Convert md tutorials to rst and copy them to the website

docs/pyproject.toml

@@ -14,6 +14,8 @@ jaxlib = "^0.4.25"
 numpyro = "^0.14.0"
 sphinxcontrib-mermaid = "^0.9.2"
 polars = "^0.20.16"
+matplotlib = "^3.8.3"
+sphinx-autodoc-typehints = "^2.1.0"
 
 
 [build-system]

docs/source/conf.py

@@ -32,12 +32,24 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.mathjax",
     "sphinxcontrib.mermaid",
+    "sphinx_autodoc_typehints",
 ]
 
+# Simplifies printing of type hints
+set_type_checking_flag = True
+typehints_fully_qualified = False
+
+# Avoid appending the full module name to the class name
+add_module_names = False
+
 templates_path = ["_templates"]
 exclude_patterns = []
 
-todo_include_todos = True
+# Default deph for documentation
+toc_deph = 2
+
+# We don't want that explicitly
+todo_include_todos = False
 
 
 # -- Options for HTML output -------------------------------------------------

docs/source/general/ctoc.rst

@@ -2,7 +2,7 @@ Complete Table Of Contents
 ==========================
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 3
 
    ../msei_reference/index
    ../test_reference/index

docs/source/msei_reference/model.rst

@@ -1,18 +1,18 @@
 MSEI Model
 ==========
 
-Hospitalizations
-----------------
+Hospital Admissions
+-------------------
 
-.. automodule:: pyrenew.model.hospitalizations
+.. automodule:: pyrenew.model.admissionsmodel
    :members:
    :undoc-members:
    :show-inheritance:
 
 Reproduction Number Renewal Infections
 --------------------------------------
 
-.. automodule:: pyrenew.model.rtinfectionsrenewal
+.. automodule:: pyrenew.model.rtinfectionsrenewalmodel
    :members:
    :undoc-members:
    :show-inheritance:

model/README.md

@@ -12,4 +12,4 @@ pip install git+https://github.com/cdcent/cfa-pyrenew.git
 
 ## Demo
 
-The [`docs`](docs) folder contains quarto documents to get you started. It simulates observed hospitalizations using a simple renewal process model and then fits it using a No-U-Turn Sampler.
+The [`docs`](docs) folder contains quarto documents to get you started. It simulates observed hospital admissions using a simple renewal process model and then fits it using a No-U-Turn Sampler.