update to verkko v2.2.1 #51111
update to verkko v2.2.1 #51111
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🚧 Files skipped from review as they are similar to previous changes (2)
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/verkko/build.sh (1)
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10-22: LGTM: Overall script structure is sound.The unchanged parts of the script maintain good practices:
- OS-specific handling for macOS (Darwin) to ensure compatibility with system Boost.
- Proper build process with clean and parallel make.
- Correct installation of binaries and libraries to $PREFIX.
As a minor suggestion for improved readability, consider adding a comment before the Darwin-specific block explaining its purpose, e.g.:
# Remove built-in Boost library on macOS to use system Boost instead if [ "$(uname)" == "Darwin" ]; then ... fi
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📒 Files selected for processing (2)
- recipes/verkko/build.sh (1 hunks)
- recipes/verkko/meta.yaml (3 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/verkko/meta.yaml
🔇 Additional comments (3)
recipes/verkko/build.sh (3)
4-4: LGTM: Directory creation is appropriate.Creating the
$PREFIX/bindirectory ensures that the subsequent operations have a valid target location. This is a good practice in build scripts.
6-8: LGTM: Appropriate compilation and linking flags set.The added environment variable exports are crucial for the build process:
LDFLAGScorrectly adds the$PREFIX/libto the library search path.CFLAGSandCXXFLAGSboth include the-O3optimization flag, which is suitable for release builds.CXXFLAGSalso includes the prefix include directory in the include search path.These changes ensure that the build process uses the correct libraries and include files from the conda environment, and applies appropriate optimizations.
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1-22: Overall LGTM with a request for version verification.The changes to the build script are appropriate and improve the build process by setting correct compilation and linking flags. The overall structure of the script is sound and follows good practices for bioconda recipes.
However, I noticed that the PR objectives mention updating verkko to version 2.2.1, but this version update is not reflected in the build script. Could you please verify that the version update is handled correctly, possibly in other files of the PR that are not included in this review?
To verify the version update, please run the following command:
✅ Verification successful
Version update verified in
recipes/verkko/meta.yaml.The PR correctly updates verkko to version 2.2.1 in
recipes/verkko/meta.yamlusing templating syntax.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for version update in meta.yaml file # Expected result: Should show the updated version number (2.2.1) rg --type yaml 'version:\s*2\.2\.1' recipes/verkko/meta.yamlLength of output: 62
Script:
#!/bin/bash # Description: Search the entire repository for version 2.2.1 to verify the update # Expected result: Should show occurrences of '2.2.1' indicating the version update rg '2\.2\.1'Length of output: 12013
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@mencian I think the issue is the change to compiler{'rust'} rather than the explicit version. For some reason that changes the build path output (see #48088). It's incorrect to use rukki 0.3.0 since the code is specifically a submodule in verkko so a specific tag was tested/built with verkko and 0.3.0 might not be it. |
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Reverting to an explicit version of rust did the trick; apologies for not looking into the previous PRs. |
Updating to bug fix release of verkko v2.2.1
Summary by CodeRabbit
New Features
verkkopackage to 2.2.1.Bug Fixes
Documentation