v5.2.0

This is feature release, with a ton of new features. We've now switched entirely to CMake for our build system.

Breaking changes

• The autotools ./configure build system has been removed
• Parsing of booleans has changed [#2828][https://github.com//pull/2828] ([bendudson][https://github.com/bendudson]).
  See the manual page for details.
• Previously, the Solver implementations passed the loop counter to
  the iter argument of call_monitors, but since the iteration has
  already been completed when the monitors are called, this results in
  iter always being one less than the number of completed
  monitor-steps at the point when the moniters are called, which is
  confusing. Now, monitors are called with the current number of
  completed monitor-steps.

What's Changed

• Switch (partially) to regions by @dschwoerer in #2439
• Allow static builds with Sundials by @bendudson in #2740
• Merge v5.1.0 into next by @ZedThree in #2756
• Fix sphinx configuration (next) by @dschwoerer in #2763
• Bump required C++ standard to 17 by @ZedThree in #2719
• Merge recent CI and maintenance fixes back into next by @ZedThree in #2768
• Remove deprecated autotools build system by @ZedThree in #2769
• Refactor PetscVector to use buffered writes by @ZedThree in #2713
• Merge recent CI and maintenance fixes back into next again by @dschwoerer in #2783
• Add BOUT_HOST_DEVICE to accessor operators for GPU by @ggeorgakoudis in #2806
• Fix hypre compilation in next branch by @bendudson in #2791
• Some recent maintenance fixes back into next from master by @dschwoerer in #2815
• ADIOS 2 I/O by @bendudson in #2766
• More consistent parsing of boolean inputs (Breaking change) by @bendudson in #2828
• Updating README by @bendudson in #2826
• Remove propietary data (next) by @dschwoerer in #2831
• Work around pip changes by @dschwoerer in #2824
• Track regions that fields are valid over by @dschwoerer in #2324
• Fixing elm-pb example to match v3 results by @bendudson in #2809
• Remove tools/pylib/post_bout by @ZedThree in #2843
• Fix a bunch of clang-tidy issues in Options by @ZedThree in #2841
• Remove unused format.hxx header by @ZedThree in #2848
• Replace MAYBE_UNUSED macro with C++17 [[maybe_unused]] by @ZedThree in #2849
• Remove Options::OptionValue nested class by @ZedThree in #2852
• Use C++17 inline variables to remove some linker hacks by @ZedThree in #2850
• Read fields from ADIOS2 restart files by @bendudson in #2857
• Update CUDA standard to cxx17, add CI build test by @ggeorgakoudis in #2856
• Cleanup Parallel BoundaryCode by @dschwoerer in #2629
• Tweak clang-tidy config by @ZedThree in #2865
• Remove backtrace example, move into docs instead by @ZedThree in #2842
• Various minor C++17 fixes and improvements by @ZedThree in #2862
• Options: Delete copy constructor and copy assignment by @bendudson in #2861
• Do not specify redundant class in ctor by @dschwoerer in #2869
• Make check for zoidberg much faster by @dschwoerer in #2870
• Fix all header guards by @ZedThree in #2872
