MSEI Reference docs added

CDCgov · Mar 18, 2024 · 15a9327 · 15a9327
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diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -2,6 +2,10 @@
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../model/src'))
+
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
@@ -14,11 +18,25 @@
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = []
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosectionlabel',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.duration',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.inheritance_diagram',
+    'sphinx.ext.todo',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.mathjax',
+]
 
 templates_path = ['_templates']
 exclude_patterns = []
 
+todo_include_todos = True
+
 
 
 # -- Options for HTML output -------------------------------------------------

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -3,16 +3,19 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to CFA Multisignal Renewal's documentation!
-===================================================
+CFA Multisignal Renewal Documentation
+=====================================
+
+Welcome, CFA wishes you a nice day!
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 4
    :caption: Contents:
 
+   msei_reference/index
 
 
-Indices and tables
+Indices And Tables
 ==================
 
 * :ref:`genindex`

diff --git a/docs/source/msei_reference/basic.rst b/docs/source/msei_reference/basic.rst
@@ -0,0 +1,7 @@
+Basic Renewal Model Module
+==========================
+
+.. automodule:: pyrenew.basic
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/msei_reference/convolve.rst b/docs/source/msei_reference/convolve.rst
@@ -0,0 +1,7 @@
+Convolution Utility Module
+==========================
+
+.. automodule:: pyrenew.convolve
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/msei_reference/distutil.rst b/docs/source/msei_reference/distutil.rst
@@ -0,0 +1,7 @@
+Distribution Utility Module
+===========================
+
+.. automodule:: pyrenew.distutil
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/msei_reference/index.rst b/docs/source/msei_reference/index.rst
@@ -0,0 +1,15 @@
+MSEI Reference
+==============
+
+.. toctree::
+   :maxdepth: 4
+
+   observation
+   regression
+   distutil
+   convolve
+   infection
+   basic
+   transform
+   process
+   math
diff --git a/docs/source/msei_reference/infection.rst b/docs/source/msei_reference/infection.rst
@@ -0,0 +1,7 @@
+Infection Module
+================
+
+.. automodule:: pyrenew.infection
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/msei_reference/math.rst b/docs/source/msei_reference/math.rst
@@ -0,0 +1,7 @@
+Math Utility Module
+===================
+
+.. automodule:: pyrenew.math
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/msei_reference/observation.rst b/docs/source/msei_reference/observation.rst
@@ -0,0 +1,7 @@
+Observation Module
+==================
+
+.. automodule:: pyrenew.observation
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/msei_reference/process.rst b/docs/source/msei_reference/process.rst
@@ -0,0 +1,7 @@
+Process Module
+==============
+
+.. automodule:: pyrenew.process
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/msei_reference/regression.rst b/docs/source/msei_reference/regression.rst
@@ -0,0 +1,7 @@
+Regression Module
+==================
+
+.. automodule:: pyrenew.regression
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/msei_reference/transform.rst b/docs/source/msei_reference/transform.rst
@@ -0,0 +1,7 @@
+Transform Utility Module 
+========================
+
+.. automodule:: pyrenew.transform
+   :members:
+   :undoc-members:
+   :show-inheritance: