From aa87658fccdef9472c028655782e8fc4f95b5c6a Mon Sep 17 00:00:00 2001
From: "samira.vandenbogaard" <samira.vandenbogaard@gmail.com>
Date: Mon, 16 Dec 2024 11:44:42 +0100
Subject: [PATCH] bugfixes

---
 .readthedocs.yaml |  1 +
 docs/conf.py      | 13 +++++++++++--
 docs/index.rst    | 14 ++++++++++++++
 3 files changed, 26 insertions(+), 2 deletions(-)
 create mode 100644 docs/index.rst

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 7d9ef1a..3f1a5f9 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -18,6 +18,7 @@ build:
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/conf.py
+  source: docs/docs
 
 # Optionally build your docs in additional formats such as PDF and ePub
 # formats:
diff --git a/docs/conf.py b/docs/conf.py
index f72e500..1a96967 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -2,7 +2,7 @@
 
 # -- Project information
 
-project = 'Lumache'
+project = 'PAModelpy'
 copyright = '2024, iAMB, RWTH Aachen University'
 author = 'Samira van den Bogaard'
 
@@ -17,6 +17,7 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.intersphinx',
+    'myst_parser',  # Add this for Markdown support
 ]
 
 intersphinx_mapping = {
@@ -32,4 +33,12 @@
 html_theme = 'sphinx_rtd_theme'
 
 # -- Options for EPUB output
-epub_show_urls = 'footnote'
\ No newline at end of file
+epub_show_urls = 'footnote'
+
+# Enable specific MyST features
+myst_enable_extensions = [
+    "colon_fence",  # Support for ::: directives
+    "deflist",      # Support for definition lists
+    "html_admonition",  # HTML-style admonitions
+    "html_image",   # Use HTML-style <img> tags
+]
\ No newline at end of file
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000..1c744ef
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,14 @@
+Welcome to PAModelpy
+===
+
+The PAModelpy package is designed to integrate protein constraints and protein sectors into protein allocation models (PAMs).
+In this documentation, you can find all the information you need to get build and analyze PAMs.
+
+Table of Contents
+===
+.. toctree::
+   :glob:
+   :maxdepth: 2
+   :caption: Table of Contents
+
+   *.md
\ No newline at end of file