From dcad7585c7c0d979511acb4406ca617936cae85f Mon Sep 17 00:00:00 2001 From: Henrik Finsberg Date: Thu, 6 Nov 2025 17:03:51 +0100 Subject: [PATCH 1/2] Pin jupyter-book --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index edd9ebc..854240b 100644 --- a/pyproject.toml +++ b/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]"] From 9eb28c6f26f13e31a28c8641bff5a0b6c0f9b469 Mon Sep 17 00:00:00 2001 From: Henrik Finsberg Date: Thu, 6 Nov 2025 18:00:04 +0100 Subject: [PATCH 2/2] Fix dolfinx api change v0.10 --- src/mri2mesh/cli.py | 2 +- src/mri2mesh/mesh/basic.py | 16 +++++++++++----- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/src/mri2mesh/cli.py b/src/mri2mesh/cli.py index 3de48e8..cbcc733 100644 --- a/src/mri2mesh/cli.py +++ b/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 diff --git a/src/mri2mesh/mesh/basic.py b/src/mri2mesh/mesh/basic.py index f0964de..86a7878 100644 --- a/src/mri2mesh/mesh/basic.py +++ b/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),