v0.8.0

This is a major release with a number of important bug fixes and new features. Users are advised to upgrade.

Full Changelog: v0.7.3...v0.8.0

Major changes

• Remove deprecated fem.FunctionSpace function by @francesco-ballarin in #2818
• Import mpi4py early for MPI initialisation by @garth-wells in #2826
• Improve documentation of pack_coefficients by @jpdean in #2822
• Use pyproject.toml for install of Python part by @chrisrichardson in #2707
• Fix bounding box leaf collision check by @jorgensd in #2850
• Switch to nanobind by @garth-wells in #2820
• Remove unnecessary calls to compute_graph_edges by @IgorBaratta in #2856
• Remove call to compute_graph_edges in compute_owned_indices by @IgorBaratta in #2875
• Remove remaning MPI_Alltoall(v) calls by @garth-wells in #2868
• Add test of symmetric tensor elements by @mscroggs in #2880
• Add test of quadrature element by @mscroggs in #2870
• Speed up non-matching interpolation data and add extrapolation parameter by @jorgensd in #2858
• Let PETSc choose default LU solver within NewtonSolver by @jhale in #2803
• Implement interpolation for quadrature elements by @mscroggs in #2878
• Encourage proper management of subspaces in user code by @IgorBaratta in #2916
• Expose transpose_dofmap in dolfinx.fem by @jorgensd in #2932
• Add CITATION.cff by @mscroggs in #2953
• Fix create_submesh by generalising sub index map creation by @jpdean in #2890
• Split mesh and mesh topology MPI communicators by @garth-wells in #2925
• Implementation performance improvements when concatenating function spaces for PETSc by @garth-wells in #2945
• Generalise topology to take multiple cell types by @chrisrichardson in #2979
• Improvements to demo_helmholtz.py and demo_scattering_boundary_conditions.py by @BillMaZengou in #2992
• Replace deprecated ffcx.element_interface.QuadratureElement with basix.ufl.quadrature_element by @mscroggs in #2956
• Allow for blocked elements with block size 1 by @mscroggs in #2955
• Custom C/C++ kernel demo by @jhale in #2983
• Implement VTK I/O for arbitrary degree tetrahedron cells by @mscroggs in #2985
• Fix IndexMap->global_to_local() by @jorgensd in #2963
• Fix leak for MPI_Datatype by @garth-wells in #3031
• Dofmap builder preparation for mixed topology by @chrisrichardson in #3025
• Add interface to mesh::Geometry for multiple cmaps and dofmaps by @chrisrichardson in #3035
• Simplify Form constructor by adding a struct for integral data by @jpdean in #3045
• Fix doc in demo_poisson.py by @BillMaZengou in #2984
• Implement VTK I/O for arbitrary degree hex cells by @mscroggs in #2982
• Wrap discrete_gradient in Python by @mscroggs in #3037
• Wrap create_nonmatching_meshes_interpolation_data in Python by @mscroggs in #3039
• Wrap entities_to_geometry in Python by @mscroggs in #3038
• Ruff format mk2 by @jhale in #3044
• Add matrix-free solver python demo by @IgorBaratta in #3028
• C++ demos document generation by @ampdes in #3052
• Add maps for mixed-domain assembly by @jpdean in #3056
• Add mixed-domain matrix assembly for facet integrals (codimension 0) by @jpdean in #3079
• Support DG-0 functions in VTXWriter by @jorgensd in #3107
• Replace NumPy's logical_and and logical_or by @michalhabera in #3115
• Reuse mesh when saving to VTX by @massimiliano-leoni in #2738
• Add numpy interface to dolfinx.cpp.mesh.extract_topology by @jorgensd in #3075
• Improve mesh refinement documentation by @jorgensd in #3010
• Topology computation for mixed topology by @chrisrichardson in #2994
• Refactor la.Vector.norm by @nate-sime in #3108
• Complex variables stored correctly in VTXWriter by @jorgensd in #2831
• Fix interior facet permutations by @anzil in #3009
• Support evaluation of facets in dolfinx.fem.Expression by @jorgensd in #3062
• Make PETSc optional (ed JH: in C++) by @chrisrichardson in #3123
• Dof transform name updates by @garth-wells in #3149
• Re-name overloaded create_form function by @garth-wells in #3003
• Fix determine point ownership when majority of points in receiving mesh is outside in-mesh by @mleoni-pf in #3110
• Support creation of meshes from Basix elements from Python by @garth-wells in #2960
• Add mixed-domain vector assembly by @jpdean in #3087
• Remove gdim input to UFL elements, move value_shape to function space by @mscroggs in #2996

