fix: yield proper error message in case a local git source file is not retrievable by johanneskoester · Pull Request #3892 · snakemake/snakemake

johanneskoester · 2025-12-19T12:38:00Z

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

Bug Fixes
- Improved error messages when loading workflow files from Git — messages now indicate a consistent, user-facing path and suggest that a local clone may be outdated when relevant.
- Clarified failure reporting for non-Git file access to provide better traceability.

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coderabbitai · 2025-12-19T12:38:42Z

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The pull request is closed.

📝 Walkthrough

Walkthrough

Introduce log_path for consistent error reporting and wrap the local Git git.show call in a try/except to raise a WorkflowError with a message (including log_path) when the Git command fails; update non-Git failure messages to use log_path.

Changes

Cohort / File(s)	Summary
Error handling & error-message normalization `src/snakemake/sourcecache.py`	Add `log_path` derived from `source_file`; wrap `LocalGitFile` `git.Repo(...).git.show(...)` in try/except to catch `GitCommandError` and raise `WorkflowError` with `log_path` and an update-suggestion; update non-Git failure path to report `log_path` in error messages.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Check try/except correctly narrows scope and only catches intended GitCommandError.
Verify log_path calculation is correct for varied source_file inputs.
Confirm error messages include log_path and do not leak sensitive paths.

Possibly related PRs

fix: yield proper error message in case a local git source file is not retrievable #3892 — Modifies _open logic in src/snakemake/sourcecache.py with similar log_path usage and a wrapped git.show call to raise WorkflowError.

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run `@coderabbitai generate docstrings` to improve docstring coverage.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and specifically describes the main change: improving error messaging when a local git source file cannot be retrieved.
Description check	✅ Passed	The PR description follows the repository template with both QC checklist items completed, though it lacks a detailed description of the changes above the checklist.

📜 Recent review details

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Review profile: CHILL

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📥 Commits

Reviewing files that changed from the base of the PR and between 60cbbfa and 24c3550.

📒 Files selected for processing (1)

src/snakemake/sourcecache.py (1 hunks)

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github-actions · 2025-12-19T12:39:06Z

Please format your code with pixi run format

coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/snakemake/sourcecache.py (1)
454-464: Excellent error handling improvement! Consider adding exception chaining.

The try/except wrapper and helpful error message with actionable suggestion significantly improve the user experience.

Consider using raise ... from e to preserve the exception chain for better debugging:
🔎 Suggested improvement for exception chaining
             except git.GitCommandError as e:
-               raise WorkflowError(
+               raise WorkflowError(
                    f"Failed to get local git source file {log_path}: {e}. "
                    "Is the local git clone up to date?"
-               )
+               ) from e
This follows Python best practices for exception handling and helps developers trace the root cause when debugging.

📜 Review details

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 005c92d and 60cbbfa.

📒 Files selected for processing (1)

src/snakemake/sourcecache.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

**/*.py

⚙️ CodeRabbit configuration file

**/*.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.
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Do not suggest return type annotation if a function or method does not contain a return statement.

Files:

src/snakemake/sourcecache.py

🪛 Ruff (0.14.8)

src/snakemake/sourcecache.py

461-464: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

461-464: Avoid specifying long messages outside the exception class

(TRY003)

470-470: Do not catch blind exception: Exception

(BLE001)

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GitHub Check: tests (4, windows-2022, py313)
GitHub Check: tests (9, ubuntu-latest, py312)
GitHub Check: tests (9, windows-2022, py313)
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GitHub Check: tests (4, ubuntu-latest, py313)
GitHub Check: tests (2, ubuntu-latest, py311)

🔇 Additional comments (2)

src/snakemake/sourcecache.py (2)

449-450: LGTM! Good refactoring for consistent error messages.

Introducing log_path improves error message consistency and ensures secrets are not leaked in logs.

472-472: LGTM! Consistent error message improvement.

Using log_path here ensures consistent, secret-free error messages across all failure paths.

🤖 I have created a release *beep* *boop* --- ## [9.14.6](v9.14.5...v9.14.6) (2026-01-08) ### Bug Fixes * create local clone of git repos for source files from hosting providers ([#3643](#3643)) ([d2f8aba](d2f8aba)) * create potentially missing .snakemake folder in case of very long command lines for spawned jobs ([#3894](#3894)) ([4b431dd](4b431dd)) * make ilp solver enumeration lazy ([#3900](#3900)) ([30e1509](30e1509)) * Prevent broken report_href links by using deterministic report IDs with fixed prefix length ([#3889](#3889)) ([6d8f4d8](6d8f4d8)) * refactor LoggerManager setup and scope ([#3851](#3851)) ([f46d904](f46d904)) * yield proper error message in case a local git source file is not retrievable ([#3892](#3892)) ([ed79cae](ed79cae)) ### Documentation * explain how to pass nested config via CLI ([#3885](#3885)) ([9d8c539](9d8c539)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

fix

60cbbfa

coderabbitai Bot reviewed Dec 19, 2025

View reviewed changes

fmt

24c3550

johanneskoester merged commit ed79cae into main Dec 19, 2025
55 of 57 checks passed

johanneskoester deleted the fix/error_local_git_source_file branch December 19, 2025 18:39

snakemake-bot mentioned this pull request Dec 19, 2025

chore(main): release 9.14.6 #3893

Merged

coderabbitai Bot mentioned this pull request Jan 3, 2026

fix: create local clone of git repos for source files from hosting providers #3643

Merged

2 tasks

coderabbitai Bot mentioned this pull request Jan 16, 2026

fix: ensure that git repos backing source files are fetched only once per run #3928

Merged

2 tasks

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fix: yield proper error message in case a local git source file is not retrievable#3892

fix: yield proper error message in case a local git source file is not retrievable#3892
johanneskoester merged 2 commits intomainfrom
fix/error_local_git_source_file

johanneskoester commented Dec 19, 2025 •

edited by coderabbitai Bot

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johanneskoester commented Dec 19, 2025 • edited by coderabbitai Bot Loading Uh oh! There was an error while loading. Please reload this page.

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johanneskoester commented Dec 19, 2025 •

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