Swap out references to pre-commit with prek (#645)

This PR removes the repos reliance on `pre-commit` in favour of `prek`.
`prek` is faster, has a welcoming community, and is the future of
linting. `prek` supports `.pre-commit-config.yaml` so no need to change
anything really, and in the future we could consider moving towards its
custom `prek.toml` format.

As part of this work I have uninstalled @pre-commit-ci. We weren't
configuring it any more (i.e. no `ci:` block in
`.pre-commit-config.yaml`) and it was causing bugs #644.

Fixes #644.

Author: paddyroddy

.github/workflows/linting.yml

@@ -14,50 +14,50 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
-      - name: Cache pre-commit
+      - name: Cache prek
         uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
-          path: ~/.cache/pre-commit
-          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+          path: ~/.cache/prek
+          key: prek-${{ hashFiles('.pre-commit-config.yaml') }}
 
       - name: Set up python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
         with:
           python-version: "3.x"
 
       - name: Install dependencies
-        run: python -m pip install pre-commit
+        run: python -m pip install prek
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files --color always --verbose
+      - name: Run prek
+        run: prek run --all-files --color always --verbose
 
   lint-the-template:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
-      - name: Cache pre-commit
+      - name: Cache prek
         uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
-          path: ~/.cache/pre-commit
-          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+          path: ~/.cache/prek
+          key: prek-${{ hashFiles('.pre-commit-config.yaml') }}
 
       - name: Set up python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
         with:
           python-version: "3.x"
 
       - name: Install dependencies
-        run: python -m pip install cookiecutter pre-commit
+        run: python -m pip install cookiecutter prek
 
       - name: Create template
         run: cookiecutter . --no-input --output-dir cookie-template
 
-      - name: Run pre-commit
+      - name: Run prek
         run: |-
           git add .
-          pre-commit run --all-files --color always --verbose
+          prek run --all-files --color always --verbose
         working-directory: cookie-template/python-template
 
   lint-prose:

CONTRIBUTING.md

@@ -26,8 +26,8 @@ To contribute a change, please:
 
 1. Create a new branch (or fork if you're not in [@UCL-ARC/collaborations]).
 2. Modify an existing page, create a new one, or tweak the template. a. Run
-   [pre-commit] which will lint your changes. b. Check
-   the tests pass if you modified the template (`pytest -s`).
+   [prek] which will lint your changes. b. Check the tests pass if you modified
+   the template (`pytest -s`).
 3. Open a _pull request_ (PR) with changes.
 4. Ask someone who did not contribute to the PR from [@UCL-ARC/collaborations]
    to review it. If it should have two reviewers, you can also request a review
@@ -90,7 +90,7 @@ See the [jekyll docs] for more info.
 [open an issue]: https://github.com/UCL-ARC/python-tooling/issues/new/choose
 [Discussions tab]: https://github.com/UCL-ARC/python-tooling/discussions
 [Research software engineers]: https://society-rse.org/about/history
-[pre-commit]: https://pre-commit.com
+[prek]: https://prek.j178.dev
 [@UCL-ARC/collaborations]: https://github.com/orgs/UCL-ARC/teams/collaborations
 [@UCL-ARC/collaborations-python-tooling]: https://github.com/orgs/UCL-ARC/teams/collaborations-python-tooling
 [uv tool]: https://docs.astral.sh/uv/guides/tools

docs/pages/ci.md

@@ -11,7 +11,7 @@ layout: default
 | [AppVeyor](https://www.appveyor.com/docs/)                                            | Continuous integration and continuous delivery platform.                                                                                            | <span class="label label-yellow">Good</span> |
 | [Bamboo](https://confluence.atlassian.com/bamboo/bamboo-documentation-289276551.html) | Atlassian continuous integration and continuous delivery platform.                                                                                  | <span class="label label-yellow">Good</span> |
 | [Travis CI](https://docs.travis-ci.com/)                                              | Continuous integration and continuous delivery platform.                                                                                            | <span class="label label-yellow">Good</span> |
-| [pre-commit.ci](https://pre-commit.ci/)                                               | A bot that adds a pre-commit job to your GitHub Actions CI, and can automatically fix most trivial linting failures. Free for open-source projects. | <span class="label label-green">Best</span>  |
+| [pre-commit.ci](https://pre-commit.ci/)                                               | A bot that adds a pre-commit job to your GitHub Actions CI, and can automatically fix most trivial linting failures. Free for open-source projects. | <span class="label label-yellow">Good</span> |
 
 <details><summary> <span class="label label-green">Best</span>  explanation</summary><!-- markdownlint-disable-line MD033 -->
 We have many projects using GitHub CI and, it has good integration with GitHub itself, and is free for public repositories (with limited free monthly minutes for private repositories).

docs/pages/linting.md

@@ -13,7 +13,8 @@ for some of these.
 
 | Name                                                    | Short description                                                                                                                                                                                     |                      🚦                      |
 | ------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------------------------------------------: |
-| [pre-commit](https://pre-commit.com/)                   | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below.                                     | <span class="label label-green">Best</span>  |
+| [prek](https://prek.j178.dev/)                          | A rust-powered improvement on `pre-commit`. Known for its friendlier community and feature rich implementation.                                                                                       | <span class="label label-green">Best</span>  |
+| [pre-commit](https://pre-commit.com/)                   | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below.                                     | <span class="label label-yellow">Good</span> |
 | [ruff-format](https://github.com/astral-sh/ruff)        | A drop-in replacement for `black` (and also super fast). A nice "no-need to think" code formatter. If you have your own opinions about code style, you might not like this.                           | <span class="label label-green">Best</span>  |
 | [ruff](https://github.com/astral-sh/ruff)               | A fast linter which incorporates a range of other linters. Notably [isort](https://pycqa.github.io/isort/) can be included as a [ruff rule](https://docs.astral.sh/ruff/rules/) (which we recommend). | <span class="label label-green">Best</span>  |
 | [toml-sort](https://github.com/pappasam/toml-sort)      | Sorts TOML files which are now part of PEP 8.                                                                                                                                                         | <span class="label label-green">Best</span>  |

docs/pages/tutorial.md

@@ -396,33 +396,33 @@ tox -e docs
 from the root of the project repository.
 The built documentation will be output to a directory `site`.
 
