Merge branch 'main' into mleoni/add_xdmffile_read_function

.github/workflows/oneapi.yml

@@ -56,7 +56,7 @@ jobs:
           conda list
 
       - name: Install Basix
-        run: pip install --no-build-isolation git+https://github.com/FEniCS/basix.git@${{ needs.fenicsx-refs.outputs.basix_ref }}
+        run: uv pip install --no-build-isolation git+https://github.com/FEniCS/basix.git@${{ needs.fenicsx-refs.outputs.basix_ref }}
 
       - name: Clone FFCx
         uses: actions/checkout@v4
@@ -82,8 +82,8 @@ jobs:
 
       - name: Install UFL and FFCx modules
         run: |
-          pip install --no-build-isolation git+https://github.com/FEniCS/ufl.git@${{ needs.fenicsx-refs.outputs.ufl_ref }}
-          pip install --no-build-isolation ffcx/
+          uv pip install --no-build-isolation git+https://github.com/FEniCS/ufl.git@${{ needs.fenicsx-refs.outputs.ufl_ref }}
+          uv pip install --no-build-isolation ffcx/
 
       - name: Build and run DOLFINx C++ unit tests (serial and MPI)
         run: |
@@ -102,7 +102,7 @@ jobs:
           ctest -R demo -R mpi_2
 
       - name: Build DOLFINx Python interface
-        run: pip -v install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Developer" python/
+        run: uv pip -v install --no-build-isolation --config-settings=cmake.build-type="Developer" python/
       - name: Run DOLFINx demos (Python, serial)
         run: python -m pytest -v -n=2 -m serial --durations=10 python/demo/test.py
       - name: Run DOLFINx demos (Python, MPI (np=2))

.github/workflows/windows.yml

@@ -104,7 +104,7 @@ jobs:
           (Get-Content __init__.py).Replace('# WINDOWSDLL', 'import os; os.add_dll_directory("D:/a/dolfinx/dolfinx-install/bin"); os.add_dll_directory("C:/Program Files (x86)/Intel/oneAPI/mpi/2021.12/opt/mpi/libfabric/bin")') | Set-Content __init__.py
           Get-Content __init__.py
 
-      - uses: mpi4py/[email protected].7
+      - uses: mpi4py/[email protected].8
         with:
           mpi: "intelmpi"
 

