fix doc build

Author: dionhaefner

docs/conf.py

@@ -12,6 +12,8 @@
 
 from tesseract_jax import __version__
 
+here = Path(__file__).parent.resolve()
+
 project = "Tesseract-JAX"
 copyright = "2025, Pasteur Labs"
 author = "The Tesseract-JAX Team @ Pasteur Labs + OSS contributors"
@@ -78,8 +80,9 @@
 # Do not execute notebooks during build (just take existing output)
 nb_execution_mode = "off"
 
-# Copy example notebooks to demo_notebooks folder on every build
-for example_notebook in Path("../examples").glob("*/demo.ipynb"):
-    # Copy the example notebook to the docs folder
-    dest = (Path("demo_notebooks") / example_notebook.parent.name).with_suffix(".ipynb")
-    shutil.copyfile(example_notebook, dest)
+# Copy example notebooks to docs/examples folder on every build
+for example_dir in Path("../examples").glob("*/"):
+    # Copy the example directory to the docs folder
+    shutil.copytree(
+        example_dir, here / "examples" / example_dir.name, dirs_exist_ok=True
+    )

docs/demo_notebooks/.gitignore

@@ -0,0 +1,2 @@
+**/*
+!.gitignore

docs/examples/.gitignore

@@ -13,7 +13,7 @@ def vector_sum(x, y):
 jax.grad(vector_sum)(x, y) # 🎉
 ```
 
-Want to learn more? See how to [get started](content/get-started.md) with Tesseract-JAX, explore the [API reference](content/api.md), or learn by [example](demo_notebooks/simple.ipynb).
+Want to learn more? See how to [get started](content/get-started.md) with Tesseract-JAX, explore the [API reference](content/api.md), or learn by [example](examples/simple/demo.ipynb).
 
 ## License
 
@@ -36,8 +36,9 @@ content/api
 :maxdepth: 2
 :hidden:
 
-demo_notebooks/simple.ipynb
-demo_notebooks/cfd.ipynb
+examples/simple/demo.ipynb
+examples/cfd/demo.ipynb
+examples/fem-shapeopt/demo.ipynb
 ```
 
 ```{toctree}