Merge pull request #101 from Pressio/fix_99

Remove "Abstract" from "AbstractXYZ" class names

Author: eparish1

romtools/__init__.py

@@ -80,7 +80,7 @@
 
 ## Representative abstract base classes
 
-- `AbstractTrialSpace`
+- `TrialSpace`
   - This class defines the minimum API requirements for a trial space
 
   - Constructing a trial space relies on utilities like truncaters, orthogonalizers, etc. Abstract classes, and
@@ -92,7 +92,7 @@
       - splitters
       - truncaters
 
-- `AbstractParameterSpace`
+- `ParameterSpace`
   - This class defines the minimum API of a parameter space. These parameter spaces are used in workflows for
     running/building ROMs
 

romtools/hyper_reduction/ecsw.py

@@ -81,7 +81,7 @@
 import numpy as np
 
 
-class AbstractECSWsolver(abc.ABC):
+class ECSWsolver(abc.ABC):
     '''
     Abstract base class for ECSW solvers
 
@@ -129,7 +129,7 @@ def __call__(self, full_mesh_lhs: np.ndarray, full_mesh_rhs: np.array, tolerance
 #       this function because tau can't be specified
 
 
-class ECSWsolverNNLS(AbstractECSWsolver):
+class ECSWsolverNNLS(ECSWsolver):
     '''
     Given a linear system with left-hand side full_mesh_lhs and right-hand side full_mesh_rhs compute sample mesh indices and weights for ECSW using the non-negative least squares algorithm from Chapman et al. 2016
     DOI: 10.1002/nme.5332.
@@ -330,7 +330,7 @@ def _construct_linear_system(residual_snapshots: np.ndarray,
     return full_mesh_lhs, full_mesh_rhs
 
 
-def ecsw_fixed_test_basis(ecsw_solver: AbstractECSWsolver,
+def ecsw_fixed_test_basis(ecsw_solver: ECSWsolver,
                           residual_snapshots: np.ndarray,
                           test_basis: np.ndarray,
                           n_var: int,
@@ -340,7 +340,7 @@ def ecsw_fixed_test_basis(ecsw_solver: AbstractECSWsolver,
     ECSW implementation for a fixed test basis, such as POD-Galerkin projection
 
     Args:
-        ecsw_solver: AbstractECSWsolver object corresponding to a child class with concrete implementations such as ECSWsolverNNLS.
+        ecsw_solver: ECSWsolver object corresponding to a child class with concrete implementations such as ECSWsolverNNLS.
         residual_snapshots: (n_dof*n_var, n_snap) numpy ndarray, where n_dof is the number of mesh degrees of freedom (DoFs) (nodes, volumes, or elements), n_var is the number of residual variables, and n_snap is the number of snapshots
         test_basis: (n_dof*n_var, n_mode) numpy ndarray, where n_mode is the number of modes in the basis.
         n_var: int, the number of residual variables (e.g. for fluid flow, residual variable could be mass, x-momentum, y-momentum, z-momentum, and energy)
@@ -361,15 +361,15 @@ def ecsw_fixed_test_basis(ecsw_solver: AbstractECSWsolver,
 
     return ecsw_solver(full_mesh_lhs, full_mesh_rhs, tolerance)
 
-def ecsw_varying_test_basis(ecsw_solver: AbstractECSWsolver,
+def ecsw_varying_test_basis(ecsw_solver: ECSWsolver,
                             full_mesh_lhs: np.ndarray,
                             full_mesh_rhs: np.ndarray,
                             tolerance: np.double):
     '''
     ECSW implementation for a varying test basis, such as Least-Squares Petrov-Galerkin projection
 
