Update PhyloAcc recipe #51090
Update PhyloAcc recipe #51090
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request updates the Changes
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/phyloacc/meta.yaml (1)
38-38: Consider adding an upper bound to the Snakemake version requirement.The update to
snakemake-minimal >=8.0aligns with the PR objective to ensure compatibility with Snakemake version 8. However, removing the upper bound constraint might lead to potential compatibility issues with future major versions of Snakemake.Consider adding an upper bound to prevent potential issues with future major versions:
- - snakemake-minimal >=8.0 + - snakemake-minimal >=8.0,<9.0This ensures compatibility with Snakemake 8.x versions while preventing potential issues with Snakemake 9.0 and beyond.
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- recipes/phyloacc/meta.yaml (2 hunks)
🔇 Additional comments (2)
recipes/phyloacc/meta.yaml (2)
14-14: LGTM: Build number increment is correct.Incrementing the build number from 0 to 1 is appropriate when updating the recipe without changing the package version. This change follows Conda packaging best practices.
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1-67: Summary of changes and recommendationsThe changes to the PhyloAcc recipe align with the PR objectives to ensure compatibility with Snakemake version 8. Here's a summary of the review:
- The build number increment is correct and follows best practices.
- The Snakemake version requirement has been updated, but consider adding an upper bound to prevent potential issues with future major versions.
- A new dependency for SLURM execution has been added. Please clarify if this is necessary for all users and consider adding a version constraint.
Overall, the changes look good, but addressing the suggestions above would further improve the recipe's robustness and maintainability.
| @@ -35,7 +35,8 @@ requirements: | |||
| - matplotlib-base >=3.5 | |||
| - biopython >=1.79 | |||
| - numpy >=1.22 | |||
| - snakemake-minimal >=7.3,<8.0 | |||
| - snakemake-minimal >=8.0 | |||
| - snakemake-executor-plugin-slurm | |||
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💡 Codebase verification
🛠️ Refactor suggestion
Add version constraints to the snakemake-executor-plugin-slurm dependency.
The addition of snakemake-executor-plugin-slurm in recipes/phyloacc/meta.yaml is necessary for SLURM support. To ensure compatibility and prevent potential issues in the future, it's recommended to specify version constraints for this dependency. This approach aligns with how other executor plugins are managed in the codebase.
-
Example:
- - snakemake-executor-plugin-slurm + - snakemake-executor-plugin-slurm >=0.2.0,<1.0.0
Replace
0.2.0with the minimum required version that is compatible with PhyloAcc.
🔗 Analysis chain
Clarify the necessity of the new SLURM plugin dependency and consider adding a version constraint.
The addition of snakemake-executor-plugin-slurm suggests that PhyloAcc now supports SLURM execution through Snakemake. However, there are a few points to consider:
- Is this plugin necessary for all users, or should it be an optional dependency?
- The version of this new dependency is not specified, which could lead to potential compatibility issues in the future.
To better understand the usage of this plugin in the PhyloAcc codebase, let's run the following script:
If the plugin is indeed necessary, consider adding a version constraint to ensure compatibility:
- - snakemake-executor-plugin-slurm
+ - snakemake-executor-plugin-slurm >=0.1.0,<1.0.0Replace 0.1.0 with the minimum required version that works with PhyloAcc.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Search for usage of SLURM-related configurations or the new plugin in the PhyloAcc codebase
# Test: Search for SLURM-related configurations or mentions of the new plugin
rg --type python -i '(slurm|snakemake.*executor.*plugin)'
Length of output: 90
Script:
#!/bin/bash
# Description: Search for usage of SLURM-related configurations or the new plugin in the PhyloAcc codebase
# Test: Search for SLURM-related configurations or mentions of the new plugin across all relevant file types
rg -i '(slurm|snakemake.*executor.*plugin)'
Length of output: 10311
|
@BiocondaBot please add label |
Changed dependencies to allow for snakemake 8
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snakemake-minimalto support newer features.PhyloAccpackage.