Merge branch 'main' into main

FEniCS · Sep 15, 2024 · 6fda65d · 6fda65d
2 parents 5baf1c2 + 9635a82
commit 6fda65d
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diff --git a/.github/workflows/pyvista.yml b/.github/workflows/pyvista.yml
@@ -20,8 +20,8 @@ jobs:
       # For pyvista/pyvistaqt
       DISPLAY: ":99.0"
       PYVISTA_OFF_SCREEN: true
-      PYVISTA_QT_VERSION: 0.11.0
-      PYVISTA_VERSION: 0.43.10
+      PYVISTA_QT_VERSION: 0.11.1
+      PYVISTA_VERSION: 0.44.1
       QT_DEBUG_PLUGINS: 1
 
       PETSC_ARCH: ${{ matrix.petsc_arch }}

diff --git a/cpp/cmake/templates/DOLFINXConfig.cmake.in b/cpp/cmake/templates/DOLFINXConfig.cmake.in
@@ -12,13 +12,17 @@ find_dependency(MPI REQUIRED)
 find_dependency(spdlog REQUIRED)
 find_dependency(pugixml REQUIRED)
 
+if(POLICY CMP0167)
+  cmake_policy(SET CMP0167 NEW)  # Boost CONFIG mode
+endif()
+
 # Check for Boost
 if(DEFINED ENV{BOOST_ROOT} OR DEFINED BOOST_ROOT)
   set(Boost_NO_SYSTEM_PATHS on)
 endif()
 set(Boost_USE_MULTITHREADED $ENV{BOOST_USE_MULTITHREADED})
 set(Boost_VERBOSE TRUE)
-find_dependency(Boost 1.70 REQUIRED COMPONENTS timer)
+find_package(Boost 1.70 REQUIRED timer)
 
 if(@ufcx_FOUND@)
   find_dependency(ufcx)

diff --git a/cpp/dolfinx/mesh/generation.h b/cpp/dolfinx/mesh/generation.h
@@ -37,36 +37,36 @@ enum class DiagonalType
 namespace impl
 {
 template <std::floating_point T>
-Mesh<T> build_tri(MPI_Comm comm, std::array<std::array<double, 2>, 2> p,
+Mesh<T> build_tri(MPI_Comm comm, std::array<std::array<T, 2>, 2> p,
                   std::array<std::int64_t, 2> n,
                   const CellPartitionFunction& partitioner,
                   DiagonalType diagonal);
 
 template <std::floating_point T>
-Mesh<T> build_quad(MPI_Comm comm, const std::array<std::array<double, 2>, 2> p,
+Mesh<T> build_quad(MPI_Comm comm, const std::array<std::array<T, 2>, 2> p,
                    std::array<std::int64_t, 2> n,
                    const CellPartitionFunction& partitioner);
 
 template <std::floating_point T>
 std::vector<T> create_geom(MPI_Comm comm,
-                           std::array<std::array<double, 3>, 2> p,
+                           std::array<std::array<T, 3>, 2> p,
                            std::array<std::int64_t, 3> n);
 
 template <std::floating_point T>
 Mesh<T> build_tet(MPI_Comm comm, MPI_Comm subcomm,
-                  std::array<std::array<double, 3>, 2> p,
+                  std::array<std::array<T, 3>, 2> p,
                   std::array<std::int64_t, 3> n,
                   const CellPartitionFunction& partitioner);
 
 template <std::floating_point T>
 Mesh<T> build_hex(MPI_Comm comm, MPI_Comm subcomm,
-                  std::array<std::array<double, 3>, 2> p,
+                  std::array<std::array<T, 3>, 2> p,
                   std::array<std::int64_t, 3> n,
                   const CellPartitionFunction& partitioner);
 
