
4-5: LGTM: Correct installation commands with a suggestion for error handling.The installation commands are correct and follow good practices:
- Using
install -dto create the directory is appropriate.- Using
installto copy the executable and set permissions is correct.- The use of
${PREFIX}is consistent with conda build practices.However, consider adding a check to ensure the kmercamel executable exists before attempting to install it:
install -d "${PREFIX}/bin" +if [ ! -f kmercamel ]; then + echo "Error: kmercamel executable not found" >&2 + exit 1 +fi install kmercamel "${PREFIX}/bin/"This addition will provide better error handling if the build process fails.
recipes/kmercamel/meta.yaml (3)
13-14: Consider addingrun_exportssectionThe build section correctly sets the initial build number to 0. However, as mentioned in the PR objectives, it's recommended to add a
run_exportssection to avoid API, ABI, and CLI breakage issues.Consider adding the
run_exportssection based on your versioning strategy. For example:build: number: 0 run_exports: - {{ pin_subpackage('kmercamel', max_pin='x.x') }}This example pins the major and minor version. Adjust the
max_pinvalue according to your versioning strategy.
27-29: Consider adding more comprehensive testsThe current test command checks for the presence of "KmerCamel" in the help output, which is a good basic check. However, to ensure the tool functions correctly, consider adding more comprehensive tests.
For example, you could add:
- A version check:
kmercamel --version- A simple functional test using example data (if available)
Example:
test: commands: - kmercamel -h 2>&1 | grep "KmerCamel" - kmercamel --version # Add a functional test if possible, e.g.: # - kmercamel -i example_input.txt -o test_output.txt # - diff test_output.txt expected_output.txt
36-36: Remove extra blank lines at the end of the fileThe static analysis tool detected extra blank lines at the end of the file. To adhere to YAML best practices, please remove these extra blank lines.
about: home: https://github.com/OndrejSladky/kmercamel/ license: MIT license_file: LICENSE.txt summary: KmerCamel🐫 - compressing k-mer sets using masked superstrings - -🧰 Tools
🪛 yamllint
[warning] 36-36: too many blank lines
(1 > 0) (empty-lines)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/kmercamel/build.sh (1 hunks)
- recipes/kmercamel/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/kmercamel/meta.yaml
[warning] 36-36: too many blank lines
(1 > 0) (empty-lines)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/kmercamel/build.sh (2)
1-1: LGTM: Correct shebang for a bash script.The shebang
#!/bin/bashis appropriate for a bash script and is generally more portable than using/usr/bin/env bash.
1-5: Overall assessment: Well-structured build script with minor suggestions for improvement.The
build.shscript is concise and follows conda build practices. It correctly uses environment variables for compiler settings and appropriate commands for installation. The suggested improvements (quoting variable expansions and adding an existence check for the executable) are minor and aimed at enhancing robustness. The script should function as intended for building and installing kmercamel.recipes/kmercamel/meta.yaml (4)
1-6: LGTM: Package metadata is well-structuredThe package metadata section is correctly defined using Jinja2 templating for version and checksum, which is a good practice for maintainability. The package name and version are properly structured.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-11: LGTM: Source section is correctly configuredThe source section is well-structured, using variables for consistency and including the necessary elements: filename, URL, and SHA256 checksum for integrity verification. This follows Bioconda best practices.
16-25: LGTM: Requirements are well-definedThe requirements section is correctly structured with appropriate build, host, and run dependencies. The inclusion of make, C++ compiler, zlib, and glpk seems suitable for the KmerCamel project.
31-35: LGTM: About section is complete and informativeThe about section provides all the necessary information including the home URL, license type, license file location, and a concise summary of the tool's functionality. This follows Bioconda best practices for recipe metadata.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/kmercamel/meta.yaml (2)
30-32: LGTM: Test section provides a basic check. Consider enhancing tests.The current test command checks if the kmercamel help output contains "KmerCamel", which is a good basic check to ensure the package is installed and can be executed.
Consider enhancing the test section with more comprehensive tests if available, such as:
- Checking for specific expected output or version information.
- Running a simple analysis with sample data, if feasible.
- Verifying the presence of important executable files or libraries.
Example of an enhanced test section:
test: commands: - kmercamel -h 2>&1 | grep "KmerCamel" - kmercamel --version 2>&1 | grep "{{ version }}" - test -f $PREFIX/bin/kmercamel # Add more specific tests here if available
39-39: Minor: Remove extra blank lines at the end of the file.There are extra blank lines at the end of the file that can be removed.
Please remove the extra blank lines at the end of the file.
