ci: update ci tools and apply formatting changes

.github/workflows/documentation.yaml → .github/workflows/documentation.yml

@@ -1,6 +1,10 @@
 name: documentation
 
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
 
 permissions:
   contents: write
@@ -10,18 +14,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+
       - uses: actions/setup-python@v5
+
       - name: Install dependencies
         run: |
           pip install sphinx sphinx_rtd_theme myst_parser
-      - name: Sphinx build
+
+      - name: Build Sphinx documentation
         run: |
           sphinx-build docs _build
+
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3
-        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/add-sphinx-pipeline' }}
         with:
-          publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_branch: gh-pages
           publish_dir: _build/
           force_orphan: true

.gitignore

@@ -164,4 +164,4 @@ runs/
 *jpg
 
 # data
-data/
+data/

.pre-commit-config.yaml

@@ -0,0 +1,79 @@
+# To use:
+#
+#     pre-commit run -a
+#
+# Or:
+#
+#     pre-commit install  # (runs every time you commit in git)
+#
+# To update this file:
+#
+#     pre-commit autoupdate
+#
+# See https://github.com/pre-commit/pre-commit
+
+repos:
+  # Standard hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-xml
+      - id: check-yaml
+        args: ["--allow-multiple-documents"]
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+        exclude_types: [rst]
+      - id: fix-byte-order-marker
+      - id: requirements-txt-fixer
+  # Python hooks
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.4
+    hooks:
+      - id: ruff-format
+      - id: ruff
+        name: ruff-isort
+        args: [
+            "--select=I",
+            "--fix"
+            ]
+      - id: ruff
+        name: ruff-pyupgrade
+        args: [
+            "--select=UP",
+            "--fix"
+            ]
+      - id: ruff
+        name: ruff-pydocstyle
+        args: [
+            "--select=D",
+            "--ignore=D100,D101,D102,D103,D104,D105,D106,D107,D401",
+            "--fix",
+            ]
+        stages: [pre-commit]
+        pass_filenames: true
+      - id: ruff
+        name: ruff-check
+        args: [
+            "--select=F,PT,B,C4,T20,S,N",
+            "--ignore=T201,N812,B006,S101,S311,S607,S603",
+            "--fix"
+            ]
+        stages: [pre-commit]
+        pass_filenames: true
+  # Spellcheck in comments and docs
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        args: ['--write-changes', '--ignore-words-list=theses,fom,NED,ENU']
+
+ci:
+    autoupdate_schedule: quarterly