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base repository: snakemake/snakemake
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base: v9.11.6
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head repository: snakemake/snakemake
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compare: v9.11.7
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  • 5 commits
  • 10 files changed
  • 6 contributors

Commits on Sep 30, 2025

  1. fix: source_path not mounted (#3738)

    fixes #3737
    
    ### 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**
    * Source cache is now mounted in Singularity/Apptainer runs whenever the
    cache directory exists, even if extra container arguments are provided;
    a debug message is logged when the cache is missing.
    
    * **Tests**
    * Added an integration test validating source-cache binding alongside
    custom bind arguments.
    * Added a sample workflow rule to verify copying a source file to an
    output inside a container.
    <!-- end of auto-generated comment: release notes by coderabbit.ai -->
    
    ---------
    
    Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
    Co-authored-by: Cade Mirchandani <[email protected]>
    3 people authored Sep 30, 2025
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  2. chore: bump logger interface version (#3758)

    The logger plugin interface is now at 2.0.0, bumping the version
    required here.
    cademirch authored Sep 30, 2025
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Commits on Oct 1, 2025

  1. fix: Add type annotations in logging module (#3757)

    Was trying to understand the logging system better and ended up filling
    in most of the missing type annotations. These were mostly pretty clear,
    but there are a few potential issues:
    
    - The first argument of `is_quiet_about()` and the `quiet` attribute of
    `DefaultFormatter` and `DefaultFilter` were annotated as `Quietness`,
    which does not seem correct. I have changed these to
    `Container[Quietness]`.
    - `LoggerManager` is a bit of a difficult case because a lot of
    attributes are `None` before `setup()` is called. I have annotated these
    with `Optional`, but it might make more sense to do the typing as if
    `setup()` had already been called, even if it's not technically correct
    just after construction.
    
    Also corrected the docstring of `get_event_level()`.
    
    ### 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).
    
    I ran the test suite applying
    [typeguard](https://typeguard.readthedocs.io) to the logging module.
    Nearly every function with added/changed annotations was covered.
    
    <!-- This is an auto-generated comment: release notes by coderabbit.ai
    -->
    ## Summary by CodeRabbit
    
    - New Features
    - Improved logging output: clearer messages, enhanced color/TTY
    handling, and finer control over quietness and failed-log visibility.
    
    - Refactor
    - Standardized and strengthened public logging interfaces, handlers,
    formatters, and filters for more predictable terminal and file output.
    
    - Documentation
    - Updated logging docs to reflect clarified behaviors and configuration
    options.
    
    - Chores
    - Broad typing and public API alignment to improve maintainability
    without changing user-facing behavior.
    <!-- end of auto-generated comment: release notes by coderabbit.ai -->
    jlumpe authored Oct 1, 2025
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  2. docs: mastodon announcements (#3723)

    This is the new announcement action for the Snakemake announcement bot
    on Mastodon (https://fediscience.org/@snakemake)
    
    Its message is basic. Please have a look.
    
    Note, that the CI has to run in release mode before anything can be told
    for its workings.
    
    edit - PS: the PR is labelled "docs" in lack for a better conventional
    commit category.
    
    
    <!-- This is an auto-generated comment: release notes by coderabbit.ai
    -->
    ## Summary by CodeRabbit
    
    * **New Features**
    * Releases are now automatically announced on Mastodon, sharing version,
    highlights, changelog links, and release notes to keep users informed
    without monitoring the repo.
    
    * **Chores**
    * CI now posts Mastodon release announcements only for official release
    commits tied to changelog updates, ensuring accurate, gated, and timely
    notifications.
    <!-- end of auto-generated comment: release notes by coderabbit.ai -->
    
    ---------
    
    Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
    cmeesters and coderabbitai[bot] authored Oct 1, 2025
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  3. chore(main): release 9.11.7 (#3762)

    🤖 I have created a release *beep* *boop*
    ---
    
    
    ##
    [9.11.7](v9.11.6...v9.11.7)
    (2025-10-01)
    
    
    ### Bug Fixes
    
    * Add type annotations in logging module
    ([#3757](#3757))
    ([63404b2](63404b2))
    * source_path not mounted
    ([#3738](#3738))
    ([86e30b3](86e30b3))
    
    
    ### Documentation
    
    * mastodon announcements
    ([#3723](#3723))
    ([7da1b18](7da1b18))
    
    ---
    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 Oct 1, 2025
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