Changed landing page, TOC/sidebar

Author: BSchilperoort

CONTRIBUTING.md

@@ -1,7 +1,7 @@
-# processing
+# Contributing Guide
 
 This repositary includes python modules for running the STEMMUS-SCOPE model in a
-notebook. 
+notebook.
 
 The workflow is executed using python and MATLAB on a Unix-like system.
 The python packages are listed in the
@@ -17,7 +17,7 @@ Run the commands below in a terminal:
 ```sh
 # Download and install Conda
 wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-pypy3-Linux-x86_64.sh
-bash Mambaforge-pypy3-Linux-x86_64.sh 
+bash Mambaforge-pypy3-Linux-x86_64.sh
 -b -p ~/mamba
 
 # Update base environment
@@ -51,7 +51,7 @@ Snellius, see the script
 on how to load the module.
 </details>
 
-# Run jupyter notebook
+## Run jupyter notebook
 
 **On Snellius:**
 
@@ -69,18 +69,18 @@ interactively.
    "InputPath" and "OutputPath".
 3. click on the `Remote Desktop` in the
 Launcher. Click on the `Applications`. You will find the 'MATLAB' software under
-the `Research`. 
+the `Research`.
 4. After clicking on 'MATLAB', it asks for your account information that is
 connected to a MATLAB license.
 5. Open the file `run_model_in_matlab_dev.m` and set the paths inside the script.
 6. Then, run the main script `run_model_in_matlab_dev.m`.
 
-# Recipe of model execution
+## Recipe of model execution
 
 The execution of the model includes following steps:
 
 - Update/set config files
-- Create input directories, prepare input files 
+- Create input directories, prepare input files
 - Run the model
 - Create output directories, prepare output files
 - Create exe file

README.md

@@ -1,4 +1,3 @@
-# PyStemmusScope
 
 <!-- (Customize these badges with your own links, and check https://shields.io/ or https://badgen.net/ to see which other badges are available.) -->
 
@@ -18,7 +17,6 @@
 [![cffconvert](https://github.com/EcoExtreML/stemmus_scope_processing/actions/workflows/cffconvert.yml/badge.svg)](https://github.com/EcoExtreML/stemmus_scope_processing/actions/workflows/cffconvert.yml)
 [![markdown-link-check](https://github.com/EcoExtreML/stemmus_scope_processing/actions/workflows/markdown-link-check.yml/badge.svg)](https://github.com/EcoExtreML/stemmus_scope_processing/actions/workflows/markdown-link-check.yml) -->
 
-
 This repositary includes python modules for running the STEMMUS-SCOPE model in a jupyter
 notebook.
 
@@ -87,7 +85,7 @@ Snellius, see the script
 on how to load the module.
 </details>
 
-# Run jupyter notebook
+## Run jupyter notebook
 
 Open a terminal and run:
 
@@ -110,7 +108,7 @@ interactively.
 Currently, running the notebook on CRIB is not supported because MATLAB Runtime
 can not be installed there.
 
-# Recipe of model execution
+## Recipe of model execution
 
 The execution of the model includes following steps:
 

docs/index.rst

@@ -3,25 +3,25 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
+PyStemmusScope documentation
+****************************
 
-.. include:: ../README.md
-   :parser: myst_parser.sphinx_
+Welcome to the documentation of PyStemmusScope, a python package that enables researchers
+to use the MATLAB-based STEMMUS-SCOPE model.
 
-.. toctree::
-  :maxdepth: 2
-  :caption: Contents:
-  :hidden:
+`STEMMUS-SCOPE <https://gmd.copernicus.org/articles/14/1379/2021/>`_ is an integrated
+soil-plant-atmosphere continuum model based on the models
+`SCOPE <https://github.com/Christiaanvandertol/SCOPE/>`_ and
+`STEMMUS <https://blog.utwente.nl/stemmus/introduction/>`_, and models
+canopy photosynthesis, fluorescence, and the transfer of energy, mass, and momentum.
 
-  Readme <readme_link>
-  Project Setup <project_setup.md>
-  Developer Readme <README.dev.md>
-  Contributing <contributing_link>
-  Code of Conduct <CODE_OF_CONDUCT.md>
-  Changelog <CHANGELOG.md>
+For a guide on how to setup and run the model, see the :doc:`user guide <readme_link>`.
+If you are interested in contributing to the PyStemmusScope code, see the
+:doc:`contributing guide <contributing_link>`.
 
-Indices and tables
-==================
+.. toctree::
+  :maxdepth: 0
+  :hidden:
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+  User guide <readme_link>
+  Contributing guide <contributing_link>

docs/readme_link.rst

@@ -1,2 +1,4 @@
+User Guide
+**********
 .. include:: ../README.md
    :parser: myst_parser.sphinx_