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

johanneskoester · web-flow · commit 91cc3ef0f24b · 2025-05-23T11:40:23.000+02:00
### QC
&lt;!-- Make sure that you can tick the boxes below. --&gt;

* [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).


&lt;!-- This is an auto-generated comment: release notes by coderabbit.ai
--&gt;

## Summary by CodeRabbit

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

&lt;!-- end of auto-generated comment: release notes by coderabbit.ai --&gt;
diff --git a/src/snakemake/dag.py b/src/snakemake/dag.py
@@ -2415,7 +2415,7 @@ async def collect_potential_dependencies(self, job, known_producers):
                                 ),
                                 False,
                             )
-                    except MissingRuleException as ex:
+                    except MissingRuleException:
                         # no dependency found
                         yield PotentialDependency(file, None, False)
 
diff --git a/src/snakemake/jobs.py b/src/snakemake/jobs.py
@@ -957,9 +957,10 @@ async def cleanup(self):
             ]
         )
         if to_remove:
+            formatted = ", ".join(map(fmt_iofile, to_remove))
             logger.info(
-                "Removing output files of failed job {}"
-                " since they might be corrupted:\n{}".format(self, ", ".join(to_remove))
+                f"Removing output files of failed job {self}"
+                f" since they might be corrupted:\n{formatted}"
             )
             for f in to_remove:
                 await f.remove()

Original file line number	Diff line number	Diff line change
`@@ -2415,7 +2415,7 @@ async def collect_potential_dependencies(self, job, known_producers):`
`2415`	`2415`	`),`
`2416`	`2416`	`False,`
`2417`	`2417`	`)`
`2418`		`- except MissingRuleException as ex:`
	`2418`	`+ except MissingRuleException:`
`2419`	`2419`	`# no dependency found`
`2420`	`2420`	`yield PotentialDependency(file, None, False)`
`2421`	`2421`
Original file line number	Diff line number	Diff line change
`@@ -957,9 +957,10 @@ async def cleanup(self):`
`957`	`957`	`]`
`958`	`958`	`)`
`959`	`959`	`if to_remove:`
	`960`	`+ formatted = ", ".join(map(fmt_iofile, to_remove))`
`960`	`961`	`logger.info(`
`961`		`- "Removing output files of failed job {}"`
`962`		`- " since they might be corrupted:\n{}".format(self, ", ".join(to_remove))`
	`962`	`+ f"Removing output files of failed job {self}"`
	`963`	`+ f" since they might be corrupted:\n{formatted}"`
`963`	`964`	`)`
`964`	`965`	`for f in to_remove:`
`965`	`966`	`await f.remove()`