Add the first version of the website (with documentation) (#65)

* Add the first version of the website/documentation

In addition:

- Remove experiment description and config files

Since sample configuration files of the experiments and the experiment
descriptions are now available in the website, they have been removed
from the main chemex code base.

- Add DNA/RNA atom names and scalar coupling

- Add circular shift to D-/cos-CEST plots

- Correct some examples

- Correct `statistics.toml` formatting

- Move from Levenshtein to rapidfuzz

- Fix bugs due to new Rich version

- Change license to GPL version 3

* Add GitHub actions for the website deployment

* Correct links in the documentation

* Add github action to publish to PyPI

Author: gbouvignies

.github/workflows/deploy.yml

@@ -0,0 +1,45 @@
+name: Deploy to GitHub Pages
+
+on:
+  release:
+    types: [published]
+    paths:
+      - ".github/workflows/deploy.yml"
+      - "website/**"
+    # Review gh actions docs if you want to further define triggers, paths, etc
+    # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#on
+
+jobs:
+  deploy:
+    name: Deploy to GitHub Pages
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./website
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v3
+        with:
+          node-version: 18
+          cache: npm
+          cache-dependency-path: website/package-lock.json
+      - name: Install dependencies
+        run: npm ci
+      - name: Build website
+        run: npm run build
+
+      # Popular action to deploy to GitHub Pages:
+      # Docs: https://github.com/peaceiris/actions-gh-pages#%EF%B8%8F-docusaurus
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          # Build output to publish to the `gh-pages` branch:
+          publish_dir: ./website/build
+          # The following lines assign commit authorship to the official
+          # GH-Actions bot for deploys to `gh-pages` branch:
+          # https://github.com/actions/checkout/issues/13#issuecomment-724415212
+          # The GH actions bot is used by default if you didn't specify the two fields.
+          # You can swap them out with your own user credentials.
+          user_name: github-actions[bot]
+          user_email: 41898282+github-actions[bot]@users.noreply.github.com

.github/workflows/publish-to-test-pypi.yml

@@ -0,0 +1,38 @@
+name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+        .
+    - name: Publish distribution 📦 to Test PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_url: https://test.pypi.org/legacy/
+    - name: Publish distribution 📦 to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test-deploy.yml

@@ -0,0 +1,30 @@
+name: Test deployment
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - ".github/workflows/test-deploy.yml"
+      - "website/**"
+    # Review gh actions docs if you want to further define triggers, paths, etc
+    # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#on
+
+jobs:
+  test-deploy:
+    name: Test deployment
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./website
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v3
+        with:
+          node-version: 18
+          cache: npm
+          cache-dependency-path: website/package-lock.json
+      - name: Install dependencies
+        run: npm ci
+      - name: Test build website
+        run: npm run build

.pre-commit-config.yaml

@@ -1,46 +1,39 @@
 repos:
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.1.0
-      hooks:
-          - id: trailing-whitespace
-          - id: end-of-file-fixer
-          - id: check-added-large-files
-          - id: check-case-conflict # Check for files that would conflict in case-insensitive filesystems
-          - id: check-merge-conflict # Check for files that contain merge conflict strings.
-          - id: check-toml # Check toml files for parseable syntax.
-          - id: debug-statements # Check for debugger imports and py37+ `breakpoint()` calls in python source.
-          - id: forbid-new-submodules # Check for git submodules
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-case-conflict # Check for files that would conflict in case-insensitive filesystems
+      - id: check-merge-conflict # Check for files that contain merge conflict strings.
+      - id: check-toml # Check toml files for parseable syntax.
+      - id: debug-statements # Check for debugger imports and py37+ `breakpoint()` calls in python source.
+      - id: forbid-new-submodules # Check for git submodules
 
-    - repo: https://github.com/pycqa/flake8
-      rev: 4.0.1
-      hooks:
-          - id: flake8
+  - repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
+    hooks:
+      - id: flake8
 
-    - repo: https://github.com/bwhmather/ssort
-      rev: v0.10.2
-      hooks:
-          - id: ssort
+  - repo: https://github.com/bwhmather/ssort
+    rev: v0.11.6
+    hooks:
+      - id: ssort
 
-    - repo: https://github.com/asottile/reorder_python_imports
-      rev: v2.7.1
-      hooks:
-          - id: reorder-python-imports
-            args: [--py39-plus]
+  - repo: https://github.com/asottile/reorder_python_imports
+    rev: v3.8.2
+    hooks:
+      - id: reorder-python-imports
+        args: [--py39-plus]
 
-    - repo: https://github.com/asottile/pyupgrade
-      rev: v2.31.0
-      hooks:
-          - id: pyupgrade
-            args: [--py39-plus, --keep-runtime-typing]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.37.3
+    hooks:
+      - id: pyupgrade
+        args: [--py39-plus, --keep-runtime-typing]
 
-    - repo: https://github.com/codespell-project/codespell
-      rev: v2.1.0
-      hooks:
-          - id: codespell
-            args: ["-L", "reson,noe,2st,3st,ba,ser"]
-
-    - repo: https://github.com/psf/black
-      rev: 22.1.0 # Replace by any tag/version: https://github.com/psf/black/tags
-      hooks:
-          - id: black
-            language_version: python3.9
+  - repo: https://github.com/psf/black
+    rev: 22.8.0 # Replace by any tag/version: https://github.com/psf/black/tags
+    hooks:
+      - id: black
+        language_version: python3.9