replace pre-commit with prek

.github/workflows/code_quality_and_tests.yml

@@ -10,7 +10,7 @@ env:
   FORCE_COLOR: "1"
 
 jobs:
-  pre-commit:
+  prek:
     name: Code quality checks
     runs-on: "ubuntu-latest"
     steps:
@@ -21,8 +21,8 @@ jobs:
         with:
           os: "ubuntu-latest"
           python: "3.10"
-      - name: Compute pre-commit cache key
-        id: pre-commit-cache
+      - name: Compute prek cache key
+        id: prek-cache
         shell: python
         run: |
           import hashlib
@@ -31,18 +31,18 @@ jobs:
           python = "py{}.{}".format(*sys.version_info[:2])
           payload = sys.version.encode() + sys.executable.encode()
           digest = hashlib.sha256(payload).hexdigest()
-          result = "${{ runner.os }}-{}-{}-pre-commit".format(python, digest[:8])
+          result = "${{ runner.os }}-{}-{}-prek".format(python, digest[:8])
           with open(os.environ['GITHUB_OUTPUT'], 'a') as f: f.write(f"result={result}\n")
-      - name: Restore pre-commit cache
+      - name: Restore prek cache
         uses: actions/cache@v4
         with:
-          path: ~/.cache/pre-commit
-          key: ${{ steps.pre-commit-cache.outputs.result }}-${{ hashFiles('.pre-commit-config.yaml') }}
+          path: ~/.cache/prek
+          key: ${{ steps.prek-cache.outputs.result }}-${{ hashFiles('.prek-config.yaml') }}
           restore-keys: |
-            ${{ steps.pre-commit-cache.outputs.result }}-
-      - name: Run pre-commits
+            ${{ steps.prek-cache.outputs.result }}-
+      - name: Run preks
         run: |
-          uv run --group cicd pre-commit run -a
+          uv run --group cicd prek run -a
         shell: bash
   pytest:
     name: Tests with Python ${{ matrix.python }} / ${{ matrix.os }}

.pre-commit-config.yaml

@@ -1,3 +1,6 @@
+# priorieties are like stages at which hooks run.
+# hooks using the same priority run simultaneously.
+# hooks running simultaneously may run into conflicts when operating on/ changing the same files!
 exclude: "^data/.*|^tests/fixtures/.*"
 
 repos:
@@ -6,83 +9,104 @@ repos:
     rev: v6.0.0
     hooks:
       - id: trailing-whitespace
+        priority: 00
       - id: end-of-file-fixer
+        priority: 01
       - id: check-docstring-first
+        priority: 02
       - id: check-yaml
+        priority: 03
       - id: debug-statements
+        priority: 04
       - id: detect-private-key
+        priority: 05
       - id: check-executables-have-shebangs
+        priority: 06
       - id: check-toml
+        priority: 07
       - id: check-case-conflict
+        priority: 08
       - id: check-added-large-files
+        priority: 09
 
   # Black (reads [tool.black] from pyproject.toml)
   - repo: https://github.com/psf/black
     rev: 25.9.0
     hooks:
       - id: black
+        priority: 10
 
   # isort (reads [tool.isort] from pyproject.toml)
   - repo: https://github.com/PyCQA/isort
     rev: 6.0.1
     hooks:
       - id: isort
+        priority: 20
 
   # pyupgrade (no TOML config; keep args here)
   - repo: https://github.com/asottile/pyupgrade
     rev: v3.20.0
     hooks:
       - id: pyupgrade
         args: ["--py310-plus"]
+        priority: 30
 
   # Flake8 (reads [tool.flake8] via plugin)
   - repo: https://github.com/PyCQA/flake8
     rev: 7.3.0
     hooks:
       - id: flake8
+        priority: 40
         additional_dependencies:
           - flake8-pyproject
 
-  # Security linter (reads [tool.bandit] from pyproject.toml)
-  - repo: https://github.com/PyCQA/bandit
-    rev: "1.8.6"
+  # Strip Jupyter outputs
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
     hooks:
-      - id: bandit
-        args: ["-c", "pyproject.toml"]          # tell bandit to read pyproject
-        additional_dependencies: ["bandit[toml]"]  # ensure TOML support
+      - id: nbstripout
+        priority: 50
+
+  # Run tools on notebooks via nbQA (inherits configs)
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.9.1
+    hooks:
+      - id: nbqa-black
+        priority: 10  # run when black runs
+      - id: nbqa-isort
+        priority: 20  # run when isort runs
+      - id: nbqa-flake8
+        priority: 40  # run when flake8 runs
 
