feat: check consistency of output file mtimes (must be newer than input files) by johanneskoester · Pull Request #3050 · snakemake/snakemake

johanneskoester · 2024-08-26T13:26:39Z

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

New Features
- Enhanced output file handling to ensure that output files are not older than their corresponding input files, preventing potential execution issues.
Improvements
- Improved clarity in variable naming for better readability and understanding of output path handling.

… after completion of each job in order to detect any clock skew issues.

coderabbitai · 2024-08-26T13:26:47Z

Walkthrough

The changes involve enhancements to the output file handling logic in the snakemake/dag.py file. The variable f has been renamed to output_path for clarity. Additionally, new logic has been introduced to check the modification times of output files against their corresponding input files, raising a WorkflowError if discrepancies are found.

Changes

File	Change Summary
snakemake/dag.py	Renamed variable `f` to `output_path` for clarity; added logic to check output file modification times against input files, raising `WorkflowError` for discrepancies.

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coderabbitai

Actionable comments posted: 0

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Files that changed from the base of the PR and between 9a60046 and dd5f9ed.

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snakemake/dag.py (3 hunks)

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snakemake/dag.py (1)

Pattern **/*.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.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

Additional comments not posted (2)

snakemake/dag.py (2)

698-700: Check directory flagging for output files.

The function now includes a loop to check if output files are correctly flagged as directories. This is a good addition to ensure that directory outputs are correctly identified.

The code changes are approved.

716-735: Check for clock skew issues.

The function now includes logic to check if output files are older than the newest input file. This is a crucial addition to handle potential clock skew issues in distributed environments. The error message provides detailed information about the discrepancy and suggests addressing potential clock skew problems.

The code changes are approved.

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snakemake/dag.py

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snakemake/dag.py

sonarqubecloud · 2024-08-28T14:48:51Z

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

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snakemake/dag.py

🤖 I have created a release *beep* *boop* --- ## [8.19.0](v8.18.2...v8.19.0) (2024-08-29) ### Features * check consistency of output file mtimes (must be newer than input files) ([#3050](#3050)) ([666cf62](666cf62)) * print host name when executing workflow ([#3048](#3048)) ([b0ff787](b0ff787)) ### Bug Fixes * `mem` and `disk` inference fixes ([#3040](#3040)) ([7530794](7530794)) * avoid error accessing superclass in ioutils ([#3056](#3056)) ([a66a5f5](a66a5f5)) * disable execute after print compilation ([#3041](#3041)) ([86ed3cd](86ed3cd)) * download report assets upon package build such that reports become possible offline (cont. of [#2904](#2904)) ([#3026](#3026)) ([e8dad4b](e8dad4b)) ### Documentation * Add 'Editor integrations' section to Installation page ([#3045](#3045)) ([9a4006d](9a4006d)) * Fix typo (seesee to see) ([#3037](#3037)) ([de201fb](de201fb)) * various documentation fixes ([#3052](#3052)) ([b11460c](b11460c)) --- 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>

…ut files) (snakemake#3050)  ### 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 - **New Features** - Enhanced output file handling to ensure that output files are not older than their corresponding input files, preventing potential execution issues. - **Improvements** - Improved clarity in variable naming for better readability and understanding of output path handling.

🤖 I have created a release *beep* *boop* --- ## [8.19.0](snakemake/snakemake@v8.18.2...v8.19.0) (2024-08-29) ### Features * check consistency of output file mtimes (must be newer than input files) ([snakemake#3050](snakemake#3050)) ([666cf62](snakemake@666cf62)) * print host name when executing workflow ([snakemake#3048](snakemake#3048)) ([b0ff787](snakemake@b0ff787)) ### Bug Fixes * `mem` and `disk` inference fixes ([snakemake#3040](snakemake#3040)) ([7530794](snakemake@7530794)) * avoid error accessing superclass in ioutils ([snakemake#3056](snakemake#3056)) ([a66a5f5](snakemake@a66a5f5)) * disable execute after print compilation ([snakemake#3041](snakemake#3041)) ([86ed3cd](snakemake@86ed3cd)) * download report assets upon package build such that reports become possible offline (cont. of [snakemake#2904](snakemake#2904)) ([snakemake#3026](snakemake#3026)) ([e8dad4b](snakemake@e8dad4b)) ### Documentation * Add 'Editor integrations' section to Installation page ([snakemake#3045](snakemake#3045)) ([9a4006d](snakemake@9a4006d)) * Fix typo (seesee to see) ([snakemake#3037](snakemake#3037)) ([de201fb](snakemake@de201fb)) * various documentation fixes ([snakemake#3052](snakemake#3052)) ([b11460c](snakemake@b11460c)) --- 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>

johanneskoester added 2 commits August 26, 2024 15:24

feat: check mtime consistency of output files

3022b3a

feat: check consistency of output file mtimes (newer and input files)…

dd5f9ed

… after completion of each job in order to detect any clock skew issues.

coderabbitai bot reviewed Aug 26, 2024

View reviewed changes

johanneskoester changed the title ~~Feat/check-mtime-consistency~~ feat: check consistency of output file mtimes (must be newer than input files) Aug 26, 2024

fix

6b707e5

coderabbitai bot reviewed Aug 26, 2024

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fix coroutine usage

980ad68

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johanneskoester added 2 commits August 27, 2024 16:19

fixes

a8d9c4a

fix

18c7826

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johanneskoester added 2 commits August 28, 2024 16:47

fix for temp files

ca791f4

fix

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johanneskoester merged commit 666cf62 into main Aug 28, 2024

johanneskoester deleted the feat/check-mtime-consistency branch August 28, 2024 14:56

github-actions bot mentioned this pull request Aug 28, 2024

chore(main): release 8.19.0 #3051

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coderabbitai bot mentioned this pull request Sep 9, 2024

fix: ensure that CLI help is formatted deterministically and set defaults are displayed properly (based on preliminary work by @keszybz) #3081

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This was referenced Sep 20, 2024

fix: improve runtime complexity of post-job checkpoint handling #3096

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fix: omit storage downloads during dryrun in workflows with checkpoints #3100

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coderabbitai bot mentioned this pull request Nov 12, 2024

fix: add missing output check #2966

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This was referenced Nov 22, 2024

feat: assume checkpoint safe temp files #3218

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fix: ensure that intermediate files in job groups do not cause spurious mtime errors when checking for consistency with output files #3220

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coderabbitai bot mentioned this pull request Mar 14, 2025

feat: Enable saving and reloading IOCache object #3386

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feat: check consistency of output file mtimes (must be newer than input files)#3050

feat: check consistency of output file mtimes (must be newer than input files)#3050
johanneskoester merged 8 commits intomainfrom
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