• Fix a bunch of clang-tidy warnings in region.hxx by @ZedThree in #2871
• Add number of OpenMP threads to dump file by @dschwoerer in #2868
• elm-pb model fix sheath boundary by @bendudson in #2876
• Some minor fixes, docs, ... by @dschwoerer in #2886
• Reintroduce removed copy function marked deprecated by @dschwoerer in #2891
• CI: Adopt for no sudo in container by @dschwoerer in #2883
• Fixes for the python interface by @dschwoerer in #2892
• Update SUNDIALS support (rebase onto next) by @ZedThree in #2896
• Prefer ADIOS2 over ADIOS in more cases by @dschwoerer in #2905
• Improve parallel boundary regions by @dschwoerer in #2648
• Improve ParallelBoundary code by @dschwoerer in #2649
• Fix metrics in Laplace inversion by @bendudson in #2914
• Fix some include issues by @ZedThree in #2919
• Fix version checking for SUNDIALS by @Steven-Roberts in #2922
• CI: Bump python dependencies by @ZedThree in #2929
• Add getters for Laplacian flags by @ZedThree in #2916
• MPCDF update by @dschwoerer in #2921
• CVODE solver: Pass linear flag to rhs() by @bendudson in #2932
• Add CVODE mxorder option back, now deprecated by @Steven-Roberts in #2949
• Fmt update by @dschwoerer in #2961
• Fix typos in laplacian inversion documentation (credit @MigMadeira) by @bshanahan in #2965
• Next IMEX issue by @maggul in #2930
• CMake: Replace include SourceRuns with SourceCompiles by @bendudson in #2970
• Some more examples fixes by @tomc271 in #2951
• Bump externalpackages/googletest from 0953a17 to 6dae7eb by @dependabot[bot] in #2981
• Update numpy requirement from ~=2.0.0 to ~=2.1.1 by @dependabot[bot] in #2973
• naulin laplace: Acceptance tolerances after maxits by @bendudson in #2983
• Use consistently signed char by @dschwoerer in #2987
• BoutMask non-const operator by @bendudson in #2988
• Add LC gitlab CI for GPU build/run tests by @ggeorgakoudis in #2989
• Fix exception message by @dschwoerer in #3003
• Update numpy requirement from ~=2.1.1 to ~=2.1.2 by @dependabot[bot] in #2984
• Ensure pointer is checked before dereferencing by @dschwoerer in #3002
• Fix: preserve regionID by @dschwoerer in #3000
• Try to do the right thing for linking netCDF::netcdf by @dschwoerer in #2995
• master branch will be 5.1.2 not 5.2.0 by @dschwoerer in #2994
• Read 2D variables into Field3D by @bendudson in #2975
• Add .zpm for sign-independent coding by @dschwoerer in #2888
• Fix iteration counts change all iter rebase by @dschwoerer in #2882
• Fix or delete examples by @bendudson in #2811
• CI: Bump all ubuntu images by @ZedThree in #2977
• Fix circular header dependency: mesh.hxx <-> griddata.hxx by @ZedThree in #3008
• Add isFci also to mesh by @dschwoerer in #3001
• CI: clang-tidy-review tweaks by @ZedThree in #3016
• Replace deprecated boututils.file_import by @ZedThree in #3017
• Merge v5.1.1 into next by @ZedThree in #2978
• Bump externalpackages/googletest from 6dae7eb to d144031 by @dependabot[bot] in #3019
• Backward Euler solver improvements by @bendudson in #3009
• Fix compilation warnings with SUNDIALS 7.1.0 by @st...

