Black formatter (#278)

Author: ndem0

docs/source/installation.rst

@@ -11,7 +11,6 @@ EZyRB requires:
 - scipy
 - matplotlib
 - scikit-learn
-- torch (for neural network-based methods)
 
 Install via pip
 ---------------

ezyrb/__init__.py

@@ -1,11 +1,24 @@
 """EZyRB package"""
 
 __all__ = [
-    'Database', 'Snapshot', 'Reduction', 'POD', 'Approximation', 'RBF',
-    'Linear', 'GPR', 'ANN', 'KNeighborsRegressor',
-    'RadiusNeighborsRegressor', 'AE', 'ReducedOrderModel', 'PODAE',
-    'RegularGrid', 'MultiReducedOrderModel', 'SklearnApproximation',
-    'SklearnReduction'
+    "Database",
+    "Snapshot",
+    "Reduction",
+    "POD",
+    "Approximation",
+    "RBF",
+    "Linear",
+    "GPR",
+    "ANN",
+    "KNeighborsRegressor",
+    "RadiusNeighborsRegressor",
+    "AE",
+    "ReducedOrderModel",
+    "PODAE",
+    "RegularGrid",
+    "MultiReducedOrderModel",
+    "SklearnApproximation",
+    "SklearnReduction",
 ]
 
 from .database import Database

ezyrb/approximation/__init__.py

@@ -1,9 +1,14 @@
 """EZyRB package"""
 
 __all__ = [
-    'Approximation', 'RBF', 'Linear', 'GPR',
-    'ANN', 'KNeighborsRegressor', 'RadiusNeighborsRegressor',
-    'SklearnApproximation'
+    "Approximation",
+    "RBF",
+    "Linear",
+    "GPR",
+    "ANN",
+    "KNeighborsRegressor",
+    "RadiusNeighborsRegressor",
+    "SklearnApproximation",
 ]
 
 from .approximation import Approximation

ezyrb/approximation/ann.py

@@ -46,7 +46,16 @@ class ANN(Approximation):
         >>> print(y_pred)
         >>> print(len(ann.loss_trend))
         >>> print(ann.loss_trend[-1])
+
+    .. note::
+        This module provides a wrapper around sklearn's MLPRegressor for
+        multidimensional function approximation using feed-forward neural
+        networks. It is not intended for deep learning tasks, but rather for
+        approximating functions based on given data points. For more advanced
+        deep learning applications, consider using dedicated libraries such as
+        :ref:`PINA`.
     """
+
     def __init__(
         self,
         layers,

ezyrb/approximation/approximation.py

@@ -10,6 +10,7 @@ class Approximation(ABC):
     All the classes that implement the input-output mapping should be inherited
     from this class.
     """
+
     @abstractmethod
     def fit(self, points, values):
         """Abstract `fit`"""

ezyrb/approximation/gpr.py

@@ -1,6 +1,7 @@
 """
 Module wrapper exploiting `GPy` for Gaussian Process Regression
 """
+
 import logging
 import numpy as np
 from scipy.optimize import minimize
@@ -40,19 +41,24 @@ class GPR(Approximation):
         >>> print(np.allclose(y, y_pred))
 
     """
+
     def __init__(self, kern=None, normalizer=True, optimization_restart=20):
         """
         Initialize a Gaussian Process Regressor.
-        
+
         :param kern: Kernel object from sklearn. Default is None.
         :param bool normalizer: Whether to normalize values. Default is True.
         :param int optimization_restart: Number of restarts for optimization.
             Default is 20.
         """
 
-        logger.debug("Initializing GPR with kernel=%s, normalizer=%s, "
-                     "optimization_restart=%d",
-                     kern, normalizer, optimization_restart)
+        logger.debug(
+            "Initializing GPR with kernel=%s, normalizer=%s, "
+            "optimization_restart=%d",
+            kern,
+            normalizer,
+            optimization_restart,
+        )
         self.X_sample = None
         self.Y_sample = None
         self.kern = kern
@@ -67,8 +73,11 @@ def fit(self, points, values):
         :param array_like points: the coordinates of the points.
         :param array_like values: the values in the points.
         """
-        logger.debug("Fitting GPR with points shape: %s, values shape: %s",
-                     np.array(points).shape, np.array(values).shape)
+        logger.debug(
+            "Fitting GPR with points shape: %s, values shape: %s",
+            np.array(points).shape,
+            np.array(values).shape,
+        )
         self.X_sample = np.array(points)
         self.Y_sample = np.array(values)
         if self.X_sample.ndim == 1:
@@ -80,8 +89,10 @@ def fit(self, points, values):
 
         logger.debug("Creating GaussianProcessRegressor")
         self.model = GaussianProcessRegressor(
-            kernel=self.kern, n_restarts_optimizer=self.optimization_restart,
-            normalize_y=self.normalizer)
+            kernel=self.kern,
+            n_restarts_optimizer=self.optimization_restart,
+            normalize_y=self.normalizer,
+        )
         self.model.fit(self.X_sample, self.Y_sample)
         logger.info("GPR fitted successfully")
 
@@ -118,14 +129,14 @@ def optimal_mu(self, bounds, optimization_restart=10):
         def min_obj(X):
             return -1 * np.linalg.norm(self.predict(X.reshape(1, -1), True)[1])
 
-        initial_starts = np.random.uniform(bounds[:, 0],
-                                           bounds[:, 1],
-                                           size=(optimization_restart, dim))
+        initial_starts = np.random.uniform(
+            bounds[:, 0], bounds[:, 1], size=(optimization_restart, dim)
+        )
 
         # Find the best optimum by starting from n_restart different random
         # points.
         for x0 in initial_starts:
-            res = minimize(min_obj, x0, bounds=bounds, method='L-BFGS-B')
+            res = minimize(min_obj, x0, bounds=bounds, method="L-BFGS-B")
 
             if res.fun < min_val:
                 min_val = res.fun

ezyrb/approximation/kneighbors_regressor.py

@@ -14,9 +14,9 @@ class KNeighborsRegressor(NeighborsRegressor):
 
     :param kwargs: arguments passed to the internal instance of
         KNeighborsRegressor.
-    
+
     :Example:
-    
+
         >>> import numpy as np
         >>> from ezyrb import KNeighborsRegressor
         >>> x = np.random.uniform(-1, 1, size=(20, 2))
@@ -26,12 +26,14 @@ class KNeighborsRegressor(NeighborsRegressor):
         >>> new_x = np.array([[0.5, 0.5]])
         >>> y_pred = knn.predict(new_x)
     """
+
     def __init__(self, **kwargs):
         """
         Initialize a K-Neighbors Regressor.
-        
+
         :param kwargs: Arguments passed to sklearn's KNeighborsRegressor.
         """
-        logger.debug("Initializing KNeighborsRegressor with kwargs: %s",
-                     kwargs)
+        logger.debug(
+            "Initializing KNeighborsRegressor with kwargs: %s", kwargs
+        )
         self.regressor = Regressor(**kwargs)

ezyrb/approximation/linear.py

@@ -20,10 +20,11 @@ class Linear(Approximation):
         of the convex hull of the input points. If not provided, then the
         default is numpy.nan.
     """
+
     def __init__(self, fill_value=np.nan):
         """
         Initialize a Linear interpolator.
-        
+
         :param float fill_value: Value for points outside the convex hull.
             Default is numpy.nan.
         """
@@ -38,33 +39,41 @@ def fit(self, points, values):
         :param array_like points: the coordinates of the points.
         :param array_like values: the values in the points.
         """
-        logger.debug("Fitting Linear with points shape: %s, "
-                     "values shape: %s",
-                     np.array(points).shape, np.array(values).shape)
+        logger.debug(
+            "Fitting Linear with points shape: %s, " "values shape: %s",
+            np.array(points).shape,
+            np.array(values).shape,
+        )
         # the first dimension is the list of parameters, the second one is
         # the dimensionality of each tuple of parameters (we look for
         # parameters of dimensionality one)
         as_np_array = np.array(points)
         if not np.issubdtype(as_np_array.dtype, np.number):
             logger.error("Invalid points format/dimension")
-            raise ValueError('Invalid format or dimension for the argument'
-                             '`points`.')
+            raise ValueError(
+                "Invalid format or dimension for the argument" "`points`."
+            )
 
         if as_np_array.shape[-1] == 1:
             as_np_array = np.squeeze(as_np_array, axis=-1)
             logger.debug("Squeezed points array")
 
-        if as_np_array.ndim == 1 or (as_np_array.ndim == 2
-                                     and as_np_array.shape[1] == 1):
+        if as_np_array.ndim == 1 or (
+            as_np_array.ndim == 2 and as_np_array.shape[1] == 1
+        ):
             logger.debug("Using 1D interpolation")
-            self.interpolator = interp1d(as_np_array, values, axis=0,
-                                         bounds_error=False,
-                                         fill_value=self.fill_value)
+            self.interpolator = interp1d(
+                as_np_array,
+                values,
+                axis=0,
+                bounds_error=False,
+                fill_value=self.fill_value,
+            )
         else:
             logger.debug("Using ND interpolation")
-            self.interpolator = LinearNDInterp(points,
-                                               values,
-                                               fill_value=self.fill_value)
+            self.interpolator = LinearNDInterp(
+                points, values, fill_value=self.fill_value
+            )
         logger.info("Linear fitted successfully")
 
     def predict(self, new_point):

ezyrb/approximation/neighbors_regressor.py

@@ -7,14 +7,14 @@
 class NeighborsRegressor(Approximation):
     """
     A generic superclass for wrappers of *NeighborsRegressor from sklearn.
-    
+
     This class provides a common interface for neighbor-based regression methods.
 
     :param kwargs: Arguments passed to the internal instance of
         *NeighborsRegressor.
-    
+
     :Example:
-    
+
         >>> import numpy as np
         >>> from ezyrb import KNeighborsRegressor
         >>> x = np.random.uniform(-1, 1, size=(20, 2))
@@ -23,6 +23,7 @@ class NeighborsRegressor(Approximation):
         >>> knn.fit(x, y)
         >>> y_pred = knn.predict(x[:5])
     """
+
     def fit(self, points, values):
         """
         Construct the interpolator given `points` and `values`.

ezyrb/approximation/radius_neighbors_regressor.py

@@ -11,9 +11,9 @@ class RadiusNeighborsRegressor(NeighborsRegressor):
 
     :param kwargs: arguments passed to the internal instance of
         RadiusNeighborsRegressor.
-    
+
     :Example:
-    
+
         >>> import numpy as np
         >>> from ezyrb import RadiusNeighborsRegressor
         >>> x = np.random.uniform(-1, 1, size=(20, 2))
@@ -23,10 +23,11 @@ class RadiusNeighborsRegressor(NeighborsRegressor):
         >>> new_x = np.array([[0.0, 0.0]])
         >>> y_pred = rnn.predict(new_x)
     """
+
     def __init__(self, **kwargs):
         """
         Initialize a Radius Neighbors Regressor.
-        
+
         :param kwargs: Arguments passed to sklearn's RadiusNeighborsRegressor.
         """
         self.regressor = Regressor(**kwargs)