Update pre-commit

[forsyth2]

Summary

Objectives:

• Update pre-commit dependencies based on running pre-commit autoupdate

Issue resolution:

• Closes Dependabot note to update pre-commit versions.

Select one: This pull request is...

• a bug fix: increment the patch version
• a small improvement: increment the minor version
• a new feature: increment the minor version
• an incompatible (non-backwards compatible) API change: increment the major version

Small Change

• To merge, I will use "Squash and merge". That is, this change should be a single commit.
• Logic: I have visually inspected the entire pull request myself.
• Pre-commit checks: All the pre-commits checks have passed.

[Copilot]

Pull request overview

This PR updates the repository’s pre-commit toolchain pins (via pre-commit autoupdate) so local QA tooling and pre-commit hooks run newer formatter/linter/type-checker versions.

Changes:

• Bumped pinned QA tool versions in the conda dev environment (black/isort/mypy).
• Updated pre-commit hook revisions and switched default_stages to [pre-commit].

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
conda/dev.yml	Updates pinned QA tool versions used in the dev conda environment.
.pre-commit-config.yaml	Updates hook revs and adjusts the default pre-commit stage.

Suppressed comments (2)

conda/dev.yml:46

• isort is pinned to 9.0.0b2, which is a pre-release (beta). If you don’t explicitly want to test isort 9.x, pin to the latest stable release instead to reduce churn and risk of formatter/import-order changes across contributors and CI.

  - isort ==9.0.0b2

.pre-commit-config.yaml:23

• isort is pinned to 9.0.0b2, which is a beta pre-release. If stability is preferred, use the latest stable isort release and keep the pin consistent with conda/dev.yml and pyproject.toml’s qa extra.

  - repo: https://github.com/PyCQA/isort
    rev: 9.0.0b2

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[Copilot]

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated no new comments.

Suppressed comments (2)

.pre-commit-config.yaml:24

• .pre-commit-config.yaml says tool versions should match conda/dev.yml and pyproject.toml, but isort is updated here to rev: 9.0.0b2 while the other files still pin isort==6.0.1. This mismatch can cause different formatting/import-order behavior depending on how the tools are installed/run.

  # Can run individually with `pre-commit run isort --all-files`
  - repo: https://github.com/PyCQA/isort
    rev: 9.0.0b2
    hooks:

pyproject.toml:55

• The qa extra is supposed to match conda/dev.yml and .pre-commit-config.yaml, but mypy is still pinned to 1.18.2 while the other files use 2.3.0, and pre-commit was changed to 2.3.0 (a downgrade) while conda pins 4.3.0. This will make QA environments inconsistent and may break hook execution.

    "isort==6.0.1",
    "mypy==1.18.2",
    "pre-commit==2.3.0",
    "types-PyYAML >=6.0.0",

[forsyth2]

@tomvothecoder I was going to rely on the Copilot review, but unfortunately I still have some open questions. Would you mind reviewing this PR and answering my questions? Thanks!

[forsyth2]

Everything in this file was changed automatically after running pre-commit autoupdate, so I assume everything is correct here. That said, do you know why the default_stages name changes here?

[tomvothecoder]

I remember seeing a warning that commit was deprecated in favor of pre-commit. Not sure why, maybe because pre-commit is the more accurate term since it runs before the commit goes through.

[forsyth2]

pre-commit autoupdate wants this to be 9.0.0b2 but apparently that's not on conda-forge, so I left conda/dev.yml and pyproject.toml as using 6.0.1 for isort. Is that the correct course of action?

[forsyth2]

The build workflow doesn't work if it's set to 6.0.1 elsewhere.

[xylar]

This is an known issue with pre-commit autoupdate. We switched to pre-commit-update, a separate tool, in our auto-update workflow to avoid this issue:
https://github.com/E3SM-Project/polaris/blob/main/.github/workflows/pre_commit_update_workflow.yml
We run this workflow automatically once a month to get the latest pre-commit. I would recommend adding it to all your repos.

[forsyth2]

Thanks @xylar!

[xylar]

I will add it here (on zppy-interfaces) and you can add it elsewhere if you like it.

[forsyth2]

That'd be great, thanks again!

[xylar]

Suggested change

	rev: 9.0.0b2
	rev: 8.0.1

8.0.1

[tomvothecoder]

This is an known issue with pre-commit autoupdate. We switched to pre-commit-update, a separate tool, in our auto-update workflow to avoid this issue: E3SM-Project/polaris@main/.github/workflows/pre_commit_update_workflow.yml We run this workflow automatically once a month to get the latest pre-commit. I would recommend adding it to all your repos.

This is a good idea for all of the other e3sm tools repos. I will take note. Thanks Xylar.

[forsyth2]

@rljacob This PR (along with related PRs for other repos: E3SM-Project/zppy#851, E3SM-Project/zstash#453, E3SM-Project/e3sm-comms#7) addresses the Dependabot issue.

[forsyth2]

@xylar Would you recommend just merging this PR now, then merge #57, and then check if anything new comes up based on what that shows?

[xylar]

No, I would downgrade pre-commit to whatever the latest non-beta version is first, then you can merge this, then #57. Or we could merge #57 instead of this and it will generate a PR exactly like this but without the beta version.

[forsyth2]

Or we could merge #57 instead of this and it will generate a PR exactly like this but without the beta version.

@xylar Ok, that seems to be the most straight-forward option; I think we should just do that. I'll merge #57.

[forsyth2]

Replaced by #58.