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docs: note about parameter inheritance when using the "use rule with" pattern#3500

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docs/params-inheritance
Apr 1, 2025
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docs: note about parameter inheritance when using the "use rule with" pattern#3500
johanneskoester merged 1 commit into
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docs/params-inheritance

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@johanneskoester johanneskoester commented Apr 1, 2025 •
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Description

QC

  • 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).

Summary by CodeRabbit

  • Documentation
    • Enhanced guidance on modifying workflow rule parameters.
    • Clarifies that when updating parameters, unaltered keyword arguments are preserved while new positional arguments and other properties (like inputs and outputs) fully replace existing values.

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📝 Walkthrough

Walkthrough

This pull request updates the documentation for Snakemake workflows in the docs/snakefiles/rules.rst file. It adds a new note clarifying the behavior when modifying the params property in a rule. Specifically, the note explains that keyword arguments not redefined after the with clause are inherited, while positional arguments provided after with overwrite the original ones, and properties like input and output are completely replaced. The update aims to provide clearer guidance on parameter modification in rule inheritance.

Changes

File(s) Change Summary
docs/snakefiles/rules.rst Added a note clarifying that when modifying params in a rule: keyword arguments not explicitly redefined are inherited, positional arguments overwrite, and all other properties (e.g., input and output) are completely replaced.

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@johanneskoester johanneskoester changed the title Docs/params-inheritance docs: note about parameter inheritance when using the "use rule with" pattern Apr 1, 2025
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Actionable comments posted: 0

🧹 Nitpick comments (1)
docs/snakefiles/rules.rst (1)

2934-2939: Enhance Clarity for Parameter Inheritance Note

The new note clearly describes the behavior for modifying the params property using with. It accurately explains that:

  • Unmodified keyword params are inherited.
  • Positional params provided after with completely replace the original positional ones.
  • All other properties (e.g. input, output, etc.) are entirely overwritten by those specified after with.

To further improve clarity, consider:

  • Replacing terms like “are overwritten” with “are replaced” for consistency with the notion of replacement.
  • Adding a brief example or bullet points to illustrate the difference between keyword and positional parameter handling.

For example, you might consider this diff for refinement:

-    Positional `params` arguments of the original rule are overwritten, if positional `params` arguments are given after `with`.
+    Positional `params` arguments of the original rule are replaced when new positional arguments are provided after `with`.

This would enhance readability and ensure the documentation is immediately clear to users.

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  • docs/snakefiles/rules.rst (1 hunks)
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@johanneskoester johanneskoester merged commit 8f6a8eb into main Apr 1, 2025
@johanneskoester johanneskoester deleted the docs/params-inheritance branch April 1, 2025 12:46
@snakemake-bot snakemake-bot mentioned this pull request Apr 1, 2025
Merged
johanneskoester pushed a commit that referenced this pull request Apr 1, 2025
@snakemake-bot
chore(main): release 9.1.4 (#3501)
270d240 
🤖 I have created a release *beep* *boop*
---


##
[9.1.4](v9.1.3...v9.1.4)
(2025-04-01)


### Bug Fixes

* Fix map call in report creation
([#3503](#3503))
([44754cc](44754cc))
* in the report, do not render toggle labels if there is more than one
label eligible for a toggle
([#3502](#3502))
([3be8ca9](3be8ca9))
* only inform about storage cleanup in case of --verbose mode
([#3494](#3494))
([62bbbf5](62bbbf5))
* provide causing rule to workflow error during checkpoint handling
([#3499](#3499))
([b4cbe5d](b4cbe5d))
* rerun-trigger regression
([#3492](#3492))
([811742d](811742d))


### Documentation

* note about parameter inheritance when using the "use rule with"
pattern ([#3500](#3500))
([8f6a8eb](8f6a8eb))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).
kjohnsen pushed a commit to kjohnsen/snakemake that referenced this pull request Dec 15, 2025
@johanneskoester @kjohnsen
docs: note about parameter inheritance when using the "use rule with"…
69fd5a0 
… pattern (snakemake#3500)

### Description

<!--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

- **Documentation**
  - Enhanced guidance on modifying workflow rule parameters.
- Clarifies that when updating parameters, unaltered keyword arguments
are preserved while new positional arguments and other properties (like
inputs and outputs) fully replace existing values.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->
kjohnsen pushed a commit to kjohnsen/snakemake that referenced this pull request Dec 15, 2025
@snakemake-bot @kjohnsen
chore(main): release 9.1.4 (snakemake#3501)
046dd62 
🤖 I have created a release *beep* *boop*
---


##
[9.1.4](snakemake/snakemake@v9.1.3...v9.1.4)
(2025-04-01)


### Bug Fixes

* Fix map call in report creation
([snakemake#3503](snakemake#3503))
([44754cc](snakemake@44754cc))
* in the report, do not render toggle labels if there is more than one
label eligible for a toggle
([snakemake#3502](snakemake#3502))
([3be8ca9](snakemake@3be8ca9))
* only inform about storage cleanup in case of --verbose mode
([snakemake#3494](snakemake#3494))
([62bbbf5](snakemake@62bbbf5))
* provide causing rule to workflow error during checkpoint handling
([snakemake#3499](snakemake#3499))
([b4cbe5d](snakemake@b4cbe5d))
* rerun-trigger regression
([snakemake#3492](snakemake#3492))
([811742d](snakemake@811742d))


### Documentation

* note about parameter inheritance when using the "use rule with"
pattern ([snakemake#3500](snakemake#3500))
([8f6a8eb](snakemake@8f6a8eb))

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