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


##
[9.0.0](v8.30.0...v9.0.0)
(2025-03-14)


### ⚠ BREAKING CHANGES

* Logging refactor & add LoggerPluginInterface
([#3107](#3107))

### Features

* [#3412](#3412) - keep
shadow folder of failed job if --keep-incomplete flag is set.
([#3430](#3430))
([22978c3](22978c3))
* add flag --report-after-run to automatically generate the report after
a successfull workflow run
([#3428](#3428))
([b0a7f03](b0a7f03))
* add flatten function to IO utils
([#3424](#3424))
([67fa392](67fa392))
* add helper functions to parse input files
([#2918](#2918))
([63e45a7](63e45a7))
* Add option to print redacted file names
([#3089](#3089))
([ba4d264](ba4d264))
* add support for validation of polars dataframe and lazyframe
([#3262](#3262))
([c7473a6](c7473a6))
* added support for rendering dag with mermaid js
([#3409](#3409))
([7bf8381](7bf8381))
* adding --replace-workflow-config to fully replace workflow configs
(from config: directive) with --configfile, instead of merging them
([#3381](#3381))
([47504a0](47504a0))
* Dynamic module name
([#3401](#3401))
([024dc32](024dc32))
* Enable saving and reloading IOCache object
([#3386](#3386))
([c935953](c935953))
* files added in rule params with workflow.source_path will be available
in used containers
([#3385](#3385))
([a6e45bf](a6e45bf))
* Fix keep_local in storage directive and more freedom over remote
retrieval behaviour
([#3410](#3410))
([67b4739](67b4739))
* inherit parameters of use rule and extend/replace individual items
them when using 'with' directive
([#3365](#3365))
([93e4b92](93e4b92))
* Logging refactor & add LoggerPluginInterface
([#3107](#3107))
([86f1d6e](86f1d6e))
* Maximal file size for checksums
([#3368](#3368))
([b039f8a](b039f8a))
* Modernize package configuration using Pixi
([#3369](#3369))
([77992d8](77992d8))
* multiext support for named input/output
([#3372](#3372))
([05e1378](05e1378))
* optionally auto-group jobs via temp files in case of remote execution
([#3378](#3378))
([cc9bba2](cc9bba2))


### Bug Fixes

* `--delete-all-output` ignores `--dry-run`
([#3265](#3265))
([23fef82](23fef82))
* 3342 faster touch runs and warning messages for non-existing files
([#3398](#3398))
([cd9c3c3](cd9c3c3))
* add default value to max-jobs-per-timespan
([#3043](#3043))
([2959abe](2959abe))
* checkpoints inside modules are overwritten
([#3359](#3359))
([fba3ac7](fba3ac7))
* Convert Path to IOFile
([#3405](#3405))
([c58684c](c58684c))
* Do not perform storage object cleanup with --keep-storage-local-copies
set ([#3358](#3358))
([9a6d14b](9a6d14b))
* edgecases of source deployment in case of remote execution
([#3396](#3396))
([5da13be](5da13be))
* enhance error message formatting for strict DAG-building mode
([#3376](#3376))
([a1c39ee](a1c39ee))
* fix bug in checkpoint handling that led to exceptions in case
checkpoint output was missing upon rerun
([#3423](#3423))
([8cf4a2f](8cf4a2f))
* force check all required outputs
([#3341](#3341))
([495a4e7](495a4e7))
* group job formatting
([#3442](#3442))
([f0b10a3](f0b10a3))
* in remote jobs, upload storage in topological order such that
modification dates are preserved (e.g. in case of group jobs)
([#3377](#3377))
([eace08f](eace08f))
* only skip eval when resource depends on input
([#3374](#3374))
([4574c92](4574c92))
* Prevent execution of conda in apptainer when not explicitly requested
in software deployment method
([#3388](#3388))
([c43c5c0](c43c5c0))
* print filenames with quotes around them in RuleException
([#3269](#3269))
([6baeda5](6baeda5))
* Re-evaluation of free resources
([#3399](#3399))
([6371293](6371293))
* ReadTheDocs layout issue due to src directory change
([#3419](#3419))
([695b127](695b127))
* robustly escaping quotes in generated bash scripts (v2)
([#3297](#3297))
([#3389](#3389))
([58720bd](58720bd))
* Show apptainer image URL in snakemake report
([#3407](#3407))
([45f0450](45f0450))
* Update ReadTheDocs configuration for documentation build to use Pixi
([#3433](#3433))
([3f227a6](3f227a6))


