Add coix tutorials (#18)

* Added tutorial notebooks * Fixed typos and bug (changed factor to unit node) in tutorial 2 * fixed formating * fixed indentation and issue with level-one headlines * Changes order of tutorials * . * fixed doc generation * Update README * . * delete empty cell * changes proposed in comments --------- Co-authored-by: Du Phan <[email protected]>
jax-ml · Mar 27, 2024 · 766b9ca · 766b9ca
1 parent 709f9e6
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diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,5 @@
+docs/notebooks
+
 # Compiled python modules.
 *.pyc
 

diff --git a/README.md b/README.md
@@ -4,8 +4,7 @@
 [![Documentation Status](https://readthedocs.org/projects/coix/badge/?version=latest)](https://coix.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/coix.svg)](https://badge.fury.io/py/coix)
 
-Inference Combinators in JAX (Coix) is a machine learning framework used to
-develop inference algorithms that are composed of probabilistic programs.
+Coix (COmbinators In jaX) is a flexible and backend-agnostic implementation of inference combinators [(Stites and Zimmermann et al., 2021)](https://arxiv.org/abs/2103.00668), a set of program transformations for compositional inference with probabilistic programs. Coix ships with backends for numpyro and oryx, and a set of pre-implemented losses and utility functions that allows to implement and run a wide variety of inference algorithms out-of-the-box.
 
 *This is not an officially supported Google product.*
 
diff --git a/docs/conf.py b/docs/conf.py
@@ -164,11 +164,18 @@
 
 # -- Copy notebook files
 
-if not os.path.exists("tutorials"):
-  os.makedirs("tutorials")
+if not os.path.exists("notebooks"):
+  os.makedirs("notebooks")
+
+if not os.path.exists("notebooks/figures"):
+  os.makedirs("notebooks/figures")
 
 for src_file in glob.glob("../notebooks/*.ipynb"):
-  shutil.copy(src_file, "tutorials/")
+  shutil.copy(src_file, "notebooks/")
+
+for src_file in glob.glob("../notebooks/figures/*"):
+  shutil.copy(src_file, "notebooks/figures/")
+
 
 # add index file to `notebooks` path, `:orphan:` is used to
 # tell sphinx that this rst file needs not to be appeared in toctree
@@ -198,7 +205,7 @@
 for src_file in glob.glob("../notebooks/*.ipynb") + glob.glob(
     "../examples/*.py"
 ):
-  toctree_path = "tutorials/" if src_file.endswith("ipynb") else "examples/"
+  toctree_path = "notebooks/" if src_file.endswith("ipynb") else "examples/"
   filename = os.path.splitext(src_file.split("/")[-1])[0]
   png_path = "_static/img/" + toctree_path + filename + ".png"
   # use Coix logo if not exist png file

diff --git a/docs/index.rst b/docs/index.rst
@@ -25,6 +25,9 @@ Coix Documentation
    :caption: Tutorials and Examples
    :name: tutorials
 
+   notebooks/tutorial_part1_vae
+   notebooks/tutorial_part2_api
+   notebooks/tutorial_part3_smcs
    examples/anneal
    examples/anneal_oryx
    examples/gmm_oryx

diff --git a/notebooks/figures/smcs_nvi.png b/notebooks/figures/smcs_nvi.png
diff --git a/notebooks/tutorial_part1_vae.ipynb b/notebooks/tutorial_part1_vae.ipynb
diff --git a/notebooks/tutorial_part2_api.ipynb b/notebooks/tutorial_part2_api.ipynb
diff --git a/notebooks/tutorial_part3_smcs.ipynb b/notebooks/tutorial_part3_smcs.ipynb