mmcdermott · Oufattole · Jul 3, 2024 · Jun 13, 2024 · Jun 13, 2024 · Jun 13, 2024
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/README.md b/README.md
@@ -46,15 +46,15 @@ This repository consists of two key pieces:
    what is more advanced is the efficient construction, storage, and loading of tabular features for the
    candidate AutoML models, enabling a far more extensive search over different featurization strategies.
 
-### Scripts and Examples
+## Scripts and Examples
 
 See `tests/test_integration.py` for an example of the end-to-end pipeline being run on synthetic data. This
 script is a functional test that is also run with `pytest` to verify the correctness of the algorithm.
 
 For an end to end example over MIMIC-IV, see the [companion repository](https://github.com/mmcdermott/MEDS_TAB_MIMIC_IV)
 For an end to end example over Philips eICU, see the [eICU companion repository](https://github.com/mmcdermott/MEDS_TAB_EICU).
 
-### Core CLI Scripts Overview
+## Core CLI Scripts Overview
 
 1. **`meds-tab-describe`**: This command processes MEDS data shards to compute the frequencies of different code-types
 
@@ -124,7 +124,7 @@ For an end to end example over Philips eICU, see the [eICU companion repository]
 
 6. **`meds-tab-xgboost-sweep`**: Conducts an Optuna hyperparameter sweep to optimize over `window_sizes`, `aggregations`, and `min_code_inclusion_frequency`, aiming to enhance model performance and adaptability.
 
-### Additional CLI Scripts
+## Additional CLI Scripts
 
 1. **`generate-permutations`**: Generates and prints a sorted list of all permutations from a comma separated input. This is provided for the convenience of sweeping over all possible combinations of window sizes and aggregations.
-## Additional CLI Scripts
-
-1. **`generate-permutations`**: Generates and prints a sorted list of all permutations from a comma separated input. This is provided for the convenience of sweeping over all possible combinations of window sizes and aggregations.
+## Additional CLI Scripts
+
+1. **`generate-permutations`**: Generates and prints all permutations from a comma-separated input, aiding in sweeping over combinations of window sizes and aggregations.
-## Additional CLI Scripts
-
-1. **`generate-permutations`**: Generates and prints a sorted list of all permutations from a comma separated input. This is provided for the convenience of sweeping over all possible combinations of window sizes and aggregations.
+## Additional CLI Scripts
+
+1. **`generate-permutations`**: Generates and prints all permutations from a comma-separated input, aiding in sweeping over combinations of window sizes and aggregations.
 
@@ -149,7 +149,7 @@ For an end to end example over Philips eICU, see the [eICU companion repository]
 
 # How does MEDS-Tab Work?
 
-#### What do you mean "tabular pipelines"? Isn't _all_ structured EHR data already tabular?
+## What do you mean "tabular pipelines"? Isn't _all_ structured EHR data already tabular?
 
 This is a common misconception. _Tabular_ data refers to data that can be organized in a consistent, logical
 set of rows/columns such that the entirety of a "sample" or "instance" for modeling or analysis is contained

diff --git a/docs/assets/main_fig.png b/docs/assets/main_fig.png
diff --git a/docs/assets/meds_logo.png b/docs/assets/meds_logo.png
diff --git a/docs/assets/pivot.png b/docs/assets/pivot.png
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
+esgpt @ git+https://github.com/mmcdermott/EventStreamGPT
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