Update kmer-db #49740
Update kmer-db #49740
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request updates the The requirements section is significantly altered, with the removal of A new Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (5)
recipes/kmer-db/build.sh (2)
9-9: Approve make command update with a suggestion for cross-platform compatibilityThe updated
makecommand is a good improvement:
- It utilizes parallel jobs based on
CPU_COUNT, which can significantly speed up the build process.- The use of
g++-12aligns with the installation of gcc@12 for macOS.However, to ensure cross-platform compatibility, consider using a conditional statement to set the compiler.
Consider updating the make command as follows:
-make -j${CPU_COUNT} CXX=g++-12 +if [ "$uname_S" == "Darwin" ]; then + make -j${CPU_COUNT} CXX=g++-12 +else + make -j${CPU_COUNT} CXX=${CXX} +fiThis change will use
g++-12on macOS and fall back to the environment'sCXXvariable on other systems, ensuring better cross-platform compatibility.
1-11: Summary of changes and suggestionsThe modifications to the build script align well with the PR objectives. The addition of OS-specific handling and the use of
g++-12on macOS are good improvements for cross-platform compatibility and proper compilation.To recap the suggested changes:
- Fix the syntax error in the OS detection block and improve its robustness.
- Update the
makecommand to use conditional compilation based on the OS.These changes will enhance the script's reliability and cross-platform compatibility.
Would you like assistance in implementing these changes or creating a GitHub issue to track these improvements?
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[error] 4-4: Couldn't find 'fi' for this 'if'.
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[error] 4-4: Couldn't parse this if expression. Fix to allow more checks.
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recipes/kmer-db/meta.yaml (3)
1-1: Version update approved. Consider documenting potential breaking changes.The version update from 1.11.1 to 2.2.0 is significant. This major version bump might introduce breaking changes.
Consider adding a comment in the recipe or updating the package documentation to highlight any potential breaking changes or new features in this version.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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33-33: Consider adding more comprehensive tests.Given the significant version update, it might be beneficial to add more comprehensive tests to ensure all functionalities are working as expected.
Consider adding tests that exercise new features or changes introduced in version 2.2.0.
34-40: Extra section changes approved. Add newline at end of file.The addition of new platforms and appropriate linting skips are good changes.
Please add a newline character at the end of the file to address the yamllint warning.
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[error] 40-40: no new line character at the end of file
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🪛 Shellcheck
recipes/kmer-db/build.sh
[error] 4-4: Couldn't find 'fi' for this 'if'.
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[error] 4-4: Couldn't parse this if expression. Fix to allow more checks.
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🪛 yamllint
recipes/kmer-db/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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[error] 40-40: no new line character at the end of file
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🔇 Additional comments (3)
recipes/kmer-db/meta.yaml (3)
8-10: Build section changes approved.The build number reset and the addition of
run_exportsare appropriate for this version update. The pinning strategy helps ensure compatibility with dependent packages.
13-14: Source section changes approved. Addressinguses_vcs_urllint.The switch to using GitHub sources with a git revision tag aligns with the PR objectives and is a good practice for version control.
The
uses_vcs_urllint has been appropriately skipped in theextrasection. To verify the git URL and revision, run:This should return the commit hash for the v2.2.0 tag if it exists.
✅ Verification successful
Verification Successful
The
git_urlandgit_revspecified inrecipes/kmer-db/meta.yamlare valid and correctly reference thev2.2.0tag.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Verify git URL and revision git ls-remote https://github.com/refresh-bio/kmer-db.git v2.2.0Length of output: 123
19-21: Requirements changes approved. Verifyzlibremoval.The addition of
nasmand explicit C compiler are good changes. However, the removal ofzlibneeds verification.Please verify that
zlibis no longer required. Run the following to check forzlibusage in the source code:If there are no matches, it confirms that
zlibis no longer used.
recipes/kmer-db/build.sh
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| uname_S=`uname -s 2>/dev/null || echo not` | ||
| if [ "$uname_S" == "Darwin" ]; then brew install gcc@12; |
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Fix syntax error and improve robustness of OS-specific setup
The OS detection is a good addition for cross-platform compatibility. However, there are a few issues to address:
- The
ifstatement is not properly closed withfi. - The
brew installcommand might fail if Homebrew is not installed or if the user doesn't have sufficient permissions.