     Args:
-        ecsw_solver: AbstractECSWsolver object corresponding to a child class with concrete implementations such as ECSWsolverNNLS.
+        ecsw_solver: ECSWsolver object corresponding to a child class with concrete implementations such as ECSWsolverNNLS.
         full_mesh_lhs: (n_snap*n_rom, n_dof) numpy ndarray, where n_snap is the number of residual snapshots, n_rom is the ROM dimension, and n_dof is the number of mesh degrees of freedom (DoFs) (nodes, volumes, or elements)
         full_mesh_rhs: (n_snap*n_rom,) numpy array
         tolerance: Double, the ECSW tolerance parameter. Lower values of tolerance will result in more mesh DoF samples

romtools/trial_space.py

@@ -65,14 +65,14 @@
 
 import abc
 import numpy as np
-from romtools.trial_space_utils.truncater import AbstractTruncater, NoOpTruncater
-from romtools.trial_space_utils.shifter import AbstractShifter, NoOpShifter
-from romtools.trial_space_utils.scaler import AbstractScaler
-from romtools.trial_space_utils.splitter import AbstractSplitter, NoOpSplitter
-from romtools.trial_space_utils.orthogonalizer import AbstractOrthogonalizer, NoOpOrthogonalizer
+from romtools.trial_space_utils.truncater import Truncater, NoOpTruncater
+from romtools.trial_space_utils.shifter import Shifter, NoOpShifter
+from romtools.trial_space_utils.scaler import Scaler
+from romtools.trial_space_utils.splitter import Splitter, NoOpSplitter
+from romtools.trial_space_utils.orthogonalizer import Orthogonalizer, NoOpOrthogonalizer
 
 
-class AbstractTrialSpace(abc.ABC):
+class TrialSpace(abc.ABC):
     '''
     Abstract base class for trial space implementations.
 
@@ -142,7 +142,7 @@ def matrix_to_tensor(n_var, matrix_input):
     return output_matrix
 
 
-class DictionaryTrialSpace(AbstractTrialSpace):
+class DictionaryTrialSpace(TrialSpace):
     '''
     ##Reduced basis trial space (no truncation).
 
@@ -205,7 +205,7 @@ def get_basis(self):
         return self.__basis
 
 
-class TrialSpaceFromPOD(AbstractTrialSpace):
+class TrialSpaceFromPOD(TrialSpace):
     '''
     ##POD trial space (constructed via SVD).
 
@@ -225,20 +225,20 @@ class TrialSpaceFromPOD(AbstractTrialSpace):
 
     def __init__(self,
                  snapshot_tensor,
-                 truncater:      AbstractTruncater      = NoOpTruncater(),
-                 shifter:        AbstractShifter        = NoOpShifter(),
-                 splitter:       AbstractSplitter       = NoOpSplitter(),
-                 orthogonalizer: AbstractOrthogonalizer = NoOpOrthogonalizer(),
+                 truncater:      Truncater      = NoOpTruncater(),
+                 shifter:        Shifter        = NoOpShifter(),
+                 splitter:       Splitter       = NoOpSplitter(),
+                 orthogonalizer: Orthogonalizer = NoOpOrthogonalizer(),
                  svdFnc = None):
         '''
         Constructor for the POD trial space.
 
         Args:
             snapshot_tensor (np.ndarray): Snapshot data tensor
-            truncater (AbstractTruncater): Class that truncates the basis.
-            shifter (AbstractShifter): Class that shifts the basis.
-            splitter (AbstractSplitter): Class that splits the basis.
-            orthogonalizer (AbstractOrthogonalizer): Class that orthogonalizes
+            truncater (Truncater): Class that truncates the basis.
+            shifter (Shifter): Class that shifts the basis.
+            splitter (Splitter): Class that splits the basis.
+            orthogonalizer (Orthogonalizer): Class that orthogonalizes
                 the basis.
             svdFnc: a callable to use for computing the SVD on the snapshots data.
                 IMPORTANT: must conform to the API of [np.linalg.svd](https://numpy.org/doc/stable/reference/generated/numpy.linalg.svd.html#numpy-linalg-svd).
@@ -296,7 +296,7 @@ def get_basis(self):
         return self.__basis
 
 
-class TrialSpaceFromScaledPOD(AbstractTrialSpace):
+class TrialSpaceFromScaledPOD(TrialSpace):
     '''
     ##POD trial space (constructed via scaled SVD).
 
