Update ucsc-pslcdnafilter to 472 #51700
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/ucsc-pslcdnafilter/include.macos.patch (1)
1-27: Consider adding CI tests for cross-platform compatibility.Since these changes are specifically for macOS compatibility, consider adding CI tests to verify the build process works correctly across different platforms (Linux, macOS) to catch potential issues early.
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📒 Files selected for processing (3)
- recipes/ucsc-pslcdnafilter/build.sh (2 hunks)
- recipes/ucsc-pslcdnafilter/include.macos.patch (1 hunks)
- recipes/ucsc-pslcdnafilter/meta.yaml (3 hunks)
🔇 Additional comments (10)
recipes/ucsc-pslcdnafilter/build.sh (2)
11-11: LGTM: Consistent optimization flagsAdding
-O3toCXXFLAGSmatches the optimization level already present inCFLAGS, ensuring consistent compiler optimization across C and C++ code.
21-22: LGTM: Improved executable installationThe two-step process of explicitly setting permissions before moving the executable is a better practice than direct copying because it:
- Ensures correct executable permissions (0755)
- Uses move operation which is more efficient than copy
recipes/ucsc-pslcdnafilter/include.macos.patch (3)
15-16: LGTM! Consistent include path configuration.The addition of
-I${PREFIX}/includetoKENT_INCmaintains consistency with the common.mk changes.
23-24: Verify Python 3 compatibility before removing version constraint.While removing the Python 2.7 dependency is good, we should ensure the script is compatible with Python 3 before making it version-agnostic.
Let's check for potential Python 2/3 compatibility issues:
#!/bin/bash # Description: Check for common Python 2/3 compatibility issues in the script # Look for print statements, unicode handling, etc. # Test: Search for Python 2-specific syntax that might break in Python 3 rg -A 2 "print [^(]|unicode|basestring|raw_input|xrange|\.iteritems\(\)|\.itervalues\(\)|\.iterkeys\(\)" "kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed" # Test: Look for division operations that might behave differently rg -A 2 "[^/]/[^/]" "kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed"
7-8: LGTM! Verify header availability in conda-build environment.The addition of
-I${PREFIX}/includetoHG_INCis correct and follows Conda packaging guidelines.Let's verify the headers are available in the conda-build environment:
✅ Verification successful
Addition of ${PREFIX}/include path is correct and verified
The modification is verified to be correct because:
- It's a standard pattern used across all UCSC tools in the repository (identical patches exist in ucsc-bigwigsummary, ucsc-blat, ucsc-fatotwobit, etc.)
- The package has host dependencies (libpng, mysql-connector-c, zlib, etc.) that require their headers to be found during build
- The build.sh already sets up INCLUDE_PATH and CXXFLAGS to use ${PREFIX}/include, making this change consistent with the overall build configuration
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check if critical headers are present in PREFIX/include # Note: This helps ensure the build will succeed with the new include path # Test: List header files in ${PREFIX}/include that might be required fd . "${PREFIX}/include" -t f -e .h -e .hppLength of output: 452
Script:
#!/bin/bash # Let's verify if the patch file exists and examine its content fd -t f "include.macos.patch" recipes # Check if there are any header files referenced in the patch rg -A 2 "\.h" recipes/ucsc-pslcdnafilter/include.macos.patch # Look for any build-related files that might give us context about required headers fd -t f "build.sh|meta.yaml" recipes/ucsc-pslcdnafilterLength of output: 495
Script:
#!/bin/bash # Let's examine the build.sh and meta.yaml for dependencies that might require headers cat recipes/ucsc-pslcdnafilter/meta.yaml cat recipes/ucsc-pslcdnafilter/build.sh # Check if similar patches exist in other UCSC tools to validate this is a common pattern head -n 10 recipes/ucsc-*/include.macos.patchLength of output: 6478
recipes/ucsc-pslcdnafilter/meta.yaml (5)
14-15: LGTM! Platform-specific patches are properly configured.The patch configuration correctly handles both Linux and macOS platforms using conditional selectors.
Line range hint
19-21: LGTM! Proper version pinning configuration.The
run_exportssection correctly usespin_subpackagewithmax_pin=None, ensuring exact version matching which helps prevent ABI incompatibilities.
45-46: LGTM! URL improvements and version-specific documentation.The URL updates are good improvements:
- Using HTTPS for security
- Version-specific documentation link ensures accuracy
Also applies to: 54-54
3-4: Verify version compatibility for the significant version bump.The update from version 469 to 472 is a significant jump. Since this is a bioinformatics tool, we should ensure there are no breaking changes in the tool's interface.
31-37: Verify if zlib is required at runtime.While zlib is listed as a host dependency, it's not included in the run dependencies. If the tool uses compression functionality, zlib might be needed at runtime.
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