CHANGELOG.md

Changelog

[v5.1.0](https://github.com/boutproject/BOUT-dev/tree/v5.1.0

Full Changelog

• Update RELEASE_HOWTO.md [#2741][boutproject#2741] ([dschwoerer][https://github.com/dschwoerer])
• Remove h5py - we only support netcdf [#2735][boutproject#2735] ([dschwoerer][https://github.com/dschwoerer])
• CI: Install dnf5 for Fedora [#2731][boutproject#2731] ([dschwoerer][https://github.com/dschwoerer])
• Improving compatibility with fmt 10 [#2730][boutproject#2730] ([dschwoerer][https://github.com/dschwoerer])
• Bump clang-tidy-review version [#2726][boutproject#2726] ([ZedThree][https://github.com/ZedThree])
• Revert sundials detection [#2725][boutproject#2725] ([dschwoerer][https://github.com/dschwoerer])
• Fix static CI build [#2724][boutproject#2724] ([dschwoerer][https://github.com/dschwoerer])
• CI install natsort [#2723][boutproject#2723] ([bendudson][https://github.com/bendudson])
• Fix FV::Div_a_Grad_perp Y alignment [#2722][boutproject#2722] ([bendudson][https://github.com/bendudson])
• Generate BOUT++ tar via boutpp backend [#2708][boutproject#2708] ([dschwoerer][https://github.com/dschwoerer])
• Build containers in GHA CI [#2511][boutproject#2511] ([dschwoerer][https://github.com/dschwoerer])
• Update to dnf5 (master) [#2732][boutproject#2732] ([dschwoerer][https://github.com/dschwoerer])
• Solver improvements [#2716][boutproject#2716] ([bendudson][https://github.com/bendudson])
• Get mesh outputs after physics init [#2714][boutproject#2714] ([bendudson][https://github.com/bendudson])
• Remove unnecessary check for aligned fields when applying twist-shift [#2711][boutproject#2711] ([dschwoerer][https://github.com/dschwoerer])
• Do not try to run SLEPc or PETSc in configure [#2709][boutproject#2709] ([dschwoerer][https://github.com/dschwoerer])
• Update make dist invocation [#2707][boutproject#2707] ([dschwoerer][https://github.com/dschwoerer])
• Add support for PETSc & SLEPc 3.18 / 3.19 [#2704][boutproject#2704] ([ZedThree][https://github.com/ZedThree])
• mesh:paralleltransform is a section [#2702][boutproject#2702] ([dschwoerer][https://github.com/dschwoerer])
• Remove last uses of bout::globals::dump [#2699][boutproject#2699] ([ZedThree][https://github.com/ZedThree])
• Docs: Fix default branch for "suggest edit" [#2697][boutproject#2697] ([ZedThree][https://github.com/ZedThree])
• CI: do not run on removed old ubuntu [#2695][boutproject#2695] ([dschwoerer][https://github.com/dschwoerer])
• isUniform: Do not fail if numbers are only almost equal [#2693][boutproject#2693] ([dschwoerer][https://github.com/dschwoerer])
• Docs for docs improvements [#2690][boutproject#2690] ([dschwoerer][https://github.com/dschwoerer])
• Recommend requirements.txt for dependencies [#2689][boutproject#2689] ([dschwoerer][https://github.com/dschwoerer])
• Fall back to pkgconfig for finding netcdf-cxx4 [#2686][boutproject#2686] ([dschwoerer][https://github.com/dschwoerer])
• Fix pvode warnings [#2684][boutproject#2684] ([dschwoerer][https://github.com/dschwoerer])
• Python: If we are on a tag, we should use that as version [#2683][boutproject#2683] ([dschwoerer][https://github.com/dschwoerer])
• CI: switch to openmpi for fedora GHA [#2682][boutproject#2682] ([dschwoerer][https://github.com/dschwoerer])
• Fix SUNDIALS Context construction for MPICH [#2678][boutproject#2678] ([dschwoerer][https://github.com/dschwoerer])
• Fix versions after release [#2669][boutproject#2669] ([dschwoerer][https://github.com/dschwoerer])
• Some fixes for tokamak-2fluid example [#2668][boutproject#2668] ([ZedThree][https://github.com/ZedThree])
• Fix some warnings and deprecated headers [#2666][boutproject#2666] ([ZedThree][https://github.com/ZedThree])
• Improve docs + fix boutpp docs (master) [#2664][boutproject#2664] ([dschwoerer][https://github.com/dschwoerer])
• Fix some warnings [#2661][boutproject#2661] ([dschwoerer][https://github.com/dschwoerer])
• Error early with in-source-builds [#2660][boutproject#2660] ([dschwoerer][https://github.com/dschwoerer])
• Squash optional [#2659][boutproject#2659] ([dschwoerer][https://github.com/dschwoerer])
• Merge v5 into next - resolve conflicts [#2658][boutproject#2658] ([dschwoerer][https://github.com/dschwoerer])
• Update bundled boututils and boutdata [#2657][boutproject#2657] ([dschwoerer][https://github.com/dschwoerer])

v5.0.0

Full Changelog

Breaking changes

• BoutMesh::GlobalNy now counts points from all y-boundaries. Previously it only counted points from the boundaries at the upper and lower edges of the logical grid, even if there was another boundary in the grid. #1829
• invert_laplace free function removed #1834
• Most factories and create methods standardised. Run bin/bout-v5-factory-upgrader.py on your physics models to update them #1842 #2087
• We now use fmt for all our string formatting, instead of the printf-style formatting. This affects calls to Output, BoutException/ParseException, DataFile, OptionsReader, and MsgStack/TRACE. Run bin/bout-v5-format-upgrader.py on your physics models to update them. #1847
• The option laplacexy:y_bndry_dirichlet has been deprecated. Use laplacexy:y_bndry=dirichlet instead. #1789
• The variable BOUT_VERSION, and the macros REVISION, BOUT_VERSION_STRING and BOUT_VERSION_DOUBLE have been replaced with constexpr variables in the bout::version namespace. REVISION is found in include/bout/revision.hxx, while the rest are in include/bout/version.hxx. Both files are generated at configure time. Run bin/bout-v5-macro-upgrader.py to update. #1920
• The MUMPS Laplacian inversion wrapper has been removed. It is still possible to use MUMPS for Laplacian inversions through the PETSc wrapper. #2018
• The using namespace bout::globals statement has been removed from physics_model.hxx, and PhysicsModel has gained public mesh and dump members. Custom mains, free functions and legacy models will need to be updated to either use bout::globals::mesh or Field::getMesh() in free functions. #2042
• The LaplaceShoot Laplacian implementation was removed. There are very few cases, if any, where this implementation actually works. #2177
• PhysicsModel expects the options datadir and dump_format to have been set; this is only a problem if you don't call BoutInitialise. #2062
• dz is now a Field2D, and Coordinates::zlength() also returns a Field2D. In most cases, wrapping these in a call to getUniform in order to get a BoutReal will do the correct thing. If checks are enabled, getUniform will throw an exception if its argument is not uniform (that is, that all values are identical). #2025