Please apply the following changes to fix the syntax error and improve robustness:
uname_S=`uname -s 2>/dev/null || echo not`
-if [ "$uname_S" == "Darwin" ]; then brew install gcc@12;
+if [ "$uname_S" == "Darwin" ]; then
+ if ! command -v brew &> /dev/null; then
+ echo "Homebrew is required but not installed. Please install Homebrew first."
+ exit 1
+ fi
+ if ! brew install gcc@12; then
+ echo "Failed to install gcc@12. Please check your Homebrew installation and permissions."
+ exit 1
+ fi
+fiThis change will:
- Properly close the
ifstatement. - Check if Homebrew is installed before attempting to use it.
- Handle potential failures when installing gcc@12.
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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.
| uname_S=`uname -s 2>/dev/null || echo not` | |
| if [ "$uname_S" == "Darwin" ]; then brew install gcc@12; | |
| uname_S=`uname -s 2>/dev/null || echo not` | |
| if [ "$uname_S" == "Darwin" ]; then | |
| if ! command -v brew &> /dev/null; then | |
| echo "Homebrew is required but not installed. Please install Homebrew first." | |
| exit 1 | |
| fi | |
| if ! brew install gcc@12; then | |
| echo "Failed to install gcc@12. Please check your Homebrew installation and permissions." | |
| exit 1 | |
| fi | |
| fi |
🧰 Tools
🪛 Shellcheck
[error] 4-4: Couldn't find 'fi' for this 'if'.
(SC1046)
[error] 4-4: Couldn't parse this if expression. Fix to allow more checks.
(SC1073)
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (3)
recipes/kmer-db/meta.yaml (3)
1-11: LGTM! Improved version management and cross-platform support.The update to version 2.2.1 and the addition of system-specific variables and SHA256 checksums greatly improve the recipe's cross-platform support. This change aligns well with the PR objectives of utilizing GitHub sources and supporting submodules.
Consider adding a comment explaining the significant version jump from 1.11.1 to 2.2.1, if there are any notable changes or reasons for this update.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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37-39: Consider expanding test coverage.While the current test command is valid, it might be beneficial to add more comprehensive tests to ensure the functionality of the updated version.
Consider adding more specific test commands, such as:
test: commands: - kmer-db > /dev/null - kmer-db --version - kmer-db --helpThis will help verify that the basic functionality and command-line interface are working as expected.
40-46: LGTM! Extra section added to improve cross-platform support and linting.The addition of the
extrasection withadditional-platformsimproves cross-platform support, which is great. Theskip-lintsentries are necessary due to the new build process using pre-built binaries.Consider adding a comment explaining why these specific lints are being skipped, to provide context for future maintainers.
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[error] 46-46: no new line character at the end of file
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- recipes/kmer-db/build.sh
🧰 Additional context used
🪛 yamllint
recipes/kmer-db/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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[error] 46-46: no new line character at the end of file
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🔇 Additional comments (2)
recipes/kmer-db/meta.yaml (2)
26-27: LGTM! Source configuration updated to use GitHub releases.The change to use GitHub releases instead of archives aligns perfectly with the PR objectives. This approach ensures that submodules are included, which was a key goal of this update. The use of variables for system-specific URLs and SHA256 checksums improves maintainability and cross-platform support.
19-23: LGTM! Build configuration updated correctly.The build number reset and the addition of the
run_exportssection are appropriate for the new version. The simplified build script suggests a shift to using pre-built binaries, which aligns with the PR objectives.To ensure the build process is correct, please run the following script:
recipes/kmer-db/meta.yaml
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| - osx-arm64 | ||
| skip-lints: | ||
| - uses_vcs_url | ||
| - missing_hash |
There was a problem hiding this comment.
Add a newline character at the end of the file.
To comply with YAML best practices and resolve the linting error, please add a newline character at the end of the file.
Apply this change to add a newline at the end of the file:
- uses_vcs_url
- missing_hash
+📝 Committable suggestion
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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.
| - missing_hash | |
| - uses_vcs_url | |
| - missing_hash | |
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🪛 yamllint
[error] 46-46: no new line character at the end of file
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/kmer-db/meta.yaml (2)
1-11: LGTM! Good job on multi-architecture support.The update to version 2.2.1 and the addition of system-specific variables and checksums for different architectures are well-implemented. This change improves the package's compatibility across various platforms.
