Clean and formatting

Author: paloma-martinez

geos-mesh/src/geos/mesh/utils/multiblockModifiers.py

@@ -1,9 +1,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
-# SPDX-FileContributor: Martin Lemay, Paloma Martinez
+# SPDX-FileContributor: Martin Lemay, Paloma Martinez, Jacques Franc
 from typing import Union
 import logging
-# import re
 
 from vtkmodules.vtkCommonDataModel import ( vtkCompositeDataSet, vtkDataObjectTreeIterator, vtkMultiBlockDataSet,
                                             vtkUnstructuredGrid, vtkDataSet )
@@ -37,10 +36,10 @@ def mergeBlocks(
             Defaults to None, an internal logger is used.
 
     Returns:
-        vtkUnstructuredGrid: Merged dataset or input mesh if it's already a single block
+        vtkUnstructuredGrid: Merged dataset or input mesh if it's already a single block.
 
     Raises:
-        geos.utilsVTKError ():
+        geos.utils.VTKError (): Error raised during call of VTK function
 
     .. Note::
         Default filling values:
@@ -52,27 +51,31 @@ def mergeBlocks(
 
     """
     if logger is None:
-        logger: Logger = getLogger( "mergeBlocks", True )
+        logger = getLogger( "mergeBlocks", True )
 
     vtkLogger.SetStderrVerbosity( vtkLogger.VERBOSITY_TRACE )
     logger.addFilter( RegexExceptionFilter() )  # will raise VTKError if captured VTK Error
+
+    logCurrentLevel: int = logger.getEffectiveLevel()
     logger.setLevel( logging.DEBUG )
 
     # Fill the partial attributes with default values to keep them during the merge.
     if keepPartialAttributes and not fillAllPartialAttributes( inputMesh, logger ):
         logger.warning( "Failed to fill partial attributes. Merging without keeping partial attributes." )
 
+    outputMesh: vtkUnstructuredGrid
+
     if Version( vtk.__version__ ) >= Version( "9.5" ):
         filter: vtkMergeBlocks = vtkMergeBlocks()
         filter.SetInputData( inputMesh )
         filter.Update()
 
-        outputMesh: vtkUnstructuredGrid = filter.GetOutputDataObject( 0 )
+        outputMesh = filter.GetOutputDataObject( 0 )
 
     else:
         if inputMesh.IsA( "vtkDataSet" ):
             logger.warning( "Input mesh is already a single block." )
-            outputMesh = inputMesh
+            outputMesh = vtkUnstructuredGrid.SafeDownCast( inputMesh )
         else:
             with VTKCaptureLog() as captured_log:
 
@@ -87,10 +90,12 @@ def mergeBlocks(
                     af.AddInputData( block )
                     iterator.GoToNextItem()
                 af.Update()
-                captured_log.seek( 0 )  #be kind let's just rewind
+                captured_log.seek( 0 )
                 captured = captured_log.read().decode()
 
             logger.debug( captured.strip() )
-            outputMesh: vtkUnstructuredGrid = af.GetOutputDataObject( 0 )
+            outputMesh = af.GetOutputDataObject( 0 )
+
+    logger.setLevel( logCurrentLevel )
 
     return outputMesh

geos-mesh/tests/conftest.py

@@ -165,7 +165,6 @@ def _get_dataset( datasetType: str ) -> Union[ vtkMultiBlockDataSet, vtkPolyData
             vtkFilename = "data/displacedFaultempty.vtm"
         elif datasetType == "multiblockGeosOutput":
             # adapted from example GEOS/inputFiles/compositionalMultiphaseWell/simpleCo2InjTutorial_smoke.xml
-            reader: vtkXMLMultiBlockDataReader = vtkXMLMultiBlockDataReader()
             vtkFilename = "data/simpleReservoirViz_small_000478.vtm"
         elif datasetType == "fracture":
             vtkFilename = "data/fracture_res5_id.vtu"

geos-mesh/tests/test_multiblockModifiers.py

@@ -3,21 +3,22 @@
 # SPDX-FileContributor: Paloma Martinez
 # SPDX-License-Identifier: Apache 2.0
 # ruff: noqa: E402 # disable Module level import not at top of file
+# mypy: disable-error-code="operator"
 import pytest
 
 from vtkmodules.vtkCommonDataModel import vtkMultiBlockDataSet, vtkUnstructuredGrid
 from geos.mesh.utils import multiblockModifiers
 