• The parallel boundaries BNDRY_PAR_FWD and BNDRY_PAR_BKWD have been expanded to distinguish between the inner and outer boundaries in x; the enums have been replaced with BNDRY_PAR_*_XIN, and BNDRY_PAR_*_XOUT for both FWD and BKWD. #2025
• Support for reading/writing HDF5 files has been removed ahead of completely refactoring the I/O
• Support for reading/writing HDF5 files has been removed ahead of completely refactoring the I/O systems. #2208
• Removed the Karniadakis time solver. Other choices for split-operator schemes are: splitrk (built-in), imexbdf2 (requires PETSc), and arkode (requires SUNDIALS) #2241
• Conversion of Option to bool is now stricter. Previously, only tested (case-insensitively) if first character was 'n', 'f', '0', 'y', 't', or '1'. Now only allow (still case-insensitively but checking full strings) 'n', 'no', 'f', 'false', '0', 'y', 'yes', 't', 'true', or '1'. #2282
• Having any unused options remaining after the first call to the physics model rhs is now an error. Set input:error_on_unused_options = false for old behaviour #2210
• Input options are now case sensitive. Run bin/bout-v5-input-file-upgrader.py to automatically fix the most common library options #2210
• Input options are now required to be either a section or a value, and not both. This requires renaming the restart section to restart_files. bin/bout-v5-input-file-upgrader.py can automatically make this change. #2277
• Options are now only implicitly-castable to types stored in the internal variant. Other types now require a call to Options::as<T>() #2341
• The Laplacian inversion solver LaplacePDD ("pdd") has been removed. This implementation had some quite significant drawbacks that made it not terribly useful in practice #3566
• Datafile and bout::globals::dump have been removed in favour of OptionsNetCDF. Uses of SAVE_ONCE/REPEAT inside PhysicsModel code will still work for the time being; outside of PhysicsModel methods, these macros will need to be manually replaced. See the file IO changes for v5 docs for more details. #2209

v5.0.0 (2023-01-10)

Full Changelog

• Provide overloaded virtual function also in derived class [#2653][boutproject#2653] ([dschwoerer][https://github.com/dschwoerer])
• Workaround PETSc clobbering MPI functions with its macros [#2637][boutproject#2637] ([ZedThree][https://github.com/ZedThree])
• Fix use of removed Datafile in Laplacian constructor; update docs [#2636][boutproject#2636] ([ZedThree][https://github.com/ZedThree])
• Fix SAVE_ONCE for Vector2/3D [#2633][boutproject#2633] ([ZedThree][https://github.com/ZedThree])
• Ensure FCI test only runs if we have zoidberg [#2607][boutproject#2607] ([dschwoerer][https://github.com/dschwoerer])
• Ignore hist_hi which is reset upon restart [#2606][boutproject#2606] ([dschwoerer][https://github.com/dschwoerer])
• Clang format everything [#2605][boutproject#2605] ([ZedThree][https://github.com/ZedThree])
• Fix FV operators in double null configurations [#2626][boutproject#2626] ([bendudson][https://github.com/bendudson])
• Fix shell script shebangs [#2625][boutproject#2625] ([bendudson][https://github.com/bendudson])
• Document FV::Div_a_Grad_perp operator [#2613][boutproject#2613] ([bendudson][https://github.com/bendudson])
• Fix input file expressions docs [#2612][boutproject#2612] ([johnomotani][https://github.com/johnomotani])
• Fix mkdir_p [#2611][boutproject#2611] ([dschwoerer][https://github.com/dschwoerer])
• CI: Fix black workflow [#2603][boutproject#2603] ([ZedThree][https://github.com/ZedThree])
• Upload boutpp to pypi [#2600][boutproject#2600] ([dschwoerer][https://github.com/dschwoerer])
• Insert Options attributes with initializer_list [#2598][boutproject#2598] ([bendudson][https://github.com/bendudson])
• cmake install fixes [#2596][boutproject#2596] ([dschwoerer][https://github.com/dschwoerer])
• Better versioning for BOUT++ [#2595][boutproject#2595] ([dschwoerer][https://github.com/dschwoerer])
• Set width for tables [#2592][boutproject#2592] ([dschwoerer][https://github.com/dschwoerer])
• Improve boutpp compatibility with numpy [#2589][boutproject#2589] ([dschwoerer][https://github.com/dschwoerer])
• Remove references to Travis in CI scripts [#2588][boutproject#2588] ([dschwoerer][https://github.com/dschwoerer])
• Documentation fixes [#2585][boutproject#2585] ([bendudson][https://github.com/bendudson])
• Add deprecation warning to configure [#2582][boutproject#2582] ([ZedThree][https://github.com/ZedThree])
• Add requires for FFTW to tests [#2579][boutproject#2579] ([dschwoerer][https://github.com/dschwoerer])
• Correct and add missing info to docs for x/y/z values in input file expressions [#2578][boutproject#2578] ([johnomotani][https://github.com/johnomotani])
• Change unbalanced brackets check [#2571][boutproject#2571] ([bendudson][https://github.com/bendudson])
• Remove LaplacePDD implementation [#2567][boutproject#2567] ([ZedThree][https://github.com/ZedThree])
• Remove two unused private ShiftedMetric::shiftz overloads [#2566][boutproject#2566] ([ZedThree][https://github.com/ZedThree])
• Fully remove deprecated Field3D.background [#2565][boutproject#2565] ([ZedThree][https://github.com/ZedThree])
• Improve CMake docs [#2564][boutproject#2564] ([ZedThree][https://github.com/ZedThree])
• CI: Fixes for clang-tidy-review [#2562][boutproject#2562] ([ZedThree][https://github.com/ZedThree])
• Use MPI_COMM_NULL rather than nullptr [#2560][boutproject#2560] ([bendudson][https://github.com/bendudson])
• PeriodicX option in cyclic Laplace solver [#2557][boutproject#2557] ([bendudson][https://github.com/bendudson])
• Output BoutException.what() in PhysicsModel main() [#2546][boutproject#2546] ([bendudson][https://github.com/bendudson])
• Print whether an option was marked as conditionally used [#2542][boutproject#2542] ([dschwoerer][https://github.com/dschwoerer])
• Only destroy MatP in LaplaceXZ if it exists [#2541][boutproject#2541] ([dschwoerer][https://github.com/dschwoerer])
• Fix some issues with parallel BCs [#2540][boutproject#2540] ([dschwoerer][https://github.com/dschwoerer])
• Bump clang-tidy-review version (next) [#2539][boutproject#2539] ([ZedThree][https://github.com/ZedThree])
• Rename FV::Div_a_Grad_perp to FV::Div_a_Grad_perp [#2536][boutproject#2536] ([dschwoerer][https://github.com/dschwoerer])
• Do not require mpi to be runnable [#2532][boutproject#2532] ([dschwoerer][https://github.com/dschwoerer])
• Use localmesh not m in LaplaceXZ constructor [#2528][boutproject#2528] ([bendudson][https://github.com/bendudson])
