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fix: ensure correct topological order when touching group job outputs#3181

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johanneskoester merged 2 commits intomainfrom
fix/touch-order-group
Nov 1, 2024
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fix: ensure correct topological order when touching group job outputs#3181
johanneskoester merged 2 commits intomainfrom
fix/touch-order-group

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@johanneskoester johanneskoester commented Nov 1, 2024 •
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fixes #3165

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 management of asynchronous tasks in job processing, enhancing performance and reliability.
    • Updated output verification process for jobs to ensure protected outputs are correctly checked.

  • Refactor

    • Reorganized task creation logic to streamline job processing.

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coderabbitai bot commented Nov 1, 2024 •
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📝 Walkthrough
📝 Walkthrough

Walkthrough

The changes in this pull request focus on the GroupJob class within the snakemake/jobs.py file. The postprocess method has been modified to improve asynchronous task management by moving the async with asyncio.TaskGroup() context manager outside of the job processing loop. This adjustment allows for the creation of a single task group per job level. Additionally, the check_protected_output method has been updated to ensure that protected outputs are verified for each job in the group, enhancing the robustness of output checks.

Changes

File Change Summary
snakemake/jobs.py - Modified postprocess method in GroupJob to move async with asyncio.TaskGroup() outside the loop for better task management.
- Updated check_protected_output method to iterate over jobs and verify protected outputs for each job.

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@johanneskoester johanneskoester mentioned this pull request Nov 1, 2024
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@johanneskoester johanneskoester changed the title fix: ensure correct topological order when touching group jobs fix: ensure correct topological order when touching group job outputs Nov 1, 2024
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sonarqubecloud bot commented Nov 1, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

@johanneskoester johanneskoester merged commit 5924a3e into main Nov 1, 2024
@johanneskoester johanneskoester deleted the fix/touch-order-group branch November 1, 2024 18:35
@github-actions github-actions bot mentioned this pull request Nov 1, 2024
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johanneskoester pushed a commit that referenced this pull request Nov 1, 2024
@github-actions
chore(main): release 8.25.1 (#3180)
45b921f 
🤖 I have created a release *beep* *boop*
---


##
[8.25.1](v8.25.0...v8.25.1)
(2024-11-01)


### Bug Fixes

* ensure correct topological order when touching group job outputs
([#3181](#3181))
([5924a3e](5924a3e))
* ensure version agnostic robust pickling of pandas, polars and numpy
data structures passed as params to Python scripts or notebooks
([#3175](#3175))
([eb11137](eb11137))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
@mbhall88
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mbhall88 commented Nov 3, 2024

Thanks Johannes. I'll test it out in the next week or two.

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@coderabbitai coderabbitai bot mentioned this pull request Mar 11, 2025
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@coderabbitai coderabbitai bot mentioned this pull request Dec 5, 2025
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clock skew error with grouped rules

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@johanneskoester @mbhall88