Consider adding a comment explaining the purpose of the
systemvariable for better readability:{% set system = "x64_linux" %} # [linux and x86_64] # Used to select the correct binary for the current platform🧰 Tools
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[error] 1-1: syntax error: found character '%' that cannot start any token
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36-40: LGTM! Good addition of a help command test.The addition of the
kmer-db -helptest is a good improvement. It helps ensure that the basic functionality of the package is working correctly.Consider adding one more test to check the version of the installed package:
test: commands: - kmer-db > /dev/null - kmer-db -help - kmer-db -version | grep {{ version }}This will help verify that the correct version is installed.
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recipes/kmer-db/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/kmer-db/meta.yaml (5)
26-27: LGTM! Good switch to GitHub releases.The update to use GitHub releases instead of the archive is a good change. This ensures that submodules are included, addressing the concern mentioned in the PR objectives. The use of variables for the URL and SHA256 is also a good practice for maintainability.
47-47: LGTM! Newline issue resolved.The newline character has been added at the end of the file, addressing the issue mentioned in the past review comments.
Line range hint
1-47: Overall, good improvements with some minor issues to address.This update to the kmer-db recipe brings several positive changes:
- Version update to 2.2.1
- Multi-architecture support
- Switch to GitHub releases for source
- Addition of run_exports
- Improved test commands
Please address the following points:
- Clarify the change in the build process (using pre-built binaries)
- Verify the accuracy of the about section
- Consider adding a version check to the test commands
- Remove unnecessary skip-lints
Once these issues are addressed, the recipe will be in excellent shape for merging.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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13-23: LGTM! Good addition of run_exports.The reset of the build number and the addition of the
run_exportssection are appropriate for this update. The pinning strategy looks good and aligns with the PR objectives.Could you please clarify the change in the build process? It seems we're now using pre-built binaries instead of building from source. Is this intentional and aligned with Bioconda best practices?
To verify the contents of the downloaded archive, please run the following script:
#!/bin/bash # Description: Verify the contents of the downloaded kmer-db archive # Download the archive curl -LO https://github.com/refresh-bio/kmer-db/releases/download/v2.2.1/kmer-db-v2.2.1_x64_linux.tar.gz # List the contents of the archive tar -tvf kmer-db-v2.2.1_x64_linux.tar.gz # Check if the kmer-db binary is present and executable tar -xOf kmer-db-v2.2.1_x64_linux.tar.gz kmer-db > /dev/null && echo "kmer-db binary found and extracted successfully" || echo "Failed to extract kmer-db binary"
Line range hint
29-34: Verify the accuracy of the about section.The about section remains unchanged. Please verify that the home URL, summary, and license information are still accurate for version 2.2.1.
Run the following script to check for any changes in the project's README or LICENSE files:
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recipes/kmer-db/meta.yaml
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| extra: | ||
| additional-platforms: | ||
| - linux-aarch64 | ||
| - osx-arm64 | ||
| skip-lints: | ||
| - uses_vcs_url | ||
| - missing_hash |
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Good addition of platform support, but skip-lints need review.
The addition of support for linux-aarch64 and osx-arm64 is excellent for broader compatibility.
However, the skip-lints for 'uses_vcs_url' and 'missing_hash' seem unnecessary given the changes made in the source section. The recipe now uses a GitHub release URL (not a VCS URL) and includes a SHA256 hash. Consider removing these skip-lints:
extra:
additional-platforms:
- linux-aarch64
- osx-arm64
- skip-lints:
- - uses_vcs_url
- - missing_hash📝 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.
| extra: | |
| additional-platforms: | |
| - linux-aarch64 | |
| - osx-arm64 | |
| skip-lints: | |
| - uses_vcs_url | |
| - missing_hash | |
| extra: | |
| additional-platforms: | |
| - linux-aarch64 | |
| - osx-arm64 |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/kmer-db/meta.yaml (3)
13-23: LGTM: Build section updates with a minor suggestion.The package name and version are correctly set, and resetting the build number to 0 for the new version is appropriate. The addition of the
run_exportssection with proper version pinning is an excellent practice for dependency management.The build script has been simplified to copy the binary directly. While this works, it might be more robust to add an error check:
script: mkdir -p ${PREFIX}/bin && cp -r kmer-db ${PREFIX}/bin || exit 1This ensures the build fails if the copy operation doesn't succeed.
