Update Snippy: restrict samtools to version <=1.20

[pmenzel]

this is a workaround to make snippy work again.

samtools should be version <= 1.20, as Snippy fails to run with samtools v1.21, see tseemann/snippy#598

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[pmenzel]

please review @rpetit3

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request involves modifications to the meta.yaml file for the snippy package. The primary change is the update of the package version from 4.6.0 to 5, indicating a new build iteration. The sha256 hash remains unchanged. Additionally, the requirements section has been updated to restrict the version of samtools from >=1.10 to >=1.10,<=1.20, which limits the acceptable versions to a specific range. This alteration aims to address compatibility issues with later versions of samtools. The overall structure of the meta.yaml file, including sections for build, test, about, and extra, remains unchanged.

Possibly related PRs

• Update meta.yaml for spec2vec #49857: Updates to version constraints for dependencies in the meta.yaml file for spec2vec.
• 2024.4 #50977: Version update in the meta.yaml file for biobb_structure_checking.
• Update recipe for ViroConstrictor #51038: Changes to dependency specifications in the meta.yaml for viroconstrictor.
• Update PhyloAcc recipe #51090: Increment of the build number in the meta.yaml file for phyloacc.
• Update hmftools-bam-tools to 1.3_beta #51142: Version update in the meta.yaml for hmftools-bam-tools.
• Update meta.yaml #51213: Build number update in the meta.yaml for rseqc.
• Update snakemake: remove toposort as dependency #51412: Version update in the meta.yaml for snakemake.
• [biobb_analysis] update 5.0.0 #51431: Version update in the meta.yaml for biobb_analysis.
• [biobb_cmip] update 5.0.0 #51453: Version update in the meta.yaml for biobb_cmip.
• [biobb_flexdyn] update 5.0.0 #51605: Version update in the meta.yaml for biobb_flexdyn.

Suggested labels

please review & merge

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 11ec7d5 and aae1bbb.

📒 Files selected for processing (1)

• recipes/snippy/meta.yaml (2 hunks)

🔇 Additional comments (2)

recipes/snippy/meta.yaml (2)

15-15: LGTM: Build number increment is appropriate.

The build number increment is correct as it reflects the dependency constraint update.

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25-25: LGTM: Samtools version constraint addresses known compatibility issues.

The addition of <=1.20 constraint for samtools is well-justified:

• Prevents issues with samtools v1.21 as documented in Snippy's GitHub issues
• Follows Bioconda's best practices for dependency version pinning
• Consistent with other carefully pinned dependencies in the recipe (e.g., vcflib, snpeff)

Let's verify if any other recipes depend on snippy and might be affected:

✅ Verification successful

Let me analyze the output. The search found several recipes that depend on snippy, but I need to check if they specifically depend on the samtools version constraint. Let me generate scripts to check this.

---

Based on the search results, I can now provide a final response:

Verified: The samtools version constraint is safe and properly managed across dependencies.

The version constraint samtools >=1.10,<=1.20 in snippy is compatible with its dependent packages. The only other package showing a samtools dependency is nullarbor, which requires samtools >=1.9, making it fully compatible with snippy's constraint.

The version pinning appears well-considered as:

• It maintains compatibility with nullarbor's requirement
• Other key dependencies in snippy are also carefully version-constrained (e.g., vcflib, snpeff) to prevent known issues
• The upper bound helps prevent potential compatibility issues with future samtools versions

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Search for recipes that depend on snippy
rg -l "(?i)snippy.*\d" recipes/*/meta.yaml

Length of output: 320876

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Script:

#!/bin/bash
# Check the dependencies section in the found recipes for samtools version constraints
rg -A 10 -B 10 "samtools" recipes/snippy/meta.yaml recipes/pgcgap/meta.yaml recipes/pathogist/meta.yaml recipes/nullarbor/meta.yaml recipes/bactopia-variants/meta.yaml recipes/agrvate/meta.yaml

Length of output: 2263

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