use the acellera docs theme

Author: stefdoerr

doc/source/_static/custom.css

@@ -4,6 +4,8 @@
 import os
 from pathlib import Path
 
+from acellera_docs_theme import apply
+
 # Drop the timestamp from moleculekit log lines in rendered tutorial output.
 os.environ.setdefault("MOLECULEKIT_LOG_FORMAT", "%(name)s - %(levelname)s - %(message)s")
 
@@ -36,7 +38,6 @@
     ".md": "myst-nb",
 }
 
-templates_path = ["_templates"]
 exclude_patterns = ["build", "**/.ipynb_checkpoints"]
 
 # -- MyST / MyST-NB ----------------------------------------------------------
@@ -54,69 +55,17 @@
 nb_execution_timeout = 300  # some system-prep cells take ~60s
 nb_merge_streams = True  # combine consecutive stream outputs into a single block
 
-# -- HTML output -------------------------------------------------------------
-
-html_theme = "pydata_sphinx_theme"
-html_static_path = ["_static"]
-html_css_files = ["custom.css"]
-html_show_sourcelink = True  # per-page Markdown source link (LLM-friendly)
-html_logo = "_static/img/acellera_new_web.png"
-html_favicon = "_static/img/acellera-logo-16x16.png"
-html_context = {"default_mode": "light"}  # the brand navbar colours assume light mode
-
-html_theme_options = {
-    "logo": {
-        "image_light": "_static/img/acellera_new_web.png",
-        "image_dark": "_static/img/acellera_new_web.png",
-        "text": "MoleculeKit",
-    },
-    "header_links_before_dropdown": 5,
-    "show_toc_level": 2,
-    "navigation_depth": 3,
-    "use_edit_page_button": False,
-    "navigation_with_keys": False,
-    "footer_start": ["copyright"],
-    "footer_end": [],
-    "icon_links": [
-        {
-            "name": "Acellera",
-            "url": "https://www.acellera.com",
-            "icon": "_static/img/acellera-logo-white.png",
-            "type": "local",
-        },
-        {
-            "name": "Twitter",
-            "url": "https://twitter.com/acellera",
-            "icon": "fab fa-twitter",
-            "type": "fontawesome",
-        },
-        {
-            "name": "GitHub",
-            "url": "https://github.com/Acellera/moleculekit",
-            "icon": "fab fa-github-square",
-            "type": "fontawesome",
-        },
-        {
-            "name": "LinkedIn",
-            "url": "https://www.linkedin.com/company/acellera/",
-            "icon": "fab fa-linkedin",
-            "type": "fontawesome",
-        },
-        {
-            "name": "Youtube",
-            "url": "https://www.youtube.com/user/acelleralive",
-            "icon": "fab fa-youtube",
-            "type": "fontawesome",
-        },
-    ],
-}
+# -- Acellera unified branding ----------------------------------------------
 
-html_sidebars = {
-    "**": ["sidebar-nav-bs.html"],
-}
+apply(
+    globals(),
+    project_name="MoleculeKit",
+    github_repo="Acellera/moleculekit",
+)
 
 # -- LLM full-corpus artifact ------------------------------------------------
 
+
 def _emit_llms_full_txt(app, exception):
     """build-finished hook: concatenate every rendered page source into llms-full.txt."""
     if exception is not None:

doc/source/_static/img/acellera-logo-16x16.png

@@ -63,8 +63,8 @@ openmm = [
 [dependency-groups]
 test = ["pytest>=8.4.2", "pytest-xdist", "jupytext", "nbclient", "ipykernel"]
 docs = [
+  "acellera-docs-theme @ git+https://github.com/Acellera/acellera-docs-theme.git",
   "sphinx",
-  "pydata-sphinx-theme",
   "myst-nb",
   "sphinx-design",
   "sphinx-copybutton",