Merge pull request #3 from jorgensd/dokken/v0.7.0

Dokken/v0.7.0

.github/workflows/build_docs.yml

@@ -21,9 +21,9 @@ jobs:
     env:
       PYTHONPATH: /usr/local/lib/python3/dist-packages:/usr/local/lib:/usr/local/dolfinx-real/lib/python3.10/dist-packages
       DEB_PYTHON_INSTALL_LAYOUT: deb_system
-      PYVISTA_JUPYTER_BACKEND: "static"
+      PYVISTA_JUPYTER_BACKEND: "html"
     runs-on: ubuntu-22.04
-    container: dolfinx/dolfinx:v0.6.0-r1
+    container: dolfinx/dolfinx:v0.7.2
     steps:
       # This action sets the current path to the root of your github repo
       - uses: actions/checkout@v4
@@ -33,8 +33,7 @@ jobs:
           apt-get install -y graphviz-dev libgl1-mesa-glx xvfb
 
       - name: Update pip
-        # Pin setuptools for old dolfinx due to https://github.com/FEniCS/ffcx/issues/553
-        run: python3 -m pip install --upgrade pip setuptools==65.5.1
+        run: python3 -m pip install --upgrade pip setuptools
 
       - name: Install dependencies
         run: python3 -m pip install -e ".[dev]"

.github/workflows/publish.yml

@@ -15,7 +15,7 @@ concurrency:
   group: "pages"
   cancel-in-progress: true
 
-jobs:  
+jobs:
   build-docs:
     uses: ./.github/workflows/build_docs.yml
 
@@ -44,8 +44,8 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Pages
-        uses: actions/configure-pages@v3
+        uses: actions/configure-pages@v4
 
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v3

README.md

@@ -8,6 +8,8 @@ in DOLFINx.
 A short summary of the various components {cite}`DOLFINx2023` can be found below.
 ![Components of FEniCS](components_of_fenics.png)
 
+The tutorial is currently built for `v0.7.x` of DOLFINx, for older versions see: https://github.com/jorgensd/FEniCS23-tutorial/releases
+
 ```{bibliography}
 :filter: cited and ({"README"} >= docnames)
 ```

pyproject.toml

@@ -1,17 +1,17 @@
-[build-system] # Require setuptool version due to https://github.com/pypa/setuptools/issues/2938
-requires = ["setuptools>=61.0.0", "pip>=23.1"]
+[build-system]
+requires = ["setuptools>=64.4.0", "wheel", "pip>=22.3"]
 
 [project]
 name = "FEniCS23"
-version = "0.6.0"
+version = "0.7.0"
 description = "Tutorial for FENiCS 2023"
 authors = [{ name = "Jørgen S. Dokken", email = "dokken@simula.no" }]
 license = { file = "LICENSE" }
 readme = "README.md"
 dependencies = [
-    "fenics-dolfinx==0.6.0",
+    "fenics-dolfinx>=0.7.0",
     "pygraphviz",
-    "pyvista",
+    "pyvista[all]>=0.43.0",
     "ipyparallel",
     "tqdm",
 ]

src/approximations.py

@@ -19,6 +19,7 @@
 import pyvista
 import numpy as np
 import dolfinx
+import dolfinx.fem.petsc
 from mpi4py import MPI
 import ufl
 from petsc4py import PETSc
@@ -49,7 +50,7 @@ class Projector():
 
     _A: PETSc.Mat  # The mass matrix
     _b: PETSc.Vec  # The rhs vector
-    _lhs: dolfinx.fem.FormMetaClass  # The compiled form for the mass matrix
+    _lhs: dolfinx.fem.Form  # The compiled form for the mass matrix
     _ksp: PETSc.KSP  # The PETSc solver
     _x: dolfinx.fem.Function  # The solution vector
     _dx: ufl.Measure  # Integration measure
@@ -90,6 +91,8 @@ def __init__(self,
             opts[k] = v
         opts.prefixPop()
         self._ksp.setFromOptions()
+        for opt in opts.getAll().keys():
+            del opts[opt]
 
         # Set matrix and vector PETSc options
         self._A.setOptionsPrefix(prefix)
@@ -158,8 +161,7 @@ def h(mesh: dolfinx.mesh.Mesh):
 
 # We can now evaluate the expression at the point 0.5 in the reference element for any cell (this coordinate is then pushed forward to the given input cell).
 # For instance, we can evaluate this expression in the cell with index 0 with
-
-compiled_h.eval([0])
+compiled_h.eval(mesh, np.array([0], dtype=np.int32))
 
 # We can also interpolate functions from an expression into any suitable function space by calling
 
@@ -176,7 +178,7 @@ def h(mesh: dolfinx.mesh.Mesh):
 
 
 V_projector = Projector(
-    V, petsc_options={"ksp_type": "preonly", "pc_type": "lu"})
+    V, petsc_options={"ksp_type": "pre_only", "pc_type": "lu"})
 uh = V_projector.project(h(V.mesh))
 
 pyvista.start_xvfb(1.0)
@@ -186,7 +188,7 @@ def h(mesh: dolfinx.mesh.Mesh):
 
 def plot_1D_scalar_function(u: dolfinx.fem.Function, title: str):
     u_grid = pyvista.UnstructuredGrid(
-        *dolfinx.plot.create_vtk_mesh(u.function_space))
+        *dolfinx.plot.vtk_mesh(u.function_space))
     u_grid.point_data["u"] = u.x.array
     warped = u_grid.warp_by_scalar()
     plotter = pyvista.Plotter()
@@ -205,7 +207,7 @@ def plot_1D_scalar_function(u: dolfinx.fem.Function, title: str):
 
 
 W_projector = Projector(
-    W, petsc_options={"ksp_type": "preonly", "pc_type": "lu"})
+    W, petsc_options={"ksp_type": "pre_only", "pc_type": "lu"})
 wh = W_projector.project(h(W.mesh))
 
 

src/code_generation.py

@@ -33,4 +33,4 @@
 # We can look at the assembly code for the local matrix. We start by inspecting the signature of the `tabulate_tensor` function,
 # that computes the local element matrix
 
-os.system("head -523 ufl_formulation.c | tail +476")
+os.system("head -336 ufl_formulation.c | tail +283")

src/form_compilation.py

@@ -7,6 +7,7 @@
 import numpy as np
 import ufl
 from mpi4py import MPI
+import dolfinx.fem.petsc
 import dolfinx
 
 # + tags=["hide-output"]
@@ -122,7 +123,7 @@ def u_init(x, sigma=0.1, mu=0.3):
 
 uh = dolfinx.fem.Function(V)
 petsc_options = {"ksp_type": "preonly",
-                 "pc_type": "lu", "pc_factor_solver_type": "mumps"}
+                 "pc_type": "lu", "pc_factor_mat_solver_type": "mumps"}
 problem = dolfinx.fem.petsc.LinearProblem(
     a_compiled, L_compiled, u=uh, bcs=[], petsc_options=petsc_options)