Setup readme as main docs page

Author: BSchilperoort

README.md

@@ -8,18 +8,18 @@
 [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu)
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 [![github license badge](https://img.shields.io/github/license/EcoExtreML/stemmus_scope_processing)](https://github.com/EcoExtreML/stemmus_scope_processing)
+[![Documentation Status](https://readthedocs.org/projects/pystemmusscope/badge/?version=latest)](https://pystemmusscope.readthedocs.io/en/latest/?badge=latest)
 
-<!-- [![RSD](https://img.shields.io/badge/rsd-pystemmusscope-00a3e3.svg)](https://www.research-software.nl/software/pystemmusscope) 
-[![workflow pypi badge](https://img.shields.io/pypi/v/pystemmusscope.svg?colorB=blue)](https://pypi.python.org/project/pystemmusscope/) 
+<!-- [![RSD](https://img.shields.io/badge/rsd-pystemmusscope-00a3e3.svg)](https://www.research-software.nl/software/pystemmusscope)
+[![workflow pypi badge](https://img.shields.io/pypi/v/pystemmusscope.svg?colorB=blue)](https://pypi.python.org/project/pystemmusscope/)
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-[![Documentation Status](https://readthedocs.org/projects/stemmus_scope_processing/badge/?version=latest)](https://stemmus_scope_processing.readthedocs.io/en/latest/?badge=latest)
-[![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) 
+[![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 notebook. 
+This repositary includes python modules for running the STEMMUS-SCOPE model in a notebook.
 
 The workflow is executed using python and MATLAB Runtime on a Unix-like system.
 The python packages are listed in the
@@ -65,7 +65,7 @@ In a terminal:
 # Download MATLAB Runtime for Linux
 wget https://ssd.mathworks.com/supportfiles/downloads/R2021a/Release/6/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R2021a_Update_6_glnxa64.zip
 
-# Unzip the file 
+# Unzip the file
 unzip MATLAB_Runtime_R2021a_Update_6_glnxa64.zip
 
 # Install it
@@ -114,7 +114,7 @@ can not be installed there.
 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
 

docs/conf.py

@@ -17,9 +17,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u"PyStemmusScope"
-copyright = u"2022, Netherlands eScience Center"
-author = u"Sarah Alidoost"
+project = "PyStemmusScope"
+copyright = "2022, Netherlands eScience Center"
+author = "Sarah Alidoost"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -76,6 +76,20 @@
 #
 # html_theme_options = {}
 
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    "**": [
+        'globaltoc.html',
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
+    ]
+}
+
+
 # -- Options for Intersphinx
 
 intersphinx_mapping = {'python': ('https://docs.python.org/3', None),

docs/contributing_link.rst

@@ -0,0 +1,2 @@
+.. include:: ../CONTRIBUTING.md
+   :parser: myst_parser.sphinx_

docs/index.rst

@@ -3,12 +3,21 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to PyStemmusScope's documentation!
-==========================================================
+
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_
 
 .. toctree::
   :maxdepth: 2
   :caption: Contents:
+  :hidden:
+
+  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>
 
 Indices and tables
 ==================

docs/readme_link.rst

@@ -0,0 +1,2 @@
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_