✨ build website based on notebooks for documentation

.github/workflows/test_tutorial.yaml

@@ -1,10 +1,10 @@
-name: Test tutorial
+name: Test tutorial and publish website
 
 on:
   - push
 
 jobs:
-  format:
+  test_tutorial:
     name: Check tutorial
     runs-on: ubuntu-latest
     steps:
@@ -24,4 +24,23 @@ jobs:
         run: |
           cd scripts
           papermill 0_Tutorial.ipynb 0_Tutorial_out.ipynb -p epochs 4
-
+  website:
+    name: Publish notebooks as website
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          pip install sphinx sphinx-book-theme myst-nb
+      - name: Build website
+        run: |
+          cd docs
+          sphinx-build -n --keep-going -b html ./ ./_build/
+      - name: Publish workflow as website
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build

docs/conf.py

@@ -0,0 +1,98 @@
+# 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
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+# -- Project information -----------------------------------------------------
+
+project = 'CLASTER'
+copyright = '2022, Marc Pielies Avelli'
+author = 'Marc Pielies Avelli'
+version = '2024.05.29'
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autodoc.typehints',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.intersphinx',
+    'myst_nb',
+    'sphinx.ext.napoleon',
+    # 'sphinx_new_tab_link',
+]
+
+#  https://myst-nb.readthedocs.io/en/latest/computation/execute.html
+nb_execution_mode = "off"
+
+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
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', 'jupyter_execute','.DS_Store']
+
+
+# Intersphinx options
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "scikit-learn": ("https://scikit-learn.org/stable/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+}
+
+# -- Options for HTML output -------------------------------------------------
+
+# 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 = "CLASTER"
+html_theme = "sphinx_book_theme"
+# html_logo = "_static/logo-wide.svg"
+# html_favicon = "_static/logo-square.svg"
+html_theme_options = {
+    "github_url": "https://github.com/RasmussenLab/CLASTER",
+    "repository_url": "https://github.com/RasmussenLab/CLASTER",
+    "repository_branch": "master",
+    "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"]

docs/index.rst

@@ -0,0 +1,14 @@
+Claster
+=======
+Modeling nascent RNA transcription from chromatin landscape and structure
+
+
+.. include:: ../Readme.md
+   :parser: myst_parser.sphinx_
+   :start-line: 3
+
+.. toctree::
+    :maxdepth: 2
+    :caption: Tutorial:
+
+    nbs/0_Tutorial.ipynb

docs/nbs/0_Tutorial.ipynb

@@ -0,0 +1 @@
+../../scripts/0_Tutorial.ipynb