fix: cleanup update-marked output files of failed jobs if there was no backup to restore them by johanneskoester · Pull Request #3843 · snakemake/snakemake

johanneskoester · 2025-11-20T15:35:03Z

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
- Cleanup now preserves outputs that were restored or explicitly marked to be kept after errors.
- Restore-after-update now reports success/failure so restored outputs are correctly retained during cleanup.
- Group-level cleanup simplified to rely on per-job cleanup to avoid accidental removal of recovered files.
Tests
- Added a test validating cleanup behavior after a failed update to ensure updated outputs are removed or preserved as intended.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

…o backup to restore them

coderabbitai · 2025-11-20T15:35:14Z

📝 Walkthrough

Walkthrough

Modifies Job.cleanup to accept skip_outputs and update cleanup selection; Job.postprocess tracks outputs restored from backup and passes them to cleanup to avoid removal. Removes GroupJob.cleanup. persistence.restore_output now returns a boolean indicating whether a backup was restored. Adds a failing-update test and test data.

Changes

Cohort / File(s)	Summary
Job cleanup & postprocess `src/snakemake/jobs.py`	`Job.cleanup` signature changed to accept `skip_outputs: Sequence[_IOFile]` and now skips removing outputs listed there. `Job.postprocess` collects `skip_cleanup_outputs` for outputs restored from backup and calls `cleanup(skip_cleanup_outputs)` on error or completion. `GroupJob.cleanup` implementation removed; group cleanup delegated to individual jobs.
Persistence restore return value `src/snakemake/persistence.py`	`restore_output` changed to return `bool` (False if no backup, True after successful restore); docstring and control flow updated to return explicit boolean results.
Tests and test data `tests/test_update_flag_fail_cleanup/Snakefile`, `tests/test_update_flag_fail_cleanup/in.txt`, `tests/tests.py`	Adds a test workflow and input to exercise a failing update scenario and a new test `test_update_flag_fail_cleanup()` asserting updated outputs are handled/cleaned as expected after failure.
Manifest `requirements.txt`	(Unchanged listing present in diff manifest)

Sequence Diagram

sequenceDiagram
    participant Post as Job.postprocess
    participant Persist as persistence.restore_output
    participant Cleanup as Job.cleanup
    participant FS as Filesystem

    Post->>Persist: attempt to restore backup for updated output
    alt restore returns True
        Persist->>FS: restore file/dir from backup
        Persist-->>Post: True
        Post->>Post: add output to skip_cleanup_outputs
    else restore returns False
        Persist-->>Post: False
    end
    Post->>Cleanup: cleanup(skip_outputs=skip_cleanup_outputs)
    Cleanup->>FS: remove outputs NOT in skip_outputs

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Pay attention to:
- All call sites and overrides of Job.cleanup to ensure the new signature is used.
- Job.postprocess branches that populate skip_cleanup_outputs and interplay with update/restore logic.
- Removal of GroupJob.cleanup and any group lifecycle assumptions.
- Callers of persistence.restore_output now handling the boolean return.

Possibly related PRs

fix: backup output files marked for update and restore them in case of job failures #3833: Changes update/restore handling and cleanup coordination for updated outputs — directly related to skip-cleanup behavior.
fix: rerun jobs if previously failed but rule was changed afterwards (thanks to @laf070810 for bringing this up) #3237: Modifies Job.postprocess and cleanup/error-handling flows — closely related to these changes.
fix: avoid checking output files in immediate-submit mode #3569: Alters Job.postprocess (ignore_missing_output handling) and intersects with postprocess/update logic here.

Suggested reviewers

cmeesters

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 15.38% 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 PR title clearly and concisely summarizes the main change: fixing cleanup of update-marked output files when jobs fail and no backup exists.
Description check	✅ Passed	The PR description follows the repository template and addresses both required checklist items with checked boxes indicating test coverage and documentation requirements.

✨ Finishing touches

📝 Generate docstrings

🧪 Generate unit tests (beta)

Create PR with unit tests
Post copyable unit tests in a comment
Commit unit tests in branch fix/update-cleanup

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src/snakemake/jobs.py (4 hunks)
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🧠 Learnings (3)

📚 Learning: 2025-05-23T09:40:24.474Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3600
File: src/snakemake/jobs.py:960-964
Timestamp: 2025-05-23T09:40:24.474Z
Learning: In the `cleanup` method of the `Job` class in `src/snakemake/jobs.py`, files in the `to_remove` list should be formatted with `fmt_iofile` without specifying `as_output=True` or `as_input=True` parameters, as these files should be displayed as generic files rather than specifically as output files.

