fix: rerun-trigger regression by cademirch · Pull Request #3492 · snakemake/snakemake

cademirch · 2025-03-28T21:26:45Z

Edit: This is reverting 4430e23, which changed the default for rerun-trigger for the docs. Presumably because RerunTrigger.all() gives the actual enum values which don't render nicely.

Will need to find a better solution. Any thoughts @fgvieira?

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

New Features
- Updated the CLI default so that all available triggers for job reruns are enabled by default, ensuring a more comprehensive and consistent behavior that aligns with workflow configurations.

fixes 3491

coderabbitai · 2025-03-28T21:26:54Z

📝 Walkthrough

Walkthrough

The change updates the default value for the --rerun-triggers argument in the get_argument_parser function of the CLI. Previously, it used RerunTrigger.choices(), and now it has been changed to RerunTrigger.all(), ensuring that all available rerun triggers are enabled by default. The help text remains unchanged, and no modifications were made to the exported or public entities.

Changes

File	Change Summary
src/snakemake/cli.py	Modified default value for `--rerun-triggers` argument in `get_argument_parser`: changed from `RerunTrigger.choices()` to `RerunTrigger.all()`.

Assessment against linked issues

Objective	Addressed	Explanation
Ensure that changes to shell directive content trigger a rerun (#3491)	✅

Possibly related PRs

docs: fix rerun-triggers default #3403 – Modifies the default value for the --rerun-triggers argument in the same file.

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johanneskoester

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coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/snakemake/cli.py (1)

724-724: Approving the fix for rerun-trigger default value

This change restores the correct default value for the --rerun-triggers argument, ensuring that all available rerun triggers are enabled by default. This aligns with the help text description at line 726 which states "By default, all triggers are used..."

The change fixes the regression mentioned in PR title by replacing RerunTrigger.choices() with RerunTrigger.all().

Consider adding a unit test that verifies the default value of --rerun-triggers to prevent similar regressions in the future.

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Reviewing files that changed from the base of the PR and between 17f0d9b and 01026e1.

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src/snakemake/cli.py (1 hunks)

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src/snakemake/cli.py

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fgvieira · 2025-03-30T17:55:24Z

But why doesn't RerunTrigger.choices() trigger the re-runs? It should be the same as RerunTrigger.all(), no?

cademirch · 2025-03-30T18:00:48Z

But why doesn't RerunTrigger.choices() trigger the re-runs? It should be the same as RerunTrigger.all(), no?

.choices() returns list[str] whereas .all() returns list[RerunTrigger].

See this comment #3491 (comment)

fgvieira · 2025-03-30T18:20:02Z

But that is a string when set by the user, so a list[str] should also work as choices, no? Unless it is parsed by

snakemake/src/snakemake/cli.py

Line 725 in 17f0d9b

parse_func=RerunTrigger.parse_choices_set,

and the defaults are not...

As for the docs, what I discussed with @johanneskoester at the time, was that the proper way would actually by to fix the parsing of the options by sphinx-argparse.

cademirch · 2025-03-30T18:22:58Z

That’s a good question. User supplied strings are parsed into RerunTrigger. I guess the defaults are not?

…

On Sun, Mar 30, 2025 at 11:20 Filipe G. Vieira ***@***.***> wrote: But that is a string when set by the user, so a list[str] should also work as choices, no? Unless it is parsed by https://github.com/snakemake/snakemake/blob/17f0d9b1edd321a8470d1552ead314532f2b3910/src/snakemake/cli.py#L725 and the defaults are not... — Reply to this email directly, view it on GitHub <#3492 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKVQJ4UBAKZ7DWKA5SSZQB32XAYWTAVCNFSM6AAAAAB2APCM6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONRUGY4DINZQGA> . You are receiving this because you authored the thread.Message ID: ***@***.***> [image: fgvieira]*fgvieira* left a comment (snakemake/snakemake#3492) <#3492 (comment)> But that is a string when set by the user, so a list[str] should also work as choices, no? Unless it is parsed by https://github.com/snakemake/snakemake/blob/17f0d9b1edd321a8470d1552ead314532f2b3910/src/snakemake/cli.py#L725 and the defaults are not... — Reply to this email directly, view it on GitHub <#3492 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKVQJ4UBAKZ7DWKA5SSZQB32XAYWTAVCNFSM6AAAAAB2APCM6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONRUGY4DINZQGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

johanneskoester · 2025-04-01T12:48:44Z

Merging this for now to avoid the regression

🤖 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).

@fgvieira

fixes snakemake#3491 Edit: This is reverting 4430e23, which changed the default for rerun-trigger for the docs. Presumably because `RerunTrigger.all()` gives the actual enum values which don't render nicely. Will need to find a better solution. Any thoughts @fgvieira?  ### 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 - **New Features** - Updated the CLI default so that all available triggers for job reruns are enabled by default, ensuring a more comprehensive and consistent behavior that aligns with workflow configurations.

🤖 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).

fix: rerun-trigger regression

01026e1

fixes 3491

cademirch requested a review from johanneskoester as a code owner March 28, 2025 21:26

coderabbitai Bot reviewed Mar 28, 2025

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johanneskoester approved these changes Apr 1, 2025

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johanneskoester merged commit 811742d into snakemake:main Apr 1, 2025

snakemake-bot mentioned this pull request Apr 1, 2025

chore(main): release 9.1.4 #3501

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fix: rerun-trigger regression#3492

fix: rerun-trigger regression#3492
johanneskoester merged 1 commit into
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cademirch:fix-shell-rerun-regression

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