diff --git a/README.md b/README.md
index a073fcf0..1c6213ac 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,6 @@
-![UM-bridge_map](https://raw.githubusercontent.com/UM-Bridge/benchmarks/main/UM-bridge_map.png "UQ-Model-UM")
+# UM-Bridge
+
+![UM-bridge_map](https://raw.githubusercontent.com/UM-Bridge/benchmarks/main/docs/source/images/UM-bridge_map.png "UQ-Model-UM")
**UM-Bridge** is a universal interface that makes any numerical model accessible from any programming language or higher-level software, with a main focus on uncertainty quantification (UQ). It accelerates development from method research to applications and from prototype to supercomputer, enabling you to:
@@ -10,7 +12,7 @@
UM-Bridge only assumes that a model returns an output vector for a given input, and possibly offers derivatives and configuration options. That makes UM-Bridge suitable for fields like **UQ, optimization or machine learning**.
-![UQ-Model-UM](https://raw.githubusercontent.com/UM-Bridge/benchmarks/main/UQ-Model-UM.png "UQ-Model-UM")
+![UQ-Model-UM](https://raw.githubusercontent.com/UM-Bridge/benchmarks/main/docs/source/images/UQ-Model-UM.png "UQ-Model-UM")
Try out this Python example! It passes an input to a simple 1D test model running on a remote server and prints the model's output.
@@ -56,7 +58,7 @@ We are happy to actively support the development of new integrations!
## Opinions
-
+
> *I love Uncertainty Quantification. But I don't love fiddling around with complex numerical solver routines. UM-Bridge takes the pain away from doing UQ with complex models.*
@@ -67,7 +69,7 @@ We are happy to actively support the development of new integrations!
-
+
> *OpenGoSim develops and supports Pflotran-OGS, an open-source reservoir
@@ -83,7 +85,7 @@ geological uncertainty on CO2 storage.*
-
+
> *The UQ software that I develop is in Matlab, which is great for prototyping
diff --git a/docs/generate_documentation.sh b/docs/generate_documentation.sh
index a041da80..6967e165 100755
--- a/docs/generate_documentation.sh
+++ b/docs/generate_documentation.sh
@@ -15,6 +15,10 @@ cp ../.readthedocs.yaml docs_output
# Create index files
cp ../benchmarks/README.md docs_output/markdown/forward-benchmarks.md
cat > docs_output/source/forward-benchmarks/index.rst << EOF
+================
+Propagation benchmarks
+================
+
.. include:: ../markdown/forward-benchmarks.md
:parser: myst_parser.sphinx_
@@ -27,6 +31,10 @@ EOF
cp ../benchmarks/README.md docs_output/markdown/inverse-benchmarks.md
cat > docs_output/source/inverse-benchmarks/index.rst << EOF
+================
+Inverse benchmarks
+================
+
.. include:: ../markdown/inverse-benchmarks.md
:parser: myst_parser.sphinx_
@@ -39,6 +47,11 @@ EOF
cp ../models/README.md docs_output/markdown/models.md
cat > docs_output/source/models/index.rst << EOF
+================
+Models
+================
+
+
.. include:: ../markdown/models.md
:parser: myst_parser.sphinx_
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 5491b7e1..8bf8f724 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -18,7 +18,7 @@
# -- Project information -----------------------------------------------------
project = 'UM-Bridge'
-copyright = '2022, UM-Bridge Team'
+copyright = '2024, UM-Bridge Team'
author = 'UM-Bridge Team'
@@ -45,7 +45,8 @@
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
-html_theme = 'alabaster'
+html_theme = 'cloud'
+html_sidebars = { '**': ['globaltoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html'] }
# 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,
diff --git a/OpenGoSim_logo.png b/docs/source/images/OpenGoSim_logo.png
similarity index 100%
rename from OpenGoSim_logo.png
rename to docs/source/images/OpenGoSim_logo.png
diff --git a/UM-bridge_map.png b/docs/source/images/UM-bridge_map.png
similarity index 100%
rename from UM-bridge_map.png
rename to docs/source/images/UM-bridge_map.png
diff --git a/UQ-Model-UM.png b/docs/source/images/UQ-Model-UM.png
similarity index 100%
rename from UQ-Model-UM.png
rename to docs/source/images/UQ-Model-UM.png
diff --git a/lorenzo_tamellini_picture.png b/docs/source/images/lorenzo_tamellini_picture.png
similarity index 100%
rename from lorenzo_tamellini_picture.png
rename to docs/source/images/lorenzo_tamellini_picture.png
diff --git a/mikkel_lykkegaard_picture.png b/docs/source/images/mikkel_lykkegaard_picture.png
similarity index 100%
rename from mikkel_lykkegaard_picture.png
rename to docs/source/images/mikkel_lykkegaard_picture.png
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 21eb300a..0ed2555e 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -3,9 +3,6 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-UM-Bridge documentation
-======================================
-
.. include:: ../markdown/main.md
:parser: myst_parser.sphinx_
@@ -14,19 +11,28 @@ Getting started
.. toctree::
:glob:
- :maxdepth: 1
-
+ :maxdepth: 2
+
/quickstart
/tutorial
/umbridge/contributing
+
+Documentation
+---------------------
+
+.. toctree::
+ :glob:
+ :maxdepth: 1
+
/umbridge/index
+
Propagation Benchmarks
-----------------------
.. toctree::
:glob:
- :maxdepth: 1
+ :maxdepth: 2
/forward-benchmarks/index
@@ -35,7 +41,7 @@ Inference Benchmarks
.. toctree::
:glob:
- :maxdepth: 1
+ :maxdepth: 2
/inverse-benchmarks/index
@@ -45,19 +51,11 @@ Models
.. toctree::
:glob:
- :maxdepth: 1
+ :maxdepth: 2
/models/index
-About
---------------------
-
-.. toctree::
- :glob:
- :maxdepth: 1
-
- /about
-
-
+Search
+--------------------
* :ref:`search`