ChangeLog.rst

@@ -28,7 +28,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Remove ``Mesh::size``. Use ``Mesh::num_entities`` instead.
 - Improved mesh topology computation performance.
 - Remove excessive calls to MPI init. It may now be necessary in some
-  cases to explicitly intialise MPI.
+  cases to explicitly initialise MPI.
 - Improvements to sparsity pattern computation.
 - Addition of some interfaces using ``Eigen::Map/ref`` in addition to
   ``dolfin::Array(View)``.  ``dolfin::Array(View)``interfaces will be
@@ -146,7 +146,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Require polynomial degree or finite element for Expressions in the
   Python interface (fixes Issue #355,
   https://bitbucket.org/fenics-project/dolfin/issues/355)
-- Switch to Google Test framwork for C++ unit tests
+- Switch to Google Test framework for C++ unit tests
 - Fix bug when reading domain data from mesh file for a ghosted mesh
 - Add interface for manipulating mesh geometry using (higher-order) FE
   functions: free functions set_coordinates, get_coordinates,
@@ -223,7 +223,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   #443)
 - Add quadrature rules for multimesh/cut-cell integration up to order
   6
-- Implement MPI reductions and XML ouput of Table class
+- Implement MPI reductions and XML output of Table class
 - list_timings() is now collective and returns MPI average across
   processes
 - Add dump_timings_to_xml()
@@ -324,7 +324,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   module
 - Add function Form::set_some_coefficients()
 - Remove Boost.MPI dependency
-- Change GenericMatrix::compresss to return a new matrix (7be3a29)
+- Change GenericMatrix::compress to return a new matrix (7be3a29)
 - Add function GenericTensor::empty()
 - Deprecate resizing of linear algebra via the GenericFoo interfaces
   (fixes #213)
@@ -387,7 +387,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Fixes bug where child/parent hierarchy in Python were destroyed
 - Add utility script dolfin-get-demos
 - MeshFunctions in python now support iterable protocol
-- Add timed VTK output for Mesh and MeshFunction in addtion to
+- Add timed VTK output for Mesh and MeshFunction in addition to
   Functions
 - Expose ufc::dofmap::tabulate_entity_dofs to GenericDofMap interface
 - Expose ufc::dofmap::num_entity_dofs to GenericDofMap interface
@@ -477,7 +477,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Add sparray method in the Python interface of GenericMatrix,
   requires scipy.sparse
 - Make methods that return a view of contiguous c-arrays, via a NumPy
-  array, keep a reference from the object so it wont get out of scope
+  array, keep a reference from the object so it won't get out of scope
 - Add parameter: "use_petsc_signal_handler", which enables/disable
   PETSc system signals
 - Avoid unnecessary resize of result vector for A*b
@@ -684,7 +684,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Thread-safe fixed in Function class
 - Make GenericFunction::eval thread-safe (Data class removed)
 - Optimize and speedup topology computation (mesh.init())
-- Add function Mesh::clean() for cleaning out auxilliary topology data
+- Add function Mesh::clean() for cleaning out auxiliary topology data
 - Improve speed and accuracy of timers
 - Fix bug in 3D uniform mesh refinement
 - Add built-in meshes UnitTriangle and UnitTetrahedron
@@ -761,7 +761,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   refinement
 - Add functionality for smoothing the boundary of a mesh
 - Speedup assembly over exterior facets by not using BoundaryMesh
-- Mesh refinement improvements, remove unecessary copying in Python
+- Mesh refinement improvements, remove unnecessary copying in Python
   interface
 - Clean PETSc and Epetra Krylov solvers
 - Add separate preconditioner classes for PETSc and Epetra solvers
@@ -935,7 +935,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   check range
 - Add unit tests to the memorycheck
 - Add call to clean up libxml2 parser at exit
-- Remove unecessary arguments in DofMap member functions
+- Remove unnecessary arguments in DofMap member functions
 - Remove reference constructors from DofMap, FiniteElement and
   FunctionSpace
 - Use a shared_ptr to store the mesh in DofMap objects
@@ -1215,7 +1215,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Disable PETSc by default, use --enable-petsc to enable
 - Modify ODE solver interface for u0() and f()
 - Add class ConvectionMatrix
-- Readd classes LoadVector, MassMatrix, StiffnessMatrix
+- Read classes LoadVector, MassMatrix, StiffnessMatrix
 - Add matrix factory for simple creation of standard finite element
   matrices
 - Collect static solvers in LU and GMRES
@@ -1500,7 +1500,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Update PETSc wrappers NewVector, NewMatrix, and NewGMRES
 - Fix initialization of PETSc
 - Add mono-adaptive cG(q) and dG(q) solvers (experimental)
-- Implementation of new assebly: NewFEM, using output from FFC
+- Implementation of new assembly: NewFEM, using output from FFC
 - Add access to mesh for nodes, cells, faces and edges
 - Add Tecplot I/O interface; contributed by Garth N. Wells
 
@@ -1623,7 +1623,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Optimize Lagrange polynomials
 - Optimize sparsity: use stl containers
 - Optimize choice of discrete residual for multi-adaptive solver
-- Don't save solution in benchmark proble
+- Don't save solution in benchmark problem
 - Improve computation of divergence factor for underdamped systems
 - Don't check residual on first slab for fixed time step
 - Decrease largest (default) time step to 0.1

README.md

@@ -12,6 +12,12 @@ DOLFINx is the computational environment of
 Solving Environment in C++ and Python. DOLFINx is a new version of
 DOLFIN and is actively developed.
 
+For questions about using DOLFINx, visit the [FEniCS
+Discourse](https://fenicsproject.discourse.group/) page or use the
+[FEniCS Slack channel](https://fenicsproject.slack.com/) (use
+[this](https://join.slack.com/t/fenicsproject/shared_invite/zt-1lraknsp1-6_3Js5kueDIyWgF192d3nA)
+link to sign up to the Slack channel).
+
 ## Documentation
 
 Documentation can be viewed at <https://docs.fenicsproject.org>.
@@ -191,19 +197,3 @@ Lesser General Public License for more details.
 You should have received a copy of the GNU Lesser General Public
 License along with DOLFINx. If not, see
 <https://www.gnu.org/licenses/>.
-
-## Contact
-
-For questions about using DOLFINx, visit the FEniCS Discourse page:
-
-<https://fenicsproject.discourse.group/>
-
-or use the FEniCS Slack channel:
-
-<https://fenicsproject.slack.com/>
-
-(use <https://join.slack.com/t/fenicsproject/shared_invite/zt-1lraknsp1-6_3Js5kueDIyWgF192d3nA> to sign up)
-
-For bug reports visit:
-
-<https://github.com/FEniCS/dolfinx>

cpp/CMakeLists.txt

@@ -382,7 +382,7 @@ if(NOT DOLFINX_UFCX_PYTHON)
   # Check in CONFIG mode, i.e. look for installed ufcxConfig.cmake
   find_package(ufcx 0.10 REQUIRED CONFIG)
 else()
-  # Check in MODULE mode (using FindUFCX.cmake) using Python intepreter.
+  # Check in MODULE mode (using FindUFCX.cmake) using Python interpreter.
   find_package(
     Python3
     COMPONENTS Interpreter

cpp/doc/Doxyfile

@@ -86,7 +86,7 @@ CREATE_SUBDIRS         = YES
 # level increment doubles the number of directories, resulting in 4096
 # directories at level 8 which is the default and also the maximum value. The
 # sub-directories are organized in 2 levels, the first level always has a fixed
-# numer of 16 directories.
+# number of 16 directories.
 # Minimum value: 0, maximum value: 8, default value: 8.
 # This tag requires that the tag CREATE_SUBDIRS is set to YES.
 
@@ -1007,7 +1007,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-# EXCLUDE                = 
+# EXCLUDE                =
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded

cpp/doc/source/jupytext_process.py

@@ -54,7 +54,7 @@ def process():
             with open(myst_file, "w") as fw:
                 fw.write(cpp_myst_text)
 
-            # There is a posibility to use jupyter-notebooks with C++/C kernels
+            # There is a possibility to use jupyter-notebooks with C++/C kernels
             # ipynb_file = (demo_doc_dir / fname.name).with_suffix(".ipynb")
             # jupytext.write(cpp_demo, ipynb_file, fmt="ipynb")
 

cpp/dolfinx/common/IndexMap.cpp

@@ -416,7 +416,7 @@ compute_submap_indices(const IndexMap& imap,
   // If required, preserve the order of the ghost indices
   if (order == IndexMapOrder::preserve)
   {
-    // Build (old postion, new position) list for ghosts and sort
+    // Build (old position, new position) list for ghosts and sort
     std::vector<std::pair<std::int32_t, std::int32_t>> pos;
     pos.reserve(submap_ghost.size());
     for (std::int32_t idx : submap_ghost)

cpp/dolfinx/common/sort.h

@@ -20,31 +20,29 @@
 
 namespace dolfinx
 {
-
 struct __radix_sort
 {
-
-  /// @brief Sort a range with radix sorting algorithm. The bucket
-  /// size is determined by the number of bits to sort at a time (2^BITS).
+  /// @brief Sort a range with radix sorting algorithm. The bucket size
+  /// is determined by the number of bits to sort at a time (2^BITS).
   ///
-  /// This allows usage with standard range containers of integral types, for
-  /// example
+  /// This allows usage with standard range containers of integral
+  /// types, for example
   /// @code
   /// std::array<std::int16_t, 3> a{2, 3, 1};
   /// dolfixn::radix_sort(a); // a = {1, 2, 3}
   /// @endcode
-  /// Additionally the projection based approach of the STL library is adpated,
-  /// which allows for versatile usage, for example the easy realization of an
-  /// argsort
+  /// Additionally the projection based approach of the STL library is
+  /// adapted, which allows for versatile usage, for example the easy
+  /// realization of an argsort
   /// @code
   /// std::array<std::int16_t, 3> a{2, 3, 1};
   /// std::array<std::int16_t, 3> i{0, 1, 2};
   /// dolfixn::radix_sort(i, [&](auto i){ return a[i]; }); // yields i = {2, 0,
   /// 1} and a[i] = {1, 2, 3};
   /// @endcode
   /// @tparam R Type of range to be sorted.
-  /// @tparam P Projection type to be applied on range elements to produce a
-  /// sorting index.
+  /// @tparam P Projection type to be applied on range elements to
+  /// produce a sorting index.
   /// @tparam BITS The number of bits to sort at a time.
   /// @param[in, out] range The range to sort.
   /// @param[in] P Element projection.
@@ -126,16 +124,21 @@ inline constexpr __radix_sort radix_sort{};
 /// @brief Compute the permutation array that sorts a 2D array by row.
 ///
 /// @param[in] x The flattened 2D array to compute the permutation array
-/// for.
+/// for (row-major storage).
 /// @param[in] shape1 The number of columns of `x`.
-/// @return The permutation array such that `x[perm[i]] <= x[perm[i +1]].
+/// @return The permutation array such that `x[perm[i]] <= x[perm[i
+/// +1]].
 /// @pre `x.size()` must be a multiple of `shape1`.
 /// @note This function is suitable for small values of `shape1`. Each
 /// column of `x` is copied into an array that is then sorted.
 template <typename T, int BITS = 16>
 std::vector<std::int32_t> sort_by_perm(std::span<const T> x, std::size_t shape1)
 {
   static_assert(std::is_integral_v<T>, "Integral required.");
+
+  if (x.empty())
+    return std::vector<std::int32_t>{};
+
   assert(shape1 > 0);
   assert(x.size() % shape1 == 0);
   const std::size_t shape0 = x.size() / shape1;
@@ -147,7 +150,7 @@ std::vector<std::int32_t> sort_by_perm(std::span<const T> x, std::size_t shape1)
   std::vector<T> column(shape0);
   for (std::size_t i = 0; i < shape1; ++i)
   {
-    int col = shape1 - 1 - i;
+    std::size_t col = shape1 - 1 - i;
     for (std::size_t j = 0; j < shape0; ++j)
       column[j] = x[j * shape1 + col];
 

cpp/dolfinx/fem/DirichletBC.h

@@ -338,7 +338,7 @@ class DirichletBC
     if (g->shape.size() != V->element()->value_shape().size())
     {
       throw std::runtime_error(
-          "Rank mis-match between Constant and function space in DirichletBC");
+          "Rank mismatch between Constant and function space in DirichletBC");
     }
 
     if (g->value.size() != _function_space->dofmap()->bs())

cpp/dolfinx/fem/FiniteElement.h

@@ -39,7 +39,7 @@ struct BasixElementData
       element; ///< Finite element.
   std::optional<std::vector<std::size_t>> value_shape
       = std::nullopt;    ///< Value shape. Can only be set for scalar `element`.
-  bool symmetry = false; ///< Symmetry. Should ony set set for 2nd-order tensor
+  bool symmetry = false; ///< Symmetry. Should only set set for 2nd-order tensor
                          ///< blocked elements.
 };
 
@@ -65,8 +65,8 @@ class FiniteElement
   /// for a vector in 3D or `{2, 2}` for a rank-2 tensor in 2D. Can only
   /// be set for blocked scalar `element`. For other elements and scalar
   /// elements it should be `std::nullopt`.
-  /// @param[in] symmetric Is the element a symmetric tensor? Should ony
-  /// set for 2nd-order tensor blocked elements.
+  /// @param[in] symmetric Is the element a symmetric tensor? Should
+  /// only set for 2nd-order tensor blocked elements.
   FiniteElement(const basix::FiniteElement<geometry_type>& element,
                 std::optional<std::vector<std::size_t>> value_shape
                 = std::nullopt,
@@ -792,7 +792,7 @@ class FiniteElement
   /// consistent physical element degree-of-freedom ordering. The
   /// permutation is computed in-place.
   ///
-  /// @param[in,out] doflist Indicies associated with the
+  /// @param[in,out] doflist Indices associated with the
   /// degrees-of-freedom. Size=`num_dofs`.
   /// @param[in] cell_permutation Permutation data for the cell.
   void permute(std::span<std::int32_t> doflist,
@@ -811,7 +811,7 @@ class FiniteElement
   /// element degree-of-freedom ordering. The permutation is computed
   /// in-place.
   ///
-  /// @param[in,out] doflist Indicies associated with the
+  /// @param[in,out] doflist Indices associated with the
   /// degrees-of-freedom. Size=`num_dofs`.
   /// @param[in] cell_permutation Permutation data for the cell.
   void permute_inv(std::span<std::int32_t> doflist,

cpp/dolfinx/fem/Form.h

@@ -48,8 +48,8 @@ struct integral_data
   /// @param[in] id Domain ID.
   /// @param[in] kernel Integration kernel.
   /// @param[in] entities Indices of entities to integrate over.
-  /// @param[in] coeffs Indicies of the coefficients are present
-  /// (active) in `kernel`.
+  /// @param[in] coeffs Indices of the coefficients are present (active)
+  /// in `kernel`.
   template <typename K, typename V, typename W>
     requires std::is_convertible_v<
                  std::remove_cvref_t<K>,
@@ -70,11 +70,11 @@ struct integral_data
   /// @param[in] id Domain ID.
   /// @param[in] kernel Integration kernel.
   /// @param[in] entities Indices of entities to integrate over.
-  /// @param[in] coeffs Indicies of the coefficients that are active in
+  /// @param[in] coeffs Indices of the coefficients that are active in
   /// the `kernel`.
   ///
-  /// @note This version allows `entities` to be passed as a std::span,
-  /// which is then copied.
+  /// @note This version allows `entities` to be passed as a
+  /// `std::span`, which is then copied.
   template <typename K, typename W>
     requires std::is_convertible_v<
                  std::remove_cvref_t<K>,

cpp/dolfinx/fem/assemble_matrix_impl.h

@@ -116,8 +116,8 @@ void assemble_cells(
     P1T(_Ae, cell_info1, c1, ndim0); // A =  B P1_T
 
     // Zero rows/columns for essential bcs
-    auto dofs0 = std::span(dmap0.data_handle() + c0 * num_dofs0, num_dofs0);
-    auto dofs1 = std::span(dmap1.data_handle() + c1 * num_dofs1, num_dofs1);
+    std::span dofs0(dmap0.data_handle() + c0 * num_dofs0, num_dofs0);
+    std::span dofs1(dmap1.data_handle() + c1 * num_dofs1, num_dofs1);
 
     if (!bc0.empty())
     {
@@ -255,8 +255,8 @@ void assemble_exterior_facets(
     P1T(_Ae, cell_info1, cell1, ndim0);
 
     // Zero rows/columns for essential bcs
-    auto dofs0 = std::span(dmap0.data_handle() + cell0 * num_dofs0, num_dofs0);
-    auto dofs1 = std::span(dmap1.data_handle() + cell1 * num_dofs1, num_dofs1);
+    std::span dofs0(dmap0.data_handle() + cell0 * num_dofs0, num_dofs0);
+    std::span dofs1(dmap1.data_handle() + cell1 * num_dofs1, num_dofs1);
     if (!bc0.empty())
     {
       for (int i = 0; i < num_dofs0; ++i)