Build bindash on osx #51661
Build bindash on osx #51661
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📝 WalkthroughWalkthroughThe pull request introduces modifications to the In Possibly related PRs
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/bindash/build.sh (1)
15-19: Document C++ standard requirement in meta.yaml.The build script requires C++14, which should be documented in the package metadata.
Consider adding this requirement to meta.yaml:
requirements: build: - {{ compiler('cxx') }} >=5.0 # For C++14 support
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/bindash/build.sh (1 hunks)
- recipes/bindash/meta.yaml (2 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/bindash/build.sh
[warning] 7-7: Use 'pushd ... || exit' or 'pushd ... || return' in case pushd fails.
(SC2164)
🔇 Additional comments (6)
recipes/bindash/build.sh (4)
3-5: LGTM: Environment variables are properly configured.The environment variables are correctly set up using PREFIX, maintaining compatibility with both Linux and macOS builds.
9-13: LGTM: Proper macOS-specific CMake configuration.The conditional block correctly configures CMake for macOS by disabling framework and app bundle finding, which is essential for conda/bioconda builds.
21-24: LGTM: Build and installation commands are well structured.The parallel build and installation commands follow conda-build best practices.
1-24: Verify impact on downstream dependencies.Since this is a Bioconda package build script modification, we should verify if any downstream packages depend on bindash.
✅ Verification successful
Let me verify the meta.yaml file to check if this package is used as a dependency by other packages.
Let me check if any other packages list bindash as a dependency by searching for it in requirements sections of other meta.yaml files.
Build script changes have minimal downstream impact
The verification shows that:
- No other packages in the bioconda-recipes repository depend on bindash
- The package provides run exports but is not used as a dependency elsewhere
- The changes are focused on platform-specific build configurations and don't affect the package interface
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for downstream dependencies in bioconda-recipes # Look for references to bindash in meta.yaml files rg -l "bindash" --glob "recipes/*/meta.yaml"Length of output: 70
Script:
#!/bin/bash # Check the content of bindash meta.yaml for test commands and package info cat recipes/bindash/meta.yamlLength of output: 1251
Script:
#!/bin/bash # Search for bindash in requirements sections of meta.yaml files rg -B2 -A2 "bindash" --glob "recipes/*/meta.yaml" | grep -v "name: bindash"Length of output: 1548
🧰 Tools
🪛 Shellcheck
[warning] 7-7: Use 'pushd ... || exit' or 'pushd ... || return' in case pushd fails.
(SC2164)
recipes/bindash/meta.yaml (2)
13-15: LGTM: Build configuration is properly set upThe build number increment and run_exports pinning are correctly configured to maintain ABI compatibility.
46-46: LGTM: OSX ARM64 platform support properly configuredThe addition of osx-arm64 platform support is consistent with the PR objectives and the necessary dependencies (llvm-openmp) are correctly specified in the requirements section.
| export INCLUDES="-I${PREFIX}/include" | ||
| export LIBPATH="-L${PREFIX}/lib" | ||
| export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" | ||
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| mkdir release && pushd release |
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Add error handling for directory operations.
The pushd command should handle potential failures to prevent silent build errors.
Apply this diff to add error handling:
-mkdir release && pushd release
+mkdir release || exit 1
+pushd release || 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.
| mkdir release && pushd release | |
| mkdir release || exit 1 | |
| pushd release || exit 1 |
🧰 Tools
🪛 Shellcheck
[warning] 7-7: Use 'pushd ... || exit' or 'pushd ... || return' in case pushd fails.
(SC2164)
| home: "https://github.com/zhaoxiaofei/bindash" | ||
| license: "Apache-2.0" |
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💡 Codebase verification
Update documentation URLs to point to the original repository
The verification shows that jianshu93/bindash is a fork of zhaoxiaofei/bindash (the original repository). For consistency and long-term maintainability, all URLs should point to the original repository since:
zhaoxiaofei/bindashis the parent repositoryjianshu93/bindashis marked as a fork- The README exists in both repositories
Please update the doc_url to point to the original repository: "https://github.com/zhaoxiaofei/bindash/blob/v2.3/README.md"
🔗 Analysis chain
Verify repository relationships and documentation links
The URLs point to different repositories:
- home/dev_url: "zhaoxiaofei/bindash"
- doc_url: "jianshu93/bindash"
This could lead to documentation inconsistencies or broken links if the repositories get out of sync.
Also applies to: 40-41
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify repository relationships and README existence
# Check if both repositories exist and their relationship
gh repo view zhaoxiaofei/bindash --json parent,isFork,defaultBranchRef
gh repo view jianshu93/bindash --json parent,isFork,defaultBranchRef
# Verify README existence at the specified version
gh api repos/jianshu93/bindash/contents/README.md?ref=v2.3 --jq '.sha'
Length of output: 506
Describe your pull request here
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...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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