Full rewrite of meshing for fractured domains

.gitignore

@@ -80,6 +80,7 @@ $RECYCLE.BIN/
 *.msh
 *.geo
 *.geo_unrolled
+*.xao
 
 # Restart-related time step monitoring files
 times.json

src/porepy/__init__.py

@@ -44,8 +44,8 @@
 # decided as needed
 
 from porepy.utils.common_constants import *
-from porepy.utils.porepy_types import *
 
+from porepy.utils.porepy_types import *
 
 from porepy.utils import permutations
 from porepy.utils.interpolation_tables import (
@@ -83,7 +83,7 @@
 from porepy.grids.grid import Grid
 from porepy.grids.mortar_grid import MortarGrid
 from porepy.grids.md_grid import MixedDimensionalGrid
-from porepy.grids.mdg_generation import create_mdg
+
 from porepy.grids.structured import CartGrid, TensorGrid
 from porepy.grids.simplex import TriangleGrid, TetrahedralGrid
 from porepy.grids.simplex import StructuredTriangleGrid, StructuredTetrahedralGrid
@@ -102,8 +102,10 @@
 # Fractures
 from porepy.fracs.plane_fracture import PlaneFracture, create_elliptic_fracture
 from porepy.fracs.line_fracture import LineFracture
-from porepy.fracs.fracture_network import create_fracture_network
+from porepy.fracs.ellipse_fracture import EllipticFracture
+from porepy.fracs.fracture_network_creation import create_fracture_network
 
+from porepy.grids.mdg_generation import create_mdg
 
 # Wells
 from porepy.fracs.wells_3d import (

src/porepy/applications/md_grids/mdg_library.py

@@ -201,7 +201,11 @@ def cube_with_orthogonal_fractures(
 
     """
     all_fractures = fracture_sets.orthogonal_fractures_3d(size)
-    fractures = [all_fractures[i] for i in fracture_indices]
+    # To please Mypy, we formally set the type to PlaneFracture or EllipticFracture,
+    # even though we know they are all PlaneFractures.
+    fractures: list[pp.PlaneFracture | pp.EllipticFracture] = [
+        all_fractures[i] for i in fracture_indices
+    ]
     domain = domains.nd_cube_domain(3, size)
 
     # Cast to FractureNetwork3d to avoid ambiguity leading to mypy errors

src/porepy/applications/test_utils/reference_dense_arrays.py

@@ -2704,14 +2704,14 @@
         -1.00000000e00,
         -1.00000000e00,
         -1.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
         2.50000000e-01,
         2.50000000e-01,
         2.50000000e-01,
@@ -2720,44 +2720,44 @@
         -2.50000000e-01,
         -2.50000000e-01,
         -2.50000000e-01,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
-        0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
         5.00000000e-03,
         -5.00000000e-03,
-        0.00000000e00,
-        0.00000000e00,
         5.00000000e-03,
         -5.00000000e-03,
-        5.55111512e-19,
-        -5.55111512e-19,
-        5.55111512e-19,
-        -5.55111512e-19,
-        5.55111512e-19,
-        -5.55111512e-19,
-        5.55111512e-19,
-        -5.55111512e-19,
-        0.00000000e00,
-        0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        2.77555756e-19,
+        -2.77555756e-19,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        2.77555756e-19,
+        -2.77555756e-19,
+        -0.00000000e00,
+        -0.00000000e00,
         5.00000000e-03,
         -5.00000000e-03,
-        0.00000000e00,
-        0.00000000e00,
         5.00000000e-03,
         -5.00000000e-03,
+        -0.00000000e00,
+        -0.00000000e00,
         -1.00000000e-04,
-        0.00000000e00,
-        0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
+        -0.00000000e00,
         1.00000000e-04,
-        0.00000000e00,
-        0.00000000e00,
     ]
 )
 
@@ -7947,7 +7947,7 @@
     "partition": _partition,
 }
 # test_constitutive_laws.py
-_diagonal_entries = np.zeros((9, 39))
+_diagonal_entries = np.zeros((9, 27))
 _diagonal_entries[0, :] = 1.0
 _diagonal_entries[4, :] = 1.0
 _diagonal_entries[8, :] = 1.0