@@ -315,11 +315,11 @@ class TrialSpaceFromScaledPOD(AbstractTrialSpace):
     '''
 
     def __init__(self, snapshot_tensor,
-                 truncater: AbstractTruncater,
-                 shifter: AbstractShifter,
-                 scaler: AbstractScaler,
-                 splitter: AbstractSplitter,
-                 orthogonalizer: AbstractOrthogonalizer):
+                 truncater: Truncater,
+                 shifter: Shifter,
+                 scaler: Scaler,
+                 splitter: Splitter,
+                 orthogonalizer: Orthogonalizer):
         '''
         Constructor for the POD trial space constructed via scaled SVD.
 

romtools/trial_space_utils/orthogonalizer.py

@@ -58,7 +58,7 @@
 import scipy.sparse
 
 
-class AbstractOrthogonalizer(abc.ABC):
+class Orthogonalizer(abc.ABC):
     '''
     Abstract base class
     '''
@@ -68,7 +68,7 @@ def __call__(self, my_array: np.ndarray) -> np.ndarray:
         pass
 
 
-class NoOpOrthogonalizer(AbstractOrthogonalizer):
+class NoOpOrthogonalizer(Orthogonalizer):
     '''
     No op class (doesn't do anything)
     '''
@@ -79,7 +79,7 @@ def __call__(self, my_array: np.ndarray):
         return my_array
 
 
-class EuclideanL2Orthogonalizer(AbstractOrthogonalizer):
+class EuclideanL2Orthogonalizer(Orthogonalizer):
     '''
     Orthogonalizes the basis in the standard Euclidean L2 inner product, i.e.,
     the output basis will satisfy
@@ -104,7 +104,7 @@ def __call__(self, my_array: np.ndarray):
         return my_array
 
 
-class EuclideanVectorWeightedL2Orthogonalizer(AbstractOrthogonalizer):
+class EuclideanVectorWeightedL2Orthogonalizer(Orthogonalizer):
     '''
     Orthogonalizes the basis in vector-weighted Euclidean L2 inner product,
     i.e., the output basis will satisfy

romtools/trial_space_utils/outputter.py

@@ -46,7 +46,7 @@
 import os
 import math
 import numpy as np
-from romtools.trial_space import AbstractTrialSpace
+from romtools.trial_space import TrialSpace
 
 try:
     import exodus
@@ -59,13 +59,13 @@
     pass
 
 
-def npz_output(filename: str, trial_space: AbstractTrialSpace, compress=True) -> None:
+def npz_output(filename: str, trial_space: TrialSpace, compress=True) -> None:
     '''
     Save trial space information to a compressed or uncompressed NumPy .npz file.
 
     Args:
         filename (str): The name of the output file.
-        trial_space (AbstractTrialSpace): The trial space containing shift and basis information.
+        trial_space (TrialSpace): The trial space containing shift and basis information.
         compress (bool, optional): Whether to compress the output file (default is True).
 
     Example:
@@ -81,13 +81,13 @@ def npz_output(filename: str, trial_space: AbstractTrialSpace, compress=True) ->
                  basis=trial_space.get_basis())
 
 
-def hdf5_output(output_filename: str, trial_space: AbstractTrialSpace) -> None:
+def hdf5_output(output_filename: str, trial_space: TrialSpace) -> None:
     '''
     Save trial space information to an HDF5 file.
 
     Args:
         output_filename (str): The name of the output HDF5 file.
-        trial_space (AbstractTrialSpace): The trial space containing shift and basis information.
+        trial_space (TrialSpace): The trial space containing shift and basis information.
 
     Example:
         hdf5_output("trial_space.h5", my_trial_space)
@@ -97,14 +97,14 @@ def hdf5_output(output_filename: str, trial_space: AbstractTrialSpace) -> None:
         f.create_dataset('basis', data=trial_space.get_basis())
 
 
-def exodus_ouput(output_filename: str, mesh_filename: str, trial_space: AbstractTrialSpace, var_names: list = None) -> None:
+def exodus_ouput(output_filename: str, mesh_filename: str, trial_space: TrialSpace, var_names: list = None) -> None:
     '''
     Save trial space information to an Exodus file.
 
     Args:
         output_filename (str): The name of the output Exodus file.
         mesh_filename (str): The name of the mesh file.
-        trial_space (AbstractTrialSpace): The trial space containing shift and basis information.
+        trial_space (TrialSpace): The trial space containing shift and basis information.
         var_names (list, optional): A list of variable names (default is None).
 
