Add pre-commit auto-update workflow

[forsyth2]

Add pre-commit auto-update workflow

Summary

Objectives:

• Add pre-commit auto-update workflow

Issue resolution:

• Equivalent to Add pre-commit auto-update workflow zppy-interfaces#57

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 adds automation for keeping pre-commit hook versions up to date in the
zppy repo, including a GitHub Actions workflow and a helper script to
propagate updated versions into other pinned dependency locations.

Changes:

• Add a pre_commit_update_workflow scheduled/manual GitHub Actions workflow to
  run pre-commit-update and open a PR with the results.
• Add scripts/sync_pre_commit_versions.py to sync pinned tool versions based
  on .pre-commit-config.yaml.
• Update existing pinned-version guidance and mypy hook dependencies to align
  with the new workflow/script.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 4 comments.

File	Description
scripts/sync_pre_commit_versions.py	New script to derive versions from .pre-commit-config.yaml and apply them to pinned dependency files.
conda/dev.yml	Updates QA-tool comment to describe the intended update flow.
.pre-commit-config.yaml	Adds a mypy additional_dependencies entry and a note about syncing pins.
.github/workflows/pre_commit_update_workflow.yml	New scheduled workflow to auto-update pre-commit hooks and open a PR.

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[forsyth2]

We should probably use the latest version if we can.

[xylar]

It would be worth adding dependebot to update them.

[forsyth2]

This seems to work fine for zppy-interfaces: https://github.com/E3SM-Project/zppy-interfaces/blob/main/.pre-commit-config.yaml#L44

[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated no new comments.

Suppressed comments (5)

.github/workflows/pre_commit_update_workflow.yml:18

• The workflow requests issues: write but doesn’t appear to interact with issues. Reducing token permissions to only what’s used follows least-privilege and limits blast radius if a token is misused.

permissions:
  contents: write
  pull-requests: write
  issues: write

.github/workflows/pre_commit_update_workflow.yml:29

• This workflow clones the repository later (git clone ... update-pre-commit-deps), so the initial actions/checkout step is unused work. Consider removing it to reduce runtime and avoid confusion about which working tree subsequent commands operate on.

      - uses: actions/checkout@v7

.github/workflows/pre_commit_update_workflow.yml:90

• gh pr create will fail if a PR from update-pre-commit-deps already exists (e.g., previous month’s PR still open), which would make this scheduled workflow brittle. Consider making this step idempotent by detecting an existing PR for the branch and updating it (or exiting successfully) instead of failing the run.

          gh pr create \
          --title "Update pre-commit and its dependencies" \
          --body "This PR was auto-generated to update pre-commit and its dependencies." \
          --head update-pre-commit-deps \
          --reviewer ${{ env.REVIEWERS }} \

pyproject.toml:46

• The comment says these versions “always match … .pre-commit-config.yaml”, but this list includes non-pinned constraints like types-PyYAML>=… while .pre-commit-config.yaml uses types-PyYAML with no version. Consider rewording to clarify that only pinned tool versions are meant to be synchronized.

# make sure these always match conda/dev.yml and .pre-commit-config.yaml
# (run `python scripts/sync_pre_commit_versions.py` to sync them)

scripts/sync_pre_commit_versions.py:1

• Using #!/usr/bin/env python can resolve to Python 2 or fail on systems where python isn’t installed. Since this repository targets Python 3, use python3 in the shebang for safer direct execution.

#!/usr/bin/env python

[forsyth2]

pre-commit run --all-files passes as before using this branch (despite the functional changes in conda/dev.yml)

[xylar]

Looks good! You can give it a run once this is merged and see if it works!

Got to the Actions tab, look for this one on the left (Pre-commit auto update) and then select "run workflow" on the right, choosing to run on main.

[forsyth2]

Thanks @xylar, looks like it passed! https://github.com/E3SM-Project/zppy/actions/runs/31820401775

[forsyth2]

That created #854. It required a few fixes, but I was eventually able to merge it.