add example notebook gallery

docs/Makefile

@@ -23,6 +23,7 @@ help:
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 clean:
+		rm -rf $(SOURCEDIR)/auto_examples
 		rm -rf $(BUILDDIR)/html/*
 		rm -rf $(BUILDDIR)/latex/*
 		rm -rf $(BUILDDIR)/doctrees/*

docs/conf.py

@@ -34,6 +34,7 @@ def setup(app):
     "sphinxarg.ext",
     "sphinx_rtd_theme",
     "nbsphinx",
+    "nbsphinx_link",
     "sphinx_design",
     "sphinx_copybutton",
     "sphinx_gallery.gen_gallery"
@@ -92,8 +93,8 @@ def setup(app):
 html_logo = "_static/scPortrait_logo_light.svg"
 
 #set up sphinx gallery
-sg_examples_dir = ["../examples/code_snippets"]
-sg_gallery_dir = ["auto_examples/code_snippets"]
+sg_examples_dir = ["../examples/code_snippets",]
+sg_gallery_dir = ["auto_examples/code_snippets",]
 
 sphinx_gallery_conf = {
     "doc_module": "scportrait",

docs/index.rst

@@ -58,6 +58,7 @@ Documentation
    :caption: Code Examples
 
    auto_examples/code_snippets/index
+   pages/example_notebooks.ipynb
 
 .. toctree::
    :maxdepth: 2

docs/pages/_notebook_sharded_hpa.nblink

@@ -0,0 +1,3 @@
+{
+    "path": "../../examples/notebooks/example_projects/example_2/processing_notebook.ipynb"
+}

docs/pages/_notebook_sharded_large.nblink

@@ -0,0 +1,3 @@
+{
+    "path": "../../examples/notebooks/example_projects/example_1/processing_notebook_sharded.ipynb"
+}

docs/pages/example_notebooks.ipynb

@@ -0,0 +1,44 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Example Projects"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "tags": [
+     "nbsphinx-gallery"
+    ]
+   },
+   "source": [
+    "* [Sharded Cellpose Segmentation](_notebook_sharded_large.nblink)\n",
+    "* [Sharded Cellpose Segmentation on human protein atlas images](_notebook_sharded_hpa.nblink)\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.11.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

requirements_dev.txt

@@ -43,6 +43,7 @@ sphinx
 sphinx-argparse
 sphinx-rtd-theme==2.0.0
 nbsphinx
+nbsphinx-link
 sphinx-book-theme
 sphinx-design
 sphinx-copybutton