chore: update formatting and pre-commit config

.github/dependabot.yml

@@ -1,6 +1,6 @@
 version: 2
 updates:
-# Maintain dependencies for GitHub Actions
+  # Maintain dependencies for GitHub Actions
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:

.github/workflows/ci.yml

@@ -2,7 +2,7 @@ name: Test
 
 on:
   push:
-    branches: [ "main" ]
+    branches: ["main"]
   pull_request:
   workflow_dispatch:
   schedule:
@@ -19,7 +19,7 @@ jobs:
     name: Test Python ${{ matrix.python-version }} [${{ matrix.qt-api }}]
     runs-on: ubuntu-latest
     env:
-      DISPLAY: ':99.0'
+      DISPLAY: ":99.0"
     strategy:
       fail-fast: false
       matrix:
@@ -75,7 +75,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: "3.12"
 
       - name: Install mypy and dependencies
         run: |
@@ -105,7 +105,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |

.github/workflows/release.yml

@@ -35,7 +35,7 @@ jobs:
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           changelog_increment_filename: body.md
-          extra_requirements : "cz-changeup"
+          extra_requirements: "cz-changeup"
 
       - name: Build package distributions
         id: build

.pre-commit-config.yaml

@@ -6,7 +6,6 @@ ci:
 default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
-
   # Meta hooks
   - repo: meta
     hooks:
@@ -30,14 +29,24 @@ repos:
       - id: mixed-line-ending
       - id: trailing-whitespace
 
+  # Pygrep hooks
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+      - id: text-unicode-replacement-char
+      - id: python-use-type-annotations
+
   # Lint and format with ruff
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: v0.8.1
     hooks:
       # Run the linter.
       - id: ruff
-        args: [ --fix, --show-fixes ]
+        args: [--fix, --show-fixes]
       # Run the formatter.
       - id: ruff-format
 
@@ -46,7 +55,7 @@ repos:
     rev: v4.0.0
     hooks:
       - id: commitizen
-        additional_dependencies: [ cz-changeup ]
+        additional_dependencies: [cz-changeup]
       - id: commitizen-branch
-        additional_dependencies: [ cz-changeup ]
+        additional_dependencies: [cz-changeup]
         stages: [pre-push]

docs/source/_static/custom.css

@@ -1,4 +1,8 @@
-dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple) .field-list>dt {
+dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(
+    .simple
+  )
+  .field-list
+  > dt {
   font-size: var(--font-size--small);
   text-transform: uppercase;
   background-color: var(--color-background-secondary);
@@ -8,7 +12,6 @@ span.default_value {
   font-weight: normal;
 }
 
-
 /* Fix for xarray dark mode */
 /* https://github.com/pradyunsg/furo/discussions/790#discussioncomment-9298183 */
 html,

docs/source/changelog.md

@@ -1,4 +1,5 @@
 # Changelog
 
 ```{include} ../../CHANGELOG.md
+
 ```

docs/source/contributing.rst

@@ -29,7 +29,7 @@ report <https://stackoverflow.com/help/mcve>`_, and this `article on minimal bug
 Creating a development environment
 ==================================
 
-First, you will need to install `git` and `conda` (or `mamba`).
+First, you will need to install ``git`` and ``conda`` (or ``mamba``).
 
 Installing git
 --------------
@@ -80,7 +80,7 @@ Cloning the repository
     cd erlabpy
     git remote add upstream https://github.com/kmnhan/erlabpy.git
 
-   This creates the directory `erlabpy` and connects your repository to the upstream
+   This creates the directory ``erlabpy`` and connects your repository to the upstream
    (main project) *erlabpy* repository.
 
 
@@ -297,25 +297,25 @@ add tests, follow these steps:
    return, and use this as a reference in the tests. See preexisting directories and
    tests for examples.
 