v5.1.1

What's Changed

• Fix sphinx configuration by @dschwoerer in #2762
• Prefer dnf5 for fedora CI (master) by @dschwoerer in #2764
• [RTD] add os to read the docs config by @dschwoerer in #2779
• Fix test-laplace-petsc3d by @dschwoerer in #2781
• Ensure also lower case is accepted by @dschwoerer in #2759
• CI: Increase shm size in container by @dschwoerer in #2777
• CI: user master branch for docker actions by @dschwoerer in #2780
• Bump actions/setup-python from 1 to 4 by @dependabot in #2771
• CI: Run on PETSc developement branch by @dschwoerer in #2765
• Bump stefanzweifel/git-auto-commit-action from 4 to 5 by @dependabot in #2772
• Bump ZedThree/clang-tidy-review from 0.13.1 to 0.14.0 by @dependabot in #2773
• Bump externalpackages/fmt from f0903ad to 2ac6c5c by @dependabot in #2776
• master branch will be 5.1.1 not 5.2.0 by @dschwoerer in #2784
• CI: Replace pip script with requirements.txt by @ZedThree in #2794
• Set oversubscribe flags for openmpi 5 by @dschwoerer in #2800
• CI: Bump actions/setup-python from 4 to 5 by @dependabot in #2819
• Remove propietary data (master) by @dschwoerer in #2832
• Do not excessively bump googletest by @dschwoerer in #2836
• Bump actions/cache from 3 to 4 by @dependabot in #2845
• Bump ZedThree/clang-tidy-review from 0.14.0 to 0.17.0 by @dependabot in #2846
• Add warnings about SUNDIALS versions <4 by @Steven-Roberts in #2840
• Bump codecov/codecov-action from 3 to 4 by @dependabot in #2860
• Fix name of PVODE Config file by @dschwoerer in #2903
• SUNDIALS v7 support (backport to v5) by @ZedThree in #2937
• CI: Ensure we do not timeout due to slow mirrors by @dschwoerer in #2940
• mark fmt::format() const by @tchaikov in #2942
• Update netcdf4 requirement from ~=1.6.0 to ~=1.7.1 by @dependabot in #2960
• Update boutdata and boututils submodules by @dschwoerer in #2959
• Small clang-tidy fixes for sundials solvers by @ZedThree in #2953
• Resolve merge conflict for v5.1.1-rc by @dschwoerer in #2964
• Tools for updating contributors and version numbers by @tomc271 in #2734
• V5.1.1 rc by @ZedThree in #2935
• Update jinja2 requirement from ~=3.1.0 to ~=3.1.4 by @dependabot in #2972

New Contributors

• @tchaikov made their first contribution in #2942

Full Changelog: v5.1.0...v5.1.1

v5.1.0

What's Changed

• SNB and InvertParDiv for nonuniform grids by @bendudson in #2572
• Fix error message by @dschwoerer in #2642
• Expose mixed derivatives by @dschwoerer in #2639
• Cleanup syntax by @dschwoerer in #2638
• Merge v5 into next - resolve conflicts by @dschwoerer in #2658
• Merge v5 into next by @ZedThree in #2655
• Squash optional by @dschwoerer in #2659
• Always provide applyParallelBoundary by @dschwoerer in #2640
• Fix getUniform warning by @dschwoerer in #2644
• Handle missing python better for finding numpy by @dschwoerer in #2643
• Fix some warnings and deprecated headers by @ZedThree in #2666
• Fix versions after release by @dschwoerer in #2669
• Improve docs + fix boutpp docs (master) by @dschwoerer in #2664
• Fix some warnings by @dschwoerer in #2661
• switch to BOUT_FOR and simplify Div_a_Grad_perp by @dschwoerer in #2641
• fix boutconfig's has by @dschwoerer in #2647
• Fix versions after release (next) by @dschwoerer in #2670