41-47: Consider removing unnecessary skip-lints.The addition of support for linux-aarch64 and osx-arm64 is excellent for broader compatibility. However, the skip-lints for 'should_not_be_noarch_source' and 'should_not_be_noarch_compiler' seem unnecessary given the changes made in the recipe. The recipe now uses architecture-specific binaries and doesn't involve compilation. Consider removing these skip-lints:
extra: additional-platforms: - linux-aarch64 - osx-arm64 - skip-lints: - - should_not_be_noarch_source - - should_not_be_noarch_compiler
48-49: Remove extra blank lines at the end of the file.To comply with YAML best practices and resolve the linting warning, please remove the extra blank lines at the end of the file.
Apply this change:
- should_not_be_noarch_compiler - -🧰 Tools
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[warning] 49-49: too many blank lines
(2 > 0) (empty-lines)
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recipes/kmer-db/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[warning] 49-49: too many blank lines
(2 > 0) (empty-lines)
🔇 Additional comments (3)
recipes/kmer-db/meta.yaml (3)
1-11: LGTM: Version update and multi-architecture support.The version update to 2.2.1 and the addition of system-specific variables and checksums for multiple architectures (x86_64 and arm64 for both Linux and macOS) are excellent improvements. This change aligns with the PR objectives and enhances the package's compatibility across different platforms.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
26-27: LGTM: Improved source URL and dynamic checksums.The update to use GitHub releases instead of archives in the source URL is an excellent change. This ensures that submodules are included, addressing the main objective of the PR. The use of dynamic SHA256 checksums based on the system architecture is a robust approach to support multiple platforms.
38-39: LGTM: Enhanced test coverage.The addition of the
kmer-db -helptest command is a good improvement. This helps ensure that the binary is not only present but also executable and responds to basic commands.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/kmer-db/meta.yaml (2)
13-23: Good updates to build section, with a minor suggestion.The reset of the build number to 0 for the new version and the addition of the
run_exportssection with proper pinning are excellent changes. These ensure correct version management and dependency handling.However, the build script could be improved slightly:
Consider updating the build script for better error handling and verbosity:
- script: mkdir -p ${PREFIX}/bin; ls; cp -r kmer-db ${PREFIX}/bin + script: | + mkdir -p "${PREFIX}/bin" + cp -rv kmer-db "${PREFIX}/bin/" + if [ ! -f "${PREFIX}/bin/kmer-db" ]; then + echo "Error: kmer-db binary not found or not copied correctly" + exit 1 + fiThis change adds error checking and increases verbosity, which can help with debugging if issues arise during the build process.
41-47: Consider removing unnecessary skip-lints.The addition of support for linux-aarch64 and osx-arm64 is excellent and aligns well with the multi-architecture approach in this recipe.
However, the skip-lints
should_be_noarch_genericandshould_not_be_noarch_sourceseem unnecessary:
- This package is clearly not "noarch" as it provides architecture-specific binaries.
- The source is not using a VCS URL, so the
should_not_be_noarch_sourcelint is not applicable.Consider removing the
skip-lintssection entirely:extra: additional-platforms: - linux-aarch64 - osx-arm64 - skip-lints: - - should_be_noarch_generic - - should_not_be_noarch_sourceThis will help maintain a cleaner recipe without suppressing potentially useful linter warnings in the future.
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🪛 yamllint
recipes/kmer-db/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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[warning] 48-48: too many blank lines
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🔇 Additional comments (4)
recipes/kmer-db/meta.yaml (4)
1-11: Excellent update with multi-platform support!The version update to 2.2.1 and the addition of system-specific variables and SHA256 checksums for different architectures (x86_64 and arm64 for both Linux and macOS) greatly improve the package's compatibility across platforms. This aligns well with the PR objectives and Bioconda best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
26-27: Excellent update to source URL and checksum!The change to use GitHub releases instead of the archive aligns perfectly with the PR objectives. The use of variables for the system and SHA256 checksum ensures consistency and makes the recipe more maintainable across different platforms.
