- 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 <[email protected]>

<!--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 -->

🤖 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).

…on job creation (#3866)

fixes #3852

### 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**
* Relaxed scheduling readiness checks to correctly handle pending queued
input jobs and avoid spurious assertion errors.

* **Refactor**
* Simplified tracking of queue inputs for leaner, more reliable
processing.

* **Tests**
* Updated queue-input test timing to align with the revised scheduling
behavior.

<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

…fore_update flag (#3857)

<!--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**
* Cycle detection now ignores cases involving before_update flags to
avoid false-cycle reports.
* Flag precedence corrected so update jobs take precedence over
before_update when both apply.

* **Tests**
* Added tests and fixtures covering cyclic dependency scenarios,
including a forced-rerun case, to validate the updated behavior.

<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: Johannes Koester <[email protected]>

🤖 I have created a release *beep* *boop*
---


##
[9.14.3](v9.14.2...v9.14.3)
(2025-12-08)


### Bug Fixes

* ensure that queue input jobs wait if the queue is still empty upon job
creation ([#3866](#3866))
([555ab6a](555ab6a))
* fix issues with cyclic dependencies when using the update and
before_update flag
([#3857](#3857))
([21cc94e](21cc94e))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).