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Update skder to 1.2.8 #51137

Merged
merged 3 commits into from
Oct 4, 2024
Merged

Update skder to 1.2.8 #51137

merged 3 commits into from
Oct 4, 2024

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@BiocondaBot BiocondaBot commented Oct 3, 2024

Update skder: 1.2.71.2.8

install with bioconda Conda

Info Link or Description
Recipe recipes/skder (click to view/edit other files)
Summary skDER & CiDDER: efficient & high-resolution dereplication methods for microbial genomes
Home https://github.com/raufs/skDER
Releases https://github.com/raufs/skDER/tags
Recipe Maintainer(s) @raufs
Author @raufs

This pull request was automatically generated (see docs).

Summary by CodeRabbit

  • New Features
    • Updated the skder package to version 1.2.8, enhancing its capabilities.
  • Bug Fixes
    • Improved handling of compilation commands for C++ binaries, streamlining the build process.

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Oct 3, 2024
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coderabbitai bot commented Oct 3, 2024

📝 Walkthrough

Walkthrough

The pull request updates the meta.yaml file for the skder package by incrementing the version from 1.2.7 to 1.2.8, updating the SHA256 checksum, and modifying the source URL to the new version's tarball. Additionally, the build.sh script has been altered to comment out the export of the LDFLAGS variable and remove the linker flag -Wl,-headerpad_max_install_names from the compilation commands. No other structural changes are present in either file.

Changes

File Change Summary
recipes/skder/meta.yaml - Version updated from 1.2.7 to 1.2.8
- SHA256 updated from 283e4a05...97347 to d60056e0...5237
- Source URL updated from v1.2.7.tar.gz to v1.2.8.tar.gz
recipes/skder/build.sh - Commented out export of LDFLAGS
- Removed linker flag -Wl,-headerpad_max_install_names from compilation commands
- Executable permissions applied to generated binaries

Possibly related PRs


📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 20c0d8d and f479204.

📒 Files selected for processing (1)
  • recipes/skder/build.sh (0 hunks)
💤 Files with no reviewable changes (1)
  • recipes/skder/build.sh

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
recipes/skder/build.sh (1)

Line range hint 1-14: Summary: Build script simplified, recommend thorough testing.

The build script has been simplified by removing the LDFLAGS export and the -Wl,-headerpad_max_install_names linker flag. While these changes may streamline the build process, they could potentially impact builds on certain platforms, particularly macOS.

To ensure the reliability of these changes:

  1. Test the build process on all supported platforms, especially macOS.
  2. Verify that the resulting binaries work correctly and can be relocated if necessary.
  3. Consider adding comments explaining why these flags were removed, to prevent future confusion.

If you encounter any issues during testing, you may need to reintroduce platform-specific flags or use conditional logic to apply them only when necessary.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between e18ea7d and 20c0d8d.

📒 Files selected for processing (1)
  • recipes/skder/build.sh (1 hunks)
🔇 Additional comments (2)
recipes/skder/build.sh (2)

9-10: LGTM! Simplified compilation commands.

The C++ compilation commands for skDERsum and skDERcore have been simplified, which is good for maintainability. The use of ${CXX} ensures the correct compiler is used, and the -std=c++11 flag is retained for C++11 feature support.

To ensure these changes don't introduce any issues, please verify the build process on different platforms. You can use the following script to check for any platform-specific compilation flags that might have been removed:

#!/bin/bash
# Description: Check for platform-specific compilation flags in other recipes

# Test: Search for platform-specific compilation flags in other build scripts
rg --type bash -i '(macos|darwin|linux|unix).*\$\{CXX\}'

7-8: Verify the removal of LDFLAGS and linker flag.

The LDFLAGS export and the -Wl,-headerpad_max_install_names linker flag have been commented out. This change might impact the build process, especially on macOS systems where this flag is commonly used to ensure sufficient space for modifying the install names of shared libraries.

Please confirm if this change is intentional and if it has been tested on different platforms, particularly macOS. If you need to verify the impact, you can use the following script:

✅ Verification successful

Verified: LDFLAGS and linker flag have been commented out.

The LDFLAGS export and the -Wl,-headerpad_max_install_names linker flag have been confirmed to be commented out in the recipes/skder/build.sh file. This change aligns with the review comment. However, this modification may have implications for the build process, especially on macOS systems:

  1. The removal of LDFLAGS might affect the linking process for this package.
  2. The -Wl,-headerpad_max_install_names flag is typically used on macOS to ensure sufficient space for modifying the install names of shared libraries.

To ensure this change doesn't negatively impact the build process, consider the following recommendations:

  • Test the build process on multiple platforms, particularly macOS, to verify that it still works as expected.
  • If issues arise on macOS, consider conditionally applying the LDFLAGS and linker flag only for macOS builds.
  • Document the reason for this change in a comment within the build script to provide context for future maintainers.
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if the package builds successfully on different platforms without the LDFLAGS and linker flag.

# Test: Check if there are any platform-specific build instructions
rg --type bash -i '(macos|darwin|linux|unix)'

# Test: Check for any mentions of LDFLAGS or headerpad in other build scripts
rg --type bash '(LDFLAGS|-Wl,-headerpad_max_install_names)'

Length of output: 241


Script:

#!/bin/bash
# Description: Check if the package builds successfully on different platforms without the LDFLAGS and linker flag.

# Test: Check if there are any platform-specific build instructions
rg --type sh -i 'macos|darwin|linux|unix'

# Test: Check for any mentions of LDFLAGS or headerpad in other build scripts
rg --type sh '(LDFLAGS|-Wl,-headerpad_max_install_names)'

Length of output: 208628


Script:

#!/bin/bash
# Description: Check for platform-specific build instructions and linker flag mentions.

# Test: Search for platform-specific keywords in shell scripts
rg --type sh 'macos|darwin|linux|unix'

# Test: Search for mentions of LDFLAGS or the specific linker flag in shell scripts
rg --type sh 'LDFLAGS|-Wl,-headerpad_max_install_names'

Length of output: 174781

@raufs raufs merged commit e9865fd into master Oct 4, 2024
7 checks passed
@raufs raufs deleted the bump/skder branch October 4, 2024 00:07
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