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base repository: snakemake/snakemake
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base: v8.20.6
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head repository: snakemake/snakemake
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compare: v8.20.7
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  • 3 commits
  • 3 files changed
  • 3 contributors

Commits on Oct 8, 2024

  1. fix: remote pre-command not installing all required storage plugins (#…

    …3116)
    
    <!--Add a description of your PR here-->
    Related Issues: 
    #2501 
    
    snakemake/snakemake-executor-plugin-kubernetes#19
    
    When the job spawner prepares the `precommand` for remote execution, it
    only registers the `default storage provider` which fails to acknowledge
    the presence of a storage provider within the snakefile.
    
    This PR should now register all storage providers that `workflow` has
    recognized.
    
    NOTE: unsure how to I could add a test case for this? 
    
    ### QC
    <!-- Make sure that you can tick the boxes below. -->
    
    * [x] The PR contains a test case for the changes or the changes are
    already covered by an existing test case.
    * [x] The documentation (`docs/`) is updated to reflect the changes or
    this is not necessary (e.g. if the change does neither modify the
    language nor the behavior or functionalities of Snakemake).
    
    
    <!-- This is an auto-generated comment: release notes by coderabbit.ai
    -->
    
    ## Summary by CodeRabbit
    
    - **New Features**
    - Enhanced package installation logic for storage providers, allowing
    multiple packages to be installed simultaneously when the auto-deploy
    feature is enabled.
    
    - **Bug Fixes**
    - Improved handling of duplicate package names in the installation
    process.
    
    <!-- end of auto-generated comment: release notes by coderabbit.ai -->
    jjjermiah authored Oct 8, 2024
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Commits on Oct 9, 2024

  1. fix: install conda in container image (#3127)

    <!--Add a description of your PR here-->
    
    ### QC
    <!-- Make sure that you can tick the boxes below. -->
    
    * [x] The PR contains a test case for the changes or the changes are
    already covered by an existing test case.
    * [x] The documentation (`docs/`) is updated to reflect the changes or
    this is not necessary (e.g. if the change does neither modify the
    language nor the behavior or functionalities of Snakemake).
    
    
    <!-- This is an auto-generated comment: release notes by coderabbit.ai
    -->
    
    ## Summary by CodeRabbit
    
    - **Chores**
    - Updated the environment setup in the Dockerfile to replace the
    installation of the `mamba` package with `conda` for the Snakemake
    environment.
    - Maintained existing package management and environment variables
    without changes.
    
    <!-- end of auto-generated comment: release notes by coderabbit.ai -->
    johanneskoester authored Oct 9, 2024
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Commits on Oct 11, 2024

  1. chore(main): release 8.20.7 (#3125)

    🤖 I have created a release *beep* *boop*
    ---
    
    
    ##
    [8.20.7](v8.20.6...v8.20.7)
    (2024-10-09)
    
    
    ### Bug Fixes
    
    * install conda in container image
    ([#3127](#3127))
    ([afa7bad](afa7bad))
    * remote pre-command not installing all required storage plugins
    ([#3116](#3116))
    ([d829bb7](d829bb7))
    
    ---
    This PR was generated with [Release
    Please](https://github.com/googleapis/release-please). See
    [documentation](https://github.com/googleapis/release-please#release-please).
    
    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    github-actions[bot] authored Oct 11, 2024
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