Merge branch 'main' into dokken/mixed_quadrature

Author: jorgensd

.github/workflows/ccpp.yml

@@ -93,22 +93,22 @@ jobs:
 
       - name: Install Python build dependencies
         run: |
-          pip install --upgrade -r python/build-requirements.txt
+          pip -v install --upgrade -r python/build-requirements.txt
 
       - name: Install FEniCS Python components
         run: |
-          pip install git+https://github.com/fenics/ufl.git@${{ env.ufl_ref }}
-          pip install git+https://github.com/fenics/basix.git@${{ env.basix_ref }}
-          pip install git+https://github.com/fenics/ffcx.git@${{ env.ffcx_ref }}
+          pip install --no-build-isolation git+https://github.com/fenics/ufl.git@${{ env.ufl_ref }}
+          pip install --no-build-isolation git+https://github.com/fenics/basix.git@${{ env.basix_ref }}
+          pip install --no-build-isolation git+https://github.com/fenics/ffcx.git@${{ env.ffcx_ref }}
 
       - name: Configure and install C++
         run: |
-          cmake -G Ninja -DDOLFINX_ENABLE_PETSC=false -DCMAKE_BUILD_TYPE=Developer -B build -S cpp/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -DDOLFINX_ENABLE_PETSC=false -DCMAKE_BUILD_TYPE=Developer -B build -S cpp/
           cmake --build build
           sudo cmake --install build
       - name: Build C++ unit tests
         run: |
-          cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S cpp/test/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S cpp/test/
           cmake --build build/test
       - name: Run C++ unit tests (serial)
         run: |
@@ -124,9 +124,11 @@ jobs:
           pip install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Debug" 'python/[test]'
           python -c "from mpi4py import MPI; import dolfinx; assert not dolfinx.has_petsc4py"
 
-      - name: Run mypy
+      - name: Run mypy  # Use a venv to avoid NumPy upgrades that are incompatible with numba
         working-directory: python
         run: |
+          python -m venv mypy-env
+          . ./mypy-env/bin/activate
           pip install mypy types-cffi scipy-stubs
           mypy -p dolfinx
         # mypy test
@@ -175,21 +177,24 @@ jobs:
       - name: Load environment variables
         run: cat .github/workflows/fenicsx-refs.env >> $GITHUB_ENV
 
+      - name: Install Python build dependencies
+        run: pip install -r python/build-requirements.txt
+
       - name: Install FEniCS Python components
         run: |
-          pip install git+https://github.com/FEniCS/ufl.git@${{ env.ufl_ref }}
-          pip install git+https://github.com/FEniCS/basix.git@${{ env.basix_ref }}
-          pip install git+https://github.com/FEniCS/ffcx.git@${{ env.ffcx_ref }}
+          pip install --no-build-isolation git+https://github.com/FEniCS/ufl.git@${{ env.ufl_ref }}
+          pip install --no-build-isolation git+https://github.com/FEniCS/basix.git@${{ env.basix_ref }}
+          pip install --no-build-isolation git+https://github.com/FEniCS/ffcx.git@${{ env.ffcx_ref }}
 
       - name: Configure, build and install C++ library
         run: |
-          cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -DDOLFINX_ENABLE_ADIOS2=true -DDOLFINX_ENABLE_KAHIP=true -DDOLFINX_ENABLE_PARMETIS=false -DDOLFINX_ENABLE_PETSC=true -DDOLFINX_ENABLE_SCOTCH=true -DDOLFINX_ENABLE_SLEPC=true -B build -S cpp/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -DDOLFINX_ENABLE_ADIOS2=true -DDOLFINX_ENABLE_KAHIP=true -DDOLFINX_ENABLE_PARMETIS=false -DDOLFINX_ENABLE_PETSC=true -DDOLFINX_ENABLE_SCOTCH=true -DDOLFINX_ENABLE_SLEPC=true -B build -S cpp/
           cmake --build build
           cmake --install build
 