38-39: Good addition to test commands!The new test command
kmer-db -helpprovides an additional check to ensure the package is correctly installed and functional. This improves the overall reliability of the package installation process.
Line range hint
1-48: Regarding static analysis hints
The yamllint error about the '%' character can be safely ignored. This is a false positive due to the use of Jinja2 templating in the YAML file, which is a common practice in Bioconda recipes.
The warning about too many blank lines at the end of the file has already been addressed in a previous review comment.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/kmer-db/meta.yaml (2)
13-23: Good updates to build section, with a minor suggestion.The reset of the build number to 0 for the new version and the addition of the
run_exportssection with proper version pinning are excellent changes. These updates align with Bioconda best practices and ensure proper dependency management.However, the build script could be improved slightly:
Consider updating the build script for better error handling and verbosity:
- script: mkdir -p ${PREFIX}/bin; ls; cp -r kmer-db ${PREFIX}/bin + script: | + mkdir -p "${PREFIX}/bin" + cp -v kmer-db "${PREFIX}/bin/" || { echo "Error: Failed to copy kmer-db binary"; exit 1; }This change adds error checking and increases verbosity, which can help with debugging if issues arise during the build process.
48-48: Minor: Remove extra blank lines at the end of the file.To comply with YAML best practices and resolve the linting warning, please remove the extra blank lines at the end of the file.
Apply this change:
skip-lints: - should_be_noarch_generic - should_not_be_noarch_source - -🧰 Tools
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[warning] 48-48: too many blank lines
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recipes/kmer-db/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[warning] 48-48: too many blank lines
(1 > 0) (empty-lines)
🔇 Additional comments (3)
recipes/kmer-db/meta.yaml (3)
1-11: Excellent update with improved cross-platform support!The version update to 2.2.2 and the addition of system-specific variables and SHA256 checksums for different architectures (x86_64 and arm64 for both Linux and macOS) significantly improve cross-platform support. This change aligns well with the PR objectives and follows Bioconda best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
26-27: Excellent update to source URL and checksum handling!The change to use GitHub releases instead of the archive aligns perfectly with the PR objectives. This ensures that submodules are included, which was the main goal of this update. The use of Jinja2 variables for both the system-specific URL and SHA256 checksum is a great practice, allowing for flexible and accurate package building across different platforms.
39-40: Good addition to test commands.The inclusion of
kmer-db -helpas an additional test command is a valuable improvement. This helps ensure that the installed package not only exists but also responds correctly to basic commands, enhancing the reliability of the installation process.
| extra: | ||
| additional-platforms: | ||
| - linux-aarch64 | ||
| - osx-arm64 | ||
| skip-lints: | ||
| - should_be_noarch_generic | ||
| - should_not_be_noarch_source |
There was a problem hiding this comment.
Good addition of platform support, but skip-lints need review.
The addition of support for linux-aarch64 and osx-arm64 is excellent for broader compatibility. However, the skip-lints for 'should_be_noarch_generic' and 'should_not_be_noarch_source' seem unnecessary and potentially contradictory given the nature of the package (architecture-specific binaries).
Consider removing the skip-lints section:
extra:
additional-platforms:
- linux-aarch64
- osx-arm64
- skip-lints:
- - should_be_noarch_generic
- - should_not_be_noarch_sourceThese lints are typically used for packages that should be architecture-independent, which doesn't apply to kmer-db as it provides architecture-specific binaries.
📝 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.
| extra: | |
| additional-platforms: | |
| - linux-aarch64 | |
| - osx-arm64 | |
| skip-lints: | |
| - should_be_noarch_generic | |
| - should_not_be_noarch_source | |
| extra: | |
| additional-platforms: | |
| - linux-aarch64 | |
| - osx-arm64 |
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🧹 Outside diff range and nitpick comments (1)
recipes/kmer-db/meta.yaml (1)
40-42: Good addition to test commands, with a suggestion for improvement.The addition of
kmer-db -helpto the test commands is a good practice to ensure the binary is functional. To further improve the test, consider capturing and verifying the output:test: commands: - kmer-db > /dev/null - kmer-db -help 2>&1 | grep -q "kmer-db options"This change would verify that the help output contains expected content, providing a more robust test.