New Contributors

• @BillMaZengou made their first contribution in #2984
• @ampdes made their first contribution in #3052
• @mleoni-pf made their first contribution in #3110
• @uvilla made their first contribution in #3092

All other changes

• Switch default dev-env container pull to ghcr.io by @jhale in #2806
• Rename name -> name by @mscroggs in #2809
• TST: add missing include by @minrk in #2810
• Missing from future import annotations by @minrk in #2808
• Bump version to 0.8.0.dev0 by @jhale in #2813
• Add two more cases to GitHub ISSUE_TEMPLATE: installation and general questions by @francesco-ballarin in #2814
• Post-release fixes for 0.7.0 by @jhale in #2815
• Add macOS-13 runner for conda install test by @jhale in #2816
• Update UFL element by @mscroggs in #2784
• Fix docker workflow after removal of fem.FunctionSpace function by @francesco-ballarin in #2819
• Add conda to macos-13 runner. by @jhale in #2821
• Fix redhat dockerfile by @garth-wells in #2823
• Fix conda CI tests by @garth-wells in #2824
• Remove unnecessary py.typed markers in python subpackages by @francesco-ballarin in #2833
• Drop setting dl open flags in dolfinx/__init__.py by @francesco-ballarin in #2836
• Doc string improvement by @garth-wells in #2839
• Add flake8 and isort checks on python files in cpp folder by @francesco-ballarin in #2838
• Remove unused pylit3 fron doc dependencies by @garth-wells in #2842
• Rename Basix functions by @mscroggs in #2849
• Update install instructions. by @jhale in #2851
• Pass pybind11 hint to cmake find. by @jhale in #2852
• Update computation of number of components for arbitrary value shape in xdmf_function by @IgorBaratta in #2848
• Pass cmake build type and cxx flags up to scikit-build-core by @jhale in #2853
• Remove installation of build requirements from workflows, since they are already installed in the underlying docker images by @francesco-ballarin in #2854
• Let dlx.la.Vector manage the scope of the petsc4py wrapper (#1) by @uvilla in #3092
• Fix typo in Dockerfile.end-user by @jhale in #2860
• Move upgrade of pip/setuptools from redhat workflow to redhat docker file, and remove installation of build requirements from workflows by @francesco-ballarin in #2857
• Fix CI build with OpenMPI5: remove some env variables by @garth-wells in #2865
• Use value_type and geometry_type template names by @garth-wells in #2864
• Fix pyvista demo and workflow by @francesco-ballarin in #2866
• Bump versions in Dockerfiles by @garth-wells in #2863
• Try smaller ARM runner with nanobind by @jhale in #2869
• Clean up unused includes in PETSc nanobind casters, but leave the macro available by @francesco-ballarin in #2871
• Re-enable basix element test by @francesco-ballarin in #2867
• Update .gitignore by @francesco-ballarin in #2882
• Change python/README to markdown by @garth-wells in #2883
• Updates for ufcx update by @chrisrichardson in #2886
• Make topology const in locate_dofs_topological by @IgorBaratta in #2885
• Rename dof transformation functions by @mscroggs in #2888
• Export CMAKE_PREFIX_PATH in helper installation scripts by @francesco-ballarin in #2887
• Add workflow to update stable tag to fixed tag e.g. v0.7.2. by @jhale in #2892
• Update docker-update-stable.yml by @jhale in #2893
• Change nanobind build options to remove -Os by @jorgensd in #2895
• Correct CMAKE_BUILD_TYPE in end user Docker images by @jorgensd in #2894
• Simplify CMake for Python interface build by @garth-wells in #2896
• Increase again number of cores on ARM buildjet runners while building Docker end-user image by @francesco-ballarin in #2897
• Work-around nanobind issue with std::function by @garth-wells in #2899
• Adds an action to quickly update stable image tag by @jhale in #2901
• Remove packages from pyproject project section by @jhale in #2902
