From 753fb16ddb75bfa577220c45cadf91b2a51c3f35 Mon Sep 17 00:00:00 2001
From: "Robert (Bob) Turner" <r.d.turner@sheffield.ac.uk>
Date: Thu, 26 Jan 2023 14:42:22 +0000
Subject: [PATCH 1/3] rtd needs this

---
 docs/source/requirements.txt | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/docs/source/requirements.txt b/docs/source/requirements.txt
index cd8d0a96..5f18d1f9 100644
--- a/docs/source/requirements.txt
+++ b/docs/source/requirements.txt
@@ -1,3 +1,4 @@
-sphinx==4.2.0
-sphinx-autoapi==1.8.4
-sphinx-rtd-theme==1.0.0
\ No newline at end of file
+Sphinx==5.3.0
+myst-parser==0.18.1
+sphinx-autoapi==2.0.1
+sphinx-rtd-theme==1.1.1
\ No newline at end of file

From 04d05af10a17943ede34d54c53e0b8c602daf9c5 Mon Sep 17 00:00:00 2001
From: "Robert (Bob) Turner" <r.d.turner@sheffield.ac.uk>
Date: Thu, 26 Jan 2023 14:42:36 +0000
Subject: [PATCH 2/3] support markdown

---
 docs/source/conf.py | 23 ++++++++++-------------
 setup.py            | 14 ++++++++++++--
 2 files changed, 22 insertions(+), 15 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index c78b83d9..a9aa633a 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -13,15 +13,15 @@
 import os
 import sys
 
-#Include root directory of project
+# Include root directory of project
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../..")))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'Causal Testing'
-copyright = '2021, Andrew Clark, Michael Foster, Neil Walkinshaw, Rob Hierons, Bob Turner'
-author = 'Andrew Clark, Michael Foster, Neil Walkinshaw, Rob Hierons, Bob Turner'
+project = "Causal Testing"
+copyright = "2021, Andrew Clark, Michael Foster, Neil Walkinshaw, Rob Hierons, Bob Turner"
+author = "Andrew Clark, Michael Foster, Neil Walkinshaw, Rob Hierons, Bob Turner"
 
 
 # -- General configuration ---------------------------------------------------
@@ -29,13 +29,10 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'autoapi.extension',
-    'sphinx.ext.autosectionlabel'
-]
+extensions = ["autoapi.extension", "myst_parser", "sphinx.ext.autosectionlabel"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -47,12 +44,12 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # 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,
 # so a file named "default.css" will overwrite the builtin "default.css".
-#html_static_path = ['_static']
+# html_static_path = ['_static']
 
-#Path to generate documentation from using sphinx AutoAPI
-autoapi_dirs = [os.path.abspath(os.path.join('..', '..', 'causal_testing'))]
\ No newline at end of file
+# Path to generate documentation from using sphinx AutoAPI
+autoapi_dirs = [os.path.abspath(os.path.join("..", "..", "causal_testing"))]
diff --git a/setup.py b/setup.py
index 7d2feb9f..0ac17997 100644
--- a/setup.py
+++ b/setup.py
@@ -15,9 +15,19 @@
 ]
 
 # Additional dependencies for development
-dev_requirements = ["autopep8", "isort", "pytest", "pylint", "black"]
+dev_requirements = [
+    "autopep8",
+    "isort",
+    "pytest",
+    "pylint",
+    "black",
+    "autoapi",
+    "myst-parser",
+    "sphinx-autoapi",
+    "sphinx_rtd_theme",
+]
 
-readme = open("README.md", encoding = "UTF-8").read()
+readme = open("README.md", encoding="UTF-8").read()
 
 setup(
     name="causal_testing_framework",

From bab966c85d65c4171a25c8a2a6a8d54e70f06983 Mon Sep 17 00:00:00 2001
From: "Robert (Bob) Turner" <r.d.turner@sheffield.ac.uk>
Date: Thu, 26 Jan 2023 14:42:42 +0000
Subject: [PATCH 3/3] add empty glossary

---
 docs/source/glossary.md | 3 +++
 docs/source/index.rst   | 6 ++++++
 2 files changed, 9 insertions(+)
 create mode 100644 docs/source/glossary.md

diff --git a/docs/source/glossary.md b/docs/source/glossary.md
new file mode 100644
index 00000000..b0160c1c
--- /dev/null
+++ b/docs/source/glossary.md
@@ -0,0 +1,3 @@
+# Glossary
+
+TDB
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 409be41e..007fd29d 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -27,6 +27,12 @@ Causal testing is a causal inference-driven framework for functional black-box t
 
    json_front_end
 
+.. toctree::
+   :maxdepth: 1
+   :caption: Glossary
+
+   glossary
+
 Indices and tables
 ==================