build: migrate from pre-commit to prek

[hasansezertasan]

Description

Migrates the hook runner from pre-commit to prek — a faster, Rust-based, single-binary drop-in reimplementation. .pre-commit-config.yaml is unchanged; prek reads it directly, and every existing hook (ruff, black, codespell, mypy, slotscheck, zizmor, uv-lock, …) runs as-is.

Changes

• CI (ci.yaml validate job): pip install prek + prek run --all-files instead of pre-commit; cache path/key moved to ~/.cache/prek.
• Makefile: make lint → prek run; make upgrade → prek update (prek's equivalent of pre-commit autoupdate).
• pyproject.toml lint group: pre-commit → prek. Lockfile regenerated (drops virtualenv/python-discovery).
• README: usage + local-development instructions updated.

CLI compatibility verified

prek run supports --all-files, --show-diff-on-failure, and --color (same flags as pre-commit); prek validate-config .pre-commit-config.yaml → All configs are valid.

Notes for reviewers

• Stacked on ci: adopt zizmor and harden GitHub Actions workflows #39 (both edit ci.yaml); base is ci/zizmor. Merge ci: adopt zizmor and harden GitHub Actions workflows #39 first — GitHub will retarget this to main.
• prek runs the zizmor hook from ci: adopt zizmor and harden GitHub Actions workflows #39 too, so the security gate is preserved.
• Follow-up: CONTRIBUTING.rst (added in docs: add CONTRIBUTING guide #32, not yet merged) still references pre-commit. Once docs: add CONTRIBUTING guide #32 lands, its setup instructions should be updated to prek install --install-hooks. Happy to push that to docs: add CONTRIBUTING guide #32's branch.

Closes

• Closes build: evaluate migrating from pre-commit to prek #20

Summary by Sourcery

Migrate linting hook runner from pre-commit to prek across CI, developer tooling, and documentation while keeping existing hooks and config intact.

Enhancements:

• Switch CI workflow lint job to use prek for running hooks with updated cache configuration.
• Update Makefile lint and upgrade targets to invoke prek for running and updating hooks.
• Replace pre-commit with prek in the lint dependency group and regenerate the uv lockfile to reflect the new tooling dependency.
• Refresh README instructions to reference prek for installing and running lint hooks.

[sourcery-ai]

Reviewer's guide (collapsed on small PRs)

Reviewer's Guide

Migrates the project from using pre-commit to prek for running the existing hook set in CI, local dev tooling, and dependency management, while keeping .pre-commit-config.yaml as the source of hook definitions.

Flow diagram for CI validate job using prek instead of pre-commit

flowchart TD
  A[GitHub Actions validate job] --> B[Set up Python 3.11]
  B --> C[Install prek via pip]
  C --> D[Restore/save cache at ~/.cache/prek]
  D --> E[Run prek run --show-diff-on-failure --color=always --all-files]
  E --> F[Hooks from .pre-commit-config.yaml execute]

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Flow diagram for local lint and upgrade using prek

flowchart TD
  subgraph Lint_flow
    Dev[Developer] --> M[make lint]
    M --> U1[uv run prek run --all-files]
    U1 --> H1[Hooks from .pre-commit-config.yaml execute]
  end

  subgraph Upgrade_flow
    Dev2[Developer] --> MU[make upgrade]
    MU --> U2[uv lock --upgrade and uv sync]
    U2 --> P[uv run prek update]
    P --> H2[Hook revisions updated in .pre-commit-config.yaml]
  end

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File-Level Changes

Change	Details	Files
Switch CI lint/validation job from pre-commit to prek while preserving behavior and cache efficiency.	Replace installation step to install prek via pip instead of pre-commit and remove pre-commit install invocation. Update cache step to use ~/.cache/prek and a cache key prefixed with 'prek-' while still hashing .pre-commit-config.yaml. Change the lint execution command from pre-commit run with flags to prek run with equivalent flags, keeping PYTHONPATH behavior unchanged. Rename CI step labels from pre-commit wording to prek wording for clarity.	.github/workflows/ci.yaml
Update local developer workflows in the Makefile to invoke prek instead of pre-commit for linting and hook updates.	Change the upgrade target to run uv run prek update instead of pre-commit autoupdate, and adjust its log message. Change the lint target to run uv run prek run --all-files with updated echo messaging to reference prek instead of pre-commit.	Makefile
Update documentation and dependency declarations to reference prek instead of pre-commit and regenerate the uv lockfile accordingly.	Update README usage and local development examples to show prek install/update and prek-based lint commands instead of pre-commit equivalents. Replace pre-commit with prek in the pyproject.toml lint dependency group, pinning prek>=0.4.10. Regenerate uv.lock to reflect the switch from pre-commit to prek and the resulting dependency graph changes.	README.md pyproject.toml uv.lock

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[sourcery-ai]

Hey - I've found 1 issue

Prompt for AI Agents

Please address the comments from this code review:

## Individual Comments

### Comment 1
<location path=".github/workflows/ci.yaml" line_range="28-33" />
<code_context>

-      - name: Load cached Pre-Commit Dependencies
-        id: cached-pre-commit-dependencies
+      - name: Load cached prek dependencies
+        id: cached-prek-dependencies
         uses: actions/cache@6f8efc29b200d32929f49075959781ed54ec270c # v3
         with:
-          path: ~/.cache/pre-commit/
-          key: pre-commit-|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
+          path: ~/.cache/prek/
+          key: prek-|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}

-      - name: Execute Pre-Commit
</code_context>
<issue_to_address>
**issue (performance):** Double-check that the prek cache path and key match its actual cache layout and config file.

Since the path is now `~/.cache/prek/` but the key still hashes `.pre-commit-config.yaml`, please verify that prek actually uses `~/.cache/prek/` and that `.pre-commit-config.yaml` is still the canonical config for cache invalidation (and not, for example, `prek.toml` or `pyproject.toml`).
</issue_to_address>

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[sourcery-ai]

issue (performance): Double-check that the prek cache path and key match its actual cache layout and config file.

Since the path is now ~/.cache/prek/ but the key still hashes .pre-commit-config.yaml, please verify that prek actually uses ~/.cache/prek/ and that .pre-commit-config.yaml is still the canonical config for cache invalidation (and not, for example, prek.toml or pyproject.toml).