v0.10.0.post0

What's Changed

This is a major release of DOLFINx and users are advised to upgrade.

All PRs are included below. A curated changelog is available here.

The v0.10.0 tag exists but was never released due to errors in the documentation build.

Features and API changes

• Safe default value for unbound variables in dolfinx.conf by @mleoni-pf in #3470
• Use standard C++20 (no GNU extensions) by @garth-wells in #3479
• Revised Timer, now using std::chrono by @garth-wells in #3484
• Improve Newton solver docs by @garth-wells in #3490
• Fixes to Timer logic by @garth-wells in #3488
• Allow access to logged timer data by @garth-wells in #3487
• Small updates to Newton Solver documentation. by @jhale in #3491
• C++ style improvements in subdomain demo by @garth-wells in #3493
• Demo updates for LU solver bugs by @garth-wells in #3499
• Improve readability of form in HDG demo by @jpdean in #3508
• Fix SNES NonlinearPDE class when using line search by @jhale in #3507
• Improve Topology construction and fix MPI/NBX bug by @garth-wells in #3512
• Add C++ demo that shows mixed elements and consistency fixes for element spaces by @garth-wells in #3500
• Use separately allocated data for each call to MPI_Ineighbor_allgatherv by @chrisrichardson in #3513
• Add more PETSc destruction notes to assembly functionality that creates PETSc.Mat/Vec objects by @jorgensd in #3524
• Allow specifying attribute name when reading meshtag by @mleoni-pf in #3257
• Remove jit options from function-space as we no longer generate code. by @jorgensd in #3529
• Use non-standard Python package manager uv in oneAPI CI by @Saransh-cpp in #3550
• Add FiniteElement python wrapper by @schnellerhase in #3542
• Mesh Geometry improvements for mixed topology by @garth-wells in #3575
• Modify demo_helmholtz.py to solve for plane wave solution in complex mode by @jzitelli in #3563
• VTKHDF mesh I/O by @chrisrichardson in #3576
• Use block preconditioner for mixed Poisson problem by @garth-wells in #3580
• Fix bug in coefficient packing by @garth-wells in #3645
• Add discrete curl matrix operator by @garth-wells in #3587
• Support assembly of linear forms with cell integrals on mixed-topology meshes by @jpdean in #3606
• Move SpMV from tests into MatrixCSR by @chrisrichardson in #3591
• Put FEM 'packing' functions into separate header by @garth-wells in #3621
• Mixed topology: find dS cells by @chrisrichardson in #3632
• Extend locate_entities for mixed-topology meshes by @jpdean in #3637
• Move Expression::eval to a free function with other 'assemblers' by @garth-wells in #3625
• Simplify assembler implementation interfaces by @garth-wells in #3649
• Expose _bbox_coordinates of BoundingBoxTree to users by @ordinary-slim in #3600
• Extend the mesh generation testing to the 3D cases by @schnellerhase in #3604
• Refactor LA into native and PETSc part and add assigners by @jhale in #3659
• Allow a custom cell reorder function to be passed to create_mesh by @jpdean in #3664
• Add support for Serendipity (order 2) coordinate elements by @jorgensd in #3662
• Add void* to tabulate tensor kernel by @sclaus2 in #3660
• Correct usage of input coefficients for apply_lifting of blocked operators. by @jorgensd in #3680
• Block assembly with no DirichletBC and None on diagonal by @jorgensd in #3683
• Fix finite relative-residual at 0th iteration by @RemDelaporteMathurin in #3713
• Expose Scatterer in Python layer by @chrisrichardson in #3727
• Local dual graph for branching meshes by @schnellerhase in #3730