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recipes/kmer-db/meta.yaml
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🔇 Additional comments (5)
recipes/kmer-db/meta.yaml (5)
1-11: Excellent update with improved cross-platform support!The version update and the addition of system-specific variables and SHA256 checksums for different architectures (x86_64 and arm64 for both Linux and macOS) significantly improve the package's cross-platform compatibility. This change aligns well with the PR objective of utilizing GitHub sources and supporting multiple platforms.
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19-25: Good updates to build section and dependency management!The changes in the build section are appropriate:
- Resetting the build number to 0 is correct for a new version.
- Adding the
run_exportssection withpin_subpackageis excellent for proper dependency management.- The updated build script ensures the kmer-db binary is correctly placed in the bin directory.
These changes align well with Bioconda best practices and the PR objectives.
28-29: Source URL and checksum updates align with PR objectives!The changes to the source section are excellent:
- Updating the URL to use GitHub releases instead of the archive addresses the PR's main objective of utilizing GitHub sources.
- Using the
sha256variable ensures the correct checksum is applied for each target architecture.These changes improve the recipe's reliability and cross-platform compatibility.
50-50: Ensure proper file endingTo comply with YAML best practices, please ensure that the file ends with a single newline character. This addresses both the yamllint warning and a previous review comment.
If not already present, add a newline at the end of the file:
extra: additional-platforms: - linux-aarch64 - osx-arm64 +🧰 Tools
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43-49:⚠️ Potential issueGood addition of platform support, but skip-lints need review.
The addition of support for linux-aarch64 and osx-arm64 is excellent for broader compatibility and aligns with the PR objectives.
However, as mentioned in a previous review comment, the skip-lints for 'should_be_noarch_generic' and 'should_not_be_noarch_source' seem unnecessary and potentially contradictory given the nature of the package (architecture-specific binaries).
Consider removing the skip-lints section:
extra: additional-platforms: - linux-aarch64 - osx-arm64 - skip-lints: - - should_be_noarch_generic - - should_not_be_noarch_sourceThese lints are typically used for packages that should be architecture-independent, which doesn't apply to kmer-db as it provides architecture-specific binaries.
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🧹 Outside diff range and nitpick comments (3)
recipes/kmer-db/meta.yaml (3)
13-25: LGTM: Build section updates are appropriate.The changes in the build section, including resetting the build number and adding the
run_exportssection, are well-implemented. The updated build script correctly copies the binary, aligning with the PR objective to use precompiled binaries.Consider adding a comment explaining the reason for using precompiled binaries, e.g.:
# Using precompiled binaries due to C++20 multithreading features compatibility script: | mkdir -p "${PREFIX}/bin" cp -v kmer-db "${PREFIX}/bin/" || { echo "Error: Failed to copy kmer-db binary"; exit 1; }
38-42: Consider enhancing the test command.The addition of the
kmer-db -helptest is good. To make it more robust, consider capturing and checking the output:test: commands: - kmer-db > /dev/null - kmer-db -help 2>&1 | grep -q "Usage"This change ensures that the help output contains expected content.
50-50: Remove extra blank line at the end of the file.While not a significant issue, it's generally good practice to have exactly one newline at the end of the file. Consider removing the extra blank line.
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recipes/kmer-db/meta.yaml
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🔇 Additional comments (4)
recipes/kmer-db/meta.yaml (4)
1-11: LGTM: Version update and system-specific configurations look good.The version update to 2.2.2 and the addition of system-specific variables and SHA256 checksums for different architectures are well-implemented. This approach ensures proper handling of the package across various platforms.
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27-29: LGTM: Source section updated correctly for precompiled binaries.The change to use GitHub releases in the source URL and the templated SHA256 checksum are appropriate for distributing precompiled binaries. This ensures that the correct binary is downloaded for each supported architecture.
Line range hint
1-50: Overall, the changes look good and align with the PR objectives.The update to use precompiled binaries addresses the compilation issues with clang and C++20 multithreading features. The recipe has been appropriately modified to handle different architectures and the build process has been simplified.