Applied to files:

src/snakemake/jobs.py

📚 Learning: 2024-10-14T09:42:11.571Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3140
File: snakemake/dag.py:1308-1308
Timestamp: 2024-10-14T09:42:11.571Z
Learning: In `snakemake/dag.py`, avoid flagging missing lines or indentation issues when there is no clear syntax or logical error to prevent false positives.

Applied to files:

src/snakemake/jobs.py

📚 Learning: 2025-05-06T01:37:23.382Z

Learnt from: kdm9
Repo: snakemake/snakemake PR: 3562
File: src/snakemake/checkpoints.py:90-90
Timestamp: 2025-05-06T01:37:23.382Z
Learning: In Snakemake checkpoints implementation, tracking only the first missing output for each checkpoint is sufficient, because if one output is missing, all outputs for that checkpoint are considered incomplete. This was the behavior before PR #3562 and maintained in the pluralized `checkpoints.get()` implementation.

Applied to files:

src/snakemake/jobs.py

🧬 Code graph analysis (1)

src/snakemake/jobs.py (1)

src/snakemake/persistence.py (2)

cleanup (418-420)

restore_output (311-326)

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🔇 Additional comments (4)

src/snakemake/jobs.py (4)

954-978: LGTM! The selective cleanup logic is correctly implemented.

The new skip_outputs parameter allows precise control over which outputs to preserve during cleanup. The logic correctly:

Filters outputs based on both existence and skip list membership

Handles edge cases where skip_outputs contains non-existent files

Maintains clear separation between files to remove and files to preserve

1222-1222: LGTM! Proper initialization of the skip set.

The empty set is correctly initialized to track outputs that should be preserved during cleanup.

1242-1249: LGTM! The restore and logging sequence is now correct.

The code properly addresses the previous review feedback:

restore_output is called first and its return value is checked

Logging only occurs when restoration succeeds

Outputs are added to skip_cleanup_outputs only when backup restoration succeeds

When no backup exists, the output is NOT added to the skip set, ensuring it gets cleaned up (which is the intended behavior per the PR objectives)

Based on past review comments, this change resolves the logging accuracy issue.

1321-1322: LGTM! Correct cleanup invocation.

The call to cleanup(skip_cleanup_outputs) correctly passes the set of outputs that were successfully restored from backup, ensuring they are preserved while corrupted outputs (those without backups) are removed.

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coderabbitai

Actionable comments posted: 1

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src/snakemake/persistence.py (1 hunks)

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🧠 Learnings (1)

📚 Learning: 2025-05-23T09:40:24.474Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3600
File: src/snakemake/jobs.py:960-964
Timestamp: 2025-05-23T09:40:24.474Z
Learning: In the `cleanup` method of the `Job` class in `src/snakemake/jobs.py`, files in the `to_remove` list should be formatted with `fmt_iofile` without specifying `as_output=True` or `as_input=True` parameters, as these files should be displayed as generic files rather than specifically as output files.

Applied to files:

src/snakemake/jobs.py

🧬 Code graph analysis (1)

src/snakemake/jobs.py (1)

src/snakemake/persistence.py (2)

cleanup (418-420)

restore_output (311-326)

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🔇 Additional comments (2)

src/snakemake/persistence.py (1)

311-327: Verification complete: all restore_output call sites correctly use the new boolean API

Found one call site in src/snakemake/jobs.py:1245 treating the boolean return value correctly—no stale None comparisons or legacy API usage. The implementation matches the intended semantics: False when no backup exists, True after successful restore, and exceptions propagate for real copy errors.

The optional docstring refinement (explicitly stating "False means no backup found; copy errors still raise") remains a nice-to-have but is not required.

src/snakemake/jobs.py (1)

954-978: All Job.cleanup call sites are correctly updated; type hint improvement is optional

The verification confirms that the only Job.cleanup call site (line 1321 in src/snakemake/jobs.py) is already properly using await and passing the skip_cleanup_outputs set argument. No further updates to call sites are needed.

