add notebooks to docs

.github/workflows/build_docs.yml

@@ -21,6 +21,12 @@ jobs:
           python-version: "3.12"
           cache-dependency-path: "pyproject.toml"
           cache: "pip"
+
+      - name: Download Dataset from Zenodo
+        run: |
+            mkdir -p data
+            wget -O data/dataset.zip https://zenodo.org/records/13305156/files/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip?download=1?
+            unzip -o data/dataset.zip -d data
 
       - name: Install Dependencies
         run: |

.gitignore

@@ -71,8 +71,9 @@ docs/_build/
 target/
 
 # Jupyter Notebook
-.ipynb_checkpoints
+*.ipynb_checkpoints
 *.ipynb
+!docs/**/*.ipynb
 
 # pyenv
 .python-version

docs/notebooks/quickstart.ipynb

@@ -0,0 +1,44 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ngio.core import NgffImage\n",
+    "\n",
+    "ngff_image = NgffImage(\"../../data/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr/B/03/0\")\n",
+    "print(ngff_image.levels_paths)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "dev2",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

mkdocs.yml

@@ -6,7 +6,9 @@ theme:
 
 nav:
   - Home: index.md
-  - Getting Started: getting-started.md
+  - Getting Started: 
+    - Installation: getting-started.md
+    - Getting Started: notebooks/quickstart.ipynb
   - API Reference:
     - core: api/core.md
 
@@ -22,3 +24,7 @@ plugins:
             # Use Google-style docstrings, for example
             docstring_style: google
 
+  - mkdocs-jupyter:
+      notebooks_dir: notebooks
+      execute: true
+

pyproject.toml

@@ -79,6 +79,7 @@ docs = [
     "mkdocs",
     "mkdocs-material",
     "mkdocstrings[python]",
+    "mkdocs-jupyter",
 ]