 template <std::floating_point T>
 Mesh<T> build_prism(MPI_Comm comm, MPI_Comm subcomm,
-                    std::array<std::array<double, 3>, 2> p,
+                    std::array<std::array<T, 3>, 2> p,
                     std::array<std::int64_t, 3> n,
                     const CellPartitionFunction& partitioner);
 } // namespace impl
@@ -93,7 +93,7 @@ Mesh<T> build_prism(MPI_Comm comm, MPI_Comm subcomm,
 /// @return Mesh
 template <std::floating_point T = double>
 Mesh<T> create_box(MPI_Comm comm, MPI_Comm subcomm,
-                   std::array<std::array<double, 3>, 2> p,
+                   std::array<std::array<T, 3>, 2> p,
                    std::array<std::int64_t, 3> n, CellType celltype,
                    CellPartitionFunction partitioner = nullptr)
 {
@@ -139,7 +139,7 @@ Mesh<T> create_box(MPI_Comm comm, MPI_Comm subcomm,
 /// across MPI ranks.
 /// @return Mesh
 template <std::floating_point T = double>
-Mesh<T> create_box(MPI_Comm comm, std::array<std::array<double, 3>, 2> p,
+Mesh<T> create_box(MPI_Comm comm, std::array<std::array<T, 3>, 2> p,
                    std::array<std::int64_t, 3> n, CellType celltype,
                    const CellPartitionFunction& partitioner = nullptr)
 {
@@ -163,7 +163,7 @@ Mesh<T> create_box(MPI_Comm comm, std::array<std::array<double, 3>, 2> p,
 /// @param[in] diagonal Direction of diagonals
 /// @return Mesh
 template <std::floating_point T = double>
-Mesh<T> create_rectangle(MPI_Comm comm, std::array<std::array<double, 2>, 2> p,
+Mesh<T> create_rectangle(MPI_Comm comm, std::array<std::array<T, 2>, 2> p,
                          std::array<std::int64_t, 2> n, CellType celltype,
                          CellPartitionFunction partitioner,
                          DiagonalType diagonal = DiagonalType::right)
@@ -206,7 +206,7 @@ Mesh<T> create_rectangle(MPI_Comm comm, std::array<std::array<double, 2>, 2> p,
 /// @param[in] diagonal Direction of diagonals
 /// @return Mesh
 template <std::floating_point T = double>
-Mesh<T> create_rectangle(MPI_Comm comm, std::array<std::array<double, 2>, 2> p,
+Mesh<T> create_rectangle(MPI_Comm comm, std::array<std::array<T, 2>, 2> p,
                          std::array<std::int64_t, 2> n, CellType celltype,
                          DiagonalType diagonal = DiagonalType::right)
 {
@@ -227,7 +227,7 @@ Mesh<T> create_rectangle(MPI_Comm comm, std::array<std::array<double, 2>, 2> p,
 /// across MPI ranks.
 /// @return A mesh.
 template <std::floating_point T = double>
-Mesh<T> create_interval(MPI_Comm comm, std::int64_t n, std::array<double, 2> p,
+Mesh<T> create_interval(MPI_Comm comm, std::int64_t n, std::array<T, 2> p,
                         mesh::GhostMode ghost_mode = mesh::GhostMode::none,
                         CellPartitionFunction partitioner = nullptr)
 {
@@ -278,7 +278,7 @@ namespace impl
 {
 template <std::floating_point T>
 std::vector<T> create_geom(MPI_Comm comm,
-                           std::array<std::array<double, 3>, 2> p,
+                           std::array<std::array<T, 3>, 2> p,
                            std::array<std::int64_t, 3> n)
 {
   // Extract data
@@ -327,7 +327,7 @@ std::vector<T> create_geom(MPI_Comm comm,
 
 template <std::floating_point T>
 Mesh<T> build_tet(MPI_Comm comm, MPI_Comm subcomm,
-                  std::array<std::array<double, 3>, 2> p,
+                  std::array<std::array<T, 3>, 2> p,
                   std::array<std::int64_t, 3> n,
                   const CellPartitionFunction& partitioner)
 {
@@ -375,7 +375,7 @@ Mesh<T> build_tet(MPI_Comm comm, MPI_Comm subcomm,
 
 template <std::floating_point T>
 mesh::Mesh<T> build_hex(MPI_Comm comm, MPI_Comm subcomm,
-                        std::array<std::array<double, 3>, 2> p,
+                        std::array<std::array<T, 3>, 2> p,
                         std::array<std::int64_t, 3> n,
                         const CellPartitionFunction& partitioner)
 {
@@ -418,7 +418,7 @@ mesh::Mesh<T> build_hex(MPI_Comm comm, MPI_Comm subcomm,
 
 template <std::floating_point T>
 Mesh<T> build_prism(MPI_Comm comm, MPI_Comm subcomm,
-                    std::array<std::array<double, 3>, 2> p,
+                    std::array<std::array<T, 3>, 2> p,
                     std::array<std::int64_t, 3> n,
                     const CellPartitionFunction& partitioner)
 {
@@ -464,7 +464,7 @@ Mesh<T> build_prism(MPI_Comm comm, MPI_Comm subcomm,
 }
 
 template <std::floating_point T>
-Mesh<T> build_tri(MPI_Comm comm, std::array<std::array<double, 2>, 2> p,
+Mesh<T> build_tri(MPI_Comm comm, std::array<std::array<T, 2>, 2> p,
                   std::array<std::int64_t, 2> n,
                   const CellPartitionFunction& partitioner,
                   DiagonalType diagonal)
@@ -621,7 +621,7 @@ Mesh<T> build_tri(MPI_Comm comm, std::array<std::array<double, 2>, 2> p,
 }
 
 template <std::floating_point T>
-Mesh<T> build_quad(MPI_Comm comm, const std::array<std::array<double, 2>, 2> p,
+Mesh<T> build_quad(MPI_Comm comm, const std::array<std::array<T, 2>, 2> p,
                    std::array<std::int64_t, 2> n,
                    const CellPartitionFunction& partitioner)
 {

diff --git a/docker/Dockerfile.end-user b/docker/Dockerfile.end-user
@@ -34,7 +34,7 @@
 #    echo "FROM dolfinx/dolfinx-onbuild:nightly" | docker build -f- .
 #
 
-ARG PYVISTA_VERSION=0.43.8
+ARG PYVISTA_VERSION=0.44.1
 
 # Used to set the correct PYTHONPATH for the real and complex install of
 # DOLFINx
@@ -170,7 +170,7 @@ RUN dpkgArch="$(dpkg --print-architecture)"; \
       pip install --no-cache-dir pyvista[trame]==${PYVISTA_VERSION} ;; \
     esac; \
     case "$dpkgArch" in arm64) \
-      pip install --no-cache-dir https://github.com/finsberg/vtk-aarch64/releases/download/vtk-9.3.0-cp312/vtk-9.3.0.dev0-cp312-cp312-linux_aarch64.whl && \ 
+      pip install --no-cache-dir https://github.com/finsberg/vtk-aarch64/releases/download/vtk-9.3.0-cp312/vtk-9.3.0.dev0-cp312-cp312-linux_aarch64.whl && \
       pip install --no-cache-dir pyvista[trame]==${PYVISTA_VERSION} ;; \
     esac; \
     pip cache purge

diff --git a/docker/Dockerfile.redhat b/docker/Dockerfile.redhat
@@ -7,10 +7,8 @@ FROM rockylinux/rockylinux:9
 
 ARG BUILD_NP=4
 
-ARG HDF5_SERIES=1.14
-ARG HDF5_PATCH=3
-ARG HDF5_FIX=
-ARG PETSC_VERSION=3.21.3
+ARG HDF5_VERSION=1.14.4.3
+ARG PETSC_VERSION=3.21.5
 ARG MPICH_VERSION=4.2.2
 
 WORKDIR /tmp
@@ -54,9 +52,9 @@ RUN curl -L -O https://www.mpich.org/static/downloads/${MPICH_VERSION}/mpich-${M
     rm -rf /tmp/*
 
 # Build HDF5
-RUN curl -L -O https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_SERIES}/hdf5-${HDF5_SERIES}.${HDF5_PATCH}/src/hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX}.tar.gz && \
-    tar -xf hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX}.tar.gz && \
-    cd hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX} && \
+RUN curl -L -O https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${HDF5_VERSION}.tar.gz && \
+    tar -xf hdf5_${HDF5_VERSION}.tar.gz && \
+    cd hdf5-hdf5_${HDF5_VERSION} && \
     ./configure --prefix=/usr/local --enable-parallel --enable-shared --enable-static=no && \
     make -j${BUILD_NP} install && \
     rm -rf /tmp/*

diff --git a/docker/Dockerfile.test-env b/docker/Dockerfile.test-env
@@ -13,14 +13,12 @@
 #
 
 ARG ADIOS2_VERSION=2.10.1
-ARG DOXYGEN_VERSION=1_11_0
+ARG DOXYGEN_VERSION=1_12_0
 ARG GMSH_VERSION=4_13_1
-ARG HDF5_SERIES=1.14
-ARG HDF5_PATCH=3
-ARG HDF5_FIX=
+ARG HDF5_VERSION=1.14.4.3
 ARG KAHIP_VERSION=3.16
-ARG NUMPY_VERSION=1.26.4
-ARG PETSC_VERSION=3.21.3
+ARG NUMPY_VERSION=2.1.1
+ARG PETSC_VERSION=3.21.5
 ARG SLEPC_VERSION=3.21.1
 
 ARG MPICH_VERSION=4.2.2
@@ -35,9 +33,7 @@ LABEL description="FEniCS testing and development environment with PETSc real, c
 
 ARG DOXYGEN_VERSION
 ARG GMSH_VERSION
-ARG HDF5_SERIES
-ARG HDF5_PATCH
-ARG HDF5_FIX
+ARG HDF5_VERSION
 ARG PETSC_VERSION
 ARG SLEPC_VERSION
 ARG ADIOS2_VERSION
@@ -149,7 +145,7 @@ RUN python3 -m venv ${VIRTUAL_ENV}
 
 # Install Python packages (via pip)
 RUN pip install --no-cache-dir --upgrade pip setuptools wheel && \
-    pip install --no-cache-dir numpy==${NUMPY_VERSION} && \
+    pip install --no-cache-dir cython numpy==${NUMPY_VERSION} && \
     pip install --no-cache-dir --no-build-isolation mpi4py
 
 # Install KaHIP
@@ -165,9 +161,9 @@ RUN wget -nc --quiet https://github.com/kahip/kahip/archive/v${KAHIP_VERSION}.ta
 # HDF5 overrides CMAKE_INSTALL_PREFIX by default, hence it is set
 # below to ensure that HDF5 is installed into a path where it can be
 # found.
-RUN wget -nc --quiet https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_SERIES}/hdf5-${HDF5_SERIES}.${HDF5_PATCH}/src/hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX}.tar.gz && \
-    tar xfz hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX}.tar.gz && \
-    cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DHDF5_ENABLE_PARALLEL=on -DHDF5_ENABLE_Z_LIB_SUPPORT=on -B build-dir -S hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX} && \
+RUN wget -nc --quiet https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${HDF5_VERSION}.tar.gz && \
+    tar xfz hdf5_${HDF5_VERSION}.tar.gz && \
+    cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DHDF5_ENABLE_PARALLEL=on -DHDF5_ENABLE_Z_LIB_SUPPORT=on -B build-dir -S hdf5-hdf5_${HDF5_VERSION} && \
     cmake --build build-dir && \
     cmake --install build-dir && \
     rm -rf /tmp/*
@@ -316,9 +312,7 @@ RUN apt-get -qq update && \
     make PETSC_ARCH=linux-gnu-complex128-64 ${MAKEFLAGS} all && \
     # Install petsc4py
     cd src/binding/petsc4py && \
-    pip install --no-cache-dir cython && \
     PETSC_ARCH=linux-gnu-real32-32:linux-gnu-complex64-32:linux-gnu-real64-32:linux-gnu-complex128-32:linux-gnu-real64-64:linux-gnu-complex128-64 pip -v install --no-cache-dir --no-build-isolation . && \
-    pip3 uninstall --yes cython && \
     # Cleanup
     apt-get -y purge bison flex && \
     apt-get -y autoremove && \
@@ -359,9 +353,7 @@ RUN git clone --depth=1 -b v${SLEPC_VERSION} https://gitlab.com/slepc/slepc.git
     make && \
     # Install slepc4py
     cd src/binding/slepc4py && \
-    pip3 install --no-cache-dir cython && \
     PETSC_ARCH=linux-gnu-real32-32:linux-gnu-complex64-32:linux-gnu-real64-32:linux-gnu-complex128-32:linux-gnu-real64-64:linux-gnu-complex128-64 pip -v install --no-cache-dir --no-build-isolation . && \
-    pip3 uninstall --yes cython && \
     rm -rf ${SLEPC_DIR}/CTAGS ${SLEPC_DIR}/TAGS ${SLEPC_DIR}/docs ${SLEPC_DIR}/src/ ${SLEPC_DIR}/**/obj/ ${SLEPC_DIR}/**/test/ && \
     rm -rf /tmp/*
 

diff --git a/python/dolfinx/wrappers/la.cpp b/python/dolfinx/wrappers/la.cpp
@@ -138,7 +138,7 @@ void declare_objects(nb::module_& m, const std::string& type)
              std::size_t nrows = self.num_all_rows() * bs[0];
              std::size_t ncols = self.index_map(1)->size_global() * bs[1];
              auto dense = self.to_dense();
-             assert(nrows*ncols == dense.size());
+             assert(nrows * ncols == dense.size());
              return dolfinx_wrappers::as_nbarray(std::move(self.to_dense()),
                                                  {nrows, ncols});
            })

diff --git a/python/dolfinx/wrappers/mesh.cpp b/python/dolfinx/wrappers/mesh.cpp
@@ -241,7 +241,7 @@ void declare_mesh(nb::module_& m, std::string type)
   std::string create_interval("create_interval_" + type);
   m.def(
       create_interval.c_str(),
-      [](MPICommWrapper comm, std::int64_t n, std::array<double, 2> p,
+      [](MPICommWrapper comm, std::int64_t n, std::array<T, 2> p,
          dolfinx::mesh::GhostMode ghost_mode,
          const PythonCellPartitionFunction& part)
       {
@@ -254,7 +254,7 @@ void declare_mesh(nb::module_& m, std::string type)
   std::string create_rectangle("create_rectangle_" + type);
   m.def(
       create_rectangle.c_str(),
-      [](MPICommWrapper comm, std::array<std::array<double, 2>, 2> p,
+      [](MPICommWrapper comm, std::array<std::array<T, 2>, 2> p,
          std::array<std::int64_t, 2> n, dolfinx::mesh::CellType celltype,
          const PythonCellPartitionFunction& part,
          dolfinx::mesh::DiagonalType diagonal)
@@ -269,7 +269,7 @@ void declare_mesh(nb::module_& m, std::string type)
   std::string create_box("create_box_" + type);
   m.def(
       create_box.c_str(),
-      [](MPICommWrapper comm, std::array<std::array<double, 3>, 2> p,
+      [](MPICommWrapper comm, std::array<std::array<T, 3>, 2> p,
          std::array<std::int64_t, 3> n, dolfinx::mesh::CellType celltype,
          const PythonCellPartitionFunction& part)
       {

diff --git a/python/dolfinx/wrappers/refinement.cpp b/python/dolfinx/wrappers/refinement.cpp
@@ -47,8 +47,9 @@ void export_refinement_with_variable_mesh_type(nb::module_& m)
       [](const dolfinx::mesh::Mesh<T>& mesh, bool redistribute,
          dolfinx::mesh::GhostMode ghost_mode)
       {
-        auto [mesh_refined, parent_cells] = dolfinx::refinement::refine_interval(
-            mesh, std::nullopt, redistribute, ghost_mode);
+        auto [mesh_refined, parent_cells]
+            = dolfinx::refinement::refine_interval(mesh, std::nullopt,
+                                                   redistribute, ghost_mode);
         return std::tuple(std::move(mesh_refined),
                           as_nbarray(std::move(parent_cells)));
       },