Move the documentation to the shared CCPBioSim Sphinx theme

.gitignore

@@ -69,7 +69,6 @@ cmake-build-*/
 
 # Sphinx build output
 docs/build/
-docs/source/_autosummary/
 
 # Python environments, caches, and packaging
 .venv/

docs/requirements.txt

@@ -1,7 +1,3 @@
 sphinx>=9.2,<9.3
-nbsphinx>=0.9.8,<1.0
-furo>=2025.0,<2026.0
-sphinx_copybutton>=0.5,<1.0
-sphinxcontrib-contentui>=0.2,<1.0
-sphinxcontrib-details-directive>=0.1,<1.0
+ccpbiosim-sphinx-theme>=1.3.4,<2.0
 markupsafe>=3.0,<4.0

docs/source/conf.py

@@ -13,33 +13,18 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
-    "sphinx.ext.autosummary",
-    "sphinx.ext.autodoc",
     "sphinx.ext.mathjax",
-    "sphinx.ext.viewcode",
-    "sphinx.ext.napoleon",
     "sphinx.ext.intersphinx",
     "sphinx.ext.extlinks",
-    "nbsphinx",
-    "sphinx_copybutton",
 ]
 
-autosummary_generate = True
-napoleon_google_docstring = False
-napoleon_use_param = False
-napoleon_use_ivar = True
-
 templates_path = ["_templates"]
 exclude_patterns = []
 
-
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = "furo"
-html_theme_options = {
-    "dark_logo": "logos/SIST-logo-white-text.svg",
-    "light_logo": "logos/SIST-logo-black-text.svg",
-}
-
+# The shared CCPBioSim theme.
+html_theme = "ccpbiosim_sphinx_theme"
+html_context = {"github_repo": "SIST"}
 html_static_path = ["_static"]

docs/source/index.rst

@@ -1,6 +1,16 @@
+:html_theme.sidebar_secondary.remove:
+
 SIST
 ====
 
+.. ccpbiosim-hero::
+   :logo-light: _static/logos/SIST-logo-black-text.svg
+   :logo-dark: _static/logos/SIST-logo-white-text.svg
+   :logo-alt: SIST
+   :tagline: Stress-Induced Structural Transitions in superhelical DNA
+   :button: user-guide | Get started
+   :github: CCPBioSim/SIST
+
 SIST (Stress-Induced Structural Transitions) is a program for analysing
 stress-induced structural transitions in superhelical DNA with a specified
 base sequence.
@@ -18,31 +28,81 @@ command, and regression testing against reference scientific outputs.
 Quick start
 -----------
 
-Install SIST with Conda:
+.. tab-set::
+
+   .. tab-item:: Install
+
+      Install SIST with Conda:
+
+      .. code-block:: bash
+
+         conda install -c ccpbiosim -c conda-forge -c bioconda sist
+
+   .. tab-item:: Melting
+
+      Run a melting calculation:
+
+      .. code-block:: bash
+
+         sist -a M -f sequence.fa
+
+   .. tab-item:: Competition
+
+      Run a competition calculation and write the result to a file:
+
+      .. code-block:: bash
+
+         sist -a A -f sequence.fa -o results.txt
+
+Explore the documentation
+-------------------------
+
+.. grid:: 1 2 3 3
+   :gutter: 3
+
+   .. grid-item-card:: 📖 User Guide
+      :link: user-guide
+      :link-type: doc
+
+      Calculation modes, options and output.
+
+   .. grid-item-card:: 📦 Installation
+      :link: installation
+      :link-type: doc
+
+      Install SIST with Conda or from source.
 
-.. code-block:: bash
+   .. grid-item-card:: 🔧 Source Usage
+      :link: source-usage
+      :link-type: doc
 
-   conda install -c ccpbiosim -c conda-forge -c bioconda sist
+      Run SIST and its parts from a source build.
 
-Run a melting calculation:
+   .. grid-item-card:: 🧬 Examples
+      :link: examples
+      :link-type: doc
 
-.. code-block:: bash
+      Example inputs and outputs to try.
 
-   sist -a M -f sequence.fa
+   .. grid-item-card:: 🧪 Development
+      :link: development
+      :link-type: doc
 
-Run a competition calculation and write the result to a file:
+      Building, testing and releasing SIST.
 
-.. code-block:: bash
+   .. grid-item-card:: 📝 Citation
+      :link: citation
+      :link-type: doc
 
-   sist -a A -f sequence.fa -o results.txt
+      How to cite SIST in your work.
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents
-
-   user-guide
-   installation
-   source-usage
-   examples
-   development
-   citation
+   :hidden:
+
+   User Guide <user-guide>
+   Installation <installation>
+   Source Usage <source-usage>
+   Examples <examples>
+   Development <development>
+   Citation <citation>