diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index d5c2583..b8d9db2 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -2,7 +2,7 @@
version: 2
sphinx:
- configuration: docs/conf.py
+ configuration: example-docs/conf.py
build:
os: ubuntu-20.04
@@ -15,7 +15,7 @@ python:
path: .
conda:
- environment: docs/environment.yml
+ environment: example-docs/environment.yml
submodules:
include: all
\ No newline at end of file
diff --git a/example-docs/Makefile b/example-docs/Makefile
new file mode 100644
index 0000000..2c6b4e5
--- /dev/null
+++ b/example-docs/Makefile
@@ -0,0 +1,27 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?= -j auto
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ git clone https://github.com/MDAnalysis/mdanalysis.git
+ cp conf.py mdanalysis/package/doc/sphinx/conf.py
+ cd mdanalysis/package/doc/sphinx/ && make html && cd -
+ cp -r mdanalysis/package/doc/html/ mdanalysis-docs/
+
+ # git clone https://github.com/MDAnalysis/UserGuide.git
+
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" -j auto $(SPHINXOPTS) $(O)
diff --git a/example-docs/conf.py b/example-docs/conf.py
new file mode 100644
index 0000000..853bb61
--- /dev/null
+++ b/example-docs/conf.py
@@ -0,0 +1,131 @@
+# 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:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+
+# -- Project information -----------------------------------------------------
+
+project = "MDAnalysis Sphinx theme"
+html_title = "MDAnalysis Sphinx theme"
+# 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.
+#
+import os
+import sys
+
+copyright = "2023, MDAnalysis"
+author = "MDAnalysis"
+
+# -- 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.autosummary",
+ "sphinx.ext.napoleon",
+ "sphinx.ext.doctest",
+ "sphinx.ext.extlinks",
+ "sphinx.ext.intersphinx",
+ "sphinx.ext.todo",
+ "sphinx.ext.mathjax",
+ "sphinx.ext.viewcode",
+ "nbsphinx",
+ "mdanalysis_sphinx_theme",
+ "sphinxcontrib.autodoc_pydantic",
+ "sphinx_search.extension",
+]
+
+# Autodoc settings
+autosummary_generate = True
+
+autodoc_default_options = {
+ "members": True,
+ "inherited-members": True,
+ "member-order": "bysource",
+}
+autodoc_preserve_defaults = True
+autodoc_typehints_format = "short"
+# Workaround for autodoc_typehints_format not working for attributes
+# see https://github.com/sphinx-doc/sphinx/issues/10290#issuecomment-1079740009
+python_use_unqualified_type_names = True
+
+intersphinx_mapping = {
+ "python": ("https://docs.python.org/3", None),
+ "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
+}
+
+napoleon_numpy_docstring = True
+napoleon_google_docstring = False
+napoleon_attr_annotations = True
+napoleon_custom_sections = [("attributes", "params_style")]
+napoleon_use_rtype = False
+napoleon_use_param = True
+napoleon_use_ivar = True
+napoleon_preprocess_types = 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", ".DS_Store"]
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+html_theme = "mdanalysis_sphinx_theme"
+
+# 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"]
+
+# If HTML theme settings isn't lines 90-160, remember to change customization.rst
+
+# -- HTML theme settings ------------------------------------------------
+html_show_sourcelink = True
+html_sidebars = {
+ "**": ["globaltoc.html", "localtoc.html", "searchbox.html"],
+}
+
