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fix: cache conda envs to fix performance regression introduced in https://github.com/snakemake/snakemake/pull/1300#3093

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johanneskoester merged 1 commit intomainfrom
fix/cache-conda-env
Sep 19, 2024
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fix: cache conda envs to fix performance regression introduced in https://github.com/snakemake/snakemake/pull/1300#3093
johanneskoester merged 1 commit intomainfrom
fix/cache-conda-env

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@johanneskoester johanneskoester commented Sep 19, 2024 •
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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 caching mechanism for the conda environment expansion, improving performance by reducing redundant computations.
  • Bug Fixes
    • Enhanced logic for determining cacheability of the conda environment, ensuring accurate evaluations.

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coderabbitai bot commented Sep 19, 2024 •
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Walkthrough

The changes introduce a caching mechanism for the expand_conda_env method in the Rule class within snakemake/rules.py. A new private variable _expanded_conda_env is added to track whether the conda environment has been expanded. The method checks this variable to return cached values when applicable, refining the logic for determining cacheability based on whether the conda environment is callable or contains wildcards. This modification aims to enhance efficiency by reducing redundant computations.

Changes

File Change Summary
snakemake/rules.py Added _NOT_CACHED as a private object; modified expand_conda_env method to implement caching logic.

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Files that changed from the base of the PR and between e9ce4a3 and 8d34b85.

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  • snakemake/rules.py (6 hunks)
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snakemake/rules.py (1)

Pattern **/*.py: Do not try to improve formatting.
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Additional comments not posted (6)
snakemake/rules.py (6)

70-70: LGTM!

Defining _NOT_CACHED as a private sentinel object is a good practice to indicate that a value has not been cached yet.

99-99: LGTM!

Initializing _expanded_conda_env to _NOT_CACHED is a good way to track whether the conda environment for the rule has been expanded yet.

1069-1070: Introduce caching for expanded conda environment.

The added check to return the cached value of _expanded_conda_env if it's not _NOT_CACHED is a good optimization. It avoids redundant computation of the expanded conda environment when the result is already available.

1081-1090: Refine caching logic for conda environment.

The updated logic for determining whether the conda environment is cacheable looks good:

  • If conda_env is not callable and doesn't contain wildcards, it's cacheable.
  • If conda_env is callable, the input function is applied, and caching is disabled since the result may vary.
  • Returning None if the input function returns None handles that case appropriately.

1113-1114: Store expanded conda environment for caching.

Storing the expanded conda environment in _expanded_conda_env when it's cacheable is the correct way to complete the caching mechanism. This allows the cached value to be reused in subsequent calls, improving performance.

28-28: LGTM!

Importing the contains_wildcard function is necessary for the added caching logic to determine if a conda environment contains wildcards.

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sonarqubecloud bot commented Sep 19, 2024

Quality Gate Passed Quality Gate passed

Issues
1 New issue
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 66600c4 into main Sep 19, 2024
@johanneskoester johanneskoester deleted the fix/cache-conda-env branch September 19, 2024 14:16
@github-actions github-actions bot mentioned this pull request Sep 19, 2024
Merged
johanneskoester pushed a commit that referenced this pull request Sep 20, 2024
@github-actions
chore(main): release 8.20.4 (#3094)
4baebfb 
🤖 I have created a release *beep* *boop*
---


##
[8.20.4](v8.20.3...v8.20.4)
(2024-09-20)


### Bug Fixes

* cache conda envs to fix performance regression introduced in
#1300
([#3093](#3093))
([66600c4](66600c4))
* Flatten conda pip dependencies for report rule info
([#3085](#3085))
([56a1f20](56a1f20))
* improve runtime complexity of post-job checkpoint handling
([#3096](#3096))
([ba30781](ba30781))


### Documentation

* Clarify the lookup function docstring
([#3091](#3091))
([94177d5](94177d5))
* Update lookup signature
([#3090](#3090))
([655d6a1](655d6a1))

---
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>
@coderabbitai coderabbitai bot mentioned this pull request Sep 25, 2024
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This was referenced Oct 7, 2024
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@coderabbitai coderabbitai bot mentioned this pull request Mar 26, 2025
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