### Documentation

* Add pixi setup instructions to general use tutorial
([#3382](#3382))
([115e81b](115e81b))
* fix contribution section heading levels, fix docs testing setup order
([#3360](#3360))
([051dc53](051dc53))
* fix link to github.com/snakemake/poetry-snakemake-plugin
([#3436](#3436))
([ec6d97c](ec6d97c))
* fix quoting
([#3394](#3394))
([b40f599](b40f599))
* fix rerun-triggers default
([#3403](#3403))
([4430e23](4430e23))
* fix typo 'safe' -> 'save'
([#3384](#3384))
([7755861](7755861))
* mention code formatting in the contribution section
([#3431](#3431))
([e8682b7](e8682b7))
* remove duplicated 'functions'.
([#3356](#3356))
([7c595db](7c595db))
* update broken links documentation
([#3437](#3437))
([e3d0d88](e3d0d88))
* Updating contributing guidelines with new pixi dev setup
([#3415](#3415))
([8e95a12](8e95a12))

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

Co-authored-by: snakemake-bot <snakemake-bot-admin@googlegroups.com>

…ke#3297) (snakemake#3389)

See original PR snakemake#3303

### QC

* [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 checked that the fixed behaviour is still consistent with the docs)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **Chores**
  - Updated the CI/CD workflow configuration for improved clarity.
  - Removed an outdated iterative processing example.
- **Refactor**
- Enhanced internal code styling and documentation to maintain
consistency.
- **Tests**
- Updated test configurations with dynamic parameterization and refined
output naming.
- Improved logging, debugging, and error handling across test scripts to
ensure more informative execution feedback.
- Added assertions to validate configuration and parameter values in the
test scripts.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Lucas Frérot <lucas.frerot@sorbonne-universite.fr>

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


##
[9.0.0](snakemake/snakemake@v8.30.0...v9.0.0)
(2025-03-14)


### ⚠ BREAKING CHANGES

* Logging refactor & add LoggerPluginInterface
([snakemake#3107](snakemake#3107))

### Features

* [snakemake#3412](snakemake#3412) - keep
shadow folder of failed job if --keep-incomplete flag is set.
([snakemake#3430](snakemake#3430))
([22978c3](snakemake@22978c3))
* add flag --report-after-run to automatically generate the report after
a successfull workflow run
([snakemake#3428](snakemake#3428))
([b0a7f03](snakemake@b0a7f03))
* add flatten function to IO utils
([snakemake#3424](snakemake#3424))
([67fa392](snakemake@67fa392))
* add helper functions to parse input files
([snakemake#2918](snakemake#2918))
([63e45a7](snakemake@63e45a7))
* Add option to print redacted file names
([snakemake#3089](snakemake#3089))
([ba4d264](snakemake@ba4d264))
* add support for validation of polars dataframe and lazyframe
([snakemake#3262](snakemake#3262))
([c7473a6](snakemake@c7473a6))
* added support for rendering dag with mermaid js
([snakemake#3409](snakemake#3409))
([7bf8381](snakemake@7bf8381))
* adding --replace-workflow-config to fully replace workflow configs
(from config: directive) with --configfile, instead of merging them
([snakemake#3381](snakemake#3381))
([47504a0](snakemake@47504a0))
* Dynamic module name
([snakemake#3401](snakemake#3401))
([024dc32](snakemake@024dc32))
* Enable saving and reloading IOCache object
([snakemake#3386](snakemake#3386))
([c935953](snakemake@c935953))
* files added in rule params with workflow.source_path will be available
in used containers
([snakemake#3385](snakemake#3385))
([a6e45bf](snakemake@a6e45bf))
* Fix keep_local in storage directive and more freedom over remote
retrieval behaviour
([snakemake#3410](snakemake#3410))
([67b4739](snakemake@67b4739))
* inherit parameters of use rule and extend/replace individual items
them when using 'with' directive
([snakemake#3365](snakemake#3365))
([93e4b92](snakemake@93e4b92))
* Logging refactor & add LoggerPluginInterface
([snakemake#3107](snakemake#3107))
([86f1d6e](snakemake@86f1d6e))
* Maximal file size for checksums
([snakemake#3368](snakemake#3368))
([b039f8a](snakemake@b039f8a))
* Modernize package configuration using Pixi
([snakemake#3369](snakemake#3369))
([77992d8](snakemake@77992d8))
* multiext support for named input/output
([snakemake#3372](snakemake#3372))
([05e1378](snakemake@05e1378))
* optionally auto-group jobs via temp files in case of remote execution
([snakemake#3378](snakemake#3378))
([cc9bba2](snakemake@cc9bba2))


### Bug Fixes

* `--delete-all-output` ignores `--dry-run`
([snakemake#3265](snakemake#3265))
([23fef82](snakemake@23fef82))
* 3342 faster touch runs and warning messages for non-existing files
([snakemake#3398](snakemake#3398))
([cd9c3c3](snakemake@cd9c3c3))
* add default value to max-jobs-per-timespan
([snakemake#3043](snakemake#3043))
([2959abe](snakemake@2959abe))
* checkpoints inside modules are overwritten
([snakemake#3359](snakemake#3359))
([fba3ac7](snakemake@fba3ac7))
* Convert Path to IOFile
([snakemake#3405](snakemake#3405))
([c58684c](snakemake@c58684c))
* Do not perform storage object cleanup with --keep-storage-local-copies
set ([snakemake#3358](snakemake#3358))
([9a6d14b](snakemake@9a6d14b))
* edgecases of source deployment in case of remote execution
([snakemake#3396](snakemake#3396))
([5da13be](snakemake@5da13be))
* enhance error message formatting for strict DAG-building mode
([snakemake#3376](snakemake#3376))
([a1c39ee](snakemake@a1c39ee))
* fix bug in checkpoint handling that led to exceptions in case
checkpoint output was missing upon rerun
([snakemake#3423](snakemake#3423))
([8cf4a2f](snakemake@8cf4a2f))
* force check all required outputs
([snakemake#3341](snakemake#3341))
([495a4e7](snakemake@495a4e7))
* group job formatting
([snakemake#3442](snakemake#3442))
([f0b10a3](snakemake@f0b10a3))
* in remote jobs, upload storage in topological order such that
modification dates are preserved (e.g. in case of group jobs)
([snakemake#3377](snakemake#3377))
([eace08f](snakemake@eace08f))
* only skip eval when resource depends on input
([snakemake#3374](snakemake#3374))
([4574c92](snakemake@4574c92))
* Prevent execution of conda in apptainer when not explicitly requested
in software deployment method
([snakemake#3388](snakemake#3388))
([c43c5c0](snakemake@c43c5c0))
* print filenames with quotes around them in RuleException
([snakemake#3269](snakemake#3269))
([6baeda5](snakemake@6baeda5))
* Re-evaluation of free resources
([snakemake#3399](snakemake#3399))
([6371293](snakemake@6371293))
* ReadTheDocs layout issue due to src directory change
([snakemake#3419](snakemake#3419))
([695b127](snakemake@695b127))
* robustly escaping quotes in generated bash scripts (v2)
([snakemake#3297](snakemake#3297))
([snakemake#3389](snakemake#3389))
([58720bd](snakemake@58720bd))
* Show apptainer image URL in snakemake report
([snakemake#3407](snakemake#3407))
([45f0450](snakemake@45f0450))
* Update ReadTheDocs configuration for documentation build to use Pixi
([snakemake#3433](snakemake#3433))
([3f227a6](snakemake@3f227a6))


### Documentation

* Add pixi setup instructions to general use tutorial
([snakemake#3382](snakemake#3382))
([115e81b](snakemake@115e81b))
* fix contribution section heading levels, fix docs testing setup order
([snakemake#3360](snakemake#3360))
([051dc53](snakemake@051dc53))
* fix link to github.com/snakemake/poetry-snakemake-plugin
([snakemake#3436](snakemake#3436))
([ec6d97c](snakemake@ec6d97c))
* fix quoting
([snakemake#3394](snakemake#3394))
([b40f599](snakemake@b40f599))
* fix rerun-triggers default
([snakemake#3403](snakemake#3403))
([4430e23](snakemake@4430e23))
* fix typo 'safe' -> 'save'
([snakemake#3384](snakemake#3384))
([7755861](snakemake@7755861))
* mention code formatting in the contribution section
([snakemake#3431](snakemake#3431))
([e8682b7](snakemake@e8682b7))
* remove duplicated 'functions'.
([snakemake#3356](snakemake#3356))
([7c595db](snakemake@7c595db))
* update broken links documentation
([snakemake#3437](snakemake#3437))
([e3d0d88](snakemake@e3d0d88))
* Updating contributing guidelines with new pixi dev setup
([snakemake#3415](snakemake#3415))
([8e95a12](snakemake@8e95a12))

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

Co-authored-by: snakemake-bot <snakemake-bot-admin@googlegroups.com>