From d4269a3c68054c037a723ef0641631277aa7293f Mon Sep 17 00:00:00 2001 From: Anne Reinarz Date: Fri, 17 May 2024 16:50:30 +0100 Subject: [PATCH] update documentation --- README.md | 12 ++++--- docs/generate_documentation.sh | 13 +++++++ docs/source/conf.py | 5 +-- .../source/images/OpenGoSim_logo.png | Bin .../source/images/UM-bridge_map.png | Bin .../source/images/UQ-Model-UM.png | Bin .../images/lorenzo_tamellini_picture.png | Bin .../images/mikkel_lykkegaard_picture.png | Bin docs/source/index.rst | 34 +++++++++--------- 9 files changed, 39 insertions(+), 25 deletions(-) rename OpenGoSim_logo.png => docs/source/images/OpenGoSim_logo.png (100%) rename UM-bridge_map.png => docs/source/images/UM-bridge_map.png (100%) rename UQ-Model-UM.png => docs/source/images/UQ-Model-UM.png (100%) rename lorenzo_tamellini_picture.png => docs/source/images/lorenzo_tamellini_picture.png (100%) rename mikkel_lykkegaard_picture.png => docs/source/images/mikkel_lykkegaard_picture.png (100%) 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
- Person Image + Person Image
> *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!
- Person Image + Person Image
> *OpenGoSim develops and supports Pflotran-OGS, an open-source reservoir @@ -83,7 +85,7 @@ geological uncertainty on CO2 storage.*
- Person Image + Person Image
> *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`