+# material theme options (see theme.conf for more information)
+html_theme_options = {
+ "base_url": "docs.mdanalysis.org",
+ "repo_url": "https://github.com/mdanalysis/mdanalysis/",
+ "repo_name": "mdanalysis",
+ "mda_official": True,
+}
+
+# If HTML theme settings isn't lines 90-160, remember to change customization.rst
+
+language = "en"
+html_last_updated_fmt = ""
+
+todo_include_todos = True
+
+html_use_index = True
+html_domain_indices = True
+
+nbsphinx_execute = "always"
+nbsphinx_kernel_name = "python3"
+
+extlinks = {
+ "duref": (
+ "http://docutils.sourceforge.net/docs/ref/rst/" "restructuredtext.html#%s",
+ "%s",
+ ),
+ "durole": ("http://docutils.sourceforge.net/docs/ref/rst/" "roles.html#%s", "%s"),
+ "dudir": (
+ "http://docutils.sourceforge.net/docs/ref/rst/" "directives.html#%s",
+ "%s",
+ ),
+}
diff --git a/example-docs/environment.yml b/example-docs/environment.yml
new file mode 100644
index 0000000..708660a
--- /dev/null
+++ b/example-docs/environment.yml
@@ -0,0 +1,78 @@
+name: guide
+channels:
+ - jaimergp/label/unsupported-cudatoolkit-shim
+ - conda-forge
+ - plotly
+ - defaults
+dependencies:
+ # theme
+ - ipykernel
+ - autodoc-pydantic
+ - myst-parser~=1.0
+ - wheel
+ - sphinx-autobuild
+ - sphinx>=6.2.1,<7
+
+
+ # user guide
+ - cython
+ - distributed==2021.1.0
+ - dask==2021.1.0
+ - python-graphviz
+ - pytest
+ - decorator
+ - docutils
+ - graphviz
+ - ipywidgets<8.0.0
+ - ipython
+ - ipygany
+ - jedi
+ - jinja2
+ - jupyter_contrib_nbextensions
+ - matplotlib
+ - nbclient
+ - nbconvert
+ - nbformat
+ - nbsphinx
+ - networkx
+ - nglview
+ - notebook
+ - numpy
+ - packaging
+ - parmed
+ - parso
+ - pip
+ - plotly
+ - pybtex
+ - python=3.9
+ - pyvista
+ - scikit-image
+ - scikit-learn>=1.1.2
+ - sphinxcontrib-bibtex
+ - threadpoolctl
+ - tabulate
+ - widgetsnbextension
+ - ipycytoscape>=1.3.0
+ - seaborn>=0.12.1
+ - openmm>=7.0.0
+ - pandoc
+ - moviepy
+ - ipyvtklink
+ - pip:
+ # theme
+ - readthedocs-sphinx-search
+ - beautifulsoup4
+ - css_html_js_minify
+ - lxml
+ - libsass
+
+ - sphinx_rtd_theme
+ - msmb_theme
+ - sphinx-sitemap
+ - nbval
+ - pre-commit
+ - python-slugify[unidecode]
+ - pyedr>=0.7
+ - git+https://github.com/MDAnalysis/mdanalysis@develop#egg=mdanalysis&subdirectory=package
+ - git+https://github.com/MDAnalysis/mdanalysis@develop#egg=MDAnalysisTests&subdirectory=testsuite
+ - git+https://github.com/MDAnalysis/MDAnalysisData@master#egg=MDAnalysisData
\ No newline at end of file
diff --git a/example-docs/index.rst b/example-docs/index.rst
new file mode 100644
index 0000000..3da2525
--- /dev/null
+++ b/example-docs/index.rst
@@ -0,0 +1,13 @@
+==================================
+MDAnalysis Sphinx theme Quickstart
+==================================
+
+This theme provides a responsive theme for Sphinx documentation by the Open Force Field Initiative.
+It is inspired by `Material for Sphinx `_ and `Material for MkDocs `_, but has been rewritten with the `Bulma `_ CSS framework to remove any JavaScript dependencies.
+
+
+.. toctree::
+ :caption: Examples
+ :maxdepth: 1
+
+ mdanalysis-docs/index
\ No newline at end of file
diff --git a/example-docs/make.bat b/example-docs/make.bat
new file mode 100644
index 0000000..1264db8
--- /dev/null
+++ b/example-docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.http://www.sphinx-doc.org/
+ exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd