Update to main branch (#117)

Moving CI to ubuntu 22.04/python 3.12:

    --break-system-packages and --no-build-isolation needed for most python3 -m pip install commands
    Run docker build on pull request to main and release to catch build issues
    Bump jorgensd/actions/install-dolfinx to v0.3

Cmake/nanobind:

    PETSc/petsc4py now optional, extra cmake code required

Dolfinx/basix:

    dtype: Consistently added to basix.ufl.element to work on single precision builds
    nullspace computation for rigid motions updated, ref: 

Split PETSc and non-PETSc tests on CI FEniCS/dolfinx#3184

.github/workflows/build_docs.yml

@@ -20,7 +20,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Install DOLFINx
-        uses: jorgensd/actions/install-dolfinx@v0.2.0
+        uses: jorgensd/actions/install-dolfinx@v0.3
         with:
           dolfinx: main
           ufl: main
@@ -35,7 +35,7 @@ jobs:
           cmake --install build-dir
 
       - name: Install DOLFINx-MPC (Python)
-        run: python3 -m pip -v install --config-settings=cmake.build-type="Release" --no-build-isolation  ./python/[docs]
+        run: python3 -m pip -v install --break-system-packages --config-settings=cmake.build-type="Release" --no-build-isolation  ./python/[docs]
 
       - name: Build docs
         run: jupyter book build .

.github/workflows/docker.yml

@@ -1,9 +1,11 @@
 on:
   push:
-    branches:
-      - "!*"
     tags:
       - "v*"
+  pull_request:
+    branches:
+      - release
+      - main
 
   workflow_dispatch:
 
@@ -43,6 +45,18 @@ jobs:
 
       - name: Build and push Docker image
         uses: docker/build-push-action@v5
+        with:
+          context: .
+          load: true
+          push: false
+          file: docker/Dockerfile
+          platforms: linux/amd64
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
         with:
           context: .
           push: true

.github/workflows/sonarcloud.yml

@@ -32,6 +32,9 @@ jobs:
         run: |
           apt-get -y update
           apt-get install unzip
+      - name: Update pip
+        run: |
+          python3 -m pip install --break-system-packages --upgrade pip setuptools
 
       - name: Set up JDK 17
         uses: actions/setup-java@v4
@@ -64,13 +67,13 @@ jobs:
           echo "$HOME/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
 
       - name: Install DOLFINx
-        uses: jorgensd/actions/install-dolfinx@v0.2.0
+        uses: jorgensd/actions/install-dolfinx@v0.3
         with:
           petsc_arch: ${PETSC_ARCH}
-          dolfinx: v0.8.0
-          basix: v0.8.0
-          ufl: 2024.1.0.post0
-          ffcx: v0.8.0
+          dolfinx: main
+          basix: main
+          ufl: main
+          ffcx: main
 
       - name: Run build-wrapper
         run: |
@@ -84,7 +87,7 @@ jobs:
           cmake --install build-dir
 
       - name: Install DOLFINx-MPC (Python)
-        run: python3 -m pip -v install --config-settings=cmake.build-type="Release" --no-build-isolation  ./python
+        run: python3 -m pip -v install --break-system-packages --config-settings=cmake.build-type="Release" --no-build-isolation  ./python
 
       - name: Run sonar-scanner
         env:

.github/workflows/test_mpc.yml

@@ -56,7 +56,7 @@ jobs:
       HDF5_DIR: "/usr/local/"
       MPC_BUILD_MODE: ${{ matrix.build_mode }}
       MPC_CMAKE_CXX_FLAGS: "-Wall -Werror -g -pedantic -Ofast -march=native"
-      PYTHONPATH: "/usr/local/dolfinx-${PETSC_TYPE}/lib/python3.10/dist-packages:/usr/local/lib"
+      PYTHONPATH: "/usr/local/dolfinx-${PETSC_TYPE}/lib/python3.12/dist-packages:/usr/local/lib"
       LD_LIBRARY_PATH: "/usr/local/petsc/${PETSC_ARCH}/lib/:/usr/local"
       DEB_PYTHON_INSTALL_LAYOUT: deb_system
     steps:
@@ -69,7 +69,7 @@ jobs:
           apt-get install -y clang
 
