update notebooks, doc and remove unused files.

Author: mperez-cdf

docs/vertax.html

@@ -149,14 +149,8 @@ markers = ["long: marks tests as slow (deselect with '-m \"not slow\"')"]
 
 [dependency-groups]
 dev = [
-    "furo>=2025.12.19",
-    "myst-parser>=5.0.0",
+    "jupyterlab>=4.5.7",
     "pdoc>=16.0.0",
     "pytest>=8.4.2",
     "scalene>=1.5.55",
-    "sphinx>=9.0.4",
-    "sphinx-autoapi>=3.8.0",
-    "sphinx-autodoc-typehints>=3.6.1",
-    "sphinx-book-theme>=1.2.0",
-    "sphinx-copybutton>=0.5.2",
 ]

examples/pbc_from_image.ipynb

@@ -81,7 +81,7 @@ def create_optimizer() -> PbcBilevelOptimizer:
     bop.patience = 5
     bop.inner_solver = optax.sgd(learning_rate=0.01)
     bop.outer_solver = optax.adam(learning_rate=0.0001, nesterov=True)
-    bop.bilevel_optimization_method = BilevelOptimizationMethod.AUTOMATIC_DIFFERENTIATION
+    bop.bilevel_optimization_method = BilevelOptimizationMethod.ADJOINT_STATE
     bop.loss_function_outer = cost_v2v
     # bop.loss_function_outer = cost_v2v_ias
     return bop