Update GW to v1.1.1 #51426
Update GW to v1.1.1 #51426
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces updates to the The Possibly related PRs
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recipes/gw/meta.yaml (1)
75-77: Consider optimizing test commandsThe added test commands are useful for basic verification, but they could be improved:
- The
ls -lhcommand alone doesn't provide much context about the package installation.- The
which gwandls -lh $(which gw)commands could be combined for efficiency.Consider the following suggestions:
- - ls -lh - - which gw - - ls -lh $(which gw) + - command -v gw >/dev/null 2>&1 || { echo >&2 "gw not found in PATH"; exit 1; } + - ls -lh $(command -v gw) + - gw --versionThese changes will:
- Check if
gwis in the PATH and exit with an error if it's not.- Show details of the
gwexecutable if found.- Display the version of
gw, which is a common practice for verifying correct installation.
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recipes/gw/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/gw/meta.yaml (1)
1-2: LGTM: Version and checksum updated correctlyThe version has been correctly updated to 1.1.1, and the SHA256 checksum has been changed accordingly. These changes are consistent with the PR objective to update GW to v1.1.1.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/gw/meta.yaml (1)
75-79: Approve new test commands and suggest cleanup.The new test commands provide more comprehensive and efficient checks for the package installation. They verify the executable's presence, inspect its architecture, and check the version, which are all valuable for ensuring correct package deployment.
Consider removing the commented-out line 79 to keep the file clean:
- #- gw hg19 -b https://github.com/kcleal/gw/releases/download/v1.0.0/demo1.bam -r chr8:37047270-37055161 -n > test.png; ls -lh test.pngIf this test is no longer needed, it's better to remove it entirely rather than keeping it as a comment.
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recipes/gw/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/gw/meta.yaml (2)
1-2: LGTM: Version and SHA256 updates are correct.The version has been correctly updated to 1.1.1, and the SHA256 checksum has been changed accordingly. These updates are consistent with the PR objective to update GW to v1.1.1.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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Line range hint
1-79: Summary: Approve PR for updating GW to v1.1.1The changes in this PR successfully update the GW package to version 1.1.1. The key updates include:
- Version number and SHA256 checksum have been correctly updated.
- New test commands have been added to provide more comprehensive checks for the package installation.
These changes align with the PR objectives and improve the package validation process. The update appears to be correctly implemented and ready for merging.
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recipes/gw/meta.yaml (1)
75-78: Improved test commands. Consider keeping the image generation test.The new test commands provide more comprehensive checks for the installation and functionality of the
gwpackage. These tests are more robust and less likely to fail due to environmental factors.Consider keeping the image generation test as an optional or extended test. It could be valuable for visual verification. You might want to add it back with a condition or as a separate test step:
- gw --version - if [[ "${CONDA_BUILD_CROSS_COMPILATION:-}" != "1" ]]; then gw hg19 -b https://github.com/kcleal/gw/releases/download/v1.0.0/demo1.bam -r chr8:37047270-37055161 -n > test.png && ls -lh test.png; fiThis way, the image generation test will only run when not cross-compiling, avoiding potential issues in certain build environments.
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recipes/gw/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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recipes/gw/meta.yaml (1)
1-2: LGTM! Verify SHA256 checksum.The version update to 1.1.1 is consistent with the PR objective. The SHA256 checksum has been updated accordingly.
To ensure the integrity of the package, please verify the SHA256 checksum using the following script:
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/gw/meta.yaml (1)
75-78: Improved test commands. Consider adding Linux-specific checks.The new test commands provide more comprehensive checks for the installed package, including binary verification, system information, and version checking. This improves the robustness of the package testing.
Consider adding Linux-specific checks similar to the Darwin-specific ones. This would provide more balanced testing across platforms. Here's a suggested addition:
- if [[ "$(uname)" == "Linux" ]]; then file $(which gw); ldd $(which gw); readelf -d $(which gw); fiThis addition would check the binary type, shared library dependencies, and dynamic section information on Linux systems.
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- recipes/gw/conda_build_config.yaml (1 hunks)
- recipes/gw/meta.yaml (2 hunks)
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🪛 yamllint
recipes/gw/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (6)
recipes/gw/conda_build_config.yaml (4)
1-2: Verify the intention behind updating MACOSX_DEPLOYMENT_TARGET.The macOS deployment target has been updated from 10.15 to 11. This change increases the minimum macOS version required, which could potentially exclude older macOS versions from running the package.
Please confirm if this change is intentional and necessary. Are there specific features or dependencies in the updated GW package (v1.1.1) that require macOS 11 or later?
4-5: LGTM: MACOSX_SDK_VERSION update is consistent.The update of MACOSX_SDK_VERSION to "11" is consistent with the change in MACOSX_DEPLOYMENT_TARGET. This alignment ensures that the SDK version matches the minimum deployment target, which is a good practice.
