From 75256130a030e396af3008273b3ee19b194e309b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sophia=20M=C3=A4dler?=
 <15019107+sophiamaedler@users.noreply.github.com>
Date: Fri, 15 Nov 2024 17:43:29 +0100
Subject: [PATCH] add example notebook gallery

---
 docs/Makefile                             |  1 +
 docs/conf.py                              |  5 +--
 docs/index.rst                            |  1 +
 docs/pages/_notebook_sharded_hpa.nblink   |  3 ++
 docs/pages/_notebook_sharded_large.nblink |  3 ++
 docs/pages/example_notebooks.ipynb        | 44 +++++++++++++++++++++++
 examples/notebooks                        |  2 +-
 requirements_dev.txt                      |  1 +
 8 files changed, 57 insertions(+), 3 deletions(-)
 create mode 100644 docs/pages/_notebook_sharded_hpa.nblink
 create mode 100644 docs/pages/_notebook_sharded_large.nblink
 create mode 100644 docs/pages/example_notebooks.ipynb

diff --git a/docs/Makefile b/docs/Makefile
index 101acc4..868d46e 100644
--- a/docs/Makefile
+++ b/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/*
diff --git a/docs/conf.py b/docs/conf.py
index 1243d42..5b345ac 100644
--- a/docs/conf.py
+++ b/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",
diff --git a/docs/index.rst b/docs/index.rst
index 839fcd1..a6ed7cf 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -58,6 +58,7 @@ Documentation
    :caption: Code Examples
 
    auto_examples/code_snippets/index
+   pages/example_notebooks.ipynb
 
 .. toctree::
    :maxdepth: 2
diff --git a/docs/pages/_notebook_sharded_hpa.nblink b/docs/pages/_notebook_sharded_hpa.nblink
new file mode 100644
index 0000000..0b2a521
--- /dev/null
+++ b/docs/pages/_notebook_sharded_hpa.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../examples/notebooks/example_projects/example_2/processing_notebook.ipynb"
+}
\ No newline at end of file
diff --git a/docs/pages/_notebook_sharded_large.nblink b/docs/pages/_notebook_sharded_large.nblink
new file mode 100644
index 0000000..ac0bd20
--- /dev/null
+++ b/docs/pages/_notebook_sharded_large.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../examples/notebooks/example_projects/example_1/processing_notebook_sharded.ipynb"
+}
\ No newline at end of file
diff --git a/docs/pages/example_notebooks.ipynb b/docs/pages/example_notebooks.ipynb
new file mode 100644
index 0000000..34130b5
--- /dev/null
+++ b/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
+}
diff --git a/examples/notebooks b/examples/notebooks
index e8da8c8..3b8c935 160000
--- a/examples/notebooks
+++ b/examples/notebooks
@@ -1 +1 @@
-Subproject commit e8da8c863d5f9da93805658ccd0c61761aa84f44
+Subproject commit 3b8c935e7f8f4d5559c2a4e1d08b21698212451d
diff --git a/requirements_dev.txt b/requirements_dev.txt
index 447430a..0081ee4 100644
--- a/requirements_dev.txt
+++ b/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