Merge pull request #12891 from KratosMultiphysics/core/fix-numpy-depr…

…ecation [Core][Tests] Fixing numpy copy=false
KratosMultiphysics · Nov 29, 2024 · f957ad1 · f957ad1
2 parents 1d7ec51 + 6c1f603
commit f957ad1
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Showing 8 changed files with 16 additions and 14 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -60,7 +60,9 @@ jobs:
 
     - name: CI configuration
       shell: bash
-      run: python3 kratos/python_scripts/testing/ci_utilities.py
+      run: |
+        python3 kratos/python_scripts/testing/ci_utilities.py
+        python3 -m pip install --upgrade numpy==1.26.4
 
     - name: Build
       shell: bash

diff --git a/applications/RomApplication/python_scripts/hrom_training_utility.py b/applications/RomApplication/python_scripts/hrom_training_utility.py
@@ -180,7 +180,7 @@ def AppendCurrentStepResiduals(self):
             err_msg = f"Projection strategy \'{self.projection_strategy}\' for HROM is not supported."
             raise Exception(err_msg)
 
-        np_res_mat = np.array(res_mat, copy=False)
+        np_res_mat = np.asarray(res_mat)
         self.time_step_residual_matrix_container.append(np_res_mat)
 
     def GetJacobianPhiMultiplication(self, computing_model_part):

diff --git a/applications/RomApplication/python_scripts/petrov_galerkin_training_utility.py b/applications/RomApplication/python_scripts/petrov_galerkin_training_utility.py
@@ -80,7 +80,7 @@ def AppendCurrentStepProjectedSystem(self):
             err_msg = "\'self.basis_strategy\' is not available. Select either 'jacobian' or 'residuals'."
             raise Exception(err_msg)
 
-        np_snapshots_matrix = np.array(snapshots_matrix, copy=False)
+        np_snapshots_matrix = np.asarray(snapshots_matrix)
         self.time_step_snapshots_matrix_container.append(np_snapshots_matrix)
 
     def GetJacobianPhiMultiplication(self, computing_model_part):

diff --git a/applications/RomApplication/python_scripts/rom_analysis.py b/applications/RomApplication/python_scripts/rom_analysis.py
@@ -292,7 +292,7 @@ def ModifyInitialGeometry(self):
 
                 print('Nodal variables: ', nodal_unknown_names)
 
-                s_default = np.array(s, copy=False)
+                s_default = np.asarray(s)
                 print(s_default.shape)
 
                 q, _ = nn_rom_interface.get_encode_function()(s_default)

diff --git a/applications/RomApplication/python_scripts/rom_manager.py b/applications/RomApplication/python_scripts/rom_manager.py
@@ -1008,7 +1008,7 @@ def Initialize(cls):
 
         def GetNonconvergedSolutions(cls):
             a,_ = cls._GetSolver()._GetSolutionStrategy().GetNonconvergedSolutions()
-            return np.array(a, copy=False)
+            return np.asarray(a)
 
         simulation.Initialize  = types.MethodType(Initialize, simulation)
         simulation.GetNonconvergedSolutions  = types.MethodType(GetNonconvergedSolutions, simulation)

diff --git a/kratos/python_scripts/petsc_conversion_tools.py b/kratos/python_scripts/petsc_conversion_tools.py
@@ -18,17 +18,17 @@ def __init__(self, A):  #Kratos DistributedCsrMatrix
         N = A.GetColNumbering().Size()
 
         ##pointers to the kratos arrays of values
-        self.a = np.array(A.GetDiagonalBlock().value_data(), copy=False)
-        self.oa = np.array(A.GetOffDiagonalBlock().value_data(), copy=False)
+        self.a = np.asarray(A.GetDiagonalBlock().value_data())
+        self.oa = np.asarray(A.GetOffDiagonalBlock().value_data())
 
         if(type(m) == type(PETSc.IntType)): #we can avoid doing copies
             #indices of diagonal block
-            self.i = np.array(A.GetDiagonalBlock().index1_data(), copy=False)
-            self.j = np.array(A.GetDiagonalBlock().index2_data(), copy=False)
+            self.i = np.asarray(A.GetDiagonalBlock().index1_data())
+            self.j = np.asarray(A.GetDiagonalBlock().index2_data())
 
             #indices of offdiagonal block
-            self.oi = np.array(A.GetOffDiagonalBlock().index1_data(), copy=False)
-            self.oj = np.array(A.GetOffDiagonalIndex2DataInGlobalNumbering(), copy=False)        
+            self.oi = np.asarray(A.GetOffDiagonalBlock().index1_data())
+            self.oj = np.asarray(A.GetOffDiagonalIndex2DataInGlobalNumbering())        
 
         else: #WE NEED TO COPY INDICES! since the size of the IndexType is not compatible between Kratos and PETSc
             if(A.GetComm().Rank() == 0):

diff --git a/kratos/tests/test_numpy_export_dense_matrix.py b/kratos/tests/test_numpy_export_dense_matrix.py
@@ -10,7 +10,7 @@ def test_numpy_export_dense_matrix_no_copying(self):
         KratosMatrix.fill(1.0)
 
         # Export it to numpy array (No copying is performed)
-        NumpyMatrix = np.array(KratosMatrix,copy=False)
+        NumpyMatrix = np.asarray(KratosMatrix)
 
         # Test correct creation
         for i in range(3):
@@ -35,7 +35,7 @@ def test_numpy_export_complex_dense_matrix_no_copying(self):
         KratosMatrix.fill(1.0+1.0j)
 
         # Export it to numpy array (No copying is performed)
-        NumpyMatrix = np.array(KratosMatrix,copy=False)
+        NumpyMatrix = np.asarray(KratosMatrix)
 
         # Test correct creation
         for i in range(3):

diff --git a/kratos/tests/test_vectorized_interpolation.py b/kratos/tests/test_vectorized_interpolation.py
@@ -39,7 +39,7 @@ def testVectorizedInterpolation(self):
 
         #obtaining a copy of database onto numpy array, and reshaping it into matrices
         nnodes = len(self.mp.Nodes)
-        vdata = np.array(Kratos.VariableUtils().GetSolutionStepValuesVector(self.mp.Nodes, Kratos.VELOCITY, 0, 3),copy=False).reshape(nnodes,3)
+        vdata = np.asarray(Kratos.VariableUtils().GetSolutionStepValuesVector(self.mp.Nodes, Kratos.VELOCITY, 0, 3)).reshape(nnodes,3)
         coords = np.array(Kratos.VariableUtils().GetCurrentPositionsVector(self.mp.Nodes,3)).reshape(nnodes,3)
 
         ##coordinates to search for