Merge branch 'main' into release

Author: jhale

.circleci/config.yml

@@ -122,7 +122,7 @@ jobs:
 
   build-complex:
     docker:
-      - image: ghcr.io/fenics/test-env:latest-mpich
+      - image: ghcr.io/fenics/test-env:nightly-mpich
     environment:
       DEBIAN_FRONTEND: "noninteractive"
       PETSC_ARCH: "linux-gnu-complex-32"

RELEASE.md

@@ -32,7 +32,10 @@ UFL still runs on the year-based release scheme.
 
 1. Merge `main` into `release` resolving all conflicts in favour of `main`.
 
-       git merge -Xtheirs main
+       git checkout release
+       git merge --no-commit main
+       git checkout --theirs main .
+       git diff main
 
 2. Update version numbers, e.g.
 
@@ -50,7 +53,10 @@ UFL still runs on the year-based release scheme.
 
 1. Merge `main` into `release` resolving all conflicts in favour of `main`.
 
-       git merge -Xtheirs main
+       git checkout release
+       git merge --no-commit main
+       git checkout --theirs main .
+       git diff main
 
 2. Update the version number in `setup.cfg`, e.g. `2022.2.0`.
 
@@ -62,15 +68,18 @@ UFL still runs on the year-based release scheme.
 
 1. Merge `main` into `release` resolving all conflicts in favour of `main`.
 
-       git merge -Xtheirs main
+       git checkout release
+       git merge --no-commit main
+       git checkout --theirs main .
+       git diff main
 
 2. Update the version number in `setup.cfg`, e.g. `0.5.0`.
 
 3. Update the dependency versions for `fenics-basix` and `fenics-ufl` in `setup.cfg`.
 
 4. If necessary, update the version number in `cmake/CMakeLists.txt`, e.g. `0.5.0`.
 
-5. Update the version number macros in `ffcx/code_generation/ufcx.h`. Typically this
+5. Update the version number macros in `ffcx/codegeneration/ufcx.h`. Typically this
    should match the Python version number. Remember to change the
    `UFCX_VERSION_RELEASE` to `1`.
 
@@ -82,7 +91,10 @@ UFL still runs on the year-based release scheme.
 
 1. Merge `main` into `release` resolving all conflicts in favour of `main`.
 
-       git merge -Xtheirs main
+       git checkout release
+       git merge --no-commit main
+       git checkout --theirs main .
+       git diff main
 
 2. In `cpp/CMakeLists.txt` change the version number near the top of the file,
    e.g. `0.5.0`.
@@ -92,7 +104,7 @@ UFL still runs on the year-based release scheme.
    there is no need to change anything here. However, if they don't match, you
    need to manually specify the appropriate UFCx version.
 
-4. In `python/setup.cfg` change the `VERSION` variable to e.g. `0.5.0` and
+4. In `python/setup.py` change the `VERSION` variable to e.g. `0.5.0` and
    update the depedency versions for `fenics-ffcx` and `fenics-ufl`.
 
 5. Commit and push.

cpp/CMakeLists.txt

@@ -1,6 +1,6 @@
 # ------------------------------------------------------------------------------
 # Top level CMakeLists.txt file for DOLFINx
-cmake_minimum_required(VERSION 3.16)
+cmake_minimum_required(VERSION 3.19)
 
 # ------------------------------------------------------------------------------
 # Set project name and version number
@@ -189,7 +189,7 @@ if(BASIX_PY_DIR)
   endif()
 endif()
 
-find_package(Basix REQUIRED CONFIG HINTS ${BASIX_PY_DIR})
+find_package(Basix 0.6 REQUIRED CONFIG HINTS ${BASIX_PY_DIR})
 set_package_properties(
   basix PROPERTIES
   TYPE REQUIRED

cpp/cmake/modules/FindUFCx.cmake

@@ -72,5 +72,6 @@ mark_as_advanced(UFCX_VERSION UFCX_INCLUDE_DIRS UFCX_SIGNATURE)
 find_package_handle_standard_args(
   UFCx
   REQUIRED_VARS UFCX_INCLUDE_DIRS UFCX_SIGNATURE UFCX_VERSION
-  VERSION_VAR UFCX_VERSION REASON_FAILURE_MESSAGE "UFCx could not be found."
+  VERSION_VAR UFCX_VERSION HANDLE_VERSION_RANGE REASON_FAILURE_MESSAGE
+                           "UFCx could not be found."
 )

cpp/cmake/scripts/generate-cmakefiles.py

@@ -12,7 +12,7 @@
 #
 # python cmake/scripts/generate-cmakefiles from dolfinx/cpp
 #
-cmake_minimum_required(VERSION 3.16)
+cmake_minimum_required(VERSION 3.19)
 
 set(PROJECT_NAME {project_name})
 project(${{PROJECT_NAME}} LANGUAGES C CXX)
@@ -118,7 +118,7 @@
 #
 # python cmake/scripts/generate-cmakefiles from dolfinx/cpp
 #
-cmake_minimum_required(VERSION 3.16)
+cmake_minimum_required(VERSION 3.19)
 
 set(PROJECT_NAME {project_name})
 project(${{PROJECT_NAME}} LANGUAGES C CXX)

cpp/dolfinx/CMakeLists.txt

@@ -182,7 +182,7 @@ include(CMakePackageConfigHelpers)
 write_basic_package_version_file(
   ${CMAKE_BINARY_DIR}/dolfinx/DOLFINXConfigVersion.cmake
   VERSION ${DOLFINX_VERSION}
-  COMPATIBILITY ExactVersion
+  COMPATIBILITY AnyNewerVersion
 )
 
 configure_package_config_file(

cpp/dolfinx/mesh/Mesh.cpp

@@ -322,8 +322,11 @@ mesh::create_submesh(const Mesh& mesh, int dim,
   // NOTE: Unclear what this return for prisms
   const std::size_t num_entity_dofs = layout.num_entity_closure_dofs(dim);
 
-  std::vector<std::int32_t> geometry_indices(num_entity_dofs
-                                             * submesh_to_mesh_map.size());
+  std::vector<std::int32_t> geometry_indices;
+  geometry_indices.reserve(num_entity_dofs * submesh_to_mesh_map.size());
+  std::vector<std::int32_t> submesh_x_dofmap_offsets;
+  submesh_x_dofmap_offsets.reserve(submesh_to_mesh_map.size() + 1);
+  submesh_x_dofmap_offsets.push_back(0);
   {
     const graph::AdjacencyList<std::int32_t>& xdofs = geometry.dofmap();
     const int tdim = topology.dim();
@@ -354,8 +357,9 @@ mesh::create_submesh(const Mesh& mesh, int dim,
           = closure_dofs[dim][local_entity];
 
       auto xc = xdofs.links(cell);
-      for (std::size_t j = 0; j < num_entity_dofs; ++j)
-        geometry_indices[i * num_entity_dofs + j] = xc[entity_dofs[j]];
+      for (std::int32_t entity_dof : entity_dofs)
+        geometry_indices.push_back(xc[entity_dof]);
+      submesh_x_dofmap_offsets.push_back(geometry_indices.size());
     }
   }
 
@@ -413,26 +417,18 @@ mesh::create_submesh(const Mesh& mesh, int dim,
     mesh_to_submesh_x_dof_map[submesh_to_mesh_x_dof_map[i]] = i;
 
   // Create submesh geometry dofmap
-  std::vector<std::int32_t> entity_x_dofs;
   std::vector<std::int32_t> submesh_x_dofmap_vec;
   submesh_x_dofmap_vec.reserve(geometry_indices.size());
-  std::vector<std::int32_t> submesh_x_dofmap_offsets(1, 0);
-  submesh_x_dofmap_offsets.reserve(submesh_to_mesh_map.size() + 1);
-  for (std::size_t i = 0; i < submesh_to_mesh_map.size(); ++i)
-  {
-    // Get the mesh geometry dofs for ith entity in entities
-    auto it = std::next(geometry_indices.begin(), i * num_entity_dofs);
-    entity_x_dofs.assign(it, std::next(it, num_entity_dofs));
+  std::transform(geometry_indices.cbegin(), geometry_indices.cend(),
+                 std::back_inserter(submesh_x_dofmap_vec),
+                 [&mesh_to_submesh_x_dof_map](auto x_dof)
+                 {
+                   std::int32_t x_dof_submesh
+                       = mesh_to_submesh_x_dof_map[x_dof];
+                   assert(x_dof_submesh != -1);
+                   return x_dof_submesh;
+                 });
 
-    // For each mesh dof of the entity, get the submesh dof
-    for (std::int32_t x_dof : entity_x_dofs)
-    {
-      std::int32_t x_dof_submesh = mesh_to_submesh_x_dof_map[x_dof];
-      assert(x_dof_submesh != -1);
-      submesh_x_dofmap_vec.push_back(x_dof_submesh);
-    }
-    submesh_x_dofmap_offsets.push_back(submesh_x_dofmap_vec.size());
-  }
   graph::AdjacencyList<std::int32_t> submesh_x_dofmap(
       std::move(submesh_x_dofmap_vec), std::move(submesh_x_dofmap_offsets));
 

docker/Dockerfile.oneapi

@@ -10,7 +10,7 @@ ARG HDF5_SERIES=1.12
 ARG HDF5_PATCH=2
 ARG PETSC_VERSION=3.17.5
 ARG SLEPC_VERSION=3.17.2
-ARG PYBIND11_VERSION=2.10.1
+ARG PYBIND11_VERSION=2.10.2
 ARG KAHIP_VERSION=3.14
 
 WORKDIR /tmp
@@ -20,6 +20,7 @@ RUN export DEBIAN_FRONTEND=noninteractive && \
     apt-get -qq update && \
     apt-get -yq --with-new-pkgs -o Dpkg::Options::="--force-confold" upgrade && \
     apt-get -y install \
+    bzip2 \
     cmake \
     gnupg \
     libboost-dev \
@@ -36,12 +37,10 @@ RUN export DEBIAN_FRONTEND=noninteractive && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Install oneAPI libraries
-RUN wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && \
-    apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && \
-    echo "deb https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list && \
+RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null && \
+    echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list && \
     apt-get update && \
-    apt-get install -y intel-oneapi-common-vars intel-oneapi-compiler-dpcpp-cpp \
-    intel-oneapi-mkl-devel intel-oneapi-mpi-devel intel-oneapi-python && \
+    apt-get install -y libstdc++-11-dev intel-oneapi-compiler-dpcpp-cpp intel-oneapi-mkl-devel intel-oneapi-mpi-devel intel-oneapi-python && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
@@ -100,7 +99,6 @@ RUN . /opt/intel/oneapi/setvars.sh && \
     --with-64-bit-indices=no \
     --with-fortran-bindings=no \
     --with-shared-libraries \
-    --download-hypre \
     --download-superlu_dist \
     --with-scalar-type=real && \
     make PETSC_DIR=/usr/local/petsc PETSC_ARCH=linux-gnu-real-32 ${MAKEFLAGS} all && \
@@ -110,7 +108,6 @@ RUN . /opt/intel/oneapi/setvars.sh && \
     --with-64-bit-indices=no \
     --with-fortran-bindings=no \
     --with-shared-libraries \
-    --download-hypre \
     --download-superlu_dist \
     --with-scalar-type=complex && \
     make PETSC_DIR=/usr/local/petsc PETSC_ARCH=linux-gnu-complex-32 ${MAKEFLAGS} all && \
@@ -120,7 +117,6 @@ RUN . /opt/intel/oneapi/setvars.sh && \
     --with-64-bit-indices=yes \
     --with-fortran-bindings=no \
     --with-shared-libraries \
-    --download-hypre \
     --download-superlu_dist \
     --with-scalar-type=real && \
     make PETSC_DIR=/usr/local/petsc PETSC_ARCH=linux-gnu-real-64 ${MAKEFLAGS} all && \
@@ -130,7 +126,6 @@ RUN . /opt/intel/oneapi/setvars.sh && \
     --with-64-bit-indices=yes \
     --with-fortran-bindings=no \
     --with-shared-libraries \
-    --download-hypre \
     --download-superlu_dist \
     --with-scalar-type=complex && \
     make PETSC_DIR=/usr/local/petsc PETSC_ARCH=linux-gnu-complex-64 ${MAKEFLAGS} all && \

python/test/unit/common/test_timer.py

@@ -6,23 +6,14 @@
 #
 # SPDX-License-Identifier:    LGPL-3.0-or-later
 
-import random
 from time import sleep
 
 from dolfinx import common
 
-# Seed random generator for determinism
-random.seed(0)
-
-
-def get_random_task_name():
-    """Get pseudo-random string"""
-    return hex(random.randint(0, 1e32))
-
 
 def test_context_manager_named():
     """Test that named Timer works as context manager"""
-    task = get_random_task_name()
+    task = "test_context_manager_named_str"
 
     # Execute task in the context manager
     t = common.Timer(task)

python/test/unit/fem/test_function_space.py

@@ -12,7 +12,6 @@
 from dolfinx.mesh import create_mesh, create_unit_cube
 from ufl import (Cell, FiniteElement, Mesh, TestFunction, TrialFunction,
                  VectorElement, grad, triangle)
-from ufl.log import UFLException
 
 from mpi4py import MPI
 
@@ -221,7 +220,7 @@ def test_argument_equality(mesh, V, V2, W, W2):
 def test_cell_mismatch(mesh):
     """Test that cell mismatch raises early enough from UFL"""
     element = FiniteElement("P", triangle, 1)
-    with pytest.raises(UFLException):
+    with pytest.raises(BaseException):
         FunctionSpace(mesh, element)