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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
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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]>
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chore: bump logger interface version (#3758)
The logger plugin interface is now at 2.0.0, bumping the version required here.
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Commits on Oct 1, 2025
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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 -->
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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>
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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).
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