Merge pull request #4 from scientificcomputing/pin-jupyter-book

Pin jupyter-book

Author: finsberg

pyproject.toml

@@ -32,7 +32,7 @@ mri2mesh = "mri2mesh.cli:main"
 [project.optional-dependencies]
 mesh = ["wildmeshing", "h5py"]
 test = ["pytest", "pytest-cov", "mri2mesh[mesh]"]
-docs = ["pyvista[jupyter]", "jupyter-book", "mri2mesh[mesh]"]
+docs = ["pyvista[jupyter]", "jupyter-book<2.0", "mri2mesh[mesh]"]
 
 
 

src/mri2mesh/cli.py

@@ -73,7 +73,7 @@ def dispatch(parser: argparse.ArgumentParser, argv: Optional[Sequence[str]] = No
             logger.error(f"Unknown command {command}")
             parser.print_help()
     except ValueError as e:
-        logger.error(e)
+        logger.error(e, exc_info=True, stacklevel=2)
         parser.print_help()
 
     return 0

src/mri2mesh/mesh/basic.py

@@ -189,20 +189,26 @@ def convert_mesh_dolfinx(
     import basix
     import ufl
 
+    try:
+        from dolfinx.io import gmsh as gmshio
+    except ImportError:
+        from dolfinx.io import gmshio
+
     point_array = np.load(mesh_dir / "point_array.npy")
     cell_array = np.load(mesh_dir / "cell_array.npy")
     marker = np.load(mesh_dir / "marker.npy")
 
     comm = MPI.COMM_WORLD
+
     mesh = dolfinx.mesh.create_mesh(
-        comm,
-        cell_array.astype(np.int64),
-        point_array,
-        ufl.Mesh(basix.ufl.element("Lagrange", "tetrahedron", 1, shape=(3,))),
+        comm=comm,
+        cells=cell_array.astype(np.int64),
+        x=point_array,
+        e=ufl.Mesh(basix.ufl.element("Lagrange", "tetrahedron", 1, shape=(3,))),
     )
     tdim = mesh.topology.dim
     fdim = tdim - 1
-    local_entities, local_values = dolfinx.io.gmshio.distribute_entity_data(
+    local_entities, local_values = gmshio.distribute_entity_data(
         mesh,
         tdim,
         cell_array.astype(np.int64),