• Extend blocked/nest/monolithic assembly test with a higher order vector example by @schnellerhase in #3708
• Add a demo showing how submeshes can be used to represent boundary data by @jpdean in #3711
• SNES solver interface for standard, block and nest systems by @jorgensd in #3648
• dolfinx.fem.petsc.LinearProblem for nest and block systems by @jorgensd in #3684
• Check rank/shape consistency between user provided Constants and Constants in generated UFCx code by @garth-wells in #3760
• XDMF IO for meshes using serendipity degree 2 by @mscroggs in #3731
• NonlinearProblem docstring improvements by @jhale in #3765
• Improve nested fieldsplit preconditioning setup on *Problem classes by @jorgensd in #3752
• Remove shared_vertex ghost mode option by @chrisrichardson in #3795
• Replace std::map in refinement by @chrisrichardson in #3797
• Harmonise Stokes high and low-level preconditioner setup by @jhale in #3778
• Write VTKHDF point and cell data by @chrisrichardson in #3806
• Introduce create_identity_partitioner for refined mesh partitioning by @schnellerhase in #3661
• Create parallel communication graph and support NetworkX analysis and visualiation by @garth-wells in #3803
• Doc improvements dolfinx.jit by @jhale in #3812
• Simplify PETSc wrapper solve return type by @jhale in #3810
• Improve PETSc wrapper documentation by @jhale in #3811
• Align order of create_mesh in Python layer to C++ layer by @schnellerhase in #3826
• Correct several typos in Stokes example and improve documentation formatting by @jorgensd in #3834
• Force non random order of execution for C++ tests by @schnellerhase in #3852
• Expose original cell indices by @jorgensd in #3854
• Wrap FunctionSpace.collapse by @michalhabera in #3851
• Allow dolfinx.fem.Constant to take native float as value type by @finsberg in #3847
• Generalise la::Vector to support GPUs by @garth-wells in #3855
• Remove mpiexec in cmake test target by @jhale in #3870
• Refactor dolfinx::fem::Form to use local indexing of forms, rather than integral ids by @jorgensd in #3740
• Re-enable Windows build by @jhale in #3867
• Allow copy of MatrixCSR to different storage (GPU support) by @chrisrichardson in #3886
• Rocky -> AlmaLinux for CI by @garth-wells in #3887
• Introduce dolfinx.fem.create_dofmaps by @schnellerhase in #3842
• Vertex integrals by @schnellerhase in #3726
• Support 'cast-copy' of la::MatrixCSR, la::Vector and common::Scatterer (includes GPU support) by @garth-wells in #3894
• allow stable abi builds by @minrk in #3875
• Drop Python 3.9 support by @schnellerhase in #3903
• Global dual graph computation for branching meshes by @schnellerhase in #3830
• Change interface of fem.petsc.create_vector to allow for general list of function spaces by @schnellerhase in #3694
• Fix vector block data for single function space case by @schnellerhase in #3924
• Improve python exposure of determine_point_ownership by @jorgensd in #3927
• add checks of cell tag consistency in gmshio by @pierricmora in #3342
• Support list of DG-0 + other space in VTXWriter by @ordinary-slim in #3375
• Fix "jointed" manifold mesh creation by @jorgensd in #3916
• Bugfix: mesh construction from mesh data on single process by @schnellerhase in #3936
• Handle diagonal assembly by @jorgensd in #3908
• Unification of one-sided sub-entity integrals + ridge integrals by @jorgensd in #3900
• Add XDMF-file flush functionality by @schnellerhase in #3947
• Fix interpolation_matrix for continuous spaces by @jorgensd in #3948
• Safer handling of PETSc destruction in high-level classes by @jorgensd in #3951

Other changes

• Update release instructions. by @jhale in #3460
• Bump version to 0.10 by @jhale in #3462
• Update Windows conda instructions. by @jhale in #3466
• Simplify conda weekly test by @jhale in #3467
• Add pip to dependabot by @jhale in #3464
• Fix warnings from Docker build linter by @jhale in #3463
• Spack CI update by @garth-wells in #3472
• Update version in Spack CI file by @garth-wells in #3473
• Re-enable Windows conda check using cmd.exe by @jhale in #3474
• Install all dependencies needed to run tests. by @jhale in #3475
• Improve build and optional dependency handing in Dockerfiles by @jhale in #3476
• Bump mpi4py/setup-mpi from 1.2.2 to 1.2.6 by @dependabot[bot] in #3457
• Bump adios2, HDF5, MPICH and OPENMPI in docker images. by @jorgensd in #3486
• Simplify interface to nanobind::ndarray by @garth-wells in #3496
• Bump mpi4py/setup-mpi from 1.2.6 to 1.2.7 by @dependabot[bot] in #3497
• PETSc version bump to 3.22.1 in Dockerfiles by @garth-wells in #3498
• Start simplification and consistency fixes for fem::FiniteElement by @garth-wells in #3502
• Remove loguru and old pugixml references by @jorgensd in #3503
• Remove Fides file backend by @garth-wells in #3485
• Expose set original cell index to python by @jorgensd in #3504
• Require nanobind>=2.2.0 by @francesco-ballarin in #3510
• Fix doc typo by @garth-wells in #3514
• Unify code path of DirichletBC::set by @schnellerhase in #3505
• Remove debug print by @jorgensd in #3515
• Allow mixed element with single element by @jorgensd in #3520
• Fix topological dimension of vertex-meshes by @jorgensd in #3523
• Remove error/warning when running macOS with OpenMPI by @jhale in #3525
• Check/fix for newest ruff by @jhale in #3527
• Fix typos by @mleoni-pf in #3526
• Remove pkg-config install from macOS test by @jhale in #3530
• Get FEniCSx refs from central workflow by @jhale in #3537
• Remove brew unlink by @schnellerhase in #3539
• Fix symmetric value shape by @michalhabera in #3535
• Fix domain id ordering of manually specified integration entities in Python by @jpdean in #3538
• Add AdjacencyList python wrapper by @schnellerhase in #3509
• cpp to MPI type mapping improvements by @schnellerhase in #3495
• Remove TimeLogManager and make TimeLogger singleton by @schnellerhase in #3494
• Ignore none subdomain data in form compilation subdomain checker by @jorgensd in #3541
• Unify and fix BoundingBoxtree constructor (C++) by @jorgensd in #3545
• Bump mpi4py/setup-mpi from 1.2.7 to 1.2.8 by @dependabot[bot] in #3544
• Copy x into u inside SNES Solver during Jacobian computation by @jhale in #3551
• Fix regression in FiniteElement Python wrapper by @jorgensd in #3552
• Further fixes to FiniteElement Python wrapper by @jorgensd in #3554
• Extract edge tags and vertex tags from gmsh and return a NamedTuple by @finsberg in #3547
• Fix regression from PR 3547 by @finsberg in #3560
• Add missing datatype in test_fem_pipeline by @finsberg in #3561
• Fix for mixed topology when mixing cells with different facet types by @chrisrichardson in #3572
• Single code path for mesh creation by @garth-wells in #3573
• Fix doc typos by @garth-wells in #3574
• Topology doc and code path improvements by @garth-wells in #3577
• Move Discourse and Slack to top of README by @garth-wells in #3578
• Simplify and improve Topology interface by @garth-wells in #3579
• Spelling fixes by @garth-wells in #3586
• Fix: interval refinement assertion ignores optional type by @schnellerhase in #3584
• Fix inconsistent ufl usage in demos by @schnellerhase in #3532
• Version bumps in Dockerfile by @garth-wells in #3592
• Tidy up sparse matrix code by @garth-wells in #3596
• Fix mapping of coefficients and constants for form independent compilation. by @jorgensd in #3597
• More work towards supporting mixed-topology meshes by @jpdean in #3590
• Switch to GitHub native runners by @jhale in #3601
• Update PETSc vector for mixed topology by @chrisrichardson in #3612
• Find ADIOS2 CXX only by @garth-wells in #3613
• Bump versions in Dockerfile by @garth-wells in #3614
• Bump pyvista version by @jorgensd in #3616
• Fix dofmap extraction for subsets of cells. Resolve #3607 by @jorgensd in #3615
• Use strict compiler flags when building nanobind layer in Debug mode. by @garth-wells in #3617
• Require nanobind>=2.5.0 by @francesco-ballarin in #3622
• Disable some GCC checks that trigger false positive warnings by @garth-wells in #3623
• Update documentation in petsc.py by @a-latyshev in #3626
• update DefElement links by @mscroggs in #3627
• Unpin cffi version (fixes tests for Python 3.13) by @garth-wells in #3635
• Add checks on geometry element for generated code by @garth-wells in #3633
• Update oneAPI CI by @garth-wells in #3636
• Add identifiable Python include directory name for Python wrappers by @schnellerhase in #3608
• Doc fixes and pin Sphinx version by @garth-wells in #3639
• Performance fixes and simplifications for fem::Form by @garth-wells in #3646
• Bump sphinx from 8.1.3 to 8.2.1 in /python by @dependabot[bot] in #3647
• Changes to type system by @schnellerhase in #3642
• CI use fenicsx-refs.env configuration in favor of run dependency by @schnellerhase in #3654
• Unpin Sphinx version. by @garth-wells in #3658
• Simplify: MDSPAN_IMPL_STANDARD_NAMESPACE -> md by @schnellerhase in #3655
• Include std::int64_t for distribute_entity_data by @jorgensd in #3651
• Improve code clarity in cell maps/permutations by @garth-wells in #3665
• Allow custom cell reorder function to be used in built-in meshes by @jpdean in #3666
• Unify PETSc matrix and vector factory functions by @jorgensd in #3667
• Require clang-format CI checks to pass by @garth-wells in #3669
• Build spdlog from source in Dockerfile.test-env by @jhale in #3670
• Update Dockerfile minor versions and fix spdlog by @jhale in #3671
• Pin nanobind version to 2.5.0 by @garth-wells in #3676
• Unpin nanobind version by @garth-wells in #3677
• Unify assembly functions for PETSc data structures (Python) by @garth-wells in #3668
• Bump mpi4py/setup-mpi from 1.2.8 to 1.2.9 by @dependabot[bot] in #3656
• Small doc improvement by @garth-wells in #3681
• Update pyvista.yml by @jorgensd in #3685
• Fixes for mypy by @jorgensd in #3690
• Replace numpy concat with concatenate by @schnellerhase in #3692
• Bump PETSc and SLEPc versions to newly released 3.23.0 by @schnellerhase in #3689
• Bump mpi4py/setup-mpi from 1.2.9 to 1.3.1 by @dependabot[bot] in #3688
• Stokes demo: create PETSc IS on mesh communicator by @garth-wells in #3693
• Add dolfinx.la.petsc to docs by @jhale in #3687
• Simplify SCOTCH configuration by @garth-wells in #3695
• Remove overflow issue in pybinding for entities_to_geometry by @jorgensd in #3696
• Extend VTKHDF file format to read/write higher order grids by @jorgensd in #3686
• Add dolfinx dependencies in user docker image as requirement and run end-user Docker image build in CI by @schnellerhase in #3697
• Various code fixes and simplifications by @garth-wells in #3700
• Use DOLFINX_ENABLE_* for end-user Docker by @schnellerhase in #3699
• Remove 'bug' label. 'bug' is now an issue type. by @garth-wells in #3702
• Get CMake to print some output when SCOTCH is found by @garth-wells in #3703
• Updates for macOS CI by @garth-wells in #3704
• Improve SCOTCH handling in CMake by @garth-wells in #3705
• Revert changes to end-user Docker build by @garth-wells in #3707
• Fix MacOS actions by @chrisrichardson in #3712
• Add missing ghost update in demo_mixed-poisson by @schnellerhase in #3710
• Update spack specification for PETSc optional by @chrisrichardson in #3714
• Use dtype in vtkhdf test by @mscroggs in #3715
• Remove upper bounds on dependencies. by @jhale in #3719
• Bump PETSc/SLEPc by @schnellerhase in #3720
• Fix oneapi CI by @schnellerhase in #3725
• Specify Python binding language in CMakeLists.txt by @garth-wells in #3734
• Fix signed version of radix_sort by @schnellerhase in #3724
• Refactor gmshio to use correct naming of subentities by @jorgensd in #3732
• Update scientificcomputing arm64 vtk wheel + bump pyvista and PETSc/SLEPc by @schnellerhase in #3737
• style: ascii art alignment by @tiagovla in #3739
• Bump mpi4py/setup-mpi from 1.3.1 to 1.3.2 by @dependabot[bot] in #3723
• Downgrade SLEPc by @schnellerhase in #3741
• Fix mypy by @schnellerhase in #3745
• Make dependabot check dockerfiles by @michalhabera in #3743
• Bump rockylinux/rockylinux from 9 to 10 in /docker by @dependabot[bot] in #3747
• Simplify input to non-linear problem by @jorgensd in #3751
• Set max doc length to 75 for python/dolfinx/ and python/demo/ by @schnellerhase in #3706
• Deactivate ruff 3.9 deprecation by @schnellerhase in #3757
• Pin scipy max version by @schnellerhase in #3761
• Update install docs by @garth-wells in #3762
• Capitalise CFFI in docs by @garth-wells in #3763
• Install custom built libraries to proper locations on RedHat image by @jhale in #3767
• Uniform refinement of mixed topology meshes by @chrisrichardson in #3756
• Fix mypy errors for newly typed ufl by @schnellerhase in #3768
• Bump mpi4py/setup-mpi from 1.3.2 to 1.3.3 by @dependabot[bot] in #3773
• More mypy fixes by @schnellerhase in #3772
• LinearProblem.solve return converged_reason and number_iterations by @jhale in #3774
• Use boost multiprecision for GJK by @chrisrichardson in #3770
• Remove duplicate lines from fem/petsc.py by @francesco-ballarin in #3781
• Bump PETSc and SLEPc by @schnellerhase in #3788
• Add mandatory options prefix to high-level solver classes and general tidy by @francesco-ballarin in #3785
• Tidy up interpolate.h and get ready for Mixed Topology interpolation by @chrisrichardson in #3793
• Check PETSc options prefix is not empty by @schnellerhase in #3796
• Allow optional node data to be attached to an AdjacencyList by @garth-wells in #3802
• Move conda/oneAPI CI config file by @garth-wells in #3804
• Local dual graph computation support for custom matching criteria by @schnellerhase in #3782
• Make bcs handling in fem.petsc.set_bc and fem.petsc.apply_lifting uniform by @francesco-ballarin in #3787
• Run mypy in package mode by @schnellerhase in #3807
• clang-tidy support by @schnellerhase in #3722
• Documentation update for MatrixCSR::mult by @chrisrichardson in #3809
• Update release instructions by @jhale in #3813
• Go back to LBYL programming style (instead of EAFP) and several mypy fixes in fem.petsc and la.petsc by @francesco-ballarin in #3790
• Revert some clang-tidy changes by @garth-wells in #3814
• Simplify import in Python demos by @garth-wells in #3816
• More complete Rocky (Redhat) image by @garth-wells in #3817
• Simplify mixed-domain interface by @jpdean in #3780
• Revert python/CMakeLists.txt change made in #3756 by @garth-wells in #3818
• Use cache for Spack CI by @garth-wells in #3821
• Switch from EAFP to LBYL by @schnellerhase in #3794
• Remove pyvista-specific CI (covered elsewhere) by @garth-wells in #3824
• Rationalise and simplify some CI by using Spack by @garth-wells in #3823
• Fix XDMF time series by @schnellerhase in #3829
• Remove redundant CI Actions code by @garth-wells in #3831
• Remove exposure of cpp type through VTXWriter interface by @schnellerhase in #3827
• Add default scalar type cast by @schnellerhase in #3833
• Improve CMake find modules by @garth-wells in #3835
• Add new Python versions to conda and fix CI by @garth-wells in #3839