 
-@pytest.mark.parametrize( "keepPartialAttributes, nb_pt_attributes, nb_cell_attributes, nb_field_attributes", [
+@pytest.mark.parametrize( "keepPartialAttributes, nbPointAttributes, nbCellAttributes, nbFieldAttributes", [
     ( False, 0, 16, 1 ),
     ( True, 2, 30, 1 ),
 ] )
 def test_mergeBlocks(
     dataSetTest: vtkMultiBlockDataSet,
-    nb_pt_attributes: int,
-    nb_cell_attributes: int,
-    nb_field_attributes: int,
+    nbPointAttributes: int,
+    nbCellAttributes: int,
+    nbFieldAttributes: int,
     keepPartialAttributes: bool,
 ) -> None:
     """Test the merging of a multiblock."""
@@ -27,10 +28,10 @@ def test_mergeBlocks(
     dataset = multiblockModifiers.mergeBlocks( vtkMultiBlockDataSetTest, keepPartialAttributes )
 
     assert dataset.GetCellData().GetNumberOfArrays(
-    ) == nb_cell_attributes, f"Expected {nb_cell_attributes} cell attributes after the merge, not {dataset.GetCellData().GetNumberOfArrays()}."
+    ) == nbCellAttributes, f"Expected {nbCellAttributes} cell attributes after the merge, not {dataset.GetCellData().GetNumberOfArrays()}."
 
     assert dataset.GetPointData().GetNumberOfArrays(
-    ) == nb_pt_attributes, f"Expected {nb_pt_attributes} point attributes after the merge, not {dataset.GetPointData().GetNumberOfArrays()}."
+    ) == nbPointAttributes, f"Expected {nbPointAttributes} point attributes after the merge, not {dataset.GetPointData().GetNumberOfArrays()}."
 
     assert dataset.GetFieldData().GetNumberOfArrays(
-    ) == nb_field_attributes, f"Expected {nb_field_attributes} field attributes after the merge, not {dataset.GetFieldData().GetNumberOfArrays()}."
+    ) == nbFieldAttributes, f"Expected {nbFieldAttributes} field attributes after the merge, not {dataset.GetFieldData().GetNumberOfArrays()}."

geos-posp/src/PVplugins/PVMohrCirclePlot.py

@@ -805,7 +805,6 @@ def createMohrCirclesAtTimeStep(
         """
         # get mesh and merge if needed
         meshMerged: vtkUnstructuredGrid = mergeBlocks( mesh )
-        # assert meshMerged is not None, "Input data is undefined"
 
         stressArray: npt.NDArray[ np.float64 ] = getArrayInObject( meshMerged,
                                                                    GeosMeshOutputsEnum.STRESS_EFFECTIVE.attributeName,

geos-posp/src/geos_posp/filters/GeosBlockMerge.py

@@ -145,22 +145,10 @@ def RequestData(
 
             # initialize output objects -- TODO: separate it as soon as we are sure not to alter behavior
             self.m_output = self.GetOutputData( outInfoVec, 0 )  # type: ignore[no-untyped-call]
-            # assert self.m_input is not None, "Input object is null."
-            # assert self.m_output is not None, "Output object is null."
 
             self.doMerge()
-        # except (AssertionError, ValueError, TypeError) as e:
-        #     mess: str = "Geos block merge failed due to:"
-        #     self.m_logger.error( mess )
-        #     self.m_logger.error( e, exc_info=True )
-        #     return 0
-        except ( ValueError, TypeError ) as e:
-            mess0: str = "Geos block merge failed due to:"
-            self.m_logger.critical( mess0 )
-            self.m_logger.critical( e, exc_info=True )
-            return 0
-        except RuntimeError as e:
-            self.m_logger.critical( "Geos block merge failed due to" )
+        except ( ValueError, TypeError, RuntimeError ) as e:
+            self.m_logger.critical( "Geos block merge failed due to:" )
             self.m_logger.critical( e, exc_info=True )
             return 0
         else:
@@ -191,12 +179,7 @@ def doMerge( self: Self ) -> int:
         self.mergeRankBlocks()
         if self.m_convertFaultToSurface:
             self.convertFaultsToSurfaces()
-            # assert self.m_outputMesh is not None, "Output mesh in null."
-        # except AssertionError as e:
-        #     mess: str = "Block merge failed due to:"
-        #     self.m_logger.error( mess )
-        #     self.m_logger.error( e, exc_info=True )
-        #     return 0
+
         self.m_output.ShallowCopy( self.m_outputMesh )
         return 1
 