The cleanup logic, including use of fmt_iofile without extra flags, is correct and matches the prior guideline.

The type hint mismatch (Sequence[_IOFile] vs. set at runtime) remains non-breaking but could be cleaned up by relaxing the annotation to Collection[_IOFile] if desired. This is optional and does not block the changes.

github-actions · 2025-11-21T07:44:32Z

Please format your code with pixi run format

coderabbitai

Actionable comments posted: 1

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**/*.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.
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🧠 Learnings (6)

📚 Learning: 2024-10-06T14:09:54.370Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3117
File: tests/test_wrapper/Snakefile:11-11
Timestamp: 2024-10-06T14:09:54.370Z
Learning: Changes made within test cases, such as in `tests/test_wrapper/Snakefile`, are for testing purposes and do not require updates to the project documentation.

Applied to files:

tests/test_update_flag_fail_cleanup/Snakefile
tests/tests.py

📚 Learning: 2024-12-21T15:10:31.992Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 2925
File: tests/test_nonstr_params/Snakefile:14-15
Timestamp: 2024-12-21T15:10:31.992Z
Learning: The file "test.jsonl" in tests/test_nonstr_params is automatically created by Snakemake, rather than manually generated in the Snakefile.

Applied to files:

tests/test_update_flag_fail_cleanup/Snakefile

📚 Learning: 2025-01-17T12:00:09.368Z

Learnt from: leoschwarz
Repo: snakemake/snakemake PR: 3176
File: tests/test_output_index.py:99-157
Timestamp: 2025-01-17T12:00:09.368Z
Learning: New test dependencies for Snakemake should be introduced in separate PRs rather than being added as part of feature or refactoring PRs.

Applied to files:

tests/test_update_flag_fail_cleanup/Snakefile

📚 Learning: 2025-09-08T12:39:09.146Z

Learnt from: Hocnonsense
Repo: snakemake/snakemake PR: 3714
File: tests/tests.py:1637-1644
Timestamp: 2025-09-08T12:39:09.146Z
Learning: In Snakemake module tests, targeting log-only files like "aaalog" can be an intentional test pattern to validate module behavior and error handling, even though log files aren't typically producible targets in normal workflows.

Applied to files:

tests/test_update_flag_fail_cleanup/Snakefile

📚 Learning: 2024-11-07T00:32:44.137Z

Learnt from: mbhall88
Repo: snakemake/snakemake PR: 3188
File: tests/test_script/scripts/test.sh:4-4
Timestamp: 2024-11-07T00:32:44.137Z
Learning: In test scripts within the Snakemake project, concise code is preferred over verbose error handling when simplicity suffices.

Applied to files:

tests/test_update_flag_fail_cleanup/Snakefile

📚 Learning: 2025-05-23T09:40:24.474Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3600
File: src/snakemake/jobs.py:960-964
Timestamp: 2025-05-23T09:40:24.474Z
Learning: In the `cleanup` method of the `Job` class in `src/snakemake/jobs.py`, files in the `to_remove` list should be formatted with `fmt_iofile` without specifying `as_output=True` or `as_input=True` parameters, as these files should be displayed as generic files rather than specifically as output files.

Applied to files:

tests/test_update_flag_fail_cleanup/Snakefile

🧬 Code graph analysis (1)

tests/tests.py (1)

tests/common.py (2)

dpath (33-36)

run (152-503)

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🔇 Additional comments (1)

tests/test_update_flag_fail_cleanup/Snakefile (1)

1-10: LGTM! Clean test case for update-marked output cleanup on failure.

The test workflow correctly exercises the scenario where a job with update() output fails after modifying the file, with no backup available to restore. The parse-time creation of in.txt and the deliberate failure (exit 1) after appending to the output appropriately tests the cleanup logic introduced in this PR.