       - name: Build C++ unit tests
         run: |
-          cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S cpp/test/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S cpp/test/
           cmake --build build/test
       - name: Run C++ unit tests (serial)
         run: |
@@ -201,28 +206,30 @@ jobs:
           mpirun -n 3 ctest -V --output-on-failure -R unittests
       - name: Build and run C++ regression tests (serial and MPI (np=2))
         run: |
-          cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/demo/ -S cpp/demo/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/demo/ -S cpp/demo/
           cmake --build build/demo
           cd build/demo
           ctest -V -R demo -R serial
           ctest --output-on-failure -V -R demo -R mpi_2
 
-      - name: Install Python build dependencies
-        run: pip install -r python/build-requirements.txt
-
       - name: Build Python interface
         run: |
           pip install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Debug" 'python/[test]'
           python -c "from mpi4py import MPI; import dolfinx; assert dolfinx.has_adios2; assert dolfinx.has_kahip; assert not dolfinx.has_parmetis; assert dolfinx.has_petsc; assert dolfinx.has_petsc4py; assert dolfinx.has_ptscotch; assert dolfinx.has_slepc; assert dolfinx.has_complex_ufcx_kernels"
 
-      - name: Run mypy
+      - name: Run mypy  # Use a venv to avoid NumPy upgrades that are incompatible with numba
         working-directory: python
         run: |
+          python -m venv mypy-env
+          . ./mypy-env/bin/activate
           pip install mypy types-cffi scipy-stubs
           mypy -p dolfinx
         # mypy test
         # mypy demo
 
+      - name: Numpy version
+        run: python -c "import numpy; print(numpy.__version__)"
+
       - name: Set default DOLFINx JIT options
         run: |
           mkdir -p ~/.config/dolfinx
@@ -264,19 +271,19 @@ jobs:
 
       - name: Install FEniCS Python components
         run: |
-          pip install git+https://github.com/FEniCS/ufl.git@${{ env.ufl_ref }}
-          pip install git+https://github.com/FEniCS/basix.git@${{ env.basix_ref }}
-          pip install git+https://github.com/FEniCS/ffcx.git@${{ env.ffcx_ref }}
+          pip install -r python/build-requirements.txt
+          pip install --no-build-isolation git+https://github.com/FEniCS/ufl.git@${{ env.ufl_ref }}
+          pip install --no-build-isolation git+https://github.com/FEniCS/basix.git@${{ env.basix_ref }}
+          pip install --no-build-isolation git+https://github.com/FEniCS/ffcx.git@${{ env.ffcx_ref }}
 
       - name: Configure C++
         run: |
-          cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build -S cpp/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build -S cpp/
           cmake --build build
           cmake --install build
 
       - name: Build Python interface
         run: |
-          pip install -r python/build-requirements.txt
           pip install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Debug" 'python/[docs]'
 
       - name: Build C++ interface documentation

.github/workflows/ci-spack.yml

@@ -94,15 +94,15 @@ jobs:
         run: |
           . ./spack-src/share/spack/setup-env.sh
           spack env activate .
-          cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build -S dolfinx-src/cpp/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build -S dolfinx-src/cpp/
           cmake --build build
           cmake --install build
 
       - name: Build C++ unit tests
         run: |
           . ./spack-src/share/spack/setup-env.sh
           spack env activate .
-          cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S dolfinx-src/cpp/test/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S dolfinx-src/cpp/test/
           cmake --build build/test
       - name: Run C++ unit tests (serial and MPI)
         run: |
@@ -114,7 +114,7 @@ jobs:
         run: |
           . ./spack-src/share/spack/setup-env.sh
           spack env activate .
-          cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/demo/ -S dolfinx-src/cpp/demo/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/demo/ -S dolfinx-src/cpp/demo/
           cmake --build build/demo
           cd build/demo
           ctest -V -R demo -R serial

.github/workflows/macos.yml

@@ -50,7 +50,7 @@ jobs:
         run: |
           export PATH="$(brew --prefix gfortran)/bin:$(brew --prefix bison)/bin:$PATH"
           export PATH="$(brew --prefix make)/libexec/gnubin:$PATH"
-          git clone -b release https://gitlab.com/petsc/petsc.git petsc
+          git clone --depth 1 --branch release https://gitlab.com/petsc/petsc.git petsc
           cd petsc
           python ./configure \
             --with-64-bit-indices=no \
@@ -79,19 +79,20 @@ jobs:
 
       - name: Build and install DOLFINx C++ library
         run: |
-          cmake -G Ninja -B build -S cpp/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -B build -S cpp/
           cmake --build build
           sudo cmake --install build
 
       - name: Build C++ unit tests
         run: |
-          cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S cpp/test/
+          cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S cpp/test/
           cmake --build build/test
 
       - name: Run C++ unit tests (serial)
         run: |
           cd build/test
           mpiexec -np 1 ctest -V --output-on-failure -R unittests
+
       - name: Run C++ unit tests (MPI)
         run: |
           cd build/test

README.md

@@ -1,11 +1,10 @@
 # DOLFINx
 
 [![DOLFINx CI](https://github.com/FEniCS/dolfinx/actions/workflows/ccpp.yml/badge.svg)](https://github.com/FEniCS/dolfinx/actions/workflows/ccpp.yml)
-[![Actions Docker images](https://github.com/FEniCS/dolfinx/actions/workflows/docker-end-user.yml/badge.svg)](https://github.com/FEniCS/dolfinx/actions/workflows/docker-end-user.yml)
 [![Actions Spack build](https://github.com/FEniCS/dolfinx/actions/workflows/spack.yml/badge.svg)](https://github.com/FEniCS/dolfinx/actions/workflows/spack.yml)
 [![Actions Conda install](https://github.com/FEniCS/dolfinx/actions/workflows/conda.yml/badge.svg)](https://github.com/FEniCS/dolfinx/actions/workflows/conda.yml)
 [![Actions macOS/Homebrew install](https://github.com/FEniCS/dolfinx/actions/workflows/macos.yml/badge.svg)](https://github.com/FEniCS/dolfinx/actions/workflows/macos.yml)
-[![Actions Windows/vcpkg install](https://github.com/FEniCS/dolfinx/actions/workflows/windows.yml/badge.svg)](https://github.com/FEniCS/dolfinx/actions/workflows/windows.yml)
+[![Actions Docker images](https://github.com/FEniCS/dolfinx/actions/workflows/docker-end-user.yml/badge.svg)](https://github.com/FEniCS/dolfinx/actions/workflows/docker-end-user.yml)
 
 DOLFINx is the computational environment of
 [FEniCSx](https://fenicsproject.org) and implements the FEniCS Problem
@@ -26,7 +25,7 @@ Documentation can be viewed at <https://docs.fenicsproject.org>.
 
 ### From source
 
-For detailed instructions and the list of dependencies, see
+For detailed instructions and a list of dependencies, see
 <https://docs.fenicsproject.org/dolfinx/main/python/installation>.
 
 #### C++ core
@@ -52,9 +51,9 @@ pip install --check-build-dependencies --no-build-isolation .
 
 ### Spack
 
-Spack is recommended for building DOLFINx on HPC systems. To build the
-most recent release using [Spack](https://spack.readthedocs.io/)
-(assuming a bash-compatible shell):
+To build the most recent release using
+[Spack](https://spack.readthedocs.io/) (assuming a bash-compatible
+shell):
 
 ```shell
 git clone https://github.com/spack/spack.git
@@ -65,10 +64,9 @@ spack add fenics-dolfinx+petsc+adios2 py-fenics-dolfinx cflags="-O3" fflags="-O3
 spack install
 ```
 
-See the Spack [documentation](https://spack.readthedocs.io/) for
-comprehensive instructions.
+Spack is the recommended approach for HPC systems.
 
-### Binary
+### Binary packages
 
 **Recommendations**
 
@@ -94,10 +92,9 @@ conda install -c conda-forge fenics-dolfinx mpich pyvista # Linux and macOS
 conda install -c conda-forge fenics-dolfinx pyvista pyamg # Windows
 ```
 
-*Windows only*: Windows conda packages are currently in beta testing. PETSc and
-petsc4py are not available on Windows; as an alternative we recommend using
-`pyamg` following `python/demo/demo_pyamg.py`. Because FEniCS uses just-in-time
-compilation it necessary to install [Microsoft Visual
+*Windows only*: Windows conda packages are currently in beta testing.
+PETSc and petsc4py are not available on Windows. Because FEniCS uses
+just-in-time compilation it necessary to install [Microsoft Visual
 Studio](https://visualstudio.microsoft.com/downloads/).
 
 conda is distributed with [Anaconda](https://www.anaconda.com/) and