7-12: LGTM: Addition of CFLAGS, CXXFLAGS, and LDFLAGS is consistent but verify necessity.The addition of CFLAGS, CXXFLAGS, and LDFLAGS with "-mmacosx-version-min=11" is consistent with the updated MACOSX_DEPLOYMENT_TARGET and MACOSX_SDK_VERSION. This ensures that the package is compiled and linked with macOS 11 as the minimum target across all stages of the build process.
However, these changes further emphasize the potential exclusion of older macOS versions. Please confirm that this strict requirement for macOS 11 and later is necessary for the updated GW package (v1.1.1).
1-12: Summary: Consistent update to macOS 11 target, verify compatibility requirements.The changes in this file consistently update the macOS target to version 11 across all relevant configuration settings (MACOSX_DEPLOYMENT_TARGET, MACOSX_SDK_VERSION, and compiler/linker flags). While these changes are internally consistent and well-structured, they represent a significant shift in the minimum supported macOS version.
Please verify and confirm the following:
- The GW package v1.1.1 requires features specific to macOS 11 or later.
- The impact of this change on your user base has been considered, especially for users on older macOS versions.
- This update aligns with the overall compatibility strategy for the Bioconda project.
If these points are confirmed, the changes are appropriate and can be approved.
recipes/gw/meta.yaml (2)
79-79: Clarify the rationale for commenting out the image generation test.The previous test command that generated a test image has been commented out. While the new test commands provide good coverage, the image generation test might have been valuable for ensuring the full functionality of the package.
Could you please explain the reasoning behind removing this test? If it's no longer necessary, consider removing it entirely rather than leaving it commented out. If it's still valuable but problematic in some way, we might want to explore alternatives or fixes to keep this functional test in place.
1-2: Version update looks good. Verify the new checksum.The version update to 1.1.1 is consistent with the PR objective. The SHA256 checksum has been updated accordingly.
To ensure the integrity of the package, please verify that the new SHA256 checksum is correct for the v1.1.1 release. You can run the following command to check:
Compare the output with the checksum in the meta.yaml file.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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🧹 Outside diff range and nitpick comments (1)
recipes/gw/meta.yaml (1)
76-79: Approve new test commands, consider retaining image generation test.The new test commands are good additions that help verify the package installation and provide useful information about the binary. However, the commented-out image generation test might still be valuable for visual verification of the package functionality.
Consider keeping both the new commands and the image generation test. You could add a condition to run the image generation test only on certain platforms or as an optional extended test.
Example:
- gw --version - if [[ "$CONDA_BUILD_CROSS_COMPILATION" != "1" ]]; then gw hg19 -b https://github.com/kcleal/gw/releases/download/v1.0.0/demo1.bam -r chr8:37047270-37055161 -n > test.png && ls -lh test.png; fi
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📒 Files selected for processing (1)
- recipes/gw/meta.yaml (3 hunks)
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🪛 yamllint
recipes/gw/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/gw/meta.yaml (3)
Line range hint
1-94: Overall changes align with PR objective, minor suggestions for improvement.The changes in this file successfully update the GW package to version 1.1.1, which aligns with the PR objective. The recipe structure remains consistent with Conda packaging best practices, and the new test commands enhance the package verification process.
Summary of suggestions:
- Verify the SHA256 checksum of the source tarball.
- Consider incrementing the build number to 1.
- Clarify the reason for skipping builds on osx and x86_64.
- Consider retaining the image generation test alongside the new test commands.
These minor improvements will further enhance the quality and reliability of the package update.
Line range hint
19-19: Consider incrementing build number and clarify skip condition.
The build number is currently set to 0. Consider incrementing it to 1 since this is a new version of the package.
A new skip condition has been added for osx and x86_64. Can you please clarify the reason for skipping the build on this platform? This may affect package availability for some users.
To check if this skip condition aligns with the package's compatibility, please run:
#!/bin/bash # Description: Check package compatibility information # Search for any compatibility information in the repository rg -i 'compatibility|supported.*platform|system.*requirements' --type mdAlso applies to: 34-34
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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1-2: LGTM! Verify SHA256 checksum.The version update to 1.1.1 is consistent with the PR objective. The SHA256 checksum has been updated accordingly.
Please run the following script to verify the SHA256 checksum:
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/gw/conda_build_config.yaml
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| MACOSX_SDK_VERSION: # [osx and x86_64] | ||
| - "10.15" # [osx and x86_64] | ||
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| CFLAGS: | ||
| - "-mmacosx-version-min=10.15" # [osx and x86_64] |
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All these new entries are not really used because of the skip in meta.yaml - https://github.com/bioconda/bioconda-recipes/pull/51426/files#diff-fe69e329f31bbed1cb39dcc0a94882f3501220a7ca03695a50000f1390c98cf3R34
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Ah yes, however I would like to try and get osx x64 working again in the future, so left it in for now.
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