Note: The static analysis tool reported a syntax error for the '%' character, but this can be safely ignored as it's a false positive due to the valid use of Jinja2 templating in this context.
🧰 Tools
🪛 yamllint
[warning] 39-39: too many blank lines
(1 > 0) (empty-lines)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/kmercamel/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/kmercamel/meta.yaml
[warning] 39-39: too many blank lines
(1 > 0) (empty-lines)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/kmercamel/meta.yaml (5)
1-6: LGTM: Package and version section is well-defined.The use of Jinja2 templating for version and checksum is a good practice for maintainability. The package name and version are correctly specified according to Bioconda guidelines.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-17: LGTM: Build section is correctly configured.The build number is correctly set to 0 for a new package. The run_exports section with pin_subpackage follows the instructions provided in the PR objectives and allows for minor version updates, which is a good practice for maintaining compatibility.
34-38: LGTM: About section is well-defined. Verify license information.The about section includes all necessary information as per Bioconda guidelines, including the home URL, license type, license file, and a brief summary of the package's functionality.
Please run the following script to verify the license information:
#!/bin/bash # Description: Verify the license information for KmerCamel # Test: Check if the LICENSE.txt file exists and contains the word "MIT" echo "Searching for LICENSE.txt file:" fd -i license echo "Checking content of LICENSE.txt file:" rg -i 'mit license' $(fd -i license) echo "Please review the output above to ensure the license information in meta.yaml matches the actual license file."
19-28: LGTM: Requirements section looks good. Verify dependencies.The requirements section includes appropriate build tools and dependencies for a C++ project using zlib and glpk. The use of {{ compiler('cxx') }} is correct for C++ projects in Bioconda.
Please run the following script to verify the dependencies:
8-11: LGTM: Source section is correctly defined. Verify URL and checksum.The source section follows Bioconda guidelines, and the use of the version variable in the URL is good for maintainability.
Please run the following script to verify the source URL and checksum:
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (4)
recipes/kmercamel/meta.yaml (4)
12-15: LGTM: Build settings are appropriate.The build number is correctly set to 0 for a new package. The use of
run_exportswithpin_subpackageis good for maintaining ABI compatibility.Consider adding a comment explaining the rationale behind using
max_pin="x". This can help future maintainers understand the versioning strategy.
29-31: LGTM: Test command is functional.The test command effectively checks if the kmercamel executable is available and outputs expected content.
Consider adding more comprehensive tests, such as checking for specific options or running a simple example, to ensure the tool functions correctly after installation.
33-37: LGTM: About section is well-defined.The about section correctly includes the home URL, license information, and a concise summary of the package's functionality.
Consider adding a
descriptionfield with a more detailed explanation of KmerCamel's features and use cases. This can help users better understand the tool's capabilities.
38-38: Remove extra blank lines at the end of the file.The linter detected extra blank lines at the end of the file. Please remove these to adhere to YAML best practices.
Apply this diff to fix the issue:
- -🧰 Tools
🪛 yamllint
[warning] 38-38: too many blank lines
(1 > 0) (empty-lines)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/kmercamel/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/kmercamel/meta.yaml
[warning] 38-38: too many blank lines
(1 > 0) (empty-lines)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/kmercamel/meta.yaml (3)
1-6: LGTM: Package and version definition looks good.The use of Jinja2 variables for version and SHA256 is a good practice for maintainability. The package name and version are correctly defined.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: LGTM: Source configuration is correct.The source URL is correctly defined using the version variable, which is good for maintainability. The SHA256 checksum is provided, ensuring integrity verification of the downloaded source.
18-27: LGTM: Requirements are well-defined.The build, host, and run requirements are appropriately specified. The inclusion of make and C++ compiler for building, and zlib and glpk for both host and run environments, seems consistent with the package's needs.
To ensure all necessary dependencies are included, let's verify the package requirements:
✅ Verification successful
To ensure all usages of
zlibandglpkare captured, let's search across the entire codebase:
Zlib is already included in the requirements
Thank you for your suggestion to add zlib to the requirements. However, I can confirm that zlib is already listed in both the build and run requirements of the recipe. Specifically:
requirements: build: - zlib run: - zlibTherefore, no changes are necessary regarding zlib in this recipe.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify package dependencies in the source code # Test: Search for zlib and glpk usage in the source code rg -i 'zlib|glpk' --type cppLength of output: 30
Script:
#!/bin/bash # Description: Search for zlib and glpk usage across the entire codebase rg -i 'zlib|glpk'Length of output: 303423
This adds the recipe for installing KmerCamel for computing masked superstrings for k-mer sets.
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