✨ add website for course

Author: enryH

.github/workflows/build_website.yaml

@@ -0,0 +1,49 @@
+# Build website and save it on gh-pages branch
+name: build-and-save-website
+
+# Only run this when the master branch is ch
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  # workflow_dispatch:
+
+# This job installs dependencies, builds the website and pushes it to `gh-pages`
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      - name: Build the site
+        run: |
+          sphinx-build -nW --keep-going -b html .  _build
+
+      # If we've pushed to main, push the book's HTML to github-pages
+      - if: ${{ github.ref == 'refs/heads/main' }}
+        name: Save to gh-pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_build
+          # # set it to a subfolder of the root to keep all PR previews:
+          # destination_dir: latest
+          # cname: website.com
+      - if: ${{ github.ref != 'refs/heads/main' }}
+        name: Save to gh-pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_build
+          # # create a version for an PR
+          # # will be automatically deleted in case the build in on the root
+          destination_dir: dev

.gitignore

@@ -10,3 +10,4 @@
 .bash_logout
 .profile
 .DS_Store
+_build

conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+#
+# created from notes_template: https://github.com/enryH/notes_template
+# -- Project information -----------------------------------------------------
+
+project = "Git Tutorial"
+copyright = "2025, DTU Biosustain, Informatics Platform, DSP"
+author = "Henry Webel"
+
+
+# -- General configuration ---------------------------------------------------
+
+
+extensions = [
+    "myst_nb",
+    # "sphinx_design", # https://sphinx-design.readthedocs.io/en/sbt-theme/
+    # "sphinx_copybutton", # https://sphinx-copybutton.readthedocs.io/
+    "sphinx_new_tab_link",
+]
+
+templates_path = ["_templates"]
+# As we can use percent notebooks and markdowns files, we need to exclude some files
+# additinally to the default ones (add to the list if needed)
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "**/pandoc_ipynb/inputs/*",
+    ".nox/*",
+    '.venv/*',
+    # "README.md",
+    "**/.ipynb_checkpoints/*",
+    "jupyter_execute",
+    "conf.py",
+    "check_recipes.py"
+]
+
+
+# -- Notebook related settings -----------------------------------------------
+
+# add notebooks
+#  https://myst-nb.readthedocs.io/en/latest/computation/execute.html
+nb_execution_mode = "auto"
+
+myst_enable_extensions = ["dollarmath", "amsmath"]
+
+# Plolty support through require javascript library
+# https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly
+# html_js_files = [
+#     "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"
+# ]
+
+# https://myst-nb.readthedocs.io/en/latest/configuration.html
+# Execution
+nb_execution_raise_on_error = True
+# Rendering
+nb_merge_streams = True
+
+# https://myst-nb.readthedocs.io/en/latest/authoring/custom-formats.html#write-custom-formats
+nb_custom_formats = {
+    # ".py": ["jupytext.reads", {"fmt": "py:percent"}]
+}
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# 2. Select a tempalate
+# ! you might need additional dependencies in requirements.txt
+# browse available themes: https://sphinx-themes.org/
+
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+# See:
+# https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py
+# html_title = ""
+html_theme = "sphinx_book_theme"
+# html_theme = "sphinx_book_theme" # alternative
+# html_logo = "_static/logo-wide.svg"
+# html_favicon = "_static/logo-square.svg"
+html_theme_options = {
+    "github_url": "https://github.com/biosustain/git-tutorial",
+    "repository_url": "https://github.com/biosustain/git-tutorial",
+    # "repository_branch": "main",
+    # "home_page_in_toc": True,
+    # "path_to_docs": "docs",
+    "show_navbar_depth": 1,
+    # "use_edit_page_button": True,
+    "use_repository_button": True,
+    "use_download_button": True,
+    "launch_buttons": {
+        "colab_url": "https://colab.research.google.com"
+        #     "binderhub_url": "https://mybinder.org",
+        #     "notebook_interface": "jupyterlab",
+    },
+    "navigation_with_keys": False,
+}
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']

index.md

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+```{include} README.md
+```
+
+
+```{toctree}
+:maxdepth: 1
+:hidden:
+
+instructions_251105
+instructions_241113
+
+
+```

instructions_251105.md

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+# Workshop on the 5th of November 2025
+
+> to be continued.

requirements.txt

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+sphinx
+sphinx-book-theme
+myst-nb
+ipywidgets
+sphinx-new-tab-link!=0.2.2
+jupytext