     Example:

romtools/trial_space_utils/scaler.py

@@ -75,7 +75,7 @@
 import numpy as np
 
 
-class AbstractScaler(abc.ABC):
+class Scaler(abc.ABC):
     '''
     Abstract base class
     '''
@@ -95,7 +95,7 @@ def post_scaling(self, data_tensor: np.ndarray) -> np.ndarray:
         pass
 
 
-class NoOpScaler(AbstractScaler):
+class NoOpScaler(Scaler):
     '''
     No op implementation
     '''
@@ -109,7 +109,7 @@ def post_scaling(self, data_tensor):
         return data_tensor
 
 
-class VectorScaler(AbstractScaler):
+class VectorScaler(Scaler):
     '''
     Concrete implementation designed to scale snapshot matrices by a vector.
     For a snapshot tensor $\\mathbf{S} \\in \\mathbb{R}^{N_{\\mathrm{u}} \\times N \\times K}$, the VectorScaler
@@ -162,7 +162,7 @@ def post_scaling(self, data_tensor):
         return self.__scaling_vector_matrix[None, :, None] * data_tensor
 
 
-class VariableScaler(AbstractScaler):
+class VariableScaler(Scaler):
     '''
     Concrete implementation designed for snapshot matrices involving multiple
     state variables.
@@ -259,7 +259,7 @@ def post_scaling(self, data_tensor):
         return data_tensor
 
 
-class VariableAndVectorScaler(AbstractScaler):
+class VariableAndVectorScaler(Scaler):
     '''
     Concrete implementation designed to scale snapshot matrices involving
     multiple state variables by both the variable magnitudes and an additional

romtools/trial_space_utils/shifter.py

@@ -63,7 +63,7 @@
 import numpy as np
 
 
-class AbstractShifter(abc.ABC):
+class Shifter(abc.ABC):
     '''
     Abstract implmentation
     '''
@@ -76,7 +76,7 @@ def __call__(self, my_array: np.ndarray) -> Tuple[np.ndarray, np.ndarray]:
         pass
 
 
-class NoOpShifter(AbstractShifter):
+class NoOpShifter(Shifter):
     '''
     No op implementation
     '''
@@ -88,7 +88,7 @@ def __call__(self, my_array: np.ndarray):
         return my_array, shift_vector
 
 
-class ConstantShifter(AbstractShifter):
+class ConstantShifter(Shifter):
     '''
     Shifts the data by a constant value.
     '''
@@ -118,7 +118,7 @@ def __call__(self, my_array: np.ndarray):
         return my_array-shift_vector[:, :, None], shift_vector
 
 
-class VectorShifter(AbstractShifter):
+class VectorShifter(Shifter):
     '''
     Shifts the data by a user-input vector.
     '''
@@ -135,7 +135,7 @@ def __call__(self, my_array: np.ndarray):
         return my_array-self.__shift_vector[..., None], self.__shift_vector
 
 
-class AverageShifter(AbstractShifter):
+class AverageShifter(Shifter):
     '''
     Shifts the data by the average of a data matrix.
     '''
@@ -147,7 +147,7 @@ def __call__(self, my_array: np.ndarray):
         return my_array-shift_vector[:, :, None], shift_vector
 
 
-class FirstVecShifter(AbstractShifter):
+class FirstVecShifter(Shifter):
     '''
     Shifts the data by the first vector of a data matrix.
     '''

romtools/trial_space_utils/splitter.py

@@ -86,15 +86,15 @@
 import numpy as np
 
 
-class AbstractSplitter(abc.ABC):
+class Splitter(abc.ABC):
     '''Abstract class for a splitter'''
 
     @abc.abstractmethod
     def __call__(self, my_array: np.ndarray) -> np.ndarray:
         pass
 
 
-class NoOpSplitter(AbstractSplitter):
+class NoOpSplitter(Splitter):
     '''Concrete no-op implementation'''
     def __init__(self) -> None:
         pass
@@ -103,7 +103,7 @@ def __call__(self, my_array: np.ndarray):
         return my_array
 
 
-class BlockSplitter(AbstractSplitter):
+class BlockSplitter(Splitter):
     '''
     Splits a data matrix into blocks defined by a list, e.g., for our Euler
     equation example above, we could set