Move the documentation to the shared CCPBioSim Sphinx theme

.gitignore

@@ -69,7 +69,9 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+docs/build/
+docs/source/reference/
+docs/source/api/
 
 # PyBuilder
 .pybuilder/

docs/source/conf.py

@@ -1,76 +1,78 @@
 # Configuration file for the Sphinx documentation builder.
 
+import importlib.metadata
+
 # -- Project information -----------------------------------------------------
 
 project = "prepmd"
 copyright = "2026, CCPBioSim"
 author = "CCPBioSim"
 
-version = ""
-release = ""
+release = importlib.metadata.version("prepmd")
 
 
 # -- 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",
     "myst_parser",
+    "autoapi.extension",
 ]
 
-autosummary_generate = True
-
-autodoc_member_order = "bysource"
-autodoc_typehints = "description"
-
 templates_path = ["_templates"]
 exclude_patterns = []
 
-# -- Autosummary / autodoc ---------------------------------------------------
+# -- Napoleon docstring settings --------------------------------------------
 
-autosummary_generate = True
+napoleon_google_docstring = True
+napoleon_numpy_docstring = False
+napoleon_use_param = True
+napoleon_use_ivar = True
 
-autosummary_mock_imports = [
-    "openff",
-    "openff.toolkit",
-    "sklearn",
+# -- API reference generated from the source by sphinx-autoapi --------------
+
+autoapi_dirs = ["../../prepmd"]
+autoapi_root = "reference"
+autoapi_add_toctree_entry = False
+autoapi_member_order = "groupwise"
+# Include the __init__ docstring, where the constructor arguments are documented
+autoapi_python_class_content = "both"
+autoapi_options = [
+    "members",
+    "undoc-members",
+    "show-inheritance",
+    "show-module-summary",
 ]
 
-autodoc_member_order = "bysource"
+# Show type hints in the parameter list rather than the signature
 autodoc_typehints = "description"
+add_module_names = False
+python_maximum_signature_line_length = 88
 
-autodoc_mock_imports = [
-    "openff",
-    "openff.toolkit",
-    "sklearn",
-]
 
-# -- Napoleon docstring settings --------------------------------------------
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-napoleon_google_docstring = True
-napoleon_numpy_docstring = False
-napoleon_use_param = False
-napoleon_use_ivar = True
+html_theme = "ccpbiosim_sphinx_theme"
+html_context = {"github_repo": "prepmd"}
+html_static_path = ["_static"]
 
-templates_path = ["_templates"]
-exclude_patterns = []
 
+# Some module variables are assigned twice, such as a default followed by a
+# fallback in an except block. Document each name only once.
+_documented = set()
 
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = "furo"
+def skip_repeated_members(app, what, name, obj, skip, options):
+    if name in _documented:
+        return True
+    _documented.add(name)
+    return skip
 
-html_theme_options = {
-    "light_logo": "logos/prepmd-logo-black.svg",
-    "dark_logo": "logos/prepmd-logo-white.svg",
-}
 
-html_static_path = ["_static"]
+def setup(app):
+    app.connect("autoapi-skip-member", skip_repeated_members)