• Do not document mpich from source [#2523][boutproject#2523] ([dschwoerer][https://github.com/dschwoerer])
• Improve petsc documentation [#2522][boutproject#2522] ([dschwoerer][https://github.com/dschwoerer])
• ensure zoidberg is installed for documentation [#2519][boutproject#2519] ([dschwoerer][https://github.com/dschwoerer])
• find python based on path [#2518][boutproject#2518] ([dschwoerer][https://github.com/dschwoerer])
• Add support for SUNDIALS 6 [#2517][boutproject#2517] ([dschwoerer][https://github.com/dschwoerer])
• Check the bout++Config.cmake file is working [#2513][boutproject#2513] ([dschwoerer][https://github.com/dschwoerer])
• Fix NLS detection [#2509][boutproject#2509] ([dschwoerer][https://github.com/dschwoerer])
• xgettext fixes [#2507][boutproject#2507] ([dschwoerer][https://github.com/dschwoerer])
• use git submodule for cloning on RTD [#2506][boutproject#2506] ([dschwoerer][https://github.com/dschwoerer])
• Remove zoidberg [#2505][boutproject#2505] ([dschwoerer][https://github.com/dschwoerer])
• Update PETSc docs [#2504][boutproject#2504] ([dschwoerer][https://github.com/dschwoerer])
• Make beuler/snes solver quieter by default [#2500][boutproject#2500] ([bendudson][https://github.com/bendudson])
• Various fixes and updates for CI [#2497][boutproject#2497] ([ZedThree][https://github.com/ZedThree])
• Update outer boundaries in PETSc 3D solver [#2496][boutproject#2496] ([bendudson][https://github.com/bendudson])
• Merge 4.4.1 into next [#2488][boutproject#2488] ([ZedThree][https://github.com/ZedThree])
• Fix ambiguous variant use [#2485][boutproject#2485] ([bendudson][https://github.com/bendudson])
• Move Solver input options into constructor [#2484][boutproject#2484] ([ZedThree][https://github.com/ZedThree])
• Command-line help for input options for factory created types [#2483][boutproject#2483] ([ZedThree][https://github.com/ZedThree])
• Bump fmt to 8.1.0; fix implicit cast of enum class to int [#2482][boutproject#2482] ([ZedThree][https://github.com/ZedThree])
• Simplify specifying factory creator arguments [#2481][boutproject#2481] ([ZedThree][https://github.com/ZedThree])
• Improve documentation on curvilinear differentiation [#2477][boutproject#2477] ([dschwoerer][https://github.com/dschwoerer])
• Cache Coordinates::zlength() result [#2471][boutproject#2471] ([ZedThree][https://github.com/ZedThree])
• Raise more descriptive error if converting Option fails [#2469][boutproject#2469] ([ZedThree][https://github.com/ZedThree])
• Update testing shields [#2458][boutproject#2458] ([dschwoerer][https://github.com/dschwoerer])
• Avoid exception in Options when parsing string to Field [#2457][boutproject#2457] ([dschwoerer][https://github.com/dschwoerer])
• Small CMake changes for MacOS [#2455][boutproject#2455] ([bendudson][https://github.com/bendudson])
• Add matrix coloring to beuler solver (and fix imexbdf2) [#2454][boutproject#2454] ([bendudson][https://github.com/bendudson])
• Coordinate transform for manual [#2453][boutproject#2453] ([bendudson][https://github.com/bendudson])
• Fixes for compilation on Mac / Darwin [#2450][boutproject#2450] ([bendudson][https://github.com/bendudson])
• Add timeout to GHA [#2449][boutproject#2449] ([dschwoerer][https://github.com/dschwoerer])
• add parallel boundaries to boutcore [#2448][boutproject#2448] ([dschwoerer][https://github.com/dschwoerer])
• Ignore test artifacts [#2447][boutproject#2447] ([dschwoerer][https://github.com/dschwoerer])
• Ensure 3D FCI derivatives use valid boundaries [#2446][boutproject#2446] ([dschwoerer][https://github.com/dschwoerer])
• Boutcore improvements [#2445][boutproject#2445] ([dschwoerer][https://github.com/dschwoerer])
• Only check error if function is called [#2444][boutproject#2444] ([dschwoerer][https://github.com/dschwoerer])
• bout-add-mod-path: Add support for out-of-source builds [#2442][boutproject#2442] ([dschwoerer][https://github.com/dschwoerer])
• Some cmake fixes [#2441][boutproject#2441] ([dschwoerer][https://github.com/dschwoerer])
• Do be quite without -s [#2440][boutproject#2440] ([dschwoerer][https://github.com/dschwoerer])
• Update nonlocal.rst [#2436][boutproject#2436] ([pcphp][https://github.com/pcphp])
• Improve comments for Mesh functions [#2434][boutproject#2434] ([bendudson][https://github.com/bendudson])
• CMake examples targets [#2429][boutproject#2429] ([bendudson][https://github.com/bendudson])
• Set CMAKE_BUILD_TYPE default to RelWithDebInfo [#2428][boutproject#2428] ([bendudson][https://github.com/bendudson])
• Add notes on installing SUNDIALS (next) [#2421][boutproject#2421] ([johnomotani][https://github.com/johnomotani])
• Fix BOUT_OVERRIDE_DEFAULT_OPTION() (next) [#2418][boutproject#2418] ([johnomotani][https://github.com/johnomotani])
• Note in manual that pip and conda can get the most recent cmake [#2412][boutproject#2412] ([johnomotani][https://github.com/johnomotani])
• Ensure MPI is initialised before writing [#2410][boutproject#2410] ([dschwoerer][https://github.com/dschwoerer])
• Add missing 3D metric build config flag to output [#2403][boutproject#2403] ([ZedThree][https://github.com/ZedThree])
• Hypre, outerloop & CUDA changes [#2397][boutproject#2397] ([bendudson][https://github.com/bendudson])
• Merge v4.4.0 release into next [#2396][boutproject#2396] ([ZedThree][https://github.com/ZedThree])
• Remove exessive debugging statements [#2376][boutproject#2376] ([dschwoerer][https://github.com/dschwoerer])
• Fix INVERT_BNDARY_ONE case for PCR solver [#2375][boutproject#2375] ([JosephThomasParker][https://github.com/JosephThomasParker])
• Bug fixes for imex-bdf2 solver [#2372][boutproject#2372] ([bendudson][https://github.com/bendudson])
• Fix for compiling without FFTW [#2371][boutproject#2371] ([ZedThree][https://github.com/ZedThree])
• Build BOUT++ on RTD [#2368][boutproject#2368] ([dschwoerer][https://github.com/dschwoerer])
• ctest parallel [#2367][boutproject#2367] ([dschwoerer][https://github.com/dschwoerer])
• Update documentation for ctest and Github Actions [#2366][boutproject#2366] ([dschwoerer][https://github.com/dschwoerer])
• CMake: Add SOVERSION; fix FindSUNDIALS [#2358][boutproject#2358] ([dschwoerer][https://github.com/dschwoerer])
• Fix test_coordinates [#2357][boutproject#2357] ([dschwoerer][https://github.com/dschwoerer])
• Make submodules improvements [#2353][boutproject#2353] ([dschwoerer][https://github.com/dschwoerer])
• CI: Apply black to python files in src [#2352][boutproject#2352] ([dschwoerer][https://github.com/dschwoerer])