   # Markdown formatter (reads [tool.mdformat] via plugin)
   - repo: https://github.com/hukkin/mdformat
     rev: 0.7.22
     hooks:
       - id: mdformat
+        priority: 70  # run when black runs
         additional_dependencies:
           - mdformat-gfm
           - mdformat-tables
           - mdformat_frontmatter
           - mdformat-pyproject
 
+  # Security linter (reads [tool.bandit] from pyproject.toml)
+  - repo: https://github.com/PyCQA/bandit
+    rev: "1.8.6"
+    hooks:
+      - id: bandit
+        args: ["-c", "pyproject.toml"]          # tell bandit to read pyproject
+        additional_dependencies: ["bandit[toml]"]  # ensure TOML support
+        priority: 80
+
   # Spelling checker (reads [tool.codespell] from pyproject.toml)
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.1
     hooks:
       - id: codespell
         # For Python < 3.11, TOML parsing needs tomli
         additional_dependencies: ["tomli"]
-
-  # Strip Jupyter outputs
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.1
-    hooks:
-      - id: nbstripout
-
-  # Run tools on notebooks via nbQA (inherits configs)
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.9.1
-    hooks:
-      - id: nbqa-black
-      - id: nbqa-isort
-      - id: nbqa-flake8
+        priority: 80  # run when bandit runs
 
   - repo: local
     hooks:
@@ -91,3 +115,4 @@ repos:
         entry: uv run mypy --config=pyproject.toml
         language: system
         pass_filenames: false
+        priority: 80  # run when bandit runs

Makefile

@@ -24,10 +24,10 @@ clean:
 	find . -type d -name "__pycache__" -delete
 
 
-## code quality checks and fixes via pre-commit
+## code quality checks and fixes via prek
 .PHONY: precommit
 precommit:
-	poetry run pre-commit run --all-files
+	poetry run prek run --all-files
 
 
 ## Lint using flake8, black, and isort (use `make format` to do formatting)

README.md

@@ -318,12 +318,12 @@ uv sync --group cicd
 To run code quality checks and static type checking, call:
 
 ```bash
-uv run pre-commit run -a
+uv run prek run -a
 # if you have not run 'uv sync --group cicd' previously, use instead
-uv run --group cicd pre-commit run -a
+uv run --group cicd prek run -a
 ```
 
-This runs all configured [pre-commit](https://pre-commit.com/) hooks (see [pre-commit-config.yaml](.pre-commit-config.yaml)) on all files. Some hooks may fix issues automatically, others will report issues that need to be fixed manually.
+This runs all configured [prek](https://prek.j178.dev/) hooks (see [pre-commit-config.yaml](.pre-commit-config.yaml)) on all files. Some hooks may fix issues automatically, others will report issues that need to be fixed manually.
 
 To run all tests, call:
 
@@ -336,7 +336,7 @@ uv run --group cicd pytest
 The following commands run on GitHub CI (see [tests.yml](.github/workflows/code_quality_and_tests.yml)), but can also be run locally:
 
 ```bash
-uv run --group cicd pre-commit run -a
+uv run --group cicd prek run -a
 # run tests *not marked as slow* with coverage and typeguard checks
 uv run --group cicd pytest -m "not slow"
 ```

pyproject.toml

@@ -51,8 +51,8 @@ cicd = [
     "pytest-xdist>=3.8.0,<4",
     "pytest-cov>=6.2.1,<7",
     "typeguard>=2.13.3",
-    "pre-commit>=2.16.0",
     "mypy>=1.3.0",
+    "prek>=0.3.8",
 ]
 
 [tool.hatch.build.targets.sdist]
@@ -110,7 +110,7 @@ exclude = [".git", "notebooks", "models", "data", "logs"]
 skip = "logs/**,data/**,configs/**/*template*,configs/evaluate.yaml,tests/fixtures/**.json,tests/fixtures/**.jsonl,src/kibad_llm/schema/**,tests/unit/schema/**,*.ipynb"
 ignore-words-list = "hist"
 
-# Bandit (read by pre-commit bandit with -c pyproject.toml)
+# Bandit (read by prek bandit with -c pyproject.toml)
 [tool.bandit]
 skips = ["B101", "B107", "B403"]
 # optionally exclude tests to reduce noise: