Merge pull request #168 from scientificcomputing/dokken/clarify_demo

Remove xvfb. Clarify try-except clause in demo on real spaces

Author: jorgensd

.github/workflows/build_docs.yml

@@ -11,23 +11,16 @@ env:
   DISPLAY: ":99.0"
 
 jobs:
-
   build:
     name: Test on ${{ matrix.label }}
     runs-on: ubuntu-24.04
     container: ghcr.io/fenics/dolfinx/dolfinx:${{ matrix.label }}
     strategy:
       fail-fast: false
       matrix:
-        label: [
-          "stable",
-          "nightly"
-        ]
+        label: ["stable", "nightly"]
     env:
       PUBLISH_DIR: ./_build/html
-      DISPLAY: ":99.0"
-      PYVISTA_TRAME_SERVER_PROXY_PREFIX: "/proxy/"
-      PYVISTA_TRAME_SERVER_PROXY_ENABLED: "True"
       PYVISTA_OFF_SCREEN: false
       PYVISTA_JUPYTER_BACKEND: "html"
 
@@ -36,7 +29,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Install dependencies for pyvista
-        run: apt-get update && apt-get install -y libgl1-mesa-dev xvfb
+        run: apt-get update && apt-get install -y libgl1-mesa-dev mesa-utils
 
       - name: Install dependencies
         run: |

examples/blocked_solver.py

@@ -174,7 +174,6 @@ def post_solve(solver: scifem.NewtonSolver):
 # Finally, we can visualize the solution using `pyvista`
 
 import pyvista
-pyvista.start_xvfb()
 p = pyvista.Plotter()
 topology, cell_types, geometry = dolfinx.plot.vtk_mesh(V)
 grid = pyvista.UnstructuredGrid(topology, cell_types, geometry)

examples/mark_entities.py

@@ -44,7 +44,6 @@ def inner(x):
 
 import pyvista
 
-pyvista.start_xvfb()
 vtk_grid = dolfinx.plot.vtk_mesh(mesh, cell_tag.dim, cell_tag.indices)
 grid = pyvista.UnstructuredGrid(*vtk_grid)
 grid.cell_data["Marker"] = cell_tag.values

examples/point_source.py

@@ -122,7 +122,6 @@
 
 import pyvista
 
-pyvista.start_xvfb()
 topology, cell_types, geometry = dolfinx.plot.vtk_mesh(V)
 values = np.zeros((geometry.shape[0], 3), dtype=np.float64)
 values[:, :len(uh)] = uh.x.array.real.reshape((geometry.shape[0], len(uh)))

examples/real_function_space.py

@@ -133,7 +133,7 @@ def u_exact(x):
 # and {py:func}`ufl.TestFunctions` as one would do with a {py:func}`basix.ufl.mixed_element`.
 # ```
 
-if dolfinx.__version__ == "0.8.0":
+if Version(dolfinx.__version__) == Version("0.8.0"):
     u = ufl.TrialFunction(V)
     lmbda = ufl.TrialFunction(R)
     du = ufl.TestFunction(V)
@@ -169,24 +169,24 @@ def u_exact(x):
 # We can now assemble the matrix and vector usig {py:func}`dolfinx.fem.petsc.assemble_matrix`
 # and {py:func}`dolfinx.fem.petsc.assemble_vector`.
 
-try:
+if Version(dolfinx.__version__) < Version("0.10.0"):
     A = dolfinx.fem.petsc.assemble_matrix_block(a_compiled)
-except AttributeError:
+else:
     A = dolfinx.fem.petsc.assemble_matrix(a_compiled)
 A.assemble()
 
 
-# On the main branch of DOLFINx, the `assemble_vector` function for blocked spaces has been rewritten to reflect how
+# In DOLFINx>=v0.10.0, the `assemble_vector` function for blocked spaces has been rewritten to reflect how
 # it works for standard assembly and `nest` assembly. This means that lifting is applied manually.
 # In this case, with no Dirichlet BC, we could skip those steps.
 # However, for clarity we include them here.
 
 bcs = []
-main_assembly = False
-try:
+
+
+if Version(dolfinx.__version__) < Version("0.10.0"):
     b = dolfinx.fem.petsc.assemble_vector_block(L_compiled, a_compiled, bcs=bcs)
-except AttributeError:
-    main_assembly = True
+else:
     b = dolfinx.fem.petsc.assemble_vector(L_compiled, kind="mpi")
     apply_lifting_and_set_bc(b, a_compiled, bcs=bcs)
 
@@ -197,7 +197,7 @@ def u_exact(x):
 # +
 uh = dolfinx.fem.Function(V, name="u")
 
-if main_assembly:
+if Version(dolfinx.__version__) >= Version("0.10.0"):
     # We start by inserting the value in the real space
     rh = dolfinx.fem.Function(R)
     rh.x.array[0] = h
@@ -239,7 +239,7 @@ def u_exact(x):
 pc.setType("lu")
 pc.setFactorSolverType("mumps")
 
-if main_assembly:
+if Version(dolfinx.__version__) >= Version("0.10.0"):
     xh = b.duplicate()
 else:
     xh = dolfinx.fem.petsc.create_vector_block(L_compiled)
@@ -251,7 +251,7 @@ def u_exact(x):
 # Finally, we extract the solution u from the blocked system and compute the error
 
 uh = dolfinx.fem.Function(V, name="u")
-if main_assembly:
+if Version(dolfinx.__version__) >= Version("0.10.0"):
     dolfinx.fem.petsc.assign(xh, [uh, rh])
 else:
     x_local = get_local_vectors(xh, maps)
@@ -280,7 +280,6 @@ def u_exact(x):
 # +
 vtk_mesh = dolfinx.plot.vtk_mesh(V)
 
-pyvista.start_xvfb(1.0)
 grid = pyvista.UnstructuredGrid(*vtk_mesh)
 grid.point_data["u"] = uh.x.array.real
 

examples/transfer_tags_to_submesh.py

@@ -73,9 +73,6 @@
 
 # + tags=["hide-input"]
 
-if sys.platform == "linux" and (os.getenv("CI") or pyvista.OFF_SCREEN):
-    pyvista.start_xvfb(0.05)
-
 
 def plot_mesh(mesh: dolfinx.mesh.Mesh, values=None):
     """

examples/xdmf_point_cloud.py

@@ -41,7 +41,6 @@
 
 import pyvista
 
-pyvista.start_xvfb()
 plotter = pyvista.Plotter()
 plotter.add_points(
     V.tabulate_dof_coordinates(),

pyproject.toml

@@ -30,7 +30,7 @@ adios2 = ["adios2"]
 docs = [
     "jupyter-book<2.0",
     "jupytext",
-    "pyvista[jupyter]",
+    "pyvista[all]>=0.45.0",
     "sphinxcontrib-bibtex",
     "sphinx-codeautolink",
 ]