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perf: cache mtime of scripts and notebooks#2965

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johanneskoester merged 3 commits intosnakemake:mainfrom
laf070810:script-mtime-caching
Aug 14, 2024
Merged

perf: cache mtime of scripts and notebooks#2965
johanneskoester merged 3 commits intosnakemake:mainfrom
laf070810:script-mtime-caching

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@laf070810 laf070810 commented Jul 15, 2024 •
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mtime of script or notebook is checked repeatedly when the same rule is wildcard-expanded, causing a lot of os.lstat calls repeated on the same file, which is unnecessary and can be slow on some filesystems.

This PR adds script mtime caching using functools.lru_cache. It can speedup DAG building time.

Related issues: #2920, #2949

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

    • Introduced a utility function to efficiently retrieve and cache the modification time of script files, improving performance.

  • Improvements

    • Enhanced the existing functionality to streamline file modification time checks, leading to cleaner and more maintainable logic.

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coderabbitai bot commented Aug 14, 2024 •
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Commits

Files that changed from the base of the PR and between 22d0d0f and e1ac4ba.

Walkthrough

The recent updates to the snakemake/jobs.py file introduce a new utility function, get_script_mtime, which improves the efficiency of retrieving a script's last modification time through caching. This change streamlines the existing logic in the outputs_older_than_script_or_notebook function by replacing direct calls to obtain modification times with the new utility function. The enhancements promote better performance and maintainability without altering the overall functionality.

Changes

File Change Summary
snakemake/jobs.py Added get_script_mtime function with caching via functools.lru_cache. Updated outputs_older_than_script_or_notebook to use this function for modification time retrieval, improving efficiency and maintainability.

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@johanneskoester
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johanneskoester commented Aug 14, 2024

Very good catch!

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Actionable comments posted: 1

Review details

Configuration used: CodeRabbit UI
Review profile: ASSERTIVE

Commits

Files that changed from the base of the PR and between e502312 and 22d0d0f.

Files selected for processing (1)
  • snakemake/jobs.py (3 hunks)
Additional context used
Path-based instructions (1)
snakemake/jobs.py (1)

Pattern **/*.py: Do not suggest to add trailing commas.
Do not suggest type annotations for functions that are defined inside of functions or methods.

Ruff
snakemake/jobs.py

92-92: Missing return type annotation for public function get_script_mtime

(ANN201)

92-92: Missing type annotation for function argument path

(ANN001)

Additional comments not posted (1)
snakemake/jobs.py (1)

406-409: Efficient use of get_script_mtime.

The use of get_script_mtime improves the efficiency of the function by caching the script modification times, reducing redundant filesystem checks.

@johanneskoester @coderabbitai
add type annotation
e1ac4ba 
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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sonarqubecloud bot commented Aug 14, 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 changed the title feat: add script mtime caching perf: cache mtime of scripts and notebooks Aug 14, 2024
@johanneskoester johanneskoester merged commit 405a056 into snakemake:main Aug 14, 2024
@github-actions github-actions bot mentioned this pull request Aug 14, 2024
Merged
johanneskoester pushed a commit that referenced this pull request Aug 14, 2024
@github-actions
chore(main): release 8.18.0 (#3016)
1b08a79 
🤖 I have created a release *beep* *boop*
---


##
[8.18.0](v8.17.0...v8.18.0)
(2024-08-14)


### Features

* show info on missing metadata
([#3014](#3014))
([e502312](e502312))


### Performance Improvements

* cache mtime of scripts and notebooks
([#2965](#2965))
([405a056](405a056))

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

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Introduced detailed reporting for missing metadata during workflow
execution, enhancing visibility and debugging.
- **Performance Improvements**
- Implemented caching for script and notebook modification times,
improving workflow execution efficiency.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
@coderabbitai coderabbitai bot mentioned this pull request Sep 19, 2024
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@coderabbitai coderabbitai bot mentioned this pull request Mar 13, 2025
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@johanneskoester johanneskoester johanneskoester approved these changes

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@laf070810 @johanneskoester