Merge pull request #36 from mmcdermott/docs

Docs
mmcdermott · Jul 3, 2024 · 9f4dde8 · 9f4dde8
2 parents cfba4ae + 7fe635a
commit 9f4dde8
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Showing 51 changed files with 1,516 additions and 605 deletions.
diff --git a/.gitignore b/.gitignore
@@ -70,6 +70,9 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/source/_autosummary/
+docs/source/api/
+docs/source/bin/
 
 # PyBuilder
 .pybuilder/
@@ -158,3 +161,5 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+docs/source/generated
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -8,6 +8,13 @@ build:
 python:
   install:
     - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
 
 sphinx:
   configuration: docs/source/conf.py
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
diff --git a/README.md b/README.md
diff --git a/docs/assets/dark_purple_meds_tab.png b/docs/assets/dark_purple_meds_tab.png
diff --git a/docs/assets/light_purple_meds_tab.png b/docs/assets/light_purple_meds_tab.png
diff --git a/docs/assets/main_fig.png b/docs/assets/main_fig.png
diff --git a/docs/assets/pivot.png b/docs/assets/pivot.png
diff --git a/docs/assets/white_meds_tab.png b/docs/assets/white_meds_tab.png
diff --git a/docs/generate.sh b/docs/generate.sh
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+# bash generate.sh
+
+set -e
+
+rm -rf build
+make html
+cd build/html
+python -m http.server
diff --git a/docs/make.bat b/docs/make.bat
@@ -10,6 +10,8 @@ if "%SPHINXBUILD%" == "" (
 set SOURCEDIR=source
 set BUILDDIR=build
 
+if "%1" == "" goto help
+
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
 	echo.
@@ -19,17 +21,15 @@ if errorlevel 9009 (
 	echo.may add the Sphinx directory to PATH.
 	echo.
 	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
+	echo.http://sphinx-doc.org/
 	exit /b 1
 )
 
-if "%1" == "" goto help
-
 %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 goto end
 
 :help
 %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 
 :end
-popd
+popd
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,15 +1,14 @@
 sphinx==7.1.2
 sphinx-rtd-theme==1.3.0rc1
 sphinx-collections
-recommonmark
-piccolo_theme
+sphinx_immaterial
 sphinx_subfigure
 nbsphinx
 myst_parser
 pypandoc
 linkify-it-py
-ipykernel
 omegaconf
 ipywidgets
 ipykernel
 ipython
+pydata-sphinx-theme
diff --git a/docs/source/_static/switcher.json b/docs/source/_static/switcher.json
@@ -0,0 +1,12 @@
+[
+    {
+      "version": "dev",
+      "url": "https://meds-tab.readthedocs.io/en/latest/"
+    },
+    {
+      "name": "0.0.2 (stable)",
+      "version": "v0.0.2",
+      "url": "https://meds-tab.readthedocs.io/en/stable/",
+      "preferred": true
+    }
+  ]
diff --git a/docs/source/api.rst b/docs/source/api.rst
diff --git a/docs/source/computational-performance.rst b/docs/source/computational-performance.rst