🤖 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>

<!--Add a description of your PR here-->

Fixes snakemake#3193 
Fixes snakemake#2933 

### QC
<!-- Make sure that you can tick the boxes below. -->

* [ ] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [ ] 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

- **Refactor**
- Revised handling of pending file operations to deliver more precise
and actionable feedback.
- Streamlined metadata cleanup processes to improve overall reliability
and consistency.
- Enhanced workflow routines for file cleanup, ensuring a more robust
and efficient operation.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

🤖 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>