A few minor suggestions have been made to improve the recipe further:
- Adding a comment explaining the use of precompiled binaries.
- Enhancing the test command to check the help output.
- Removing unnecessary skip-lints.
- Removing the extra blank line at the end of the file.
Once these minor adjustments are made, the PR should be ready for merging after successful tests.
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43-49:⚠️ Potential issueRemove unnecessary skip-lints.
The addition of support for linux-aarch64 and osx-arm64 is excellent for broader compatibility. However, the skip-lints for 'should_be_noarch_generic' and 'should_not_be_noarch_source' seem unnecessary and potentially contradictory given the nature of the package (architecture-specific binaries).
Consider removing the skip-lints section:
extra: additional-platforms: - linux-aarch64 - osx-arm64 - skip-lints: - - should_be_noarch_generic - - should_not_be_noarch_sourceThese lints are typically used for packages that should be architecture-independent, which doesn't apply to kmer-db as it provides architecture-specific binaries.
Likely invalid or redundant comment.
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🧹 Outside diff range and nitpick comments (2)
recipes/kmer-db/meta.yaml (2)
1-11: LGTM! Good job on improving cross-platform support.The update to version 2.2.2 and the addition of system variables and SHA256 checksums for different architectures significantly improve the package's cross-platform support. The use of Jinja2 templating for conditional inclusion is correct.
Consider adding a comment explaining the purpose of the
systemvariable for better readability:{% set system = "x64_linux" %} # [linux and x86_64] # Used to select the correct binary for the current platform🧰 Tools
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19-25: LGTM! Good improvements to build section.The changes in the build section are appropriate:
- Resetting the build number to 0 for the new version is correct.
- Adding the
run_exportssection improves dependency management.- Updating the build script to copy the pre-compiled binary instead of compiling from source aligns with the PR objectives.
- The error handling in the copy command is a good practice.
Consider adding a comment explaining why compilation is no longer needed:
script: | # Using pre-compiled binaries due to C++20 multithreading features compatibility issues mkdir -p "${PREFIX}/bin" cp -v kmer-db "${PREFIX}/bin/" || { echo "Error: Failed to copy kmer-db binary"; exit 1; }
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📒 Files selected for processing (1)
- recipes/kmer-db/meta.yaml (2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/kmer-db/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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[warning] 50-50: too many blank lines
(1 > 0) (empty-lines)
🔇 Additional comments (4)
recipes/kmer-db/meta.yaml (4)
28-29: LGTM! Appropriate changes to source section.The updates to the source section are correct and align with the switch to pre-compiled binaries:
- The URL now points to GitHub releases instead of the source archive.
- The use of the
sha256variable ensures the correct checksum is used for each platform.These changes support the PR's objective of using pre-compiled binaries to address compilation issues.
41-41: LGTM! Good addition to test commands.Adding the
kmer-db -helpcommand to the test section is a good practice. It not only checks for the existence of the command but also verifies that it runs without errors, providing a more thorough test of the installed package.
43-49:⚠️ Potential issueGood addition of platform support, but remove unnecessary skip-lints.
The addition of support for linux-aarch64 and osx-arm64 is excellent for broader compatibility. However, the skip-lints for 'should_be_noarch_generic' and 'should_not_be_noarch_source' are unnecessary and potentially contradictory given the nature of the package (architecture-specific binaries).
Remove the skip-lints section:
extra: additional-platforms: - linux-aarch64 - osx-arm64 - skip-lints: - - should_be_noarch_generic - - should_not_be_noarch_sourceThese lints are typically used for packages that should be architecture-independent, which doesn't apply to kmer-db as it provides architecture-specific binaries.
50-50:⚠️ Potential issueAdd a newline character at the end of the file.
To comply with YAML best practices and resolve the linting error, please add a newline character at the end of the file.
Apply this change to add a newline at the end of the file:
- osx-arm64 +🧰 Tools
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[warning] 50-50: too many blank lines
(1 > 0) (empty-lines)
Due to problems with compiling sources with clang (the software uses c++20 multithreading features which are available only in g++ 11 or higher) we configured package to download precompiled binaries. We would appreciate if you accept our pull request once the tests are passed.
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