Rebuild regenie recipe #52074
Rebuild regenie recipe #52074
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📝 WalkthroughWalkthroughThe pull request introduces significant modifications to the Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/regenie/build.sh (1)
20-21: Consider consolidating include path settingsThe include path is set in multiple variables (INCLUDES, CXXFLAGS, CFLAGS, and CPATH). While this works, it might be cleaner to use a single variable that others reference.
-export INCLUDES="-I${PREFIX}/include" -export CFLAGS="${CFLAGS} -O3 -I$PREFIX/include" -export CPATH="${PREFIX}/include" +export INCLUDES="-I${PREFIX}/include" +export CFLAGS="${CFLAGS} -O3 ${INCLUDES}" +export CPATH="${PREFIX}/include"
📜 Review details
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📒 Files selected for processing (18)
recipes/regenie/build.sh(1 hunks)recipes/regenie/build_failure.osx-64.yaml(0 hunks)recipes/regenie/conda_build_config.yaml(0 hunks)recipes/regenie/meta.yaml(4 hunks)recipes/regenie/patches/0001-use-shared-cxxopts.patch(0 hunks)recipes/regenie/patches/0002-import-shared-Eigen3.patch(0 hunks)recipes/regenie/patches/0003-use-conda-cmakelists.patch(0 hunks)recipes/regenie/patches/0004-fix-fail-exit-on-help.patch(0 hunks)recipes/regenie/patches/0005-use-conda-cmakelist-file.patch(0 hunks)recipes/regenie/patches/0006-fix-cmakelist-file.patch(0 hunks)recipes/regenie/patches/0007-fix-cmakelist-file-for-osx.patch(0 hunks)recipes/regenie/patches/0008-fix-cmakelist-file-for-osx-eigen4.patch(0 hunks)recipes/regenie/patches/0009-update-cmake-file-for-conda.patch(0 hunks)recipes/regenie/patches/0010-update-cmakelist-file-for-v3.2.7.patch(0 hunks)recipes/regenie/patches/0011-update-cmakelist-file-for-v3.2.9.patch(0 hunks)recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch(0 hunks)recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch(0 hunks)recipes/regenie/patches/0014-update-cmakelist.txt-for-v3.5.patch(0 hunks)
💤 Files with no reviewable changes (16)
- recipes/regenie/build_failure.osx-64.yaml
- recipes/regenie/conda_build_config.yaml
- recipes/regenie/patches/0001-use-shared-cxxopts.patch
- recipes/regenie/patches/0002-import-shared-Eigen3.patch
- recipes/regenie/patches/0003-use-conda-cmakelists.patch
- recipes/regenie/patches/0004-fix-fail-exit-on-help.patch
- recipes/regenie/patches/0005-use-conda-cmakelist-file.patch
- recipes/regenie/patches/0006-fix-cmakelist-file.patch
- recipes/regenie/patches/0007-fix-cmakelist-file-for-osx.patch
- recipes/regenie/patches/0008-fix-cmakelist-file-for-osx-eigen4.patch
- recipes/regenie/patches/0009-update-cmake-file-for-conda.patch
- recipes/regenie/patches/0010-update-cmakelist-file-for-v3.2.7.patch
- recipes/regenie/patches/0011-update-cmakelist-file-for-v3.2.9.patch
- recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch
- recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch
- recipes/regenie/patches/0014-update-cmakelist.txt-for-v3.5.patch
🔇 Additional comments (8)
recipes/regenie/build.sh (3)
6-8: LGTM: Environment variable setup follows conda-build best practices
The environment variables are correctly configured with proper prefix paths and optimization flags.
24-31: LGTM: CMake configuration follows best practices
The CMake configuration is well-structured with:
- Modern CMake syntax
- Proper compiler and flag handling
- Parallel build support
- Correct Boost configuration
10-17: Verify MKL configuration for non-Darwin platforms
The MKL threading layer is set to "GNU" for non-Darwin platforms. This is generally correct for conda-forge builds, but we should verify that regenie actually uses MKL.
✅ Verification successful
MKL configuration for non-Darwin platforms verified
The package uses MKL, and the MKL_THREADING_LAYER is appropriately set to "GNU".
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if the package actually uses MKL
rg -l "mkl" --type cmake
rg -l "MKL" --type cmake
# Check for MKL-related dependencies in meta.yaml
if [ -f meta.yaml ]; then
echo "Checking meta.yaml for MKL dependencies:"
grep -i "mkl" meta.yaml
fi
Length of output: 72
Script:
#!/bin/bash
# Search for 'MKL' in all source and configuration files
rg -l "MKL" --type cpp --type h --type py --type sh --type yaml --type cmake
# Additionally, search for 'intel' which might be related to MKL
rg -l "intel" --type cpp --type h --type py --type sh --type yaml --type cmake
Length of output: 771
recipes/regenie/meta.yaml (5)
16-18: LGTM: Build configuration changes look good
The build number increment and addition of run_exports with appropriate version pinning will help maintain compatibility with downstream recipes, as mentioned in the PR objectives.
39-43: Platform-specific OpenMP dependencies look good
The addition of platform-specific OpenMP libraries (llvm-openmp for macOS, libgomp for Linux) is correctly configured and matches the host requirements.
52-65: Documentation and metadata improvements look good
The addition of the DOI identifier and cleaned-up documentation URLs enhance the package metadata, making it more discoverable and citable in academic contexts.
Line range hint 1-65: Verify bioconda guidelines compliance
Please ensure this recipe update aligns with bioconda guidelines, particularly:
- Package versioning and compatibility with existing bioconda packages
- Dependency availability in the bioconda or conda-forge channels
#!/bin/bash
# Check if dependencies are available in bioconda/conda-forge
# and if there are any potential conflicts
# Check for boost-cpp availability in conda-forge
curl -s https://conda.anaconda.org/conda-forge/noarch/repodata.json | jq '.packages | with_entries(select(.key | contains("boost-cpp-1.74")))'
# Check for potential conflicts in other bioconda recipes
rg -g "meta.yaml" "boost-cpp.*1\.74" Line range hint 28-38: Verify MKL version constraints and dependencies
The host requirements use MKL-specific configurations:
liblapack * *mkluses MKL variantmkl >=2020.4specifies minimum version
Please verify if these version constraints are sufficient for the current regenie version's requirements.
✅ Verification successful
MKL version constraints for regenie are appropriate.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if any other bioconda recipes use different MKL version constraints with regenie
rg -g "meta.yaml" "regenie.*mkl"
Length of output: 380
Script:
#!/bin/bash
# Search the regenie meta.yaml for explicit MKL version requirements
rg -g "meta.yaml" "mkl\s*>=?\s*"
Length of output: 254
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