Update crux-toolkit to 4.2 #51625
Update crux-toolkit to 4.2 #51625
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/crux-toolkit/meta.yaml (2)
17-21: Consider adding run_exports for ABI compatibility.As per Bioconda guidelines, to prevent API/ABI breakage issues, consider adding
run_exportsto specify the version constraints for downstream packages.Example addition:
build: run_exports: - {{ pin_subpackage('crux-toolkit', max_pin='x.x') }}
23-25: Consider enhancing version test.The current test only checks if the version command works. Consider enhancing it to verify the exact version number.
test: commands: - - crux version 2> /dev/null | grep -q 'Crux version' + - crux version 2> /dev/null | grep -q "Crux version {{ version }}"
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📒 Files selected for processing (1)
- recipes/crux-toolkit/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/crux-toolkit/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/crux-toolkit/meta.yaml (4)
27-32: LGTM!The metadata section is complete and appropriate.
34-40: LGTM!The maintainers list is properly configured and includes the PR author.
1-5: Verify the new version exists.The version update looks correct. Let's verify that version 4.2 exists in the upstream repository.
✅ Verification successful
Let me try a different verification approach by checking if the version exists in the upstream repository's release page.
Version 4.2 exists and is available in the upstream repository
The verification confirms that version 4.2 exists in the upstream repository's downloads page. The version update in the meta.yaml file is correct and corresponds to a real release.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify version 4.2 exists in the upstream repository # Test: Check if the Linux distribution URL is accessible curl -I https://noble.gs.washington.edu/crux-downloads/crux-4.2/crux-4.2.Linux.x86_64.zipLength of output: 778
Script:
#!/bin/bash # Check if the version exists in the downloads page curl -s https://noble.gs.washington.edu/crux-downloads/ | grep -o "crux-4.2"Length of output: 94
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
7-11: Verify SHA256 checksums match the distribution files.The URLs have been correctly updated for the new version. Let's verify the SHA256 checksums.
recipes/crux-toolkit/meta.yaml
Outdated
| build: | ||
| number: 2 | ||
| script: "mkdir -p $PREFIX/bin; chmod a+x bin/*; cp bin/* $PREFIX/bin" |
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Reset build number for new version.
When updating to a new version, the build number should typically be reset to 0.
build:
- number: 2
+ number: 0
script: "mkdir -p $PREFIX/bin; chmod a+x bin/*; cp bin/* $PREFIX/bin"📝 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.
| build: | |
| number: 2 | |
| script: "mkdir -p $PREFIX/bin; chmod a+x bin/*; cp bin/* $PREFIX/bin" | |
| build: | |
| number: 0 | |
| script: "mkdir -p $PREFIX/bin; chmod a+x bin/*; cp bin/* $PREFIX/bin" |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/crux-toolkit/meta.yaml (1)
17-21: Consider adding run_exports for ABI stabilitySince this is a C/C++ package, consider adding
run_exportsto handle ABI compatibility as mentioned in the Bioconda guidelines. This helps ensure proper runtime dependencies are propagated to dependent packages.Example addition:
build: run_exports: - {{ pin_subpackage('crux-toolkit', max_pin='x.x') }}
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📒 Files selected for processing (1)
- recipes/crux-toolkit/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/crux-toolkit/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/crux-toolkit/meta.yaml (5)
1-5: LGTM: Version update looks correctThe version bump from 4.1 to 4.2 is properly implemented using Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
23-25: LGTM: Test configuration is appropriateThe version check test is sufficient for a binary package distribution.
27-32: LGTM: Package metadata is completeAll required metadata fields are properly specified with appropriate license information.
34-40: LGTM: Extra configuration is appropriateThe maintainers list is properly specified and the skip-lints configuration is reasonable for a binary package.
7-11: Verify package availability and checksumsLet's verify:
- The download URLs are accessible
- The package is not already in conda-forge
✅ Verification successful
Based on the results from the shell scripts, I can now generate the final response:
URLs are accessible and package is not in conda-forge
- Both Linux and Darwin download URLs return HTTP 200 OK, confirming they are accessible
- No existing
crux-toolkitpackages were found in conda-forge's repositoryNote: I've categorized this as because:
- The URLs in the recipe are valid and accessible
- The package is not already present in conda-forge, making this a valid new addition
- The SHA256 checksums are provided in the recipe, which is a required component
The original review's concerns have been adequately addressed by these verification checks.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if URLs are accessible and verify checksums echo "Checking Linux URL..." curl -sI "https://noble.gs.washington.edu/crux-downloads/crux-4.2/crux-4.2.Linux.x86_64.zip" | head -n 1 echo "Checking Darwin URL..." curl -sI "https://noble.gs.washington.edu/crux-downloads/crux-4.2/crux-4.2.Darwin.x86_64.zip" | head -n 1 # Check if package exists in conda-forge echo "Checking conda-forge..." curl -sL "https://conda.anaconda.org/conda-forge/noarch/repodata.json" | jq '.packages | keys[] | select(startswith("crux-toolkit-"))'Length of output: 544
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/crux-toolkit/meta.yaml (1)
27-29: Consider enhancing test coverage.While the current test verifies basic functionality, consider adding:
- Help command test (
crux --help)- Basic functionality test for a core command
Would you like me to provide examples of additional test commands?
