Update to work with latest FEniCSx (#200)

* Fix bounding box tree

* comment

* update test

* Add weekly test against FEniCSx v0.6

* }

* actually set the tags

* -release

* Support FEniCSx 0.6.0

* don't test released on each push

.github/workflows/weekly-tests.yml

@@ -0,0 +1,47 @@
+name: Run tests with FEniCSx releases
+
+on:
+  schedule:
+    - cron: "0 7 * * 1"
+
+jobs:
+  build-and-publish-docker-fenicsx-release:
+    name: Build testing docker image with FEniCSx release
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        fenics-version: [ "v0.6.0", "main" ]
+    steps:
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      - name: Login to DockerHub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+      - name: Build and push testing Docker image with FEniCSx ${{ matrix.fenics-version }}
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: bempp/cl-dev-env-with-dolfinx:main-fenicsx-${{ matrix.fenics-version }}
+          target: bempp-dev-env-with-dolfinx
+          build-args: |
+            FENICSX_BASIX_TAG=${{ matrix.fenics-version }}
+            FENICSX_FFCX_TAG=${{ matrix.fenics-version }}
+            FENICSX_DOLFINX_TAG=${{ matrix.fenics-version }}
+
+  build-and-test-with-fenicsx-release:
+    name: Build Bempp and run tests with FEniCSx release
+    needs:
+      - build-and-publish-docker-fenicsx-release
+    strategy:
+      matrix:
+        fenics-version: [ "v0.6.0", "main" ]
+    runs-on: ubuntu-latest
+    container: bempp/cl-dev-env-with-dolfinx:main-fenicsx-${{ matrix.fenics-version }}
+    steps:
+      - uses: actions/checkout@v2
+      - run: python3 setup.py install
+        name: Install Bempp
+      - run: python3 -m pytest -n4 --durations=50 test/unit --has-dolfin 0 --has-dolfinx 1 --has-exafmm 1
+        name: Run Bempp unit tests

bempp/api/external/fenicsx.py

@@ -108,11 +108,13 @@ def p1_trace(fenics_space):
     dof_to_vertex_map = np.zeros(num_fenics_vertices, dtype=np.int64)
     tets = fenics_mesh.geometry.dofmap
 
-    try:
+    # Support older versions of FEniCSx
+    if hasattr(tets, "get_links"):
         ntets = tets.num_nodes
         tets = [tets.get_links(i) for i in range(ntets)]
-    except AttributeError:
-        pass
+    if hasattr(tets, "links"):
+        ntets = tets.num_nodes
+        tets = [tets.links(i) for i in range(ntets)]
 
     for tet, cell_verts in enumerate(tets):
         cell_dofs = fenics_space.dofmap.cell_dofs(tet)

notebooks/helmholtz/simple_helmholtz_fem_bem_coupling_dolfinx.ipynb

@@ -1861,7 +1861,11 @@
     "plot_me[bem_x] -= slp_pot.evaluate(neumann_fun).flat\n",
     "\n",
     "fem_points = points[:, np.logical_not(bem_x)].transpose()\n",
-    "tree = dolfinx.geometry.BoundingBoxTree(mesh, 3)\n",
+    "try:\n",
+    "    # Compatibility with older versions of DOLFINx\n",
+    "    tree = dolfinx.geometry.BoundingBoxTree(mesh, 3)\n",
+    "except TypeError:\n",
+    "    tree = dolfinx.geometry.bb_tree(mesh, 3)\n",
     "midpoint_tree = dolfinx.geometry.create_midpoint_tree(\n",
     "    mesh, 3, list(range(mesh.topology.connectivity(3, 0).num_nodes))\n",
     ")\n",

test/unit/external/test_fenicsx.py

@@ -10,41 +10,39 @@ def test_p1_trace(has_dolfinx):
     """Test the trace of a P1 DOLFINx function."""
     try:
         from mpi4py import MPI
-        from dolfinx.geometry import (
-            BoundingBoxTree,
-            create_midpoint_tree,
-            compute_closest_entity,
-        )
-        from dolfinx.fem import FunctionSpace, Function
-        from dolfinx.mesh import create_unit_cube
+        import dolfinx
     except ImportError:
         if has_dolfinx:
             raise ImportError("DOLFINx is not installed")
         pytest.skip("DOLFINx must be installed to run this test")
 
-    fenics_mesh = create_unit_cube(MPI.COMM_WORLD, 2, 2, 2)
-    fenics_space = FunctionSpace(fenics_mesh, ("CG", 1))
+    fenics_mesh = dolfinx.mesh.create_unit_cube(MPI.COMM_WORLD, 2, 2, 2)
+    fenics_space = dolfinx.fem.FunctionSpace(fenics_mesh, ("CG", 1))
 
     bempp_space, trace_matrix = fenics_to_bempp_trace_data(fenics_space)
 
     fenics_coeffs = np.random.rand(fenics_space.dofmap.index_map.size_global)
     bempp_coeffs = trace_matrix @ fenics_coeffs
 
-    fenics_fun = Function(fenics_space)
+    fenics_fun = dolfinx.fem.Function(fenics_space)
     fenics_fun.vector[:] = fenics_coeffs
     bempp_fun = bempp.api.GridFunction(bempp_space, coefficients=bempp_coeffs)
 
-    tree = BoundingBoxTree(fenics_mesh, 3)
+    try:
+        tree = dolfinx.geometry.bb_tree(fenics_mesh, 3)
+    except AttributeError:
+        # Support older FEniCSx
+        tree = dolfinx.geometry.BoundingBoxTree(fenics_mesh, 3)
 
-    midpoint_tree = create_midpoint_tree(
+    midpoint_tree = dolfinx.geometry.create_midpoint_tree(
         fenics_mesh, 3, list(range(fenics_mesh.topology.connectivity(3, 0).num_nodes))
     )
 
     for cell in bempp_space.grid.entity_iterator(0):
         mid = cell.geometry.centroid
         bempp_val = bempp_fun.evaluate(cell.index, np.array([[1 / 3], [1 / 3]]))
 
-        fenics_cell = compute_closest_entity(tree, midpoint_tree, fenics_mesh, mid)[0]
+        fenics_cell = dolfinx.geometry.compute_closest_entity(tree, midpoint_tree, fenics_mesh, mid)[0]
         fenics_val = fenics_fun.eval([mid.T], [fenics_cell])
         assert np.isclose(bempp_val[0, 0], fenics_val[0])