• Bump DOLFINx release version in Spack action by @jhale in #2904
• Unfix Sphinx version and remove Sphinx Makefile by @jhale in #2908
• Add ruff to base test environment by @francesco-ballarin in #2909
• Run cmake-format on CMakeLists.txt files too on CI by @francesco-ballarin in #2910
• Purge cppimport from Dockerfiles by @francesco-ballarin in #2911
• Fix broken links to integration test workflows in RELEASE.md by @francesco-ballarin in #2915
• Update GH bug template by @garth-wells in #2912
• Fix misleading commit message when updating documentation repository by @francesco-ballarin in #2914
• Set min version for scikit-build-core by @garth-wells in #2917
• Fix test for collapsing function spaces by @jpdean in #2919
• Bump versions in oneAPI Dockerfile by @garth-wells in #2921
• Add Basix dependency to pyproject.toml by @garth-wells in #2924
• Install ptscotch in oneAPI image by @garth-wells in #2928
• Refactor build basic dofmap by @chrisrichardson in #2927
• Remove dolfinx.nls from Python documentation by @jorgensd in #2933
• Improve overview of online documentation with autosummary by @jorgensd in #2931
• Disable Spack CI 0.7.2 Python build by @garth-wells in #2939
• Update GMSH quadrilateral recombination options to force pure quadrilateral meshes by @jorgensd in #2940
• Add test of quadrature element by @mscroggs in #2907
• Work-arounds for latest doxygen release by @garth-wells in #2947
• Update names of fields in basix.ufl by @mscroggs in #2957
• Update types by @mscroggs in #2959
• Simplify mesh creation interface and algorithms by @garth-wells in #2954
• Timer fix by @jhale in #2966
• Update stokes demo tolerance by @IgorBaratta in #2964
• Add dofmap consistency check for VTXWriter and FidesWriter by @garth-wells in #2952
• Type hint fixes by @garth-wells in #2967
• Further typing fixes by @francesco-ballarin in #2969
• Remove some implicit PETSc from tests when not needed by @chrisrichardson in #2970
• Improve FFI support for calling C functions from Python/Numba by @garth-wells in #2968
• Simplify doc path in README.md by @garth-wells in #2974
• Simplify handling of scalar type for FFCx by @garth-wells in #2975
• Increase tolerance in some tests by @IgorBaratta in #2976
• Change binary stripping settings for scikit-build-core by @jhale in #2980
• Remove default CMAKE_BUILD_TYPE from end-user action by @jhale in #2981
• Add IndexMap::global_to_local to the Python interface by @jorgensd in #2972
• Update sonar-scanner version in CI by @jorgensd in #2990
• Drop [email protected] in favor of [email protected] by @francesco-ballarin in #2995
• Simplify access to wrapped C++ form classes by @garth-wells in #2977
• Fix scalar type in generate-cmakefiles.py by @IgorBaratta in #2999
• Stop cffi_utils failing on KeyError by @mscroggs in #2993
• Create 'solver' fixture for tests, and update test_complex_assembler.py to use it. by @chrisrichardson in #3001
• Small tweaks to custom cell kernel demo by @jhale in #3007
• Update all notebooks to render correctly on web page and in notebooks. by @jorgensd in #3005
• Lighter switch to ruff by @jhale in #2998
• Add 0.7.3 to bug report issue template by @jorgensd in #3014
• Bump actions/upload-artifact to v4 by @francesco-ballarin in #3015
• ADIOS2 for Spack by default by @jhale in #3017
• Fix input arguments to dolfinx.mesh.refine_plaza by @francesco-ballarin in #3018
• Another update to Spack by @jhale in #3019
• Ensure that explicitly requested packages are enabled by CMake (and otherwise fail) by @garth-wells in #3024
• Improve wording in README.md by @garth-wells in #3027
• Fix some use of deprecated Python and NumPy functionality in tests by @garth-wells in #3029
• Fix pytest marker warning and some doc typos by @garth-wells in #3030
• Updates for ruff by @garth-wells in #3033
