fix

Author: soodoku

docs/api_reference.rst

@@ -57,7 +57,7 @@ Optimizers
 ----------
 
 SciPy Optimizer
-~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~
 
 .. autoclass:: pyppur.optimizers.ScipyOptimizer
    :members:
@@ -66,7 +66,7 @@ SciPy Optimizer
    :show-inheritance:
 
 Grid Optimizer
-~~~~~~~~~~~~~
+~~~~~~~~~~~~~~
 
 .. autoclass:: pyppur.optimizers.GridOptimizer
    :members:
@@ -75,7 +75,7 @@ Grid Optimizer
    :show-inheritance:
 
 Utility Functions
-----------------
+-----------------
 
 Metrics
 ~~~~~~~
@@ -86,25 +86,25 @@ Metrics
    :show-inheritance:
 
 Preprocessing
-~~~~~~~~~~~~
+~~~~~~~~~~~~~
 
 .. automodule:: pyppur.utils.preprocessing
    :members:
    :undoc-members:
    :show-inheritance:
 
 Visualization
-~~~~~~~~~~~~
+~~~~~~~~~~~~~
 
 .. automodule:: pyppur.utils.visualization
    :members:
    :undoc-members:
    :show-inheritance:
 
 Helper Functions
----------------
+----------------
 
 Normalization
-~~~~~~~~~~~~
+~~~~~~~~~~~~~
 
 .. autofunction:: pyppur.optimizers.scipy_optimizer.normalize_projection_directions

docs/examples.rst

@@ -4,7 +4,7 @@ Examples
 This section provides comprehensive examples of using pyppur for different scenarios.
 
 Basic Usage Examples
--------------------
+--------------------
 
 Distance Distortion Example
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -68,7 +68,7 @@ Distance Distortion Example
    plt.show()
 
 Reconstruction Examples
-~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: python
 
@@ -108,10 +108,10 @@ Reconstruction Examples
    print("Untied decoder shape:", pp_untied.decoder_weights_.shape)
 
 Advanced Examples
-----------------
+-----------------
 
 Parameter Sensitivity Analysis
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: python
 
@@ -161,7 +161,7 @@ Parameter Sensitivity Analysis
    plt.show()
 
 Comparison with Other Methods
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: python
 
@@ -237,7 +237,7 @@ Comparison with Other Methods
        print(f"{method}: {time_taken:.3f} seconds")
 
 Evaluation and Metrics
-~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: python
 
@@ -316,7 +316,7 @@ Working with Large Datasets
    print(f"Processed {X_scaled.shape[0]} samples in {pp_large.fit_time_:.2f} seconds")
 
 Custom Workflows
-~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~
 
 .. code-block:: python
 

docs/pyppur.objectives.rst

@@ -5,6 +5,7 @@ pyppur.objectives package
    :members:
    :undoc-members:
    :show-inheritance:
+   :no-index:
 
 Submodules
 ----------
@@ -17,6 +18,7 @@ pyppur.objectives.base module
    :undoc-members:
    :show-inheritance:
    :exclude-members: BaseObjective, Objective
+   :no-index:
 
 pyppur.objectives.distance module
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -26,6 +28,7 @@ pyppur.objectives.distance module
    :undoc-members:
    :show-inheritance:
    :exclude-members: DistanceObjective
+   :no-index:
 
 pyppur.objectives.reconstruction module
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -34,4 +37,5 @@ pyppur.objectives.reconstruction module
    :members:
    :undoc-members:
    :show-inheritance:
-   :exclude-members: ReconstructionObjective
+   :exclude-members: ReconstructionObjective
+   :no-index:

docs/pyppur.optimizers.rst

@@ -5,6 +5,7 @@ pyppur.optimizers package
    :members:
    :undoc-members:
    :show-inheritance:
+   :no-index:
 
 Submodules
 ----------
@@ -17,6 +18,7 @@ pyppur.optimizers.base module
    :undoc-members:
    :show-inheritance:
    :exclude-members: BaseOptimizer
+   :no-index:
 
 pyppur.optimizers.scipy_optimizer module
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -26,6 +28,7 @@ pyppur.optimizers.scipy_optimizer module
    :undoc-members:
    :show-inheritance:
    :exclude-members: ScipyOptimizer
+   :no-index:
 
 pyppur.optimizers.grid_optimizer module
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -34,4 +37,5 @@ pyppur.optimizers.grid_optimizer module
    :members:
    :undoc-members:
    :show-inheritance:
-   :exclude-members: GridOptimizer
+   :exclude-members: GridOptimizer
+   :no-index:

docs/pyppur.rst

@@ -5,6 +5,7 @@ pyppur package
    :members:
    :undoc-members:
    :show-inheritance:
+   :no-index:
 
 Subpackages
 -----------

docs/pyppur.utils.rst

@@ -16,6 +16,7 @@ pyppur.utils.metrics module
    :members:
    :undoc-members:
    :show-inheritance:
+   :no-index:
 
 pyppur.utils.preprocessing module
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -24,11 +25,13 @@ pyppur.utils.preprocessing module
    :members:
    :undoc-members:
    :show-inheritance:
+   :no-index:
 
 pyppur.utils.visualization module
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. automodule:: pyppur.utils.visualization
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
+   :no-index: