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base repository: snakemake/snakemake
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base: v9.14.1
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head repository: snakemake/snakemake
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compare: v9.14.2
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  • 3 commits
  • 7 files changed
  • 4 contributors

Commits on Dec 4, 2025

  1. test: Improve logging tests (#3848)

    - Edits to `common` test module:
      - Added type annotations to many functions
      - Edits to `run()` function:
        - Documented and added type annotations for many arguments.
        - Allow `path` and `tmpdir` to be either string or `os.Pathlike`.
        - Removed unused `subpath` argument.
    - Updates to existing logging tests:
    - Added file to `test-all` Pixi task, I don't think it was actually
    being run before.
    - Added some helper functions to deduplicate code relating to counting
    log events.
    - Don't count exact number of `LOG_COUNTED` events (multiple jobs can be
    grouped under a single event), just assert at least one exists.
      - Completed `test_rule_failure` test, add expected log counts.
    - Run workflow in `test_logging_config` in temporary directory instead
    of current directory (this maybe should be using the same `run()`
    function as all the others, but isn't).
    - Added some more descriptive docstrings and type annotations to test
    functions.
    - Added new test for logging plugin.
    
    An issue I noticed that existed before this PR and I did not change: the
    `benchmark_extended` argument of the `run()` test function is used in
    some tests but its value is ignored in the function body.
    
    
    <!-- This is an auto-generated comment: release notes by coderabbit.ai
    -->
    ## Summary by CodeRabbit
    
    * **Tests**
    * Added centralized helpers to count and validate log events and
    refactored tests to use them.
    * Added a test logging plugin that emits structured JSONL events
    (including an initial logger_info record) for improved log capture and
    verification.
    
    * **Chores**
    * Introduced comprehensive type annotations and a new string/path type
    alias across test utilities for clearer typing and maintainability.
    
    <sub>✏️ Tip: You can customize this high-level summary in your review
    settings.</sub>
    <!-- end of auto-generated comment: release notes by coderabbit.ai -->
    
    ---------
    
    Co-authored-by: Cade Mirchandani <cmirchan@ucsc.edu>
    jlumpe and cademirch authored Dec 4, 2025
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Commits on Dec 5, 2025

  1. fix: correctly handle groups when retrieving storage input (#3861)

    <!--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
    
    * **Bug Fixes**
    * Improved handling of grouped workflow tasks when retrieving storage
    inputs, ensuring proper aggregation across all tasks within a group
    rather than treating them as a single unit.
      * Enhanced type safety with explicit parameter validation.
    
    <sub>✏️ Tip: You can customize this high-level summary in your review
    settings.</sub>
    
    <!-- end of auto-generated comment: release notes by coderabbit.ai -->
    johanneskoester authored Dec 5, 2025
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Commits on Dec 6, 2025

  1. chore(main): release 9.14.2 (#3863)

    🤖 I have created a release *beep* *boop*
    ---
    
    
    ##
    [9.14.2](v9.14.1...v9.14.2)
    (2025-12-05)
    
    
    ### Bug Fixes
    
    * correctly handle groups when retrieving storage input
    ([#3861](#3861))
    ([8c818f4](8c818f4))
    
    ---
    This PR was generated with [Release
    Please](https://github.com/googleapis/release-please). See
    [documentation](https://github.com/googleapis/release-please#release-please).
    snakemake-bot authored Dec 6, 2025
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