• Bump dependency versions by @garth-wells in #3032
• Re-enable a test by @garth-wells in #3034
• Add some PETSc destroy to avoid MPICH leak messages by @garth-wells in #3036
• correct typo in issue template by @mscroggs in #3042
• Remove dead code in mesh.py by @chrisrichardson in #3046
• Bump openmpi patch version by @jorgensd in #3048
• Simplify the dual_graph to use CellType rather than tdim by @chrisrichardson in #3049
• Add transformation_type enum by @mscroggs in #2989
• Simple typo by @chrisrichardson in #3055
• Improve Python test coverage by @chrisrichardson in #3053
• Better error messages if mesh dtype is not compatible with function space dtype by @mscroggs in #3043
• Check that UFCx kernel functions are not null by @garth-wells in #3057
• Remove .flake8 file by @garth-wells in #3058
• Always pass std::span by value by @garth-wells in #3059
• Make dolfinx.mesh.Mesh.input_global_indices a numpy array by @jorgensd in #3069
• Add pair header for SparsityPattern graph return type by @chrisrichardson in #3073
• Documentation fix by @chrisrichardson in #3074
• Missing C++ accessor to mesh object in create nonmatching interpolation data by @jorgensd in #3078
• Update macOS action to Sonoma/14 by @jhale in #3080
• C++ demo documentation refinements by @garth-wells in #3068
• Mark IndexMaps on communicators with size 1 as non-overlapped by @garth-wells in #3066
• Bump versions in Dockerfiles by @garth-wells in #3082
• Simplify IndexMap overlap by @garth-wells in #3085
• Switch macOS CI to arm M1 by @jhale in #3084
• Add multiple dofmaps and elements to Geometry by @chrisrichardson in #3071
• Updates for mdspan by @garth-wells in #3086
• Add option to preserve sub-IndexMap ghost ordering by @garth-wells in #3091
• Add support for mixed-domain coefficient packing by @jpdean in #3093
• Let *_apply_dof_transformation accept lists of cells in Python layer by @jorgensd in #3090
• Fix padding of xdmf vector of len < 3 by @jorgensd in #3095
• Fix sub index map destination rank computation by @jpdean in #3099
• Small change to MPI_I(s)send buffer allocation by @garth-wells in #3104
• Revert change to Python interface of non-matching interpolation data by @jorgensd in #3088
• Generalize bounds of bc for arbitrary partitioning in test_assembly_domains.py by @jorgensd in #3118
• Move piece node outside of function loop in VTKFile by @jorgensd in #3120
• Fix deprecation warning introduced in #3092 by @francesco-ballarin in #3122
• Require MPI ADIOS2 build during configuration. by @jhale in #3125
• Linting and formatting prior to 0.8 by @jhale in #3126
• Split linting and build steps in CI by @garth-wells in #3127
• Template distribute_entity_data to support multiple data-types by @jorgensd in #3119
• Bump dependency versions in Docker files by @garth-wells in #3130
• macos version bumps for CI by @garth-wells in #3131
• Make ADIOS tests compatible with 2.9 and 2.10 by @jhale in #3128
• Remove legacy detection of PETSc scalar type by @garth-wells in #3132
• Don't run build steps if linting fails by @jhale in #3134
• Use adjacencylist constructor in test by @jhale in #3139
• Remove linting from CircleCI - covered by Actions by @garth-wells in #3140
• Remove Sphinx pin from Dockerfile by @jhale in #3141
• Updates for Basix function changes by @garth-wells in #3142
• Update release instructions by @jhale in #3147
• Re-activate commented lines in hyperelastic demo by @garth-wells in #3146
• Updates for Conda weekly CI by @garth-wells in #3150
• Remove conda -y option by @garth-wells in #3152
• Run C++ unit tests on the no-PETSc CI job by @garth-wells in #3153
• Documentation improvements for dof transforms by @garth-wells in #3154
• Update Lagrange variant demo by @mscroggs in #3155
• Document transpose data storate for blocked elements by @mscroggs in #3156