…cloud jobs or logfiles) (#3168)

<!--Add a description of your PR here-->
fixes
snakemake/snakemake-executor-plugin-slurm#154

### QC
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* [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

- **New Features**
- Enhanced the naming of group jobs to include associated rule names,
improving readability and context.
- Implemented truncation for long lists of rule names, ensuring clarity.

- **Bug Fixes**
- Minor adjustments made to the formatting of the group job's name for
consistency.

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

…present in a workdir. This avoids problems in case multiple people use the same workdir and workflow. (#3169)

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

### QC
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* [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

- **New Features**
- Introduced a new function to enhance file copying while managing
permissions effectively.

- **Bug Fixes**
- Improved handling of file permissions during the copying of
environment files and deployment scripts.

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

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

### QC
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* [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

- **New Features**
- Enhanced documentation on benchmarking capabilities, modularization,
and automatic deployment of software dependencies.
- Introduced a comprehensive tutorial on interaction, visualization, and
reporting with Snakemake, including integration with Jupyter notebooks
and Datavzrd.
- Added new rules for data retrieval and visualization in Snakemake
workflows.

- **Documentation**
- Improved clarity and detail in tutorials to facilitate user
understanding and workflow integration.

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

…mmand line interface (and thereby also via workflow specific profiles). Putting this into a workflow specific profile (or specifying as argument) allows to overrule rerun triggers caused by file modification dates where the user knows better. (#3171)

### QC
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* [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

- **New Features**
- Introduced the `--consider-ancient` command-line argument for enhanced
control over input item handling.
- Added a new field in `WorkflowSettings` to store mappings for
"ancient" items.
	- Implemented a new Snakemake workflow with rules for processing files.
- Added a new FAQ section explaining how to prevent unnecessary rule
re-execution using the `--consider-ancient` option.

- **Bug Fixes**
- Improved error handling for input item parsing, ensuring correct
formats are enforced.

- **Enhancements**
- Updated input handling in the `Rule` class to support marking items as
ancient.
	- Enhanced logging for clearer feedback on input and output processing.
- Improved type hinting in `WorkflowSettings` for better data handling
capabilities.
- Added new test cases to validate the handling of ancient files in the
CLI.
<!-- 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: Sven Schrinner <[email protected]>

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### QC
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* [ ] 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 the handling of flags when cloning from input files to
shadowed files, enhancing the management of shadowed file properties.

- **Refactor**
- Streamlined the `shadowed_path` method for better efficiency by
skipping the storage object during the cloning process.

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

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


##
[8.25.0](v8.24.1...v8.25.0)
(2024-10-29)


### Features

* add first 5 rules to group name (used e.g. when naming cluster/cloud
jobs or logfiles)
([#3168](#3168))
([5657122](5657122))
* allow to mark input files of rules as ancient via the API or command
line interface (and thereby also via workflow specific profiles).
Putting this into a workflow specific profile (or specifying as
argument) allows to overrule rerun triggers caused by file modification
dates where the user knows better.
([#3171](#3171))
([6f3aed3](6f3aed3))


### Bug Fixes

* skip storage object when cloning flags for shadowed IO
([#3174](#3174))
([d733fed](d733fed))
* use permission safe copying when hidden conda files are already
present in a workdir. This avoids problems in case multiple people use
the same workdir and workflow.
([#3169](#3169))
([c98b2e7](c98b2e7))


### Documentation

* add tutorial references and small syntax fix
([#3172](#3172))
([6bee12a](6bee12a))

---
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Please](https://github.com/googleapis/release-please). See
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Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>