• Convert python interface to jinja2 [#2351][boutproject#2351] ([dschwoerer][https://github.com/dschwoerer])
• Delete integrated test of FieldFactory: replaced by unit tests [#2349][boutproject#2349] ([ZedThree][https://github.com/ZedThree])
• Convert ersatz MMS tests to use library MMS features [#2348][boutproject#2348] ([ZedThree][https://github.com/ZedThree])
• CMake rename PACKAGE_TESTS to BOUT_TESTS [#2347][boutproject#2347] ([bendudson][https://github.com/bendudson])
• Fixing up 6field-simple example in next [#2346][boutproject#2346] ([bendudson][https://github.com/bendudson])
• Fix for conditionally used boundary condition inputs in 'all' [#2345][boutproject#2345] ([ZedThree][https://github.com/ZedThree])
• speedup test-invpar [#2344][boutproject#2344] ([dschwoerer][https://github.com/dschwoerer])
• Parallel tests [#2343][boutproject#2343] ([dschwoerer][https://github.com/dschwoerer])
• Add fmt::formatter for Options [#2341][boutproject#2341] ([ZedThree][https://github.com/ZedThree])
• Add PCR Thomas Laplacian inversion solver [#2340][boutproject#2340] ([JosephThomasParker][https://github.com/JosephThomasParker])
• Rename max_nonlinear_it to max_nonlinear_iterations [#2338][boutproject#2338] ([johnomotani][https://github.com/johnomotani])
• Bump boutdata, boututils versions [#2335][boutproject#2335] ([ZedThree][https://github.com/ZedThree])
• CMake: Add option to download SUNDIALS at configure time [#2331][boutproject#2331] ([ZedThree][https://github.com/ZedThree])
• Parallel cyclic reduction [#2330][boutproject#2330] ([JosephThomasParker][https://github.com/JosephThomasParker])
• Correct descriptive text in coordinates section of manual [#2329][boutproject#2329] ([johnomotani][https://github.com/johnomotani])
• CMake: Fix a few minor issues, generate bout-config [#2328][boutproject#2328] ([ZedThree][https://github.com/ZedThree])
• Autotools: Link against PETSc first to avoid unresolved symbols from parallel HDF5 [#2327][boutproject#2327] ([dschwoerer][https://github.com/dschwoerer])
• Fix --enable-debug and --enable-checks [#2325][boutproject#2325] ([dschwoerer][https://github.com/dschwoerer])
• Do not include inner corner cells in FCI [#2323][boutproject#2323] ([dschwoerer][https://github.com/dschwoerer])
• Fix make -q [#2322][boutproject#2322] ([dschwoerer][https://github.com/dschwoerer])
• Fix for FindPETSc not being reentrant if pkg-config used (next) [#2318][boutproject#2318] ([ZedThree][https://github.com/ZedThree])
• Refactor FieldData to be base class of Field [#2313][boutproject#2313] ([ZedThree][https://github.com/ZedThree])
• Fix more documentation issues [#2310][boutproject#2310] ([ZedThree][https://github.com/ZedThree])
• CMake: Add separate configure-time option for MsgStack [#2309][boutproject#2309] ([dschwoerer][https://github.com/dschwoerer])
• Fix a couple of documentation issues [#2308][boutproject#2308] ([ZedThree][https://github.com/ZedThree])
• Fix memory leak of Coordinates in unit tests [#2306][boutproject#2306] ([ZedThree][https://github.com/ZedThree])
• Add instructions for MPCDF clusters [#2305][boutproject#2305] ([dschwoerer][https://github.com/dschwoerer])
• CVODE constraints and max_noinlinear_iterations options [#2303][boutproject#2303] ([johnomotani][https://github.com/johnomotani])
• CMake: Add coverage/sanitizers [#2302][boutproject#2302] ([ZedThree][https://github.com/ZedThree])
• CMake: Ensure compilation date/time are updated with file changes [#2301][boutproject#2301] ([ZedThree][https://github.com/ZedThree])
• CMake: Build documentation [#2300][boutproject#2300] ([ZedThree][https://github.com/ZedThree])
• Update installation suggestions for Marconi/gnu [#2299][boutproject#2299] ([johnomotani][https://github.com/johnomotani])
• CMake: Build Python API [#2298][boutproject#2298] ([dschwoerer][https://github.com/dschwoerer])
• Enable formatting of SpecificInd objects [#2297][boutproject#2297] ([bendudson][https://github.com/bendudson])
• cyclic reduction solver documentation [#2296][boutproject#2296] ([bendudson][https://github.com/bendudson])
• Faster recompile [#2294][boutproject#2294] ([dschwoerer][https://github.com/dschwoerer])
• Remove most deprecated declarations [#2291][boutproject#2291] ([ZedThree][https://github.com/ZedThree])
• Add MMS tests to CMake build [#2286][boutproject#2286] ([ZedThree][https://github.com/ZedThree])
• Remove legacy Solver API [#2285][boutproject#2285] ([ZedThree][https://github.com/ZedThree])
• Make conversion of Option to bool stricter [#2282][boutproject#2282] ([johnomotani][https://github.com/johnomotani])
• Set all boundary cells in LaplaceXZ [#2281][boutproject#2281] ([bshanahan][https://github.com/bshanahan])
• Equation numbers in manual [#2280][boutproject#2280] ([johnomotani][https://github.com/johnomotani])
• Require Options to be exactly one of either a section or a value [#2277][boutproject#2277] ([ZedThree][https://github.com/ZedThree])
• Fix some deprecation warnings in MsgStack [#2276][boutproject#2276] ([ZedThree][https://github.com/ZedThree])
• Next CMake fixes [#2275][boutproject#2275] ([bendudson][https://github.com/bendudson])
• Fix segfault when creating LaplaceXZ without passing Options [#2272][boutproject#2272] ([ZedThree][https://github.com/ZedThree])
• Bump jinja2 from 2.10.1 to 2.11.3 [#2271][boutproject#2271] ([j-b-o][https://github.com/j-b-o])
• Improve documentation [#2270][boutproject#2270] ([j-b-o][https://github.com/j-b-o])
• Restrict region for toFieldAligned() in VDDY() when not staggered [#2268][boutproject#2268] ([johnomotani][https://github.com/johnomotani])
• Fix use of uninitialised value in Delp2 (next) [#2264][boutproject#2264] ([johnomotani][https://github.com/johnomotani])
• Add "invert" timer to LaplacePetsc3dAmg [#2259][boutproject#2259] ([johnomotani][https://github.com/johnomotani])
• Make shifted paralleltransform message more helpful [#2256][boutproject#2256] ([bendudson][https://github.com/bendudson])
• Correct Monitor documentation [#2255][boutproject#2255] ([johnomotani][https://github.com/johnomotani])
• Set any extra boundary cells in LaplacePetsc3dAmg [#2254][boutproject#2254] ([johnomotani][https://github.com/johnomotani])
• Minor boutcore cleanup [#2251][boutproject#2251] ([dschwoerer][https://github.com/dschwoerer])
• Fix typos brackets->bracket in manual [#2250][boutproject#2250] ([johnomotani][https://github.com/johnomotani])
• Use zero for initial guess in test-laplace-petsc3d [#2248][boutproject#2248] ([johnomotani][https://github.com/johnomotani])
• Add unit tests for BoutMesh::load [#2245][boutproject#2245] ([ZedThree][https://github.com/ZedThree])
• Bump clang-tidy-review [#2244][boutproject#2244] ([ZedThree][https://github.com/ZedThree])
• Remove include from uuid [#2243][boutproject#2243] ([bendudson][https://github.com/bendudson])
• Remove the Karniadakis time solver [#2241][boutproject#2241] ([ZedThree][https://github.com/ZedThree])
• Tidy test-drift-instability [#2240][boutproject#2240] ([ZedThree][https://github.com/ZedThree])
• Add Backward Euler solver (rebased) [#2239][boutproject#2239] ([bendudson][https://github.com/bendudson])
• Fix LaplacePetsc3dAmg [#2237][boutproject#2237] ([johnomotani][https://github.com/johnomotani])
• [GHA] black format everything automatically [#2235][boutproject#2235] ([dschwoerer][https://github.com/dschwoerer])
• ny_inner label misleading in topology schematic [#2234][boutproject#2234] ([johnomotani][https://github.com/johnomotani])
• Rebase of boutcore improvements [#2232][boutproject#2232] ([dschwoerer][https://github.com/dschwoerer])
• Save provenance tracking info from grid file [#2230][boutproject#2230] ([johnomotani][https://github.com/johnomotani])
• Update googletest [#2228][boutproject#2228] ([ZedThree][https://github.com/ZedThree])
• Update clang tidy review [#2227][boutproject#2227] ([ZedThree][https://github.com/ZedThree])
• Only use save_repeat_run_id for dump files [#2223][boutproject#2223] ([johnomotani][https://github.com/johnomotani])
• Fix bout-add-mod-path for Python 3.9 [#2221][boutproject#2221] ([dschwoerer][https://github.com/dschwoerer])
• Docs: fix escaping [#2220][boutproject#2220] ([dschwoerer][https://github.com/dschwoerer])
• Canonicalise input files [#2218][boutproject#2218] ([ZedThree][https://github.com/ZedThree])
• Documentation for iterative parallel tridiagonal solver [#2215][boutproject#2215] ([JosephThomasParker][https://github.com/JosephThomasParker])
• Update note on zShift in grid-files section of manual [#2211][boutproject#2211] ([johnomotani][https://github.com/johnomotani])
• Make input Options case sensitive and error on unused Options [#2210][boutproject#2210] ([ZedThree][https://github.com/ZedThree])
• Replace DataFile/Dataformat with OptionsNetCDF [#2209][boutproject#2209] ([ZedThree][https://github.com/ZedThree])
• Remove HDF5 support [#2208][boutproject#2208] ([johnomotani][https://github.com/johnomotani])
• Removed bout_runners from repo, and redirected it to project site [#2202][boutproject#2202] ([loeiten][https://github.com/loeiten])
• Minor FCI improvements [#2201][boutproject#2201] ([ZedThree][https://github.com/ZedThree])
• Fix test-squash [#2197][boutproject#2197] ([ZedThree][https://github.com/ZedThree])
• Replace boutdata and boututils directories with submodules [#2196][boutproject#2196] ([johnomotani][https://github.com/johnomotani])
• Use bout_type="string" for strings in H5Format [#2193][boutproject#2193] ([johnomotani][https://github.com/johnomotani])
• Write descriptions for std::vector and std::string variables [#2190][boutproject#2190] ([johnomotani][https://github.com/johnomotani])
• Fix reading of char* in Ncxx4 [#2188][boutproject#2188] ([johnomotani][https://github.com/johnomotani])
• Use MPI_C_BOOL type instead of C++ binding MPI::Bool [#2187][boutproject#2187] ([johnomotani][https://github.com/johnomotani])
• Removing hypnotoad grid generator [#2184][boutproject#2184] ([bendudson][https://github.com/bendudson])
• Support location in Mesh::get() [#2183][boutproject#2183] ([johnomotani][https://github.com/johnomotani])
• Completely remove LaplaceShoot [#2177][boutproject#2177] ([ZedThree][https://github.com/ZedThree])
• CMake: Set PYTHONPATH for tests [#2176][boutproject#2176] ([ZedThree][https://github.com/ZedThree])
• Allow registering "unavailable" Factory options [#2173][boutproject#2173] ([ZedThree][https://github.com/ZedThree])
• Docs: note more recent version of PETSc might work, but not guaranteed [#2172][boutproject#2172] ([johnomotani][https://github.com/johnomotani])
• Testing of Coordinates [#2167][boutproject#2167] ([bendudson][https://github.com/bendudson])
• Tidy up coordinate systems with explicit directions [#2165][boutproject#2165] ([bendudson][https://github.com/bendudson])
• Upgrade all examples to use PhysicsModel [#2164][boutproject#2164] ([ZedThree][https://github.com/ZedThree])
• Stringify BOUT_REVISION when passed as a define on the command line [#2163][boutproject#2163] ([ZedThree][https://github.com/ZedThree])
• Fix CMake config file following change to netCDF cmake module [#2162][boutproject#2162] ([ZedThree][https://github.com/ZedThree])
• Fix typo in showdata gif save [#2161][boutproject#2161] ([bshanahan][https://github.com/bshanahan])
• Fix shiftOutput [#2157][boutproject#2157] ([johnomotani][https://github.com/johnomotani])
• Migrate to GitHub Actions [#2156][boutproject#2156] ([ZedThree][https://github.com/ZedThree])
• I/O for std::vector and std::string [#2153][boutproject#2153] ([johnomotani][https://github.com/johnomotani])
• Add ability to use FieldPerp in Options [#2152][boutproject#2152] ([ZedThree][https://github.com/ZedThree])
• Generate random run ID, track restarts [#2149][boutproject#2149] ([bendudson][https://github.com/bendudson])
• Add a clamp function to FieldFactory [#2147][boutproject#2147] ([bendudson][https://github.com/bendudson])
• Relax security controls on Fedora test image [#2146][boutproject#2146] ([ZedThree][https://github.com/ZedThree])
• Check DataFile grid sizes match those in existing mesh [#2145][boutproject#2145] ([ZedThree][https://github.com/ZedThree])
• Add back some missing Fields documentation (and clang-format) [#2144][boutproject#2144] ([ZedThree][https://github.com/ZedThree])
• Add test-squash for CMake [#2142][boutproject#2142] ([ZedThree][https://github.com/ZedThree])
• Merge v4.3.2 into next [#2139][boutproject#2139] ([ZedThree][https://github.com/ZedThree])
• CMake: Add option to download and build netCDF C++ API [#2138][boutproject#2138] ([ZedThree][https://github.com/ZedThree])
• Fix errors in tests/MMS/elm-pb [#2137][boutproject#2137] ([johnomotani][https://github.com/johnomotani])
• Fix a couple of typos in zoidberg.field.GEQDSK [#2136][boutproject#2136] ([ZedThree][https://github.com/ZedThree])
• Update InvertPar factory call in some examples [#2135][boutproject#2135] ([ZedThree][https://github.com/ZedThree])
• Call checkData() before returning result in Laplace inversions [#2133][boutproject#2133] ([johnomotani][https://github.com/johnomotani])
• Allow setting FFTW_EXHAUSTIVE [#2131][boutproject#2131] ([johnomotani][https://github.com/johnomotani])
• Fix two issues with build_defines header [#2130][boutproject#2130] ([ZedThree][https://github.com/ZedThree])
• Make example relocatable [#2126][boutproject#2126] ([dschwoerer][https://github.com/dschwoerer])
• Fix links to open-mpi.org and lam-mpi.org [#2123][boutproject#2123] ([tobyjamez][https://github.com/tobyjamez])
• CMake: Generate Field arithmetic operators [#2119][boutproject#2119] ([dschwoerer][https://github.com/dschwoerer])
• Suggestions for gnu build on Marconi [#2111][boutproject#2111] ([johnomotani][https://github.com/johnomotani])
• Fix some HDF5 related issues and add Mesh::getLocal{X,Y,Z}Index [#2102][boutproject#2102] ([ZedThree][https://github.com/ZedThree])
• Copy changes from boututils/boutdata [#2101][boutproject#2101] ([dschwoerer][https://github.com/dschwoerer])
• Handle FieldPerps in Datafile::varAdded() and Datafile::varPtr() (next) [#2095][boutproject#2095] ([johnomotani][https://github.com/johnomotani])
• auto-fix autoconf_build_defines.hxx.in [#2091][boutproject#2091] ([dschwoerer][https://github.com/dschwoerer])
• Fix current Travis failures in next [#2090][boutproject#2090] ([ZedThree][https://github.com/ZedThree])
• Staggered grids in InvertPar [#2087][boutproject#2087] ([johnomotani][https://github.com/johnomotani])
• Link to xBOUT in the manual [#2085][boutproject#2085] ([johnomotani][https://github.com/johnomotani])
• Bump mpark.variant to latest version [#2083][boutproject#2083] ([ZedThree][https://github.com/ZedThree])
• Bump fmt version to latest master [#2082][boutproject#2082] ([ZedThree][https://github.com/ZedThree])
• always pull fedora from fedoras registry [#2080][boutproject#2080] ([dschwoerer][https://github.com/dschwoerer])
• Allow to override packages in fedora rawhide [#2079][boutproject#2079] ([dschwoerer][https://github.com/dschwoerer])
• CI: Turn off patch coverage check [#2074][boutproject#2074] ([ZedThree][https://github.com/ZedThree])
• Correct Grad2_par2 implementation in InvertParCR [#2071][boutproject#2071] ([johnomotani][https://github.com/johnomotani])
• Minor optimization of cyclic InvertPar implementation [#2070][boutproject#2070] ([johnomotani][https://github.com/johnomotani])
• Allow descriptions of output variables; save some diagnostics for solvers [#2064][boutproject#2064] ([johnomotani][https://github.com/johnomotani])
• Fix default file format when using legacy netcdf [#2062][boutproject#2062] ([ZedThree][https://github.com/ZedThree])
• Enable staggered versions of SplitFluxDerivativeType [#2060][boutproject#2060] ([johnomotani][https://github.com/johnomotani])
• make error look nicer [#2056][boutproject#2056] ([dschwoerer][https://github.com/dschwoerer])
• Fix typo in curvature section [#2055][boutproject#2055] ([bshanahan][https://github.com/bshanahan])
• Revert name of legacy netCDF macro [#2053][boutproject#2053] ([ZedThree][https://github.com/ZedThree])
• Tighten set tolerance for LaplacePetsc3dAmg test [#2051][boutproject#2051] ([ZedThree][https://github.com/ZedThree])
• Support multiple parallel slices in ShiftedMetricInterp [#2049][boutproject#2049] ([johnomotani][https://github.com/johnomotani])
• Use C++ style casts [#2048][boutproject#2048] ([dschwoerer][https://github.com/dschwoerer])
• Improve generic factory docstring example [#2046][boutproject#2046] ([bendudson][https://github.com/bendudson])
• Fix examples warnings [#2045][boutproject#2045] ([ZedThree][https://github.com/ZedThree])
• MMS test for ShiftedMetricInterp [#2044][boutproject#2044] ([johnomotani][https://github.com/johnomotani])
• Add PhysicsModel::mesh/dump members [#2042][boutproject#2042] ([ZedThree][https://github.com/ZedThree])
• Add location checks to Div_par_K_Grad_par [#2038][boutproject#2038] ([bshanahan][https://github.com/bshanahan])
• filledFrom using lambda function [#2037][boutproject#2037] ([bendudson][https://github.com/bendudson])
• Travis: add Fedora job [#2036][boutproject#2036] ([dschwoerer][https://github.com/dschwoerer])
• Minor optimizations for ZHermiteSpline [#2035][boutproject#2035] ([johnomotani][https://github.com/johnomotani])
• Fix and unit tests for BOUT_ENUM_CLASS [#2031][boutproject#2031] ([johnomotani][https://github.com/johnomotani])
• Iterative parallel tridiagonal solver [#2030][boutproject#2030] ([JosephThomasParker][https://github.com/JosephThomasParker])
• Update the staggered grids section of the manual [#2028][boutproject#2028] ([johnomotani][https://github.com/johnomotani])
• Move compile-time feature macros to header [#2027][boutproject#2027] ([ZedThree][https://github.com/ZedThree])
• 3D metrics [#2025][boutproject#2025] ([dschwoerer][https://github.com/dschwoerer])
• Add option to build all examples with CMake, plus some minor fixes [#2021][boutproject#2021] ([ZedThree][https://github.com/ZedThree])
• Add script for creating environment module files [#2019][boutproject#2019] ([dschwoerer][https://github.com/dschwoerer])
• Remove MUMPS [#2018][boutproject#2018] ([dschwoerer][https://github.com/dschwoerer])
• Fix bug in configure when using dash as shell [#2016][boutproject#2016] ([dschwoerer][https://github.com/dschwoerer])
• Fix formatting of 'Obtaining BOUT++' section heading [#2015][boutproject#2015] ([johnomotani][https://github.com/johnomotani])
• Provide better error if fields are not compatible [#2012][boutproject#2012] ([dschwoerer][https://github.com/dschwoerer])
• Ensure quiet script isn't too verbose on error [#2011][boutproject#2011] ([dschwoerer][https://github.com/dschwoerer])
• Add boutconfig Python module with build configuration information [#2010][boutproject#2010] ([dschwoerer][https://github.com/dschwoerer])
• fix requires in options-netcdf test [#2009][boutproject#2009] ([dschwoerer][https://github.com/dschwoerer])
• Run wrapper improvements [#2007][boutproject#2007] ([dschwoerer][https://github.com/dschwoerer])
• Ensure ffts are OpenMP thread safe [#2006][boutproject#2006] ([dschwoerer][https://github.com/dschwoerer])
• Improve some error messages [#2005][boutproject#2005] ([dschwoerer][https://github.com/dschwoerer])
• Without netcdf [#2004][boutproject#2004] ([dschwoerer][https://github.com/dschwoerer])
• remove checklib dependency from unit tests [#2002][boutproject#2002] ([dschwoerer][https://github.com/dschwoerer])
• Include smaller "fmt/core.h" [#2001][boutproject#2001] ([ZedThree][https://github.com/ZedThree])
• Parallel tests [#2000][boutproject#2000] ([dschwoerer][https://github.com/dschwoerer])
• Merge v4.3.1 into next [#1999][boutproject#1999] ([ZedThree][https://github.com/ZedThree])
• fix test-laplace-petsc3d [#1985][boutproject#1985] ([dschwoerer][https://github.com/dschwoerer])
• Fix --enabled-shared for configure [#1984][boutproject#1984] ([dschwoerer][https://github.com/dschwoerer])
• Use custom main instead of PhysicsModel in test-communications [#1983][boutproject#1983] ([johnomotani][https://github.com/johnomotani])
• Conditionally show backtrace [#1974][boutproject#1974] ([dschwoerer][https://github.com/dschwoerer])
• Fix typo in Ubuntu 16.04 installation command [#1964][boutproject#1964] ([bshanahan][https://github.com/bshanahan])
• Fix typo in example/performance/communications [#1963][boutproject#1963] ([johnomotani][https://github.com/johnomotani])
• Add region argument to XZInterpolations [#1962][boutproject#1962] ([ZedThree][https://github.com/ZedThree])
• Pass method and region arguments to D2DXDY in Laplace(Field2D) [#1961][boutproject#1961] ([johnomotani][https://github.com/johnomotani])
• Field3d copy parallel slices [#1960][boutproject#1960] ([ZedThree][https://github.com/ZedThree])
• fix for running unit-test as root [#1959][boutproject#1959] ([dschwoerer][https://github.com/dschwoerer])
• Minor fixes for elm-pb and python tools [#1958][boutproject#1958] ([dschwoerer][https://github.com/dschwoerer])
• Exclude corner cells in LaplaceXY [#1957][boutproject#1957] ([ZedThree][https://github.com/ZedThree])
• Fix possible data race in MsgStack::push() [#1955][boutproject#1955] ([johnomotani][https://github.com/johnomotani])
• Update staggered grids implementation in various examples [#1954][boutproject#1954] ([johnomotani][https://github.com/johnomotani])
• Fix runtest for non-make generators [#1952][boutproject#1952] ([ZedThree][https://github.com/ZedThree])
• Ignore latexmk files [#1947][boutproject#1947] ([dschwoerer][https://github.com/dschwoerer])
• Add ShiftedMetricInterp: shifted metric using interpolation in Z [#1946][boutproject#1946] ([ZedThree][https://github.com/ZedThree])
• Add ZInterpolation, ZHermiteSpline [#1944][boutproject#1944] ([ZedThree][https://github.com/ZedThree])
• Fix some missed fmt format strings [#1943][boutproject#1943] ([ZedThree][https://github.com/ZedThree])
• Minor Travis fixes and job names [#1942][boutproject#1942] ([ZedThree][https://github.com/ZedThree])
• MsgStack and PetscLib thread safety [#1941][boutproject#1941] ([ZedThree][https://github.com/ZedThree])
• Add full perpendicular Laplacian, inverse of LaplaceXY [#1939][boutproject#1939] ([ZedThree][https://github.com/ZedThree])
• Rely on latexmk in noninteractive mode [#1938][boutproject#1938] ([dschwoerer][https://github.com/dschwoerer])
• Add extra region option for mixed derivatives [#1936][boutproject#1936] ([ZedThree][https://github.com/ZedThree])
• Various minor fixes for the sphinx docs [#1935][boutproject#1935] ([ZedThree][https://github.com/ZedThree])
• Fix segfaults from PvodeSolver [#1926][boutproject#1926] ([johnomotani][https://github.com/johnomotani])
• Fixes for staggering in lapd-drift example [#1925][boutproject#1925] ([johnomotani][https://github.com/johnomotani])
• Workaround for Petsc init/finialise not being idempotent [#1922][boutproject#1922] ([ZedThree][https://github.com/ZedThree])
• Generate version header [#1920][boutproject#1920] ([ZedThree][https://github.com/ZedThree])
• Implement BOUT_FOR for FV::div_f_v [#1918][boutproject#1918] ([bshanahan][https://github.com/bshanahan])
• pkg-config petsc (next) [#1914][boutproject#1914] ([dschwoerer][https://github.com/dschwoerer])
• CMake: find package fixes [#1912][boutproject#1912] ([ZedThree][https://github.com/ZedThree])
• Cmake fixes [#1909][boutproject#1909] ([dschwoerer][https://github.com/dschwoerer])
• Laplace performance test [#1908][boutproject#1908] ([JosephThomasParker][https://github.com/JosephThomasParker])
• CMake: enable using external mpark.variant [#1900][boutproject#1900] ([ZedThree][https://github.com/ZedThree])
• XZInterpolation rename, and passing Options to XZInterpolation objects [#1896][boutproject#1896] ([johnomotani][https://github.com/johnomotani])
• Rename death tests according to gtest recommendations [#1891][boutproject#1891] ([ZedThree][https://github.com/ZedThree])
• Add Mesh::getRegion for use in generic code [#1890][boutproject#1890] ([ZedThree][https://github.com/ZedThree])
• Petsc interface generalisation [#1889][boutproject#1889] ([cmacmackin][https://github.com/cmacmackin])
• Remove unused parameters to silence warnings in MsgStack [#1887][boutproject#1887] ([ZedThree][https://github.com/ZedThree])
• Set corner cells consistently [#1885][boutproject#1885] ([johnomotani][https://github.com/johnomotani])
• Generate report for Timers [#1882][boutproject#1882] ([ZedThree][https://github.com/ZedThree])
• CMake: fix FindSlepc for non-make generators [#1881][boutproject#1881] ([ZedThree][https://github.com/ZedThree])
• Implement toFieldAligned and fromFieldAligned for Vector3D [#1877][boutproject#1877] ([johnomotani][https://github.com/johnomotani])
• Fixes for Windows [#1874][boutproject#1874] ([ZedThree][https://github.com/ZedThree])
• Fix PETSc Laplace tests [#1859][boutproject#1859] ([ZedThree][https://github.com/ZedThree])
• Use {fmt} for all string formatting [#1847][boutproject#1847] ([ZedThree][https://github.com/ZedThree])
• Adding an adaptive, arbitrary order, Adams-Bashforth solver [#1846][boutproject#1846] ([d7919][https://github.com/d7919])
• Standardise factories [#1842][boutproject#1842] ([ZedThree][https://github.com/ZedThree])
• Macro for creating enum classes [#1841][boutproject#1841] ([johnomotani][https://github.com/johnomotani])
• Fix typo in initialisation of rgn_outer_x [#1837][boutproject#1837] ([AdamD94][https://github.com/AdamD94])
• Remove deprecated Laplacian API [#1834][boutproject#1834] ([ZedThree][https://github.com/ZedThree])
• Add remaining integrated tests to CMake build [#1833][boutproject#1833] ([ZedThree][https://github.com/ZedThree])
• Fix various warnings [#1832][boutproject#1832] ([ZedThree][https://github.com/ZedThree])
• Get latest versions of submodules [#1831][boutproject#1831] ([ZedThree][https://github.com/ZedThree])
• Require C++14 [#1830][boutproject#1830] ([ZedThree][https://github.com/ZedThree])
• Include all boundary cells in GlobalNy [#1829][boutproject#1829] ([johnomotani][https://github.com/johnomotani])
• Bump version in next to 5.0.0-alpha [#1827][boutproject#1827] ([ZedThree][https://github.com/ZedThree])
• Merge v4.3.0 into next [#1826][boutproject#1826] ([ZedThree][https://github.com/ZedThree])
• MPI wrapper class [#1808][boutproject#1808] ([cmacmackin][https://github.com/cmacmackin])
• Petsc interface [#1805][boutproject#1805] ([cmacmackin][https://github.com/cmacmackin])
• Algebraic multigrid [#1803][boutproject#1803] ([cmacmackin][https://github.com/cmacmackin])
• Allow PETSc options to be passed from BOUT.inp [#1795][boutproject#1795] ([johnomotani][https://github.com/johnomotani])
• LaplaceXY: finite difference option [#1789][boutproject#1789] ([johnomotani][https://github.com/johnomotani])
• Add macro for Scorep instrumentation of a user-defined code region [#1784][boutproject#1784] ([JosephThomasParker][https://github.com/JosephThomasParker])
• Fix some issues in hypnotoad [#1783][boutproject#1783] ([friva000][https://github.com/friva000])
• Allow user to override library option defaults [#1773][boutproject#1773] ([johnomotani][https://github.com/johnomotani])
• Construct Option with initializer_list [#1772][boutproject#1772] ([bendudson][https://github.com/bendudson])
• Add mesh options for extrapolate_{x,y} [#1760][boutproject#1760] ([bendudson][https://github.com/bendudson])
• Deprecate Laplacian::setFlags() [#1758][boutproject#1758] ([johnomotani][https://github.com/johnomotani])
• Fix advection MMS tests [#1757][boutproject#1757] ([ZedThree][https://github.com/ZedThree])
• Rename 'coordinates_type' gridfile attribute to 'parallel_transform' [#1756][boutproject#1756] ([ZedThree][https://github.com/ZedThree])
• More clang-tidy fixes [#1755][boutproject#1755] ([ZedThree][https://github.com/ZedThree])
• Add default value to Mesh::get for ints [#1754][boutproject#1754] ([JosephThomasParker][https://github.com/JosephThomasParker])
• Remove FIXME comment from interp_to [#1752][boutproject#1752] ([johnomotani][https://github.com/johnomotani])
• Build pdf manual [#1751][boutproject#1751] ([johnomotani][https://github.com/johnomotani])
• Bug fix, test and tidy SLEPc solver [#1749][boutproject#1749] ([ZedThree][https://github.com/ZedThree])
• SNB nonlocal heat flux model [#1748][boutproject#1748] ([bendudson][https://github.com/bendudson])
• Pin packages in requirements.txt for Sphinx docs [#1746][boutproject#1746] ([ZedThree][https://github.com/ZedThree])
• Don't mark Coordinates::zShift as const, can't be output [#1745][boutproject#1745] ([ZedThree][https://github.com/ZedThree])
• Laplacian: FFT include dfdz term, plus manual updates [#1744][boutproject#1744] ([johnomotani][https://github.com/johnomotani])
• Fix interpolation of staggered zShift [#1743][boutproject#1743] ([johnomotani][https://github.com/johnomotani])
• Correct calculation of Bxy when interpolating from CELL_CENTRE [#1741][boutproject#1741] ([johnomotani][https://github.com/johnomotani])
• Only call checkPositive(g) for grid cells [#1739][boutproject#1739] ([johnomotani][https://github.com/johnomotani])
• ensure make clean cleans tests [#1738][boutproject#1738] ([dschwoerer][https://github.com/dschwoerer])
• Output ParallelTransform variables [#1736][boutproject#1736] ([johnomotani][https://github.com/johnomotani])
• Fix BoutMesh decomposition on single processor [#1735][boutproject#1735] ([ZedThree][https://github.com/ZedThree])
• Deprecate some unused methods [#1734][boutproject#1734] ([ZedThree][https://github.com/ZedThree])
• make sure values() returns valid pointer [#1733][boutproject#1733] ([dschwoerer][https://github.com/dschwoerer])
• Twistshift for field-aligned variables [#1732][boutproject#1732] ([johnomotani][https://github.com/johnomotani])
• Add bout::utils::is_Field and variants [#1730][boutproject#1730] ([ZedThree][https://github.com/ZedThree])
• Deprecate Karniadakis solver [#1727][boutproject#1727] ([ZedThree][https://github.com/ZedThree])
• Make MsgStack and BoutException unit tests more flexible [#1726][boutproject#1726] ([ZedThree][https://github.com/ZedThree])
• Bugfix: use region in Coordinates::calcCovariant/calcContravariant [#1725][boutproject#1725] ([ZedThree][https://github.com/ZedThree])
• Hardcode all variables for test-solver; remove input file [#1724][boutproject#1724] ([ZedThree][https://github.com/ZedThree])
• Remove Laplace3D [#1723][boutproject#1723] ([ZedThree][https://github.com/ZedThree])
• Add function_traits template and replace SUNDIALS int type macros [#1722][boutproject#1722] ([ZedThree][https://github.com/ZedThree])
• fix nc-format [#1721][boutproject#1721] ([dschwoerer][https://github.com/dschwoerer])
• Templated Field functions and deprecate REGION enum arguments [#1720][boutproject#1720] ([johnomotani][https://github.com/johnomotani])
• More robust staggered Jacobian and RGN_NOCORNERS [#1719][boutproject#1719] ([johnomotani][https://github.com/johnomotani])
• Handle attributes for missing variables [#1718][boutproject#1718] ([bendudson][https://github.com/bendudson])
• Revert "Hypnotoad: 'H' is derivative of integral" [#1717][boutproject#1717] ([johnomotani][https://github.com/johnomotani])
• Remove deprecated invert_laplace from gyro_average [#1716][boutproject#1716] ([ZedThree][https://github.com/ZedThree])
• Lots of small clang-tidy fixes [#1715][boutproject#1715] ([ZedThree][https://github.com/ZedThree])
• Tidy up direction-type setters [#1712][boutproject#1712] ([johnomotani][https://github.com/johnomotani])
• Add implementation of Field2D::applyBoundary(BoutReal time) [#1711][boutproject#1711] ([ZedThree][https://github.com/ZedThree])
• Fix BoutMesh boundary regions [#1710][boutproject#1710] ([ZedThree][https://github.com/ZedThree])
• Don't run tests that use FFTW if not compiled with it [#1709][boutproject#1709] ([ZedThree][https://github.com/ZedThree])
• Fixes for FV::Div_a_Laplace_perp [#1707][boutproject#1707] ([bendudson][https://github.com/bendudson])
• FieldGenerate refactor [#1705][boutproject#1705] ([dschwoerer][https://github.com/dschwoerer])
• Set y-direction of FieldPerp results in ParallelTransformIdentity [#1704][boutproject#1704] ([johnomotani][https://github.com/johnomotani])
• Do not calculate parallel slices for field-aligned fields [#1703][boutproject#1703] ([johnomotani][https://github.com/johnomotani])
• Allow default value of Options to be set from another Options object [#1702][boutproject#1702] ([johnomotani][https://github.com/johnomotani])
• Fieldperp I/O [#1699][boutproject#1699] ([johnomotani][https://github.com/johnomotani])
• Set y-direction of results in ParallelTransformIdentity [#1698][boutproject#1698] ([johnomotani][https://github.com/johnomotani])
• Add support for shifting a FieldPerp toFieldAligned/fromFieldAligned [#1697][boutproject#1