• Compute modulo only once by @dschwoerer in #2645
• Set some _ROOT vars by @dschwoerer in #2652
• Add dependabot config by @dschwoerer in #2680
• Some fixes for tokamak-2fluid example by @ZedThree in #2668
• Error early with in-source-builds by @dschwoerer in #2660
• More forgiving restart inputs by @bendudson in #2676
• apply clang-format v15.0.7 and .clang-format@d8f14fdd by @dschwoerer in #2662
• Python: If we are on a tag, we should use that as version by @dschwoerer in #2683
• Recommend requirements.txt for dependencies by @dschwoerer in #2689
• Add plt.show() to example by @dschwoerer in #2687
• CI: switch to openmpi for fedora GHA by @dschwoerer in #2682
• Fix pvode warnings by @dschwoerer in #2684
• Track more build options by @dschwoerer in #2634
• Revert "Workaround for test-restart-io for recent boututils" by @dschwoerer in #2685
• Update boututils and boutdata to working versions by @dschwoerer in #2679
• Update bundled boututils and boutdata by @dschwoerer in #2657
• isUniform: Do not fail if numbers are only almost equal by @dschwoerer in #2693
• Docs for docs improvements by @dschwoerer in #2690
• Fix SUNDIALS Context construction for MPICH by @dschwoerer in #2678
• Improve checking in coords constructor by @dschwoerer in #2650
• CI: do not run on removed old ubuntu by @dschwoerer in #2695
• Fall back to pkgconfig for finding netcdf-cxx4 by @dschwoerer in #2686
• CI: Update runs-on (next) by @dschwoerer in #2696
• Docs: Fix default branch for "suggest edit" by @ZedThree in #2697
• Improve invSg calculation by @dschwoerer in #2646
• Add support for PETSc & SLEPc 3.18 / 3.19 by @ZedThree in #2704
• provide VectorMetric in vectormetric.hxx by @dschwoerer in #2706
• Remove last uses of bout::globals::dump by @ZedThree in #2699
• Remove unnecessary check for aligned fields when applying twist-shift by @dschwoerer in #2711
• The additional check is not needed by @dschwoerer in #2710
• Get mesh outputs after physics init by @bendudson in #2714
• Solver improvements by @bendudson in #2716
• Review of PR #2514 (Switch to CMake) by @tomc271 in #2694
• Do not try to run SLEPc or PETSc in configure by @dschwoerer in #2709
• Switch to CMake in CI and docs by @dschwoerer in #2514
• Update make dist invocation by @dschwoerer in #2707
• mesh:paralleltransform is a section by @dschwoerer in #2702
• Remove references to build dir from install by @dschwoerer in #2628
• CI install natsort by @bendudson in #2723
• Revert sundials detection by @dschwoerer in #2725
• Fix static CI build by @dschwoerer in #2724
• Bump clang-tidy-review version by @ZedThree in #2726
• CI: Install dnf5 for Fedora by @dschwoerer in #2731
• Build containers in GHA CI by @dschwoerer in #2511
• Generate BOUT++ tar via boutpp backend by @dschwoerer in #2708
• Remove h5py - we only support netcdf by @dschwoerer in #2735
• Update to dnf5 (master) by @dschwoerer in #2732
• Improving compatibility with fmt 10 by @dschwoerer in #2730
• Fix FV::Div_a_Grad_perp Y alignment by @bendudson in #2722
• Update RELEASE_HOWTO.md by @dschwoerer in #2741
• 5.1 release candidate by @ZedThree in #2720
• CMake: Fix version detection from git tag by @ZedThree in #2753
• Add fallback if the version has been bumped bot not tagged by @dschwoerer in #2754

New Contributors

• @tomc271 made their first contribution in #2694

Full Changelog: v5.0.0...v5.1.0

v5.0.0

What's Changed

• Parse params by @bendudson in #1706
• More expressions "improvements" by @bendudson in #1764
• Fix some issues in hypnotoad by @friva000 in #1783
• Add macro for Scorep instrumentation of a user-defined code region by @JosephThomasParker in #1784
• Merge v4.3.0 into next by @ZedThree in #1826
• Bump version in next to 5.0.0-alpha by @ZedThree in #1827
• Require C++14 by @ZedThree in #1830
• Get latest versions of submodules by @ZedThree in #1831
• Fix various warnings by @ZedThree in #1832
• Include all boundary cells in GlobalNy by @johnomotani in #1829
• Fix typo in initialisation of rgn_outer_x by @AdamD94 in #1837
• Petsc interface by @cmacmackin in #1805
• Remove deprecated Laplacian API by @ZedThree in #1834
• Add remaining integrated tests to CMake build by @ZedThree in #1833
• Rename Positon -> Context, simplify class, fix things by @bendudson in #1750
• Standardise factories by @ZedThree in #1842
• Allow user to override library option defaults by @johnomotani in #1773
• Fix PETSc Laplace tests by @ZedThree in #1859
• MPI wrapper class by @cmacmackin in #1808
• Add fmtlib locale corrections by @bendudson in #1866
• Use {fmt} for all string formatting by @ZedThree in #1847
• CMake: fix FindSlepc for non-make generators by @ZedThree in #1881
• Fixes for Windows by @ZedThree in #1874
• FieldGenerate refactor by @dschwoerer in #1705
• Remove unused parameters to silence warnings in MsgStack by @ZedThree in #1887
• Generate report for Timers by @ZedThree in #1882
• Petsc interface generalisation by @cmacmackin in #1889
• Rename death tests according to gtest recommendations by @ZedThree in #1891
• Cmake fixes by @dschwoerer in #1909
• Macro for creating enum classes by @johnomotani in #1841
• Laplace performance test by @JosephThomasParker in #1908
• Implement toFieldAligned and fromFieldAligned for Vector3D by @johnomotani in #1877
• Add v5 upgrader scripts for XZInterpolation by @ZedThree in #1919
• Workaround for Petsc init/finialise not being idempotent by @ZedThree in #1922
• Fix segfaults from PvodeSolver by @johnomotani in #1926
• Implement BOUT_FOR for FV::div_f_v by @bshanahan in #1918
• XZInterpolation rename, and passing Options to XZInterpolation objects by @johnomotani in #1896
• Fixes for staggering in lapd-drift example by @johnomotani in #1925
• Various minor fixes for the sphinx docs by @ZedThree in #1935
• Minor Travis fixes and job names by @ZedThree in #1942
• Rely on latexmk in noninteractive mode by @dschwoerer in #1938
• use system library, if GIT_SUBMODULE=OFF by @dschwoerer in #1907
• ensure make clean cleans tests by @dschwoerer in #1738
• Ignore latexmk files by @dschwoerer in #1947
• Add Mesh::getRegion for use in generic code by @ZedThree in #1890
• MsgStack and PetscLib thread safety by @ZedThree in #1941
• Add ZInterpolation, ZHermiteSpline by @ZedThree in #1944
• Add full perpendicular Laplacian, inverse of LaplaceXY by @ZedThree in #1939
• Generate version header by @ZedThree in #1920
• Update staggered grids implementation in various examples by @johnomotani in #1954
• Add ShiftedMetricInterp: shifted metric using interpolation in Z by @ZedThree in #1946
• Set corner cells consistently by @johnomotani in #1885
• Exclude corner cells in LaplaceXY by @ZedThree in #1957
• Fix some missed fmt format strings by @ZedThree in #1943
• Fix possible data race in MsgStack::push() by @johnomotani in #1955
• Add extra region option for mixed derivatives by @ZedThree in #1936
• CMake: find package fixes by @ZedThree in #1912
• Pass method and region arguments to D2DXDY in Laplace(Field2D) by @johnomotani in #1961
• CMake: enable using external mpark.variant by @ZedThree in #1900
• Fix runtest for non-make generators by @ZedThree in #1952
• fix for running unit-test as root by @dschwoerer in #1959
• Field3d copy parallel slices by @ZedThree in #1960
• Fix typo in example/performance/communications by @johnomotani in #1963
• LaplaceXY: finite difference option by @johnomotani in #1789
• Add region argument to XZInterpolations by @ZedThree in #1962
• Algebraic multigrid by @cmacmackin in #1803
• Fix typo in Ubuntu 16.04 installation command by @bshanahan in #1964
• fix test-laplace-petsc3d by @dschwoerer in #1985
• Use custom main instead of PhysicsModel in test-communications by @johnomotani in #1983
• Merge v4.3.1 into next by @ZedThree in #1999
• Include smaller "fmt/core.h" by @ZedThree in #2001
• Fix --enabled-shared for configure by @dschwoerer in #1984
• Provide better error if fields are not compatible by @dschwoerer in #2012
• Ensure quiet script isn't too verbose on error by @dschwoerer in #2011
• fix requires in options-netcdf test by @dschwoerer in #2009
• Improve some error messages by @dschwoerer in #2005
• Ensure ffts are OpenMP thread safe by @dschwoerer in #2006
• pkg-config petsc (next) by @dschwoerer in #1914
• Minor fixes for elm-pb and python tools by @dschwoerer in #1958
• Run wrapper improvements by @dschwoerer in #2007
• Fix bug in configure when using dash as shell by @dschwoerer in #2016
• Fix formatting of 'Obtaining BOUT++' section heading by @johnomotani in #2015
• Remove MUMPS by @dschwoerer in #2018
• Update the staggered grids section of the manual by @johnomotani in #2028
• remove checklib dependency from unit tests by @dschwoerer in #2002
• Fix and unit tests for BOUT_ENUM_CLASS by @johnomotani in #2031
• Parallel tests by @dschwoerer in #2000
• filledFrom using lambda function by @bendudson in #2037
• Construct Option with initializer_list by @bendudson in #1772
• Allow PETSc options to be passed from BOUT.inp by @johnomotani in #1795
• Travis: add Fedora job by @dschwoerer in #2036
• Add location checks to Div_par_K_Grad_par by @bshanahan in #2038
• Minor optimizations for ZHermiteSpline by @johnomotani in #2035
• Add Physi...

BOUT++ v4.4.2

• CMake: option to ignore a conda environment; fix for PVODE #2494 (johnomotani)
• CMake fixes for netCDF #2493 (johnomotani)
• Fix bug in PetscLib that broke no-PETSc builds #2492 (johnomotani)
• Remove tests depending on UB #2491 (j-b-o)
• Make cmake submodule update work with older versions of git #2490 (johnomotani)

BOUT++ v4.4.1

4.4.1 is a bugfix release:

• Fixed some issues building BOUT++ on MacOS
• Fixed some issues when installing
• Fixed some issues when downloading SUNDIALS and netCDF C++
• Fixed some out of date documentation
• Some improvements/fixes to the beuler/snes solver

BOUT++ v4.4.0

4.4.0 is a feature release. The main new features are:

• The CMake support has been expanded, and will replace the autotools build
  system in the next major release. See the CMake installation
  instructions
  for details on building with CMake.
• Output files can now handle FieldPerp, std::vector<int>, and
  std::string, while input options can now handle FieldPerp.
• Output and evolving variables can now have an optional description
• The boutdata and boututils python libraries have been moved to standalone
  packages. BOUT++ still comes bundled with them as submodules, but you can now
  install them separately.
• Staggered grids now work with InvertPar and split flux derivatives.
• User code can set default values that override the library's default values.
• Timing information can be output in a table at the end of the run with
  time_report:show
• Some basic provenance information tracking has been enabled: each run now
  generates a random unique ID. Hypnotoad grid files that contain a UUID will
  also be tracked.
• A new time solver has been added, an adaptive, arbitrary order Adams-Bashforth
  solver.
• FFTs can use the FFTW_EXHAUSTIVE input option.

See the full changelog for more details

BOUT++ v4.3.3

4.3.3 is a bugfix release:

• Better documentation and tests
• Fix shiftOutput for aligned fields
• Some improvements to the Python API, including support for Python's
  exponentiation operator **, and MPI-aware logging
• Fix an uninitialised variable in Delp2
• Bump the version of jinja2 from 2.10 to 2.11
• Fix for some Solvers not always using user preconditioner/Jacobian
• Some minor fixes to the build systems

BOUT++ v4.3.2

4.3.2 is a bugfix release:

• Make downloading the submodules a bit nicer, including an option for
  using non-bundled versions when using configure
• Make dz in the Python API a property
• Make Div_par_K_Grad_par check the staggered location of its inputs
• Enable split-flux derivatives on staggered fields
• Fix Grad2_par2 implementation in InvertParCR
• Fix an issue writing FieldPerps
• Make it easier to compile the examples with different versions of
  BOUT++, plus fixes for the tokamak-2fluid example
• Fix Div_par when using more than one y-guard cell
• Fix an issue with text attributes in HDF5 files

BOUT++ v4.3.1

4.3.1 is a bugfix release, with a few minor fixes to library code, notably:

• Fix the creation of the RGN_OUTER_X region
• Several small bugs in the Python API
• Preserve restart files if there's a crash during initialisation
• Fix some segfaults in the PvodeSolver
• Fix some issues with Hypnotoad (see #1783)

Other changes are mostly housekeeping changes for the BOUT++ project.