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


##
[9.11.0](v9.10.1...v9.11.0)
(2025-09-05)


### Features

* add landing page to the report containing custom metadata defined with
a YTE yaml template
([#3452](#3452))
([c754d80](c754d80))
* Issue a warning when unsupported characters are used in wildcard names
([#1587](#1587))
([fa57355](fa57355))


### Bug Fixes

* avoid checking output files in immediate-submit mode
([#3569](#3569))
([58c42cf](58c42cf))
* clarify --keep-going flag help text to distinguish runtime vs DAG
construction errors
([#3705](#3705))
([a3a8ef4](a3a8ef4))
* enable docstring assignment in `use rule ... with:` block
([#3710](#3710))
([2191962](2191962))
* fix missing attribute error in greedy scheduler settings when using
touch, dryrun or immediate submit.
([6471004](6471004))
* only trigger script with CODE label
([#3707](#3707))
([2d01f8c](2d01f8c))
* parser.py incorrectly parsing multiline f-strings
([#3701](#3701))
([06ece76](06ece76))
* parsing ordinary yaml strings
([#3506](#3506))
([ddf334e](ddf334e))
* remove temp files when using checkpoints
([#3716](#3716))
([5ff3e20](5ff3e20))
* Restore python rules changes triggering reruns. (GH:
[#3213](#3213))
([#3485](#3485))
([2f663be](2f663be))
* unit testing
([#3680](#3680))
([06ba7e6](06ba7e6))
* use queue_input_wait_time when updating queue input jobs
([#3712](#3712))
([a945a19](a945a19))


### Documentation

* output files within output directories is an error
([#2848](#2848))
([#2913](#2913))
([37272e5](37272e5))

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

) (snakemake#2913)

<!--Add a description of your PR here-->
Closes snakemake#2848, by providing the documentation suggested, and fixes a bug
found while investigating:

The `check_directory_outputs()` function relies on the sorting of file
paths to detect nested outputs. This breaks on windows as file paths are
separated with `\\` rather than `/`, which is sorted after alphanumeric
characters, rather than before.

I've fixed this, and provided a test case, but as there's not currently
a mechanism for distinguishing failures before/during execution (before
being the intended behavior, as this provides better feedback to the
user), it would pass either way. A better test would be the code below,
but I don't want to stray from the use of `run()` in the other test
cases. It may also be possible to extend run with an
`expected_exception` parameter for non-shell execution.

```
def test_github_issue2848():
    # Should fail on parsing with ChildIOException, on Windows previously failed during execution
    with api.SnakemakeApi() as snakemake_api:

        workflow_api = snakemake_api.workflow(
            resource_settings=settings.ResourceSettings(cores=1),
            snakefile=Path(dpath("test_github_issue2848/Snakefile")),
            workdir=Path(dpath("test_github_issue2848")),
        )

        dag_api = workflow_api.dag(dag_settings=settings.DAGSettings(targets={"output/c.txt", "output/dir2/d.txt"}))

        with pytest.raises(ChildIOException):
            dag_api.execute_workflow()
```

### 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

- Documentation
• Updated the docs with a sidebar note explaining that directories
marked as outputs are removed before a job runs, helping prevent
accidental file deletion.
  
- New Features
• Added an example workflow that demonstrates file and directory
management in job execution.

- Tests
• Expanded test coverage to ensure improved error handling around
workflow output parsing.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

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


##
[9.11.0](snakemake/snakemake@v9.10.1...v9.11.0)
(2025-09-05)


### Features

* add landing page to the report containing custom metadata defined with
a YTE yaml template
([snakemake#3452](snakemake#3452))
([c754d80](snakemake@c754d80))
* Issue a warning when unsupported characters are used in wildcard names
([snakemake#1587](snakemake#1587))
([fa57355](snakemake@fa57355))


### Bug Fixes

* avoid checking output files in immediate-submit mode
([snakemake#3569](snakemake#3569))
([58c42cf](snakemake@58c42cf))
* clarify --keep-going flag help text to distinguish runtime vs DAG
construction errors
([snakemake#3705](snakemake#3705))
([a3a8ef4](snakemake@a3a8ef4))
* enable docstring assignment in `use rule ... with:` block
([snakemake#3710](snakemake#3710))
([2191962](snakemake@2191962))
* fix missing attribute error in greedy scheduler settings when using
touch, dryrun or immediate submit.
([6471004](snakemake@6471004))
* only trigger script with CODE label
([snakemake#3707](snakemake#3707))
([2d01f8c](snakemake@2d01f8c))
* parser.py incorrectly parsing multiline f-strings
([snakemake#3701](snakemake#3701))
([06ece76](snakemake@06ece76))
* parsing ordinary yaml strings
([snakemake#3506](snakemake#3506))
([ddf334e](snakemake@ddf334e))
* remove temp files when using checkpoints
([snakemake#3716](snakemake#3716))
([5ff3e20](snakemake@5ff3e20))
* Restore python rules changes triggering reruns. (GH:
[snakemake#3213](snakemake#3213))
([snakemake#3485](snakemake#3485))
([2f663be](snakemake@2f663be))
* unit testing
([snakemake#3680](snakemake#3680))
([06ba7e6](snakemake@06ba7e6))
* use queue_input_wait_time when updating queue input jobs
([snakemake#3712](snakemake#3712))
([a945a19](snakemake@a945a19))


### Documentation

* output files within output directories is an error
([snakemake#2848](snakemake#2848))
([snakemake#2913](snakemake#2913))
([37272e5](snakemake@37272e5))

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