-## ✅ Using `pre-commit` to run checks when committing
+## ✅ Using `prek` to run checks when committing
 
-The package is set-up to use [pre-commit](https://pre-commit.com/), a framework for running [Git hook scripts](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) on each commit to the repository.
+The package is set-up to use [prek](https://prek.j178.dev/), a framework for running [Git hook scripts](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) on each commit to the repository.
 
 There is a `.pre-commit-config.yaml` configuration file which you can take a look at.
-With this setup `pre-commit` will run a series of fast linters, checks and formatters on the repository on every commit.
+With this setup `prek` will run a series of fast linters, checks and formatters on the repository on every commit.
 
 The main tools we recommend are [ruff](https://docs.astral.sh/ruff/), [ty](https://docs.astral.sh/ty/) and [prettier](https://prettier.io/).
 These Git hook scripts can be installed locally by running
 
 ```sh
-pre-commit install
+prek install
 ```
 
 from the root of the project repository.
 You will only need to do this once per `git clone` of the code.
 
 Once installed, the scripts will be called to inspect the changes each time `git commit` is run.
 Any failures of the checks will need to be fixed before the changes can be committed.
-Some of the `pre-commit` hooks include support for auto-fixing easy problems - in this case you will be alerted that a file has been changed by a hook and these changes need to be staged using `git add` before recommitting.
+Some of the `prek` hooks include support for auto-fixing easy problems - in this case you will be alerted that a file has been changed by a hook and these changes need to be staged using `git add` before recommitting.
 
 The hooks typically only run on the files _changed_ in a commit.
-The `pre-commit` hooks can be run against _all files in the repository_ by running
+The `prek` hooks can be run against _all files in the repository_ by running
 
 ```sh
-pre-commit run --all-files
+prek run --all-files
 ```
 
 from the root of the project repository.
-This is useful to check they will pass if the `pre-commit` configuration is updated, for example, when [adding a new plug-in](https://pre-commit.com/#plugins).
+This is useful to check they will pass if the `prek` configuration is updated, for example, when [adding a new plug-in](https://prek.j178.dev/authoring-hooks).

tests/data/test_package_generation/.github/workflows/linting.yml

@@ -13,11 +13,11 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
-      - name: Cache pre-commit
+      - name: Cache prek
         uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
-          path: ~/.cache/pre-commit
-          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+          path: ~/.cache/prek
+          key: prek-${{ hashFiles('.pre-commit-config.yaml') }}
 
       - name: Set up python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
@@ -27,7 +27,7 @@ jobs:
           cache-dependency-path: pyproject.toml
 
       - name: Install dependencies
-        run: python -m pip install pre-commit
+        run: python -m pip install prek
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files --color always --verbose
+      - name: Run prek
+        run: prek run --all-files --color always --verbose

tests/data/test_package_generation/README.md

@@ -1,6 +1,6 @@
 # Cookiecutter Test
 
-[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![prek](https://img.shields.io/badge/prek-enabled-brightgreen?logo=prek&logoColor=white)](https://github.com/j178/prek)
 [![Tests status][tests-badge]][tests-link]
 [![Linting status][linting-badge]][linting-link]
 [![Documentation status][documentation-badge]][documentation-link]

tests/data/test_package_generation/pyproject.toml

@@ -8,7 +8,7 @@ requires = [
 [dependency-groups]
 dev = [
     "build",
-    "pre-commit",
+    "prek",
     "ruff",
     "tox",
     "twine",

{{cookiecutter.project_slug}}/.github/workflows/linting.yml

@@ -13,11 +13,11 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
-      - name: Cache pre-commit
+      - name: Cache prek
         uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
-          path: ~/.cache/pre-commit
-          key: pre-commit-${{ '{{' }} hashFiles('.pre-commit-config.yaml') {{ '}}' }}
+          path: ~/.cache/prek
+          key: prek-${{ '{{' }} hashFiles('.pre-commit-config.yaml') {{ '}}' }}
 
       - name: Set up python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
@@ -27,7 +27,7 @@ jobs:
           cache-dependency-path: pyproject.toml
 
       - name: Install dependencies
-        run: python -m pip install pre-commit
+        run: python -m pip install prek
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files --color always --verbose
+      - name: Run prek
+        run: prek run --all-files --color always --verbose

{{cookiecutter.project_slug}}/README.md

@@ -1,6 +1,6 @@
 # {{cookiecutter.project_name}}
 
-[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![prek](https://img.shields.io/badge/prek-enabled-brightgreen?logo=prek&logoColor=white)](https://github.com/j178/prek)
 [![Tests status][tests-badge]][tests-link]
 [![Linting status][linting-badge]][linting-link]
 [![Documentation status][documentation-badge]][documentation-link]