Based on learnings

🤖 I have created a release *beep* *boop* --- ## [9.14.0](v9.13.7...v9.14.0) (2025-11-27) ### Features * Support Hy in script directive ([#3824](#3824)) ([2329c9e](2329c9e)) ### Bug Fixes * Add support for pathlib in `notebook` field ([#3811](#3811)) ([7b2180a](7b2180a)) * Addressed race condition in workdir_handler.py ([#3844](#3844)) ([8dbfcfb](8dbfcfb)) * cleanup update-marked output files of failed jobs if there was no backup to restore them ([#3843](#3843)) ([41f1ce8](41f1ce8)) * correct Windows callable path handling ([#3832](#3832)) ([5caad70](5caad70)) * expand env vars on resources ([#3823](#3823)) ([fcfa1bc](fcfa1bc)) * fix backup for output marked by `update` ([#3839](#3839)) ([09c64b7](09c64b7)) * Minor fixes/additions to logging module. ([#3802](#3802)) ([3b3986d](3b3986d)) * mount local storage prefix into containers ([#3840](#3840)) ([f1e8b62](f1e8b62)) * properly format input/output files in case of missing rule to produce them ([#3849](#3849)) ([69d5d24](69d5d24)) * Unpack AnnotatedString in _apply_wildcards ([#3798](#3798)) ([7886508](7886508)) ### Performance Improvements * retrieve storage inputs immediately before scheduling jobs instead of before running the entire workflow ([#3850](#3850)) ([4ac6cda](4ac6cda)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

…o backup to restore them (snakemake#3843)  ### 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 * **Bug Fixes** * Cleanup now preserves outputs that were restored or explicitly marked to be kept after errors. * Restore-after-update now reports success/failure so restored outputs are correctly retained during cleanup. * Group-level cleanup simplified to rely on per-job cleanup to avoid accidental removal of recovered files. * **Tests** * Added a test validating cleanup behavior after a failed update to ensure updated outputs are removed or preserved as intended. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub>  --------- Co-authored-by: Felix Mölder <[email protected]>

🤖 I have created a release *beep* *boop* --- ## [9.14.0](snakemake/snakemake@v9.13.7...v9.14.0) (2025-11-27) ### Features * Support Hy in script directive ([snakemake#3824](snakemake#3824)) ([2329c9e](snakemake@2329c9e)) ### Bug Fixes * Add support for pathlib in `notebook` field ([snakemake#3811](snakemake#3811)) ([7b2180a](snakemake@7b2180a)) * Addressed race condition in workdir_handler.py ([snakemake#3844](snakemake#3844)) ([8dbfcfb](snakemake@8dbfcfb)) * cleanup update-marked output files of failed jobs if there was no backup to restore them ([snakemake#3843](snakemake#3843)) ([41f1ce8](snakemake@41f1ce8)) * correct Windows callable path handling ([snakemake#3832](snakemake#3832)) ([5caad70](snakemake@5caad70)) * expand env vars on resources ([snakemake#3823](snakemake#3823)) ([fcfa1bc](snakemake@fcfa1bc)) * fix backup for output marked by `update` ([snakemake#3839](snakemake#3839)) ([09c64b7](snakemake@09c64b7)) * Minor fixes/additions to logging module. ([snakemake#3802](snakemake#3802)) ([3b3986d](snakemake@3b3986d)) * mount local storage prefix into containers ([snakemake#3840](snakemake#3840)) ([f1e8b62](snakemake@f1e8b62)) * properly format input/output files in case of missing rule to produce them ([snakemake#3849](snakemake#3849)) ([69d5d24](snakemake@69d5d24)) * Unpack AnnotatedString in _apply_wildcards ([snakemake#3798](snakemake#3798)) ([7886508](snakemake@7886508)) ### Performance Improvements * retrieve storage inputs immediately before scheduling jobs instead of before running the entire workflow ([snakemake#3850](snakemake#3850)) ([4ac6cda](snakemake@4ac6cda)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

fix: cleanup update-marked output files of failed jobs if there was n…

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…o backup to restore them

coderabbitai Bot reviewed Nov 20, 2025

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Comment thread src/snakemake/jobs.py

add testcase

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coderabbitai Bot reviewed Nov 21, 2025

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Comment thread tests/tests.py Outdated

FelixMoelder and others added 2 commits November 21, 2025 10:16

fmt

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fixes

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johanneskoester merged commit 41f1ce8 into main Nov 27, 2025
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johanneskoester deleted the fix/update-cleanup branch November 27, 2025 13:22

snakemake-bot mentioned this pull request Nov 27, 2025

chore(main): release 9.14.0 #3835

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

fix: cleanup update-marked output files of failed jobs if there was no backup to restore them#3843
johanneskoester merged 4 commits intomainfrom
fix/update-cleanup

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