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fix: Remove incomplete marker also when drop-metadata is active #3215

Merged
merged 3 commits into from
Nov 21, 2024
Merged

fix: Remove incomplete marker also when drop-metadata is active #3215

merged 3 commits into from
Nov 21, 2024

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mhulsman
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@mhulsman mhulsman commented Nov 20, 2024 •
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Fix: This PR adds back the removal of the incomplete marker file also when keep_metadata is False (i.e. --drop-metadata is active).

The removal calls were merged and put at the start of the function in #3162, but this caused loss of starttime info in the metadata record. In #3197 this was fixed, but by moving the removal call to the end of the function, the incomplete tracker file was not removed anymore when --drop-metadata was active. This PR adds the call to the removal function back also for that case, and adds a note to inform why the code is structured this way.

Summary by CodeRabbit

  • Bug Fixes

    • Improved handling of job metadata by ensuring the incomplete marker is removed only after successful metadata record creation, preserving job start time.

  • Documentation

    • Added clarifying comments to explain changes regarding the incomplete marker removal.

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coderabbitai bot commented Nov 20, 2024 •
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📝 Walkthrough
📝 Walkthrough
📝 Walkthrough

Walkthrough

The changes in this pull request focus on the finished method of the Persistence class in the snakemake/persistence.py file. The method now includes two calls to _remove_incomplete_marker(job), with the first call occurring before the creation of the metadata record to preserve the job"s start time. This adjustment is documented with a comment, while the overall structure of the class remains unchanged.

Changes

File Change Summary
snakemake/persistence.py Modified the finished method to add a call to _remove_incomplete_marker(job) before metadata creation and retained the call at the end of the method. Added a comment for clarification.

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  • johanneskoester

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Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

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0.0% Coverage on New Code
0.0% Duplication on New Code

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@johanneskoester johanneskoester merged commit a4f2e5c into snakemake:main Nov 21, 2024
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@github-actions github-actions bot mentioned this pull request Nov 21, 2024
Merged
johanneskoester pushed a commit that referenced this pull request Nov 27, 2024
@github-actions
chore(main): release 8.25.4 (#3201)
dea213d 
🤖 I have created a release *beep* *boop*
---


##
[8.25.4](v8.25.3...v8.25.4)
(2024-11-27)


### Bug Fixes

* clean env vars in apptainer
([#3199](#3199))
([76d5329](76d5329))
* ensure that intermediate files in job groups do not cause spurious
mtime errors when checking for consistency with output files
([#3220](#3220))
([4ba2bdf](4ba2bdf))
* Remove incomplete marker also when drop-metadata is active
([#3215](#3215))
([a4f2e5c](a4f2e5c))
* Remove incomplete marker for job finished only after metadata is
written ([#3197](#3197))
([6567e5f](6567e5f))
* Support versioned URLs in Asset class and fix missing versions in
Snakemake report
([#3203](#3203))
([f086f6c](f086f6c))
* update rust-script usage to recent version (v0.35.0)
[#3183](#3183)
([#3208](#3208))
([43885d7](43885d7))


### Documentation

* clarify continuously updated input section
([#3219](#3219))
([72a6994](72a6994))
* Fix typo in CHANGELOG.md
([#3198](#3198))
([0e445ed](0e445ed))
* refer to Merkle trees instead of "blockchain" in caching.rst
([#3216](#3216))
([282e5d9](282e5d9))
* remove twitter in favor of bluesky and mastodon
([#3217](#3217))
([231c6df](231c6df))
* use "dictionary" not "array" wording in config docs
([#3156](#3156))
([17aed41](17aed41))

---
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>
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@johanneskoester johanneskoester johanneskoester approved these changes

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@mhulsman @johanneskoester