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📒 Files selected for processing (1)
- recipes/crux-toolkit/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/crux-toolkit/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/crux-toolkit/meta.yaml (4)
1-5: LGTM: Version update looks correct.The package version has been properly updated to 4.2 using Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
17-25: LGTM: Appropriate compiler configuration for binary distribution.The addition of
ignore_run_exports_fromfor the C/C++ compilers is correct for pre-built binaries, as it prevents unnecessary compiler runtime dependencies.
38-44: LGTM: Recipe maintainers properly documented.Good addition of recipe maintainers, which helps with package maintenance tracking.
7-11: Verify source URLs and checksums.The URLs and checksums have been updated for the new version. Let's verify their validity.
There was a problem hiding this comment.
Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/crux-toolkit/meta.yaml (1)
22-24: Consider enhancing version test.The current test only verifies that the version command works. Consider enhancing it to verify the specific version number.
- - crux version 2> /dev/null | grep -q 'Crux version' + - crux version 2> /dev/null | grep -q "Crux version ${PKG_VERSION}"
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📒 Files selected for processing (1)
- recipes/crux-toolkit/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/crux-toolkit/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/crux-toolkit/meta.yaml (4)
1-5: LGTM! Version update looks good.The version bump to 4.2 is consistent with the PR objectives.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
26-31: LGTM! Package metadata is complete.All required metadata fields are present and properly formatted.
33-39: LGTM! Extra configuration is appropriate.The recipe maintainers list and skip-lints configuration are properly set up.
7-11: Verify source URLs and checksums.Let's verify the accessibility of the URLs and validate the checksums.
recipes/crux-toolkit/meta.yaml
Outdated
| requirements: | ||
| run: | ||
| - {{ compiler('c') }} | ||
| - {{ compiler('cxx') }} |
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Fix requirements section: Move compilers to build requirements.
The compiler requirements are incorrectly placed in the run section. Compilers are build-time dependencies and should be in the build section.
Apply this fix:
requirements:
- run:
+ build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}📝 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.
| requirements: | |
| run: | |
| - {{ compiler('c') }} | |
| - {{ compiler('cxx') }} | |
| requirements: | |
| build: | |
| - {{ compiler('c') }} | |
| - {{ compiler('cxx') }} |
There was a problem hiding this comment.
Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/crux-toolkit/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/crux-toolkit/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/crux-toolkit/meta.yaml (5)
1-5: LGTM: Version update looks correctThe version update to 4.2 is properly implemented using Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
22-24: LGTM: Test configuration is appropriateThe test command properly verifies the Crux version installation.
26-31: LGTM: Package metadata is complete and accurateAll required metadata fields are present and correctly maintained.
33-39: LGTM: Extra configuration properly updatedThe addition of recipe maintainers and skip-lints configuration is appropriate.
7-11: Verify source URLs and checksumsLet's verify that the URLs are accessible and the checksums match the downloaded files.
recipes/crux-toolkit/meta.yaml
Outdated
| requirements: | ||
| buil: | ||
| - {{ stdlib('c') }} | ||
| - {{ stdlib('cxx') }} |
There was a problem hiding this comment.
Fix requirements section issues
There are two issues in the requirements section:
- There's a typo in the
builkey (should bebuild) - The change from
compilertostdlibseems incorrect for a C/C++ project
Apply this fix:
requirements:
- buil:
- - {{ stdlib('c') }}
- - {{ stdlib('cxx') }}
+ build:
+ - {{ compiler('c') }}
+ - {{ compiler('cxx') }}📝 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.
| requirements: | |
| buil: | |
| - {{ stdlib('c') }} | |
| - {{ stdlib('cxx') }} | |
| requirements: | |
| build: | |
| - {{ compiler('c') }} | |
| - {{ compiler('cxx') }} |
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