       - name: upgrade pip
-        run: python3 -m pip install --upgrade setuptools pip
+        run: python3 -m pip install --break-system-packages --upgrade setuptools pip
 
       - name: Check formatting
         run: |
@@ -78,16 +78,16 @@ jobs:
 
       - name: Check typing
         run: |
-          python3 -m pip install mypy
+          python3 -m pip install --break-system-packages mypy
           cd python
           python3 -m mypy . --exclude=build
 
       - name: Install h5py
         run: |
-          python3 -m pip install --no-cache-dir --no-binary=h5py h5py
+          python3 -m pip install --no-build-isolation --break-system-packages --no-cache-dir --no-binary=h5py h5py
 
       - name: Install DOLFINx
-        uses: jorgensd/actions/install-dolfinx@v0.2.0
+        uses: jorgensd/actions/install-dolfinx@v0.3
         with:
           dolfinx: ${{ env.DOLFINX_BRANCH }}
           ufl: ${{ env.UFL_BRANCH }}
@@ -102,7 +102,7 @@ jobs:
           cmake --install build-dir
 
       - name: Install DOLFINx-MPC (Python)
-        run: python3 -m pip -v install --config-settings=cmake.build-type=${MPC_BUILD_MODE} --no-build-isolation  -e python/[test]
+        run: python3 -m pip -v install --break-system-packages --config-settings=cmake.build-type=${MPC_BUILD_MODE} --no-build-isolation  -e python/[test]
 
       - name: Run tests (serial)
         run: coverage run --rcfile=.coveragerc -m mpi4py -m pytest python/tests/ -vs

docker/Dockerfile

@@ -3,17 +3,17 @@ FROM ghcr.io/fenics/dolfinx/dolfinx:nightly
 WORKDIR /tmp
 
 # This argument should be the same as what-ever the python version of the dol
-ARG PYTHON_VERSION=3.10
+ARG PYTHON_VERSION=3.12
 
 # Set env variables
 ENV HDF5_MPI="ON" \
     HDF5_DIR="/usr/local"
 
-RUN python3 -m pip install -U pip setuptools
+RUN python3 -m pip install --break-system-packages -U pip setuptools
 
 # Install h5py https://github.com/h5py/h5py/issues/2222
-RUN python3 -m pip install --no-cache-dir --no-binary=h5py git+https://github.com/h5py/h5py.git
-RUN python3 -m pip install meshio 
+RUN python3 -m pip install --break-system-packages --no-cache-dir --no-binary=h5py git+https://github.com/h5py/h5py.git
+RUN python3 -m pip install --break-system-packages meshio 
 
 # Copy DOLFINX_MPC source dir
 COPY . dolfinx_mpc
@@ -23,7 +23,8 @@ RUN . /usr/local/bin/dolfinx-real-mode && \
     . /usr/local/dolfinx-real/lib/dolfinx/dolfinx.conf && \
     cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-real  -DCMAKE_BUILD_TYPE=Developer -B build-dir-real dolfinx_mpc/cpp/ && \
     ninja install -j4  -C build-dir-real && \
-    python3 -m pip install -v --no-build-isolation --check-build-dependencies --no-dependencies --target /usr/local/dolfinx-real/lib/python${PYTHON_VERSION}/dist-packages --config-settings=cmake.build-type=Developer -e dolfinx_mpc/python/[test]
+    python3 -m pip install -v --break-system-packages --no-build-isolation --check-build-dependencies \
+    --target /usr/local/dolfinx-real/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir ./dolfinx_mpc/python
 
 # Clean repo to remove build dir from pip
 RUN rm -rf dolfinx_mpc/python/build 
@@ -33,6 +34,7 @@ RUN . /usr/local/bin/dolfinx-complex-mode && \
     . /usr/local/dolfinx-complex/lib/dolfinx/dolfinx.conf && \
     cmake -G Ninja  -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-complex -DCMAKE_BUILD_TYPE=Developer -B build-dir-complex dolfinx_mpc/cpp/ && \
     ninja install -j4  -C build-dir-complex && \
-    python3 -m pip install -v --no-build-isolation --check-build-dependencies --no-dependencies --target /usr/local/dolfinx-complex/lib/python${PYTHON_VERSION}/dist-packages --config-settings=cmake.build-type=Developer -e dolfinx_mpc/python/[test]
+    python3 -m pip install --break-system-packages -v --no-build-isolation --check-build-dependencies \
+    --target /usr/local/dolfinx-complex/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir ./dolfinx_mpc/python
 
