fix: format output files in job cleanup message such that their remote query is shown instead of the local copy by johanneskoester · Pull Request #3600 · snakemake/snakemake

johanneskoester · 2025-05-23T08:52:48Z

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

Style
- Improved exception handling for cleaner code readability.
- Enhanced log message formatting for clearer output during job cleanup.

…e query is shown instead of the local copy

coderabbitai · 2025-05-23T08:52:54Z

📝 Walkthrough

Walkthrough

This update refactors exception handling in the collect_potential_dependencies method by removing an unused exception variable. It also updates the Job.cleanup method's logging to use formatted file names with the fmt_iofile function, improving the readability of log messages. No public interfaces or control flow are altered.

Changes

File(s)	Change Summary
src/snakemake/dag.py	Removed the unused exception variable from the `except MissingRuleException` clause in an async generator.
src/snakemake/jobs.py	Changed log formatting in `Job.cleanup` to use `fmt_iofile` for each file, enhancing log message clarity.

Possibly related PRs

fix: fix recent regression when printing remote storage output or log files (local path shown instead of query) #3550: Modifies the fmt_iofile.annotate function, which is used for formatting file paths in logs and is directly relevant to the logging changes in Job.cleanup.

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Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 65a5360 and 75cb598.

📒 Files selected for processing (2)

src/snakemake/dag.py (1 hunks)
src/snakemake/jobs.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

`**/*.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 the `s...

**/*.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 the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

src/snakemake/dag.py
src/snakemake/jobs.py

🧬 Code Graph Analysis (2)

src/snakemake/dag.py (1)

src/snakemake/exceptions.py (1)

MissingRuleException (413-420)

src/snakemake/jobs.py (1)

src/snakemake/io/fmt.py (1)

fmt_iofile (5-49)

⏰ Context from checks skipped due to timeout of 90000ms (35)

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GitHub Check: apidocs

🔇 Additional comments (1)

src/snakemake/dag.py (1)

2418-2420: Removed unused exception variable from except clause
Catching MissingRuleException without binding to a name removes an unused variable and cleans up the code. The control flow and behavior remain identical.

src/snakemake/jobs.py

🤖 I have created a release *beep* *boop* --- ## [9.5.1](v9.5.0...v9.5.1) (2025-05-23) ### Bug Fixes * format output files in job cleanup message such that their remote query is shown instead of the local copy ([#3600](#3600)) ([91cc3ef](91cc3ef)) * skip unnecessary schema validation inside of remote jobs ([#3601](#3601)) ([9129654](9129654)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

…e query is shown instead of the local copy (snakemake#3600) ### QC  * [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).  ## Summary by CodeRabbit - **Style** - Improved exception handling for cleaner code readability. - Enhanced log message formatting for clearer output during job cleanup.

🤖 I have created a release *beep* *boop* --- ## [9.5.1](snakemake/snakemake@v9.5.0...v9.5.1) (2025-05-23) ### Bug Fixes * format output files in job cleanup message such that their remote query is shown instead of the local copy ([snakemake#3600](snakemake#3600)) ([91cc3ef](snakemake@91cc3ef)) * skip unnecessary schema validation inside of remote jobs ([snakemake#3601](snakemake#3601)) ([9129654](snakemake@9129654)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

fix: format output files in job cleanup message such that their remot…

75cb598

…e query is shown instead of the local copy

johanneskoester requested a review from cmeesters May 23, 2025 08:53

coderabbitai bot reviewed May 23, 2025

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src/snakemake/jobs.py Show resolved Hide resolved

johanneskoester merged commit 91cc3ef into main May 23, 2025
49 checks passed

johanneskoester deleted the fix/format-io-cleanup branch May 23, 2025 09:40

snakemake-bot mentioned this pull request May 23, 2025

chore(main): release 9.5.1 #3603

Merged

coderabbitai bot mentioned this pull request Jul 29, 2025

fix: standardize handling of resources #3421

Merged

2 tasks

This was referenced Nov 20, 2025

fix: cleanup update-marked output files of failed jobs if there was no backup to restore them #3843

Merged

fix: properly format input/output files in case of missing rule to produce them #3849

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fix: format output files in job cleanup message such that their remote query is shown instead of the local copy#3600

fix: format output files in job cleanup message such that their remote query is shown instead of the local copy#3600
johanneskoester merged 1 commit intomainfrom
fix/format-io-cleanup

johanneskoester commented May 23, 2025 •

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