ci: migrate from pre-commit to prek

.github/dependabot.yml

@@ -10,3 +10,14 @@ updates:
     commit-message:
       prefix: "ci"
       include: "scope"
+
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "dependencies"
+      - "pre-commit"
+    commit-message:
+      prefix: "ci"
+      include: "scope"

.github/workflows/_test.yml

@@ -58,14 +58,10 @@ jobs:
         - name: Sync Python dependencies
           run: uv sync --no-dev --group ci
 
-        - name: Cache pre-commit
-          uses: actions/cache@v4
+        - name: Install prek
+          uses: j178/prek-action@v1
           with:
-            path: ~/.cache/pre-commit
-            key: precommit-${{ matrix.platform.runner }}-${{ matrix.python-version }}
-
-        - name: Install pre-commit
-          run: pip install pre-commit
+            install-only: true
 
         - name: Run build-test hooks
           env:
@@ -74,29 +70,29 @@ jobs:
             RUSTC_WRAPPER: "sccache"
             UV_NO_SYNC: "1"
             # Skip mypy-check - it runs in e2e_type_check workflow
-            SKIP: mypy-check
+            PREK_SKIP: mypy-check
           shell: bash
           run: |
             set +e
 
             if [[ "${{ github.event_name }}" == "pull_request" ]]; then
-              echo "Running pre-commit on PR diff against target branch: ${{ github.base_ref }}"
+              echo "Running prek on PR diff against target branch: ${{ github.base_ref }}"
               git fetch --no-tags --prune --depth=1 origin \
                 "${{ github.base_ref }}:refs/remotes/origin/${{ github.base_ref }}"
 
-              pre-commit run \
+              prek run \
                 --from-ref "origin/${{ github.base_ref }}" \
                 --to-ref "${{ github.sha }}" \
                 --show-diff-on-failure
               status=$?
             else
-              echo "Running pre-commit on all files (event: ${{ github.event_name }})"
-              pre-commit run --all-files --show-diff-on-failure
+              echo "Running prek on all files (event: ${{ github.event_name }})"
+              prek run --all-files --show-diff-on-failure
               status=$?
             fi
 
             if [ $status -ne 0 ]; then
-              echo "::error::Build-test checks failed. Please run 'uv run pre-commit run --all-files' locally."
+              echo "::error::Build-test checks failed. Please run 'prek run --all-files' locally."
               exit $status
             fi
 

.github/workflows/e2e_type_check.yml

@@ -41,27 +41,9 @@ jobs:
       - name: Sync Python dependencies
         run: uv sync --no-dev --group ci
 
-      - name: Cache pre-commit
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pre-commit
-          key: precommit-e2e-type-check-${{ matrix.python-version }}
-
-      - name: Install pre-commit
-        run: pip install pre-commit
-
       - name: Run mypy-check hook
+        uses: j178/prek-action@v1
+        with:
+          extra-args: 'mypy-check --all-files'
         env:
           UV_NO_SYNC: "1"
-        shell: bash
-        run: |
-          set +e
-
-          echo "Running mypy-check on all files (event: ${{ github.event_name }})"
-          pre-commit run mypy-check --all-files --show-diff-on-failure
-          status=$?
-
-          if [ $status -ne 0 ]; then
-            echo "::error::E2E type check failed. Please run 'uv run pre-commit run --all-files' locally."
-            exit $status
-          fi

.github/workflows/fast_check.yml

@@ -27,26 +27,10 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v7
 
-      - name: Cache pre-commit
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pre-commit
-          key: precommit-fast-check-ubuntu-latest
-
-      - name: Install pre-commit
-        run: pip install pre-commit
-
       - name: Run fast-check hooks
+        uses: j178/prek-action@v1
+        with:
+          extra-args: '--all-files'
         env:
           # Skip heavy build/test hooks - only run fast formatting/linting checks
-          SKIP: uv-lock,mypy-check,maturin-develop,cargo-test,pytest,generate-cli-docs
-        shell: bash
-        run: |
-          set +e
-
-          pre-commit run --all-files --show-diff-on-failure
-          status=$?
-          if [ $status -ne 0 ]; then
-            echo "::error::Fast check failed. Please run 'uv run pre-commit run --all-files' locally."
-            exit $status
-          fi
+          PREK_SKIP: uv-lock,mypy-check,maturin-develop,cargo-test,pytest,generate-cli-docs