 WORKDIR /root

python/CMakeLists.txt

@@ -59,7 +59,8 @@ target_link_libraries(cpp PRIVATE dolfinx_mpc)
 
 # Check for petsc4py
 execute_process(
-  COMMAND ${Python_EXECUTABLE} -c "import petsc4py; print(petsc4py.get_include())"
+  COMMAND ${Python_EXECUTABLE} -c
+          "import petsc4py; print(petsc4py.get_include())"
   OUTPUT_VARIABLE PETSC4PY_INCLUDE_DIR
   RESULT_VARIABLE PETSC4PY_COMMAND_RESULT
   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE
@@ -68,8 +69,9 @@ execute_process(
 if(NOT PETSC4PY_COMMAND_RESULT)
   message(STATUS "Found petsc4py include directory at ${PETSC4PY_INCLUDE_DIR}")
   target_include_directories(cpp PRIVATE ${PETSC4PY_INCLUDE_DIR})
+  target_compile_definitions(cpp PRIVATE HAS_PETSC4PY)
 else()
-  message(FATAL_ERROR "petsc4py could not be found.")
+  message(FATAL_ERROR "petsc4py not found.")
 endif()
 
 

python/benchmarks/bench_contact_3D.py

@@ -211,7 +211,9 @@ def demo_stacked_cubes(theta, ct, noslip, num_refinements, N0, timings=False):
     mesh.name = f"mesh_{celltype}_{theta:.2f}{type_ext:s}"
 
     # Create functionspaces
-    el = basix.ufl.element("Lagrange", mesh.topology.cell_name(), 1, shape=(mesh.geometry.dim,))
+    el = basix.ufl.element(
+        "Lagrange", mesh.topology.cell_name(), 1, shape=(mesh.geometry.dim,), dtype=default_real_type
+    )
     V = functionspace(mesh, el)
 
     # Define boundary conditions

python/benchmarks/bench_elasticity.py

@@ -16,7 +16,7 @@
 import basix.ufl
 import h5py
 import numpy as np
-from dolfinx import default_scalar_type
+from dolfinx import default_real_type, default_scalar_type
 from dolfinx.common import Timer, TimingType, list_timings
 from dolfinx.fem import (
     Constant,
@@ -49,7 +49,9 @@ def bench_elasticity_one(
         mesh = refine(mesh, redistribute=True)
 
     fdim = mesh.topology.dim - 1
-    el = basix.ufl.element("Lagrange", mesh.topology.cell_name(), 1, shape=(mesh.geometry.dim,))
+    el = basix.ufl.element(
+        "Lagrange", mesh.topology.cell_name(), 1, shape=(mesh.geometry.dim,), dtype=default_real_type
+    )
     V = functionspace(mesh, el)
 
     # Generate Dirichlet BC on lower boundary (Fixed)

python/benchmarks/bench_elasticity_edge.py

@@ -15,7 +15,7 @@
 import basix.ufl
 import h5py
 import numpy as np
-from dolfinx import default_scalar_type
+from dolfinx import default_real_type, default_scalar_type
 from dolfinx.common import Timer, TimingType, list_timings
 from dolfinx.fem import (
     Constant,
@@ -62,7 +62,9 @@ def bench_elasticity_edge(
     ct = CellType.tetrahedron if tetra else CellType.hexahedron
     mesh = create_unit_cube(MPI.COMM_WORLD, N, N, N, ct)
 
-    el = basix.ufl.element("Lagrange", mesh.topology.cell_name(), int(degree), shape=(mesh.geometry.dim,))
+    el = basix.ufl.element(
+        "Lagrange", mesh.topology.cell_name(), int(degree), shape=(mesh.geometry.dim,), dtype=default_real_type
+    )
     V = functionspace(mesh, el)
 
