tests/test_github_issue3687/Snakefile (1)

18-27: Consider ensuring parent directory exists.

The code creates a symlink at dir2/D, but the parent directory dir2 is not explicitly created. While Snakemake may handle parent directory creation for outputs automatically, consider adding explicit parent creation for robustness:

   run:
+    Path(str(output)).parent.mkdir(parents=True, exist_ok=True)
     Path(str(output)).symlink_to(f'../{input}')

Alternatively, verify that Snakemake's test framework handles this automatically.

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

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

587-599: Preserve the original stat() failure via exception chaining.

These branches now add useful context, but they still discard the original FileNotFoundError / PermissionError, which makes symlink-vs-target failures harder to diagnose. Please capture the exception and raise WorkflowError(...) from e here.

♻️ Proposed change

-        except FileNotFoundError:
+        except FileNotFoundError as e:
             if self.is_storage:
                 return Mtime(storage=mtime_in_storage)
             raise WorkflowError(
                 f"Unable to obtain modification time of file {file} although it existed before. "
                 "It could be that a concurrent process has deleted it while Snakemake "
                 "was running."
-            )
-        except PermissionError:
+            ) from e
+        except PermissionError as e:
             raise WorkflowError(
                 f"Unable to obtain modification time of file {file} because of missing "
                 "read permissions."
-            )
+            ) from e

Based on learnings: "In the snakemake codebase, use exception chaining (raise NewError(...) from original) to preserve the original exception context when re-raising or wrapping exceptions in Python files."

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@src/snakemake/io/__init__.py` around lines 587 - 599, The except handlers
that wrap FileNotFoundError and PermissionError should preserve the original
exception via exception chaining: capture the original exception (e) in both
except blocks and re-raise WorkflowError(...) using "raise WorkflowError(... )
from e" so the original stat() failure context is kept; update the
FileNotFoundError handler (the branch that returns
Mtime(storage=mtime_in_storage) when self.is_storage, otherwise raises
WorkflowError about modification time of file variable file) and the
PermissionError handler (which raises WorkflowError about missing read
permissions) to use "from e" when re-raising.