• Small README and Docker improvements by @garth-wells in #3840
• Remove Windows badge - it's alway red by @garth-wells in #3841
• Switch to vtk version that supports aarch64 wheels in end user image by @schnellerhase in #3805
• Get nestis from A instead of P by @jorgensd in #3846
• Consistency of input arguments to LinearProblem by @jorgensd in #3849
• Warn about missing IndexMap in Topology by @chrisrichardson in #3853
• Add error for missing physical groups in gmsh by @chrisrichardson in #3860
• Fix correct material/void split in loaded waveguide demo by @schnellerhase in #3843
• Fix indentation of create_mesh by @jorgensd in #3863
• Add explicit <format> includes by @francesco-ballarin in #3865
• Integrate C++ tests into project cmake by @schnellerhase in #3858
• Unpin scipy by @schnellerhase in #3871
• Fix Python-binding of Form::num_integrals by @jorgensd in #3877
• Bump actions/setup-java from 4 to 5 by @dependabot[bot] in #3874
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #3873
• Make tests work as standalone project by @schnellerhase in #3879
• Add 'Developer' CMake build type for Python wrappers by @garth-wells in #3878
• Remove MPI Python test Windows by @jhale in #3882
• Update windows.yml by @jhale in #3883
• Run Spack CI build in parallel by @garth-wells in #3888
• Disable Windows demo run by @jhale in #3889
• Spack install fix: change concretize by @garth-wells in #3890
• Cache PETSc on macos CI by @garth-wells in #3891
• Updates for Spack install tests by @garth-wells in #3892
• CI testing via Spack (experimental) by @garth-wells in #3884
• Some mypy fixes by @schnellerhase in #3896
• Small simplifications of gmsh IO interface by @schnellerhase in #3881
• Revert "Remove Windows badge - it's alway red (#3841)" by @jhale in #3898
• Fix kernel extraction on windows by @schnellerhase in #3897
• Pep-0604 - Removing typing.Union by @jorgensd in #3906
• Fix type hint regression by @schnellerhase in #3907
• Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #3910
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #3909
• Remove dynamic memory allocation in lowest-level scalar assembly functions by @garth-wells in #3914
• Rename spack-experimental-ci by @jorgensd in #3918
• Job names need to be unique for branch protection rules by @schnellerhase in #3920
• Ruff formatting 0.13.0 by @jorgensd in #3921
• Fix Windows CI for .env-file config variables. by @jorgensd in #3922
• Provide commit SHA for Spack install by @garth-wells in #3913
• Ensure dolfinx does not expose warning to user by @schnellerhase in #3905
• Improve GMSH usage in tests by @jorgensd in #3932
• Expose documentation of determine point ownership by @jorgensd in #3933
• Fix typo in binding by @jorgensd in #3935
• Remove PETSc C-binding utils from default namespace and add all spd LogLevels to Python-API by @jorgensd in #3931
• DirichletBC.dof_indices() are wrong for blocked spaces by @jorgensd in #3937
• Remove breakpoint by @jorgensd in #3939
• More fixes to DirichletBC.dof_indices by @michalhabera in #3941
• Bump PETSc/SLEPc to 3.24.0 release by @schnellerhase in #3942
• Revise documentation of Python API and demos by @jorgensd in #3940
• Bump sonarcloud by @jorgensd in #3943
• Petsc ignore type by @jorgensd in #3944
• Clean up demo postprocessing by @jorgensd in #3946
• Fix shape for vtkOriginalPointIds and vtkGhostType by @chrisrichardson in #3952
• Release-notes for 0.10 by @jorgensd in #3950

New Contributors

• @Saransh-cpp made their first contribution in #3550
• @jzitelli made their first contribution in #3563
• @a-latyshev made their first contribution in #3626
• @ordinary-slim made their first contribution in #3600
• @sclaus2 made their first contribution in #3660
• @RemDelaporteMathurin made their first contribution in #3713

Full Changelog: v0.9.0.post1...v0.10.0.post0