From efd6edd314cda5801082e194340abe5237d00d48 Mon Sep 17 00:00:00 2001
From: Jen Schripsema <jen.schripsema@gatesfoundation.org>
Date: Thu, 28 Sep 2023 12:53:46 -0600
Subject: [PATCH] updated Sphinx config to correctly apply css, corrected typos
 in .gitignore and demo docstring

---
 .gitignore                                    |  2 +-
 docs/conf.py                                  | 32 +++++++++++++------
 .../demographics/TyphoidDemographics.py       |  2 +-
 3 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/.gitignore b/.gitignore
index ffdfa61..785494c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -70,7 +70,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/emodpy-typhoid*.rst
+docs/emodpy_typhoid*.rst
 docs/modules.rst
 
 # PyBuilder
diff --git a/docs/conf.py b/docs/conf.py
index 8945d56..df7d08e 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -59,10 +59,27 @@
     'sphinx_copybutton',
     'sphinx.ext.intersphinx',
     'sphinxext.remoteliteralinclude',
-    'myst_parser',
-    'sphinx_search.extension'
+    'myst_parser', # source files written in MD or RST
+    'sphinx_search.extension', # search across entire IDM docs domain
+    'sphinx.ext.viewcode' # link to view source code
 ]
 
+myst_enable_extensions = [
+    "amsmath",
+    "attrs_inline",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "fieldlist",
+    "html_admonition",
+    "html_image",
+    "linkify",
+    "replacements",
+    "smartquotes",
+    "strikethrough",
+    "substitution",
+    "tasklist",
+]
 plantuml = 'plantweb'
 
 autodoc_default_options = {
@@ -208,18 +225,13 @@
 # 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_context = {
-    'css_files': [
-        '_static/theme_overrides.css',
-        '_static/copy_button.css'
-        ]
-}
-html_js_files = ['show_block_by_os.js']
+html_static_path = ['_static']
 
 html_css_files = ['theme_overrides.css']
 
+html_js_files = ['show_block_by_os.js'] 
+
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
diff --git a/emodpy_typhoid/demographics/TyphoidDemographics.py b/emodpy_typhoid/demographics/TyphoidDemographics.py
index b3789ca..89edbf2 100644
--- a/emodpy_typhoid/demographics/TyphoidDemographics.py
+++ b/emodpy_typhoid/demographics/TyphoidDemographics.py
@@ -81,7 +81,7 @@ def from_csv( pop_filename_in, site="No_Site", min_node_pop = 0 ):
         site: A string to identify the country, village, or trial site.
 
     Returns:
-        A :py:class:`~emodpy_malaria.demographics.MalariaDemographics` instance.
+        A :py:class:`~emodpy_typhoid.demographics.MalariaDemographics` instance.
     """
     typhoid_demog = Demog.from_csv( pop_filename_in )
     nodes = []