Cleanup pre-commit hooks and change to prek (#676)

Author: timmens

.pre-commit-config.yaml

@@ -10,16 +10,6 @@ repos:
     hooks:
       - id: yamlfix
         exclude: tests/optimagic/optimizers/_pounders/fixtures
-  - repo: local
-    hooks:
-      - id: check-mypy-versions
-        name: verify that pre-commits and pixi use the same mypy version
-        entry: python .tools/check_mypy_versions.py
-        language: python
-        always_run: true
-        require_serial: true
-        additional_dependencies:
-          - pyyaml
   - repo: local
     hooks:
       - id: update-algo-selection-code
@@ -68,20 +58,8 @@ repos:
     hooks:
       - id: yamllint
         exclude: tests/optimagic/optimizers/_pounders/fixtures
-  - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.7
-    hooks:
-      - id: docformatter
-        args:
-          - --in-place
-          - --wrap-summaries
-          - '88'
-          - --wrap-descriptions
-          - '88'
-          - --blank
-        exclude: src/optimagic/optimization/algo_options.py
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.4
+    rev: v0.15.5
     hooks:
       # Run the linter.
       - id: ruff
@@ -132,26 +110,7 @@ repos:
           )$
         args:
           - --drop-empty-cells
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1
-    hooks:
-      - id: mypy
-        files: src|tests
-        additional_dependencies:
-          - numpy >= 2
-          - packaging
-          - pandas-stubs
-          - sqlalchemy-stubs
-          - types-cffi
-          - types-openpyxl
-          - types-jinja2
-          - bokeh
 ci:
   autoupdate_schedule: monthly
   skip:
     - update-algo-selection-code
-    # Skip mypy stubtest on pre-commit.ci due to maximum size limitations. This is
-    # unlikely to get better in the future as dependencies keep growing. Local runs
-    # of pre-commit would still execute stubtest. For CI, we have a separate GitHub
-    # Action that runs stubtest.
-    - mypy

.tools/check_mypy_versions.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+import importlib.util
 import subprocess
 import sys
 from pathlib import Path
@@ -8,19 +9,15 @@
 
 # sys.executable guarantees we stay inside the pre‑commit venv
 PYTHON = [sys.executable]
-# "-m" lets us call std‑lib modules (e.g. pip) the same way
-PYTHON_MINUS_M = [*PYTHON, "-m"]
 
 
 def run(cmd: list[str], **kwargs: Any) -> None:
     subprocess.check_call(cmd, cwd=ROOT, **kwargs)
 
 
 def ensure_optimagic_is_locally_installed() -> None:
-    try:
-        run(PYTHON_MINUS_M + ["pip", "show", "optimagic"], stdout=subprocess.DEVNULL)
-    except subprocess.CalledProcessError:
-        run(PYTHON_MINUS_M + ["pip", "install", "-e", "."])
+    if importlib.util.find_spec("optimagic") is None:
+        run(["uv", "pip", "install", "--python", sys.executable, "-e", "."])
 
 
 def main() -> int:

.tools/update_algo_selection_hook.py

@@ -44,14 +44,14 @@ For regular contributors: **Clone** the [repository](https://github.com/optimagi
    local optimagic repository:
 
    ```console
-   $ pre-commit install
+   $ prek install
    ```
 
    This activates pre-commit hooks for linting and style formatting.
 
    ```{note}
-   `pre-commit` is not managed by pixi and must be installed globally. We recommend
-   installing it globally using pixi or uv.
+   `prek` is not managed by pixi and must be installed globally. You can find
+   installation instructions at [github.com/j178/prek](https://github.com/j178/prek).
    ```
 
    You can then run the test suite with:
@@ -60,8 +60,14 @@ For regular contributors: **Clone** the [repository](https://github.com/optimagi
    $ pixi run tests
    ```
 
-   which installs the development dependencies and runs pytest. To see all available
-   pixi tasks, run:
+   which installs the development dependencies and runs pytest. To run the type checker,
+   use:
+
+   ```console
+   $ pixi run mypy
+   ```
+
+   To see all available pixi tasks, run:
 
    ```console
    $ pixi task list
@@ -84,8 +90,8 @@ For regular contributors: **Clone** the [repository](https://github.com/optimagi
    You can also run the test suite locally for
    [debugging](https://effective-programming-practices.vercel.app/debugging/pdbp/objectives_materials.html).
 
-   With pre-commit installed, linters run before each commit. Commits are rejected if
-   any checks fail. Note that some linters may automatically fix errors by modifying the
+   With prek installed, linters run before each commit. Commits are rejected if any
+   checks fail. Note that some linters may automatically fix errors by modifying the
    code in-place. Remember to re-stage the files after such modifications.
 
 ```{tip}
@@ -103,9 +109,9 @@ Skip the next paragraph if you haven't worked on the documentation.
    `docs/build/html/index.html` or any other file. Similar to the online documentation,
    you can navigate to different pages simply by clicking on the links.
 
-1. Once all tests and pre-commit hooks pass locally, push your changes to your forked
-   repository and create a pull request through GitHub: Go to the Github repository of
-   your fork. A banner on your fork's GitHub repository will prompt you to open a PR.
+1. Once all tests and hooks pass locally, push your changes to your forked repository
+   and create a pull request through GitHub: Go to the Github repository of your fork. A
+   banner on your fork's GitHub repository will prompt you to open a PR.
 
    ```{note}
    Regular contributors with push access can directly push their local branch to the remote optimagic repository and initiate a PR from there.

docs/source/development/how_to_contribute.md

@@ -105,9 +105,9 @@ Your contribution should fulfill the criteria provided below.
   refactoring, it is sufficient if the function that calls it is tested. But all
   functions that are exposed to the user must have unit tests.
 
-- Enable pre-commit hooks by executing `pre-commit install` in a terminal in the root of
-  the optimagic repository. This makes sure that your formatting is consistent with what
-  we expect.
+- Enable pre-commit hooks by executing `prek install` in a terminal in the root of the
+  optimagic repository. This makes sure that your formatting is consistent with what we
+  expect.
 
 - Use `pathlib` for all file paths operations. : You can find the pathlib documentation
   [here](https://docs.python.org/3/library/pathlib.html)

docs/source/development/styleguide.md

@@ -71,7 +71,6 @@
     "    Returns:\n",
     "        pd.DataFrame: Clustered dataset.\n",
     "    \"\"\"\n",
-    "\n",
     "    x_cluster = np.random.normal(size=nclusters)\n",
     "    x_ind = np.random.normal(size=nobs_per_cluster * nclusters)\n",
     "    eps_cluster = np.random.normal(size=nclusters, scale=0.5)\n",
@@ -179,7 +178,6 @@
     "    Returns:\n",
     "        pd.DataFrame: DataFrame of average rejection rates.\n",
     "    \"\"\"\n",
-    "\n",
     "    np.zeros(nsim)\n",
     "\n",
     "    np.zeros(nsim)\n",