Last part of correction review

geos-mesh/src/geos/mesh/doctor/checks/check_fractures.py

@@ -1,30 +1,14 @@
-from dataclasses import dataclass
 import logging
-
-from typing import (
-    Collection,
-    FrozenSet,
-    Iterable,
-    Sequence,
-    Set,
-    Tuple,
-)
-
-from tqdm import tqdm
 import numpy
-
-from vtkmodules.vtkCommonDataModel import (
-    vtkUnstructuredGrid,
-    vtkCell,
-)
-from vtkmodules.vtkCommonCore import (
-    vtkPoints, )
-from vtkmodules.vtkIOXML import (
-    vtkXMLMultiBlockDataReader, )
-from vtkmodules.util.numpy_support import (
-    vtk_to_numpy, )
-from .vtk_utils import (
-    vtk_iter, )
+from dataclasses import dataclass
+from typing import Collection, Iterable, Sequence
+from tqdm import tqdm
+from vtkmodules.vtkCommonDataModel import vtkUnstructuredGrid, vtkCell
+from vtkmodules.vtkCommonCore import vtkPoints
+from vtkmodules.vtkIOXML import vtkXMLMultiBlockDataReader
+from vtkmodules.util.numpy_support import vtk_to_numpy
+from geos.mesh.doctor.checks.vtk_utils import vtk_iter
+from geos.mesh.doctor.checks.generate_fractures import Coordinates3D
 
 
 @dataclass( frozen=True )
@@ -44,7 +28,7 @@ class Result:
 
 
 def __read_multiblock( vtk_input_file: str, matrix_name: str,
-                       fracture_name: str ) -> Tuple[ vtkUnstructuredGrid, vtkUnstructuredGrid ]:
+                       fracture_name: str ) -> tuple[ vtkUnstructuredGrid, vtkUnstructuredGrid ]:
     reader = vtkXMLMultiBlockDataReader()
     reader.SetFileName( vtk_input_file )
     reader.Update()
@@ -73,9 +57,9 @@ def format_collocated_nodes( fracture_mesh: vtkUnstructuredGrid ) -> Sequence[ I
 
 
 def __check_collocated_nodes_positions(
-    matrix_points: Sequence[ Tuple[ float, float, float ] ], fracture_points: Sequence[ Tuple[ float, float, float ] ],
-    g2l: Sequence[ int ], collocated_nodes: Iterable[ Iterable[ int ] ]
-) -> Collection[ Tuple[ int, Iterable[ int ], Iterable[ Tuple[ float, float, float ] ] ] ]:
+    matrix_points: Sequence[ Coordinates3D ], fracture_points: Sequence[ Coordinates3D ], g2l: Sequence[ int ],
+    collocated_nodes: Iterable[ Iterable[ int ] ]
+) -> Collection[ tuple[ int, Iterable[ int ], Iterable[ Coordinates3D ] ] ]:
     issues = []
     for li, bucket in enumerate( collocated_nodes ):
         matrix_nodes = ( fracture_points[ li ], ) + tuple( map( lambda gi: matrix_points[ g2l[ gi ] ], bucket ) )
@@ -98,14 +82,14 @@ def my_iter( ccc ):
 
 def __check_neighbors( matrix: vtkUnstructuredGrid, fracture: vtkUnstructuredGrid, g2l: Sequence[ int ],
                        collocated_nodes: Sequence[ Iterable[ int ] ] ):
-    fracture_nodes: Set[ int ] = set()
+    fracture_nodes: set[ int ] = set()
     for bucket in collocated_nodes:
         for gi in bucket:
             fracture_nodes.add( g2l[ gi ] )
     # For each face of each cell,
     # if all the points of the face are "made" of collocated nodes,
     # then this is a fracture face.
-    fracture_faces: Set[ FrozenSet[ int ] ] = set()
+    fracture_faces: set[ frozenset[ int ] ] = set()
     for c in range( matrix.GetNumberOfCells() ):
         cell: vtkCell = matrix.GetCell( c )
         for f in range( cell.GetNumberOfFaces() ):
@@ -116,7 +100,7 @@ def __check_neighbors( matrix: vtkUnstructuredGrid, fracture: vtkUnstructuredGri
     # Finding the cells
     for c in tqdm( range( fracture.GetNumberOfCells() ), desc="Finding neighbor cell pairs" ):
         cell: vtkCell = fracture.GetCell( c )
-        cns: Set[ FrozenSet[ int ] ] = set()  # subset of collocated_nodes
+        cns: set[ frozenset[ int ] ] = set()  # subset of collocated_nodes
         point_ids = frozenset( vtk_iter( cell.GetPointIds() ) )
         for point_id in point_ids:
             bucket = collocated_nodes[ point_id ]
@@ -129,9 +113,8 @@ def __check_neighbors( matrix: vtkUnstructuredGrid, fracture: vtkUnstructuredGri
             if f in fracture_faces:
                 found += 1
         if found != 2:
-            logging.warning(
-                f"Something went wrong since we should have found 2 fractures faces (we found {found}) for collocated nodes {cns}."
-            )
+            logging.warning( f"Something went wrong since we should have found 2 fractures faces (we found {found})" +
+                             f" for collocated nodes {cns}." )
 