.pre-commit-config.yaml

@@ -1,7 +1,3 @@
-ci:
-  autofix_prs: false
-  autoupdate_schedule: 'monthly'
-
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0

README.md

@@ -15,6 +15,7 @@
 [![CI](https://github.com/cocoindex-io/cocoindex/actions/workflows/CI.yml/badge.svg?event=push&color=5B5BD6)](https://github.com/cocoindex-io/cocoindex/actions/workflows/CI.yml)
 [![release](https://github.com/cocoindex-io/cocoindex/actions/workflows/release.yml/badge.svg?event=push&color=5B5BD6)](https://github.com/cocoindex-io/cocoindex/actions/workflows/release.yml)
 [![Link Check](https://github.com/cocoindex-io/cocoindex/actions/workflows/links.yml/badge.svg)](https://github.com/cocoindex-io/cocoindex/actions/workflows/links.yml)
+[![prek](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/j178/prek/master/docs/assets/badge-v0.json)](https://github.com/j178/prek)
 [![Discord](https://img.shields.io/discord/1314801574169673738?logo=discord&color=5B5BD6&logoColor=white)](https://discord.com/invite/zpA9S2DR7s)
 
 </div>

dev/README.md

@@ -25,7 +25,7 @@ python dev/generate_cli_docs.py
 
 **Integration:**
 
-- Runs automatically as a pre-commit hook when `python/cocoindex/cli.py` is modified
+- Runs automatically as a prek hook when `python/cocoindex/cli.py` is modified
 - The generated documentation is directly imported into `docs/docs/core/cli.mdx` via MDX import
 - Provides seamless single-page CLI documentation experience without separate reference pages
 

docs/docs/contributing/guide.md

@@ -24,12 +24,12 @@ To submit your code:
 1. Fork the [CocoIndex repository](https://github.com/cocoindex-io/cocoindex)
 2. [Create a new branch](https://docs.github.com/en/desktop/making-changes-in-a-branch/managing-branches-in-github-desktop) on your fork
 3. Make your changes
-4. Run the pre-commit checks. It will be automatically triggered on `git commit` after you install the pre-commit hooks by `pre-commit install` (see [Setup Development Environment](setup_dev_environment.md)).
+4. Run the prek checks. It will be automatically triggered on `git commit` after you install the prek hooks by `prek install` (see [Setup Development Environment](setup_dev_environment.md)).
 
     :::tip
     To run them manually (same as CI):
         ```sh
-        pre-commit run --all-files
+        prek run --all-files
         ```
     :::
 

docs/docs/contributing/setup_dev_environment.md

@@ -31,10 +31,10 @@ Follow the steps below to get CocoIndex built on the latest codebase locally - i
 
 - Setup your local development environment:
 
-  - Install and enable pre-commit hooks. This ensures all checks run automatically before each commit:
+  - Install and enable prek hooks. This ensures all checks run automatically before each commit:
 
     ```sh
-    uv run pre-commit install
+    uv run prek install
     ```
 
   - (Optionally) Install all optional dependencies:
@@ -90,4 +90,6 @@ Workaround:
 
 This wrapper sets `PYTHONHOME`/`PYTHONPATH` for that command only, so embedded Python can locate the stdlib and site-packages.
 
-Note: the cargo-test pre-commit hook uses this wrapper.
+:::info
+
+The cargo-test prek hook uses this wrapper.

pyproject.toml

@@ -99,7 +99,7 @@ ci = [
     { include-group = "ci-enabled-optional-deps" },
 ]
 
-dev-local = ["pre-commit"]
+dev-local = ["prek"]
 dev = [{ include-group = "ci" }, { include-group = "dev-local" }]
 
 [tool.uv]