     # Generate Dirichlet BC (Fixed)

python/benchmarks/ref_elasticity.py

@@ -17,7 +17,7 @@
 import basix.ufl
 import h5py
 import numpy as np
-from dolfinx import default_scalar_type
+from dolfinx import default_real_type, default_scalar_type
 from dolfinx.common import Timer, TimingType, list_timings
 from dolfinx.fem import (
     Constant,
@@ -73,7 +73,9 @@ def ref_elasticity(
         # set_log_level(LogLevel.ERROR)
     N = degree * N
     fdim = mesh.topology.dim - 1
-    el = basix.ufl.element("Lagrange", mesh.topology.cell_name(), 1, shape=(mesh.geometry.dim,))
+    el = basix.ufl.element(
+        "Lagrange", mesh.topology.cell_name(), 1, shape=(mesh.geometry.dim,), dtype=default_real_type
+    )
     V = functionspace(mesh, el)
 
     # Generate Dirichlet BC on lower boundary (Fixed)

python/demos/demo_elasticity_disconnect.py

@@ -14,7 +14,7 @@
 import basix.ufl
 import gmsh
 import numpy as np
-from dolfinx import default_scalar_type
+from dolfinx import default_real_type, default_scalar_type
 from dolfinx.fem import Constant, Function, dirichletbc, functionspace, locate_dofs_topological
 from dolfinx.io import XDMFFile, gmshio
 from ufl import (
@@ -224,6 +224,7 @@ def sigma(v):
         mesh.geometry.cmap.degree,
         lagrange_variant=basix.LagrangeVariant(mesh.geometry.cmap.variant),
         shape=(V.dofmap.bs,),
+        dtype=default_real_type,
     ),
 )
 u_out = Function(V_out)

python/demos/demo_stokes.py

@@ -21,7 +21,7 @@
 import gmsh
 import numpy as np
 import scipy.sparse.linalg
-from dolfinx import common, default_scalar_type, fem, io
+from dolfinx import common, default_real_type, default_scalar_type, fem, io
 from dolfinx.io import gmshio
 from numpy.typing import NDArray
 from ufl import (
@@ -141,8 +141,8 @@ def create_mesh_gmsh(
 # The next step is the create the function spaces for the fluid velocit and pressure.
 # We will use a mixed-formulation, and we use `basix.ufl` to create the Taylor-Hood finite element pair
 
-P2 = basix.ufl.element("Lagrange", mesh.topology.cell_name(), 2, shape=(mesh.geometry.dim,))
-P1 = basix.ufl.element("Lagrange", mesh.topology.cell_name(), 1)
+P2 = basix.ufl.element("Lagrange", mesh.topology.cell_name(), 2, shape=(mesh.geometry.dim,), dtype=default_real_type)
+P1 = basix.ufl.element("Lagrange", mesh.topology.cell_name(), 1, dtype=default_real_type)
 
 TH = basix.ufl.mixed_element([P2, P1])
 W = fem.functionspace(mesh, TH)

python/demos/demo_stokes_nest.py

@@ -22,7 +22,7 @@
 import numpy as np
 import scipy.sparse.linalg
 import ufl
-from dolfinx import default_scalar_type
+from dolfinx import default_real_type, default_scalar_type
 from dolfinx.io import gmshio
 from ufl.core.expr import Expr
 
@@ -120,8 +120,8 @@ def create_mesh_gmsh(
 
 # Create the function space
 cellname = mesh.ufl_cell().cellname()
-Ve = basix.ufl.element(basix.ElementFamily.P, cellname, 2, shape=(mesh.geometry.dim,))
-Qe = basix.ufl.element(basix.ElementFamily.P, cellname, 1)
+Ve = basix.ufl.element(basix.ElementFamily.P, cellname, 2, shape=(mesh.geometry.dim,), dtype=default_real_type)
+Qe = basix.ufl.element(basix.ElementFamily.P, cellname, 1, dtype=default_real_type)
 
 V = dolfinx.fem.functionspace(mesh, Ve)
 Q = dolfinx.fem.functionspace(mesh, Qe)

python/dolfinx_mpc/mpc.cpp

@@ -33,6 +33,7 @@
 #include <nanobind/stl/string.h>
 #include <nanobind/stl/tuple.h>
 #include <nanobind/stl/vector.h>
+#include <petsc4py/petsc4py.h>
 #include <petscmat.h>
 #include <petscvec.h>
 namespace nb = nanobind;