shb84 · shb84 · Nov 29, 2025 · Nov 29, 2025 · Nov 29, 2025 · Nov 29, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,7 @@ build: Changes to the build process or tools.
 ### Test 
 
 - Updated optimization tests to reflect line search changes
+- Updated unit tests to reflect changes to synthetic data functions  
 
 ### Build
 
@@ -40,16 +41,15 @@ build: Changes to the build process or tools.
 - Simplified CONTRIBUTING 
 - Updated docs to include API changes
 
-# Refactor
+### Refactor
 
-- Changed model API by moving module `model.py` into `core` 
-- Changed plotting API (instead of `jenn.utils.plot.something()` it is now `jenn.plot_something()`)
-- Moved all plotting functions into their own modules inside `post_processsing`
-- Renamed all plotting algorithms and tweaked signatures 
-- Modified convergence history plotting to control log-scale of each axis 
-- Modified contour plotting to allow index selection of which inputs and outputs to plot 
-- Added function to plot histogram of prediction error 
-- Updated goodness of fit summary plot to also include prediction error distribution 
+- Changed API by moving module `model.py` into `core` 
+- Changed API by moving module `synthetic.py` into `synthetic_data` (synthetic functions are now modules not classes)
+- Changed API by moving module `plot` into `post_processing` 
+  - _Instead of `jenn.utils.plot.something()` it is now `jenn.plot_something()`_
+  - _Modified signature and tweaked almost all plotting functions (adjusted notebooks accordingly)_
+  - _Added plotting function to display histogram of prediction error (and added it to goodness of fit summary plots)_
+- Changed name of `utils` to `utilities` and added `_sample.py` and `_finite_difference.py` modules
 
 ## v1.0.8 (2024-06-26)
 

diff --git a/docs/examples/.ipynb_checkpoints/demo_1_sinusoid-checkpoint.ipynb b/docs/examples/.ipynb_checkpoints/demo_1_sinusoid-checkpoint.ipynb
diff --git a/docs/examples/.ipynb_checkpoints/demo_2_rastrigin-checkpoint.ipynb b/docs/examples/.ipynb_checkpoints/demo_2_rastrigin-checkpoint.ipynb
diff --git a/docs/examples/.ipynb_checkpoints/demo_4_rosenbrock-checkpoint.ipynb b/docs/examples/.ipynb_checkpoints/demo_4_rosenbrock-checkpoint.ipynb
diff --git a/docs/examples/demo_1_sinusoid.ipynb b/docs/examples/demo_1_sinusoid.ipynb
diff --git a/docs/examples/demo_2_rastrigin.ipynb b/docs/examples/demo_2_rastrigin.ipynb
diff --git a/docs/examples/demo_4_rosenbrock.ipynb b/docs/examples/demo_4_rosenbrock.ipynb
diff --git a/docs/examples/sbo_contours.pdf b/docs/examples/sbo_contours.pdf
diff --git a/docs/examples/sbo_convergence.pdf b/docs/examples/sbo_convergence.pdf
diff --git a/docs/source/sections/api.rst b/docs/source/sections/api.rst
@@ -7,7 +7,10 @@ This section describes the main API users are expected to interact with.
 .. automodule:: jenn
    :members:
 
-.. automodule:: jenn.synthetic
+.. automodule:: jenn.synthetic_data
+   :members:
+
+.. automodule:: jenn.utilities
    :members:
 
 Core API

diff --git a/notebooks/noisy_partials.ipynb b/notebooks/noisy_partials.ipynb
@@ -65,26 +65,29 @@
    "source": [
     "def generate_training_data(step_size: float = 1e-6, seed: int = 123):\n",
     "    \"\"\"Generate training data using finite difference.\"\"\"\n",
-    "    test_function = jenn.synthetic.Rastrigin\n",
     "    lb = (-1.0, -1.0)\n",
     "    ub = (1.5, 1.5)\n",
-    "    X_train, Y_train, J_train = test_function.sample(\n",
+    "    X_train, Y_train, J_train = jenn.utilities.sample(\n",
+    "        f=jenn.synthetic_data.rastrigin.compute,\n",
+    "        f_prime=jenn.synthetic_data.rastrigin.compute_partials,\n",
     "        m_random=100,\n",
     "        m_levels=0,\n",
     "        lb=lb,\n",
     "        ub=ub,\n",
-    "        dx=None,\n",
     "        random_state=seed,\n",
     "    )  # analytical partials\n",
-    "    X_train_FD, Y_train_FD, J_train_FD = test_function.sample(\n",
+    "    X_train_FD, Y_train_FD, J_train_FD = jenn.utilities.sample(\n",
+    "        f=jenn.synthetic_data.rastrigin.compute,\n",
     "        m_random=100,\n",
     "        m_levels=0,\n",
     "        lb=lb,\n",
     "        ub=ub,\n",
-    "        dx=step_size,\n",
+    "        dx=step_size,  # triggers finite difference\n",
     "        random_state=seed,\n",
-    "    )  # finite difference\n",
-    "    X_test, Y_test, J_test = test_function.sample(\n",
+    "    )\n",
+    "    X_test, Y_test, J_test = jenn.utilities.sample(\n",
+    "        f=jenn.synthetic_data.rastrigin.compute,\n",
+    "        f_prime=jenn.synthetic_data.rastrigin.compute_partials,\n",
     "        m_random=0,\n",
     "        m_levels=10,\n",
     "        lb=lb,\n",
@@ -162,7 +165,7 @@
    },
    "outputs": [],
    "source": [
-    "model, r2 = fit_rastrigin(step_size=None, gamma=1.0)"
+    "model, r2 = fit_rastrigin(gamma=1.0)"
    ]
   },
   {

diff --git a/src/jenn/__init__.py b/src/jenn/__init__.py
@@ -2,7 +2,7 @@
 # Copyright (C) 2018 Steven H. Berguin
 # This work is licensed under the MIT License.
 
-from . import core, synthetic, utils  # TODO: remove
+from . import core, synthetic_data, utilities
 from .core.model import NeuralNet
 from .post_processing import (
     metrics,
@@ -29,6 +29,6 @@
     "plot_histogram",
     "plot_residual_by_predicted",
     "plot_sensitivity_profiles",
-    "synthetic",
-    "utils",
+    "synthetic_data",
+    "utilities",
 ]