geos-pv/src/geos/pv/plugins/PVMergeBlocksEnhanced.py

@@ -114,8 +114,8 @@ def RequestData(
         inputMesh: Union[ vtkMultiBlockDataSet, vtkCompositeDataSet ] = self.GetInputData( inInfoVec, 0, 0 )
         outputMesh: vtkUnstructuredGrid = self.GetOutputData( outInfoVec, 0 )
 
-        # assert inputMesh is not None, "Input mesh is null."
-        # assert outputMesh is not None, "Output pipeline is null."
+        assert inputMesh is not None, "Input mesh is null."
+        assert outputMesh is not None, "Output pipeline is null."
 
         filter: MergeBlockEnhanced = MergeBlockEnhanced( inputMesh, True )
 
@@ -124,16 +124,10 @@ def RequestData(
 
         try:
             filter.applyFilter()
-        except ( ValueError, TypeError ) as e:
-            filter.logger.error( f"MergeBlock failed due to {e}",
-                                 exc_info=True )  #no critical as there is no reason to crash here
-            return 0
-        except RuntimeError as e:
-            filter.logger.error( f"MergeBlock failed due to {e}",
-                                 exc_info=True )  #no critical as there is no reason to crash here
+        except ( ValueError, TypeError, RuntimeError ) as e:
+            filter.logger.error( f"MergeBlock failed due to {e}", exc_info=True )
             return 0
         else:
             outputMesh.ShallowCopy( filter.getOutput() )
             outputMesh.Modified()
-
             return 1

geos-utils/src/geos/utils/Logger.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: Apache-2.0
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
-# SPDX-FileContributor: Martin Lemay
+# SPDX-FileContributor: Martin Lemay, Romain Baville, Jacques Franc
 import logging
 from typing import Any, Union, Generator
 from typing_extensions import Self
@@ -44,7 +44,7 @@
 class RegexExceptionFilter( logging.Filter ):
     """Class to regexp VTK messages rethrown into logger by VTKCaptureLog."""
 
-    pattern: str = r"ERR"  #pattern captured that will raise a vtkError
+    pattern: str = r'\bERR\|\b'  # Pattern captured that will raise a vtkError
 
     def __init__( self ) -> None:
         """Init filter with class based pattern as this is patch to logging logic."""
@@ -71,27 +71,27 @@ def VTKCaptureLog() -> Generator[ Any, Any, Any ]:
     """Hard way of adapting C-like vtkLogger to logging class by throwing in stderr and reading back from it.
 
     Returns:
-        Generator: buffering os stderr.
+        Generator: Buffering os stderr.
 
     """
     #equiv to pyvista's
     # from pyvista.utilities import VtkErrorCatcher
     # with VtkErrorCatcher() as err:
     #     append_filter.Update()
     #     print(err)
-    # original_stderr_fd = sys.stderr.fileno()
-    original_stderr_fd = 2
-    saved_stderr_fd = os.dup( original_stderr_fd )
+    # originalStderrFd = sys.stderr.fileno()
+    originalStderrFd = 2
+    savedStderrFd = os.dup( originalStderrFd )
 
     # Create a temporary file to capture stderr
     with tempfile.TemporaryFile( mode='w+b' ) as tmp:
-        os.dup2( tmp.fileno(), original_stderr_fd )
+        os.dup2( tmp.fileno(), originalStderrFd )
         try:
             yield tmp
         finally:
             # Restore original stderr
-            os.dup2( saved_stderr_fd, original_stderr_fd )
-            os.close( saved_stderr_fd )
+            os.dup2( savedStderrFd, originalStderrFd )
+            os.close( savedStderrFd )
 
 
 class CountWarningHandler( logging.Handler ):