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perf: autobump bio/sortmerna

Open snakedeploy-bot[bot] opened this issue 1 year ago • 2 comments

Automatic bump of bio/sortmerna.

Summary by CodeRabbit

  • New Features

    • Upgraded the sortmerna package from version 4.3.6 to 4.3.7, improving performance and compatibility.
    • Expanded the dependency list with multiple new packages from conda-forge, enhancing environment stability and access to updated libraries.
  • Bug Fixes

    • The update to sortmerna may include bug fixes not specified in the documentation.
  • Chores

    • Updated environment configuration files to reflect the latest package versions and dependencies.

snakedeploy-bot[bot] avatar Jun 07 '24 05:06 snakedeploy-bot[bot]

It seems sortmerna is migrating from bioconda to conda-forge and version 4.3.7 is invalid (sortmerna/sortmerna#423, conda-forge/staged-recipes#25438, bioconda/bioconda-recipes#48607)

fgvieira avatar Jun 25 '24 11:06 fgvieira

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Walkthrough

The changes involve upgrading the sortmerna package from version 4.3.6 to 4.3.7 in both the environment.linux-64.pin.txt and environment.yaml files. The dependency management strategy has been revised, replacing the previous single package reference with multiple new packages sourced from the conda-forge channel, enhancing the overall environment setup for bioinformatics tasks.

Changes

Files Change Summary
bio/sortmerna/environment.linux-64.pin.txt Updated sortmerna from version 4.3.6 to 4.3.7; replaced single package reference with multiple new package links from conda-forge.
bio/sortmerna/environment.yaml Upgraded sortmerna version from 4.3.6 to 4.3.7, indicating an update to maintain the software environment.

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coderabbitai[bot] avatar Aug 16 '24 04:08 coderabbitai[bot]

Still something wrong with the conda build: sortmerna/sortmerna#438

fgvieira avatar Feb 21 '25 07:02 fgvieira