fix: use proper callable when accessing rule proxy with associated path modifier#3763
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johanneskoester merged 2 commits intomainfrom Oct 2, 2025
Merged
fix: use proper callable when accessing rule proxy with associated path modifier#3763johanneskoester merged 2 commits intomainfrom
johanneskoester merged 2 commits intomainfrom
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📝 WalkthroughWalkthroughHandles callables wrapped in _IOFile or AnnotatedString by extracting the underlying callable and applying the existing path modifier to the callable's result via an inner(wildcards) indirection instead of calling the wrapper directly. Changes
Sequence Diagram(s)sequenceDiagram
participant Rule as Rule
participant PM as PathModifier
participant Wrapper as _IOFile / AnnotatedString
participant UF as Underlying Callable
Note over PM,Wrapper: New flow for callable inputs wrapped by helpers
Rule->>PM: register input with modifier(item)
PM->>Wrapper: detect wrapper contains callable
alt wrapper contains callable
PM->>Wrapper: extract callable (item._file.callable or item.callable)
PM->>UF: call inner(wildcards) -> UF(wildcards)
UF-->>PM: path(s)
PM-->>Rule: apply modifier(path(s))
else not wrapped callable
PM-->>Rule: apply modifier(item(wildcards) or item)
end
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src/snakemake/rules.py(1 hunks)
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**/*.py
⚙️ CodeRabbit configuration file
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
Files:
src/snakemake/rules.py
🧬 Code graph analysis (1)
src/snakemake/rules.py (1)
src/snakemake/io/__init__.py (4)
_IOFile(259-931)is_callable(310-311)is_callable(945-946)is_callable(1163-1168)
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johanneskoester
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Oct 2, 2025
🤖 I have created a release *beep* *boop* --- ## [9.11.8](v9.11.7...v9.11.8) (2025-10-02) ### Bug Fixes * use proper callable when accessing rule proxy with associated path modifier ([#3763](#3763)) ([b5d12c8](b5d12c8)) ### Documentation * add snakemake logo to automatic mastodon release posts ([#3764](#3764)) ([7b66250](7b66250)) --- 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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kjohnsen
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Dec 15, 2025
…th modifier (snakemake#3763) ### Description <!--Add a description of your PR here--> ### 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. * [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** * Ensures path modifiers are correctly applied when callable inputs are wrapped as file-like annotations, producing correct input paths. * Preserves support for unwrapped callable inputs and aligns behavior between wrapped and unwrapped callables. * Reduces unexpected path mismatches in complex workflows, improving input resolution reliability. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
kjohnsen
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Dec 15, 2025
🤖 I have created a release *beep* *boop* --- ## [9.11.8](snakemake/snakemake@v9.11.7...v9.11.8) (2025-10-02) ### Bug Fixes * use proper callable when accessing rule proxy with associated path modifier ([snakemake#3763](snakemake#3763)) ([b5d12c8](snakemake@b5d12c8)) ### Documentation * add snakemake logo to automatic mastodon release posts ([snakemake#3764](snakemake#3764)) ([7b66250](snakemake@7b66250)) --- 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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Description
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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