-4. Set the environment variable `ERLAB_TEST_DATA_DIR` to the path of the cloned
+4. Set the environment variable ``ERLAB_TEST_DATA_DIR`` to the path of the cloned
    `erlabpy-data <https://github.com/kmnhan/erlabpy-data>`_ repository in your
    development environment. This will allow the tests to access the test data.
 
 5. Now, we can work with the original `erlabpy <https://github.com/kmnhan/erlabpy>`_
    repository to write and run tests for the plugin. Add your tests in
-   `tests/io/plugins/test_<plugin_name>.py`. You can use the `test_data_dir` fixture to
-   access the test data directory. See other modules in the folder for examples.
+   ``tests/io/plugins/test_<plugin_name>.py``. You can use the ``test_data_dir`` fixture
+   to access the test data directory. See other modules in the folder for examples.
 
 6. Run the tests using `pytest <https://docs.pytest.org/>`_ and make sure they pass.
 
 7. Now, it's time to apply your changes. First, push your changes to `erlabpy-data
    <https://github.com/kmnhan/erlabpy-data>`_ and create a pull request.
 
 8. Once your pull request to `erlabpy-data <https://github.com/kmnhan/erlabpy-data>`_ is
-   merged, update the `DATA_COMMIT_HASH` and `DATA_KNOWN_HASH` attributes in
-   `tests/conftest.py`.
+   merged, update the ``DATA_COMMIT_HASH`` and ``DATA_KNOWN_HASH`` attributes in
+   ``tests/conftest.py``.
 
-   - `DATA_COMMIT_HASH` should be the commit hash of `erlabpy-data
+   - ``DATA_COMMIT_HASH`` should be the commit hash of `erlabpy-data
      <https://github.com/kmnhan/erlabpy-data>`_ that contains your test data. This will
      ensure that the version of the test data used in the tests is consistent.
 
@@ -325,7 +325,7 @@ add tests, follow these steps:
        <https://github.com/kmnhan/erlabpy-data/commits/main/>`_ page will copy the full
        hash to your clipboard.
 
-   - `DATA_KNOWN_HASH` is the file hash of the test data tarball. This will ensure that
+   - ``DATA_KNOWN_HASH`` is the file hash of the test data tarball. This will ensure that
      the test data has not been modified or corrupted since the last time the tests were
      run.
 

docs/source/reference.rst

@@ -10,12 +10,12 @@ Subpackages
 ========================   ========================
 Subpackage                 Description
 ========================   ========================
-`erlab.analysis`           Routines for analyzing ARPES data.
-`erlab.io`                 Reading and writing data.
-`erlab.plotting`           Functions related to static plotting with matplotlib.
-`erlab.interactive`        Interactive tools and widgets based on Qt and pyqtgraph
-`erlab.accessors`          `xarray accessors <https://docs.xarray.dev/en/stable/internals/extending-xarray.html>`_. You will not need to import this module directly.
-`erlab.utils`              Utility functions and classes, typically used internally.
+``erlab.analysis``         Routines for analyzing ARPES data.
+``erlab.io``               Reading and writing data.
+``erlab.plotting``         Functions related to static plotting with matplotlib.
+``erlab.interactive``      Interactive tools and widgets based on Qt and pyqtgraph
+``erlab.accessors``        `xarray accessors <https://docs.xarray.dev/en/stable/internals/extending-xarray.html>`_. You will not need to import this module directly.
+``erlab.utils``            Utility functions and classes, typically used internally.
 ========================   ========================
 
 .. currentmodule:: erlab
@@ -33,12 +33,12 @@ Subpackage                 Description
 Submodules
 ==========
 
-==================  ==================
+===================  ==================
 Submodule           Description
-==================  ==================
-`erlab.lattice`     Tools for working with real and reciprocal lattices.
-`erlab.constants`   Physical constants and functions for unit conversion.
-==================  ==================
+===================  ==================
+``erlab.lattice``   Tools for working with real and reciprocal lattices.
+``erlab.constants`` Physical constants and functions for unit conversion.
+===================  ==================
 
 .. toctree::
    :hidden: