fix: fix iofile formatting to always display the storage query if it is set, also in case of missing input exceptions#3786
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johanneskoester merged 1 commit intomainfrom Oct 11, 2025
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…is set, also in case of missing input exceptions
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📝 WalkthroughWalkthroughUpdates fmt_iofile in src/snakemake/io/fmt.py to adjust storage phrasing when neither input nor output flags are set and to change the default return value to an annotated string when no specific IO branch applies. Changes
Sequence Diagram(s)sequenceDiagram
participant Caller
participant fmt_iofile
Caller->>fmt_iofile: format IOFile (f, flags)
alt as_input or as_output
fmt_iofile-->>Caller: formatted string (uses flags)
else no IO flags
alt f.is_storage
Note right of fmt_iofile: storage_phrase = "in storage"
else not storage
Note right of fmt_iofile: storage_phrase = ""
end
fmt_iofile-->>Caller: annotate(f_str)
end
Estimated code review effort🎯 2 (Simple) | ⏱️ ~10 minutes Possibly related PRs
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johanneskoester
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Oct 11, 2025
🤖 I have created a release *beep* *boop* --- ## [9.13.1](v9.13.0...v9.13.1) (2025-10-11) ### Bug Fixes * **config:** restore $ref resolution for schemas ([#3777](#3777)) ([a3e0939](a3e0939)) * fix iofile formatting to always display the storage query if it is set, also in case of missing input exceptions ([#3786](#3786)) ([b1c29fa](b1c29fa)) --- 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
…is set, also in case of missing input exceptions (snakemake#3786) ### 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 * **New Features** * Formatted file references now clearly indicate when a file is in storage by appending “in storage” where applicable. * **Bug Fixes** * Standardized the return of formatted file paths: in non-input/output contexts, formatting now consistently returns the annotated string representation, ensuring predictable display and messaging across the app. <!-- 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* --- ## [9.13.1](snakemake/snakemake@v9.13.0...v9.13.1) (2025-10-11) ### Bug Fixes * **config:** restore $ref resolution for schemas ([snakemake#3777](snakemake#3777)) ([a3e0939](snakemake@a3e0939)) * fix iofile formatting to always display the storage query if it is set, also in case of missing input exceptions ([snakemake#3786](snakemake#3786)) ([b1c29fa](snakemake@b1c29fa)) --- 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
QC
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