Update vcf-validator to v0.10.0 #51421
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apply fixes for linting
📝 WalkthroughWalkthroughThe pull request includes several significant changes to the Possibly related PRs
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (3)
recipes/vcf-validator/meta.yaml (1)
Line range hint
39-42: Consider adding more comprehensive tests.While the existing test commands check for basic functionality, considering the significant update to version 0.10.0, it might be beneficial to add more comprehensive tests. This could include testing new features or changes introduced in this version.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
recipes/vcf-validator/build.sh (2)
4-4: Consider the order ofCXXFLAGSin the export commandCurrently, the export command prepends
-std=c++11to any existingCXXFLAGS. This ensures that the C++11 standard is used. However, if there are flags in${CXXFLAGS}that should take precedence, consider appending instead.Apply this change to append
-std=c++11:-export CXXFLAGS="-std=c++11 ${CXXFLAGS}" +export CXXFLAGS="${CXXFLAGS} -std=c++11"
17-17: Ensure consistent logging throughout the scriptThe final message
echo "Done with vcf-validator"is helpful. Consider adding informative messages at other key steps for better visibility during the build process.
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📒 Files selected for processing (3)
- recipes/vcf-validator/LICENSE_ODB (0 hunks)
- recipes/vcf-validator/build.sh (1 hunks)
- recipes/vcf-validator/meta.yaml (2 hunks)
💤 Files with no reviewable changes (1)
- recipes/vcf-validator/LICENSE_ODB
🧰 Additional context used
🔇 Additional comments (6)
recipes/vcf-validator/meta.yaml (6)
2-6: LGTM: Version update and package name formatting.The version has been correctly updated to 0.10.0 as per the PR objective. The package name is now set to lowercase, which aligns with conda packaging best practices.
15-17: LGTM: Explicit package name in run_exports.The use of the explicit package name "vcf-validator" in the pin_subpackage function is a good practice. It ensures that the correct package is pinned, reducing the risk of errors.
44-48: LGTM: Improved summary and updated license information.The summary has been refined to more accurately describe the tool's purpose. The removal of the ODB license file aligns with the PR objective of removing the libODB dependency.
50-56: LGTM: Added platform support and new maintainer.The addition of support for the osx-arm64 platform aligns with the PR objective. The inclusion of a new recipe maintainer (ebi-variation) is beneficial for the long-term maintenance of the package.
18-37: Verify comprehensive requirements list.The requirements section has been significantly expanded, which aligns with the PR objective of compiling the package directly in conda. The list appears comprehensive, including necessary build tools and runtime dependencies.
Please run the following script to verify the requirements against the project's build instructions:
#!/bin/bash # Description: Verify the requirements against the project's build instructions # Test: Check if all required dependencies are listed in the meta.yaml rg -i "cmake|make|boost|zstd|curl|openssl|bzip2|zlib" README.md | grep -v "meta.yaml" && echo "All dependencies seem to be included" || echo "Some dependencies might be missing"
8-10: Verify source URL and SHA256.The source section has been simplified to use a single tarball for all platforms, which is a good practice. The SHA256 checksum has been updated accordingly.
Please run the following script to verify the source URL and SHA256:
| cp build/bin/vcf_validator ${PREFIX}/bin | ||
| cp build/bin/vcf_assembly_checker ${PREFIX}/bin |
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Add error handling for copying binaries
Currently, the cp commands lack error handling. If the copy operation fails, the script will proceed without indication of an error.
Apply this change:
-cp build/bin/vcf_validator ${PREFIX}/bin
-cp build/bin/vcf_assembly_checker ${PREFIX}/bin
+cp build/bin/vcf_validator ${PREFIX}/bin || { echo "Failed to copy vcf_validator" >&2; exit 1; }
+cp build/bin/vcf_assembly_checker ${PREFIX}/bin || { echo "Failed to copy vcf_assembly_checker" >&2; exit 1; }📝 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.
| cp build/bin/vcf_validator ${PREFIX}/bin | |
| cp build/bin/vcf_assembly_checker ${PREFIX}/bin | |
| cp build/bin/vcf_validator ${PREFIX}/bin || { echo "Failed to copy vcf_validator" >&2; exit 1; } | |
| cp build/bin/vcf_assembly_checker ${PREFIX}/bin || { echo "Failed to copy vcf_assembly_checker" >&2; exit 1; } |
| mkdir build || { echo "Failed to create build directory" >&2; exit 1; } | ||
| cd build || { echo "Failed to go into build directory" >&2; exit 1; } | ||
| cmake -G "Unix Makefiles" .. | ||
| make -j2 || { echo "Build failed" >&2; exit 1; } |
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🛠️ Refactor suggestion
Use dynamic CPU count for parallel compilation
Instead of hardcoding -j2, use ${CPU_COUNT} to utilize the available CPU cores. This makes the build process more efficient on systems with different numbers of cores.
Apply this change:
-make -j2 || { echo "Build failed" >&2; exit 1; }
+make -j${CPU_COUNT} || { echo "Build failed" >&2; exit 1; }📝 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.
| make -j2 || { echo "Build failed" >&2; exit 1; } | |
| make -j${CPU_COUNT} || { echo "Build failed" >&2; exit 1; } |
| if ! ./build/bin/test_validation_suite; then | ||
| echo "Validation suite failed" >&2 | ||
| exit 1 | ||
| fi |
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Check for the existence of the validation suite before execution
Before running ./build/bin/test_validation_suite, ensure that the file exists to avoid execution errors.
Apply this change:
+if [ ! -f ./build/bin/test_validation_suite ]; then
+ echo "Validation suite executable not found" >&2
+ exit 1
+fi
if ! ./build/bin/test_validation_suite; then
echo "Validation suite failed" >&2
exit 1
fi📝 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.
| if ! ./build/bin/test_validation_suite; then | |
| echo "Validation suite failed" >&2 | |
| exit 1 | |
| fi | |
| if [ ! -f ./build/bin/test_validation_suite ]; then | |
| echo "Validation suite executable not found" >&2 | |
| exit 1 | |
| fi | |
| if ! ./build/bin/test_validation_suite; then | |
| echo "Validation suite failed" >&2 | |
| exit 1 | |
| fi |
|
@BiocondaBot please add label |
In this PR we:
osx-arm64In the VCF validator v0.10.0 we remove our dependency to libODB which allowed us to remove the ODB license as well.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
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...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
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