 
 def __check( vtk_input_file: str, options: Options ) -> Result:

geos-mesh/src/geos/mesh/doctor/checks/generate_fractures.py

@@ -1,10 +1,10 @@
+import logging
+import networkx
+import numpy
 from collections import defaultdict
 from dataclasses import dataclass
-import logging
 from enum import Enum
 from tqdm import tqdm
-import networkx
-import numpy
 from typing import Collection, Iterable, Mapping, Optional, Sequence, TypeAlias
 from vtk import vtkDataArray
 from vtkmodules.vtkCommonCore import vtkIdList, vtkPoints

geos-mesh/src/geos/mesh/doctor/checks/vtk_utils.py

@@ -1,25 +1,11 @@
-from dataclasses import dataclass
 import os.path
 import logging
-import sys
-from typing import (
-    Any,
-    Iterator,
-    Optional,
-)
-
-from vtkmodules.vtkCommonCore import (
-    vtkIdList, )
-from vtkmodules.vtkCommonDataModel import (
-    vtkUnstructuredGrid, )
-from vtkmodules.vtkIOLegacy import (
-    vtkUnstructuredGridWriter,
-    vtkUnstructuredGridReader,
-)
-from vtkmodules.vtkIOXML import (
-    vtkXMLUnstructuredGridReader,
-    vtkXMLUnstructuredGridWriter,
-)
+from dataclasses import dataclass
+from typing import Iterator, Optional
+from vtkmodules.vtkCommonCore import vtkIdList
+from vtkmodules.vtkCommonDataModel import vtkUnstructuredGrid
+from vtkmodules.vtkIOLegacy import vtkUnstructuredGridWriter, vtkUnstructuredGridReader
+from vtkmodules.vtkIOXML import vtkXMLUnstructuredGridReader, vtkXMLUnstructuredGridWriter
 
 
 @dataclass( frozen=True )
@@ -36,7 +22,7 @@ def to_vtk_id_list( data ) -> vtkIdList:
     return result
 
 
-def vtk_iter( l ) -> Iterator[ Any ]:
+def vtk_iter( l ) -> Iterator[ any ]:
     """
     Utility function transforming a vtk "container" (e.g. vtkIdList) into an iterable to be used for building built-ins python containers.
     :param l: A vtk container.
@@ -116,8 +102,9 @@ def read_mesh( vtk_input_file: str ) -> vtkUnstructuredGrid:
     :return: A unstructured grid.
     """
     if not os.path.exists( vtk_input_file ):
-        logging.critical( f"Invalid file path. COuld not read \"{vtk_input_file}\". Dying..." )
-        sys.exit( 1 )
+        err_msg: str = f"Invalid file path. Could not read \"{vtk_input_file}\". Dying..."
+        logging.error( err_msg )
+        raise ValueError( err_msg )
     file_extension = os.path.splitext( vtk_input_file )[ -1 ]
     extension_to_reader = { ".vtk": __read_vtk, ".vtu": __read_vtu }
     # Testing first the reader that should match
@@ -131,8 +118,9 @@ def read_mesh( vtk_input_file: str ) -> vtkUnstructuredGrid:
         if output_mesh:
             return output_mesh
     # No reader did work. Dying.
-    logging.critical( f"Could not find the appropriate VTK reader for file \"{vtk_input_file}\". Dying..." )
-    sys.exit( 1 )
+    err_msg = f"Could not find the appropriate VTK reader for file \"{vtk_input_file}\". Dying..."
+    logging.error( err_msg )
+    raise ValueError( err_msg )
 
 
 def __write_vtk( mesh: vtkUnstructuredGrid, output: str ) -> int:
@@ -170,6 +158,7 @@ def write_mesh( mesh: vtkUnstructuredGrid, vtk_output: VtkOutput ) -> int:
         success_code = __write_vtu( mesh, vtk_output.output, vtk_output.is_data_mode_binary )
     else:
         # No writer found did work. Dying.
-        logging.critical( f"Could not find the appropriate VTK writer for extension \"{file_extension}\". Dying..." )
-        sys.exit( 1 )
+        err_msg = f"Could not find the appropriate VTK writer for extension \"{file_extension}\". Dying..."
+        logging.error( err_msg )
+        raise ValueError( err_msg )
     return 0 if success_code else 2  # the Write member function return 1 in case of success, 0 otherwise.

geos-mesh/tests/test_generate_fractures.py

@@ -1,7 +1,7 @@
-from dataclasses import dataclass
 import logging
 import numpy
 import pytest
+from dataclasses import dataclass
 from typing import Iterable, Iterator, Sequence, TypeAlias
 from vtkmodules.vtkCommonDataModel import ( vtkUnstructuredGrid, vtkQuad, VTK_HEXAHEDRON, VTK_POLYHEDRON, VTK_QUAD )
 from vtkmodules.util.numpy_support import numpy_to_vtk, vtk_to_numpy