Update pipeline and format code

.github/workflows/build-and-deploy-docs.yml

@@ -1,28 +1,24 @@
+---
 # Simple workflow for deploying static content to GitHub Pages
 name: Deploy static content to Pages
-
 on:
   # Runs on pushes targeting the default branch
   push:
-    branches: ["main"]
-
+    branches: [main]
   pull_request:
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
-
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
   id-token: write
   pages: write
   contents: read
-
 # Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
 # However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
 concurrency:
-  group: "pages"
+  group: pages
   cancel-in-progress: false
-
 jobs:
   build_docs_and_deploy:
     runs-on: ubuntu-latest
@@ -34,7 +30,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: '3.11'
       - name: Install dependencies
         run: |
           pip install .
@@ -54,7 +50,7 @@ jobs:
         uses: actions/upload-pages-artifact@v3
         with:
           # Upload entire repository
-          path: "./docs/build/html"
+          path: ./docs/build/html
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v4

.github/workflows/python-package.yml

@@ -1,23 +1,20 @@
+---
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Python package
-
 on:
   push:
-    branches: ["main"]
+    branches: [main]
   pull_request:
-    branches: ["main"]
-
+    branches: [main]
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-
+        python-version: ['3.10', '3.11', '3.12', '3.13']
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

.github/workflows/python-publish.yml

@@ -1,30 +1,26 @@
+---
 # This workflow will upload a Python Package using Twine when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
 # This workflow uses actions that are not certified by GitHub.
 # They are provided by a third-party and are governed by
 # separate terms of service, privacy policy, and support
 # documentation.
-
 name: Upload Python Package
-
 on:
   release:
     types: [published]
-
 permissions:
   contents: read
-
 jobs:
   deploy:
     runs-on: ubuntu-latest
-
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: "3.x"
+          python-version: 3.x
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.pre-commit-config.yaml

@@ -1,32 +1,48 @@
+---
 repos:
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-
-  - repo: https://github.com/jsh9/cercis
-    rev: 0.2.3
-    hooks:
-      - id: cercis
-      - id: cercis-jupyter
-
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.3
-    hooks:
-      - id: prettier
-
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v6.0.0
     hooks:
-      - id: end-of-file-fixer
       - id: trailing-whitespace
-
-  - repo: https://github.com/pre-commit/pre-commit
-    rev: v3.5.0
+      - id: end-of-file-fixer
+      - id: debug-statements
+      - id: double-quote-string-fixer
+      - id: requirements-txt-fixer
+      - id: pretty-format-json
+        args: [--no-ensure-ascii, --indent=4, --no-sort-keys]
+        exclude: \.ipynb$
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.21.0
+    hooks:
+      - id: pyupgrade
+        args: [--py310-plus]
+  - repo: https://github.com/jsh9/muff-pre-commit
+    rev: 0.13.2
+    hooks:
+      - id: muff-format
+        args: [--config, muff.toml]
+  - repo: https://github.com/jsh9/blank-line-after-blocks
+    rev: 0.1.4
     hooks:
-      - id: validate_manifest
-
+      - id: blank-line-after-blocks
+      - id: blank-line-after-blocks-jupyter
+  - repo: https://github.com/lyz-code/yamlfix
+    rev: 1.18.0
+    hooks:
+      - id: yamlfix
+  - repo: https://github.com/hukkin/mdformat
+    rev: 0.7.22
+    hooks:
+      - id: mdformat
+        args: [--wrap, '79', --number]
+        additional_dependencies: [mdformat-tables]
   - repo: https://github.com/jsh9/markdown-toc-creator
-    rev: 0.0.6
+    rev: 0.0.11
     hooks:
       - id: markdown-toc-creator
+  - repo: https://github.com/jsh9/format-docstring
+    rev: 0.1.4
+    hooks:
+      - id: format-docstring
+        name: Format docstrings in .py files
+        args: [--line-length=79]

CHANGELOG.md

@@ -2,8 +2,9 @@
 
 All notable changes to this project will be documented in this file.
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
-and this project adheres to [Semantic Versioning](https://semver.org/).
+The format is based on
+[Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project
+adheres to [Semantic Versioning](https://semver.org/).
 
 ## [Unreleased]
 
@@ -27,4 +28,5 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 ### Fixed
 
 - Python 3.12 pipeline issues
-- GitHub Pages deployment workflow permissions by adding environment configuration
+- GitHub Pages deployment workflow permissions by adding environment
+  configuration

CONTRIBUTING.md

@@ -2,12 +2,16 @@
 
 ## 1. General guideline
 
-In general, contributors should make code changes on a branch, and then [create a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) to have the changes merged.
+In general, contributors should make code changes on a branch, and then
+[create a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request)
+to have the changes merged.
 
 ## 2. Install the library for development
 
-- It is strongly recommended that contributors work on code changes in an isolated Python environment
-- Use `pip install -e .` to install this library locally, so that any local code changes are reflected immediately in your current Python environment
+- It is strongly recommended that contributors work on code changes in an
+  isolated Python environment
+- Use `pip install -e .` to install this library locally, so that any local
+  code changes are reflected immediately in your current Python environment
 
 ## 3. Running local tests and linting
 
@@ -17,10 +21,14 @@ And you can run auto-formatting with the command `pre-commit run -a`.
 
 ## 4. Update the documentations
 
-If you would like to make changes to the documentations of this library, you need to install the dependencies for building documentations with the following command (from the root directory):
+If you would like to make changes to the documentations of this library, you
+need to install the dependencies for building documentations with the following
+command (from the root directory):
 
 ```
 pip install -r docs/requirements.txt
 ```
 
-To build the documentation HTML pages locally, navigate to the `docs` folder, and run `make clean html`. To view the generated HTML documentation, open the file `docs/build/html/index.html` in the browser.
+To build the documentation HTML pages locally, navigate to the `docs` folder,
+and run `make clean html`. To view the generated HTML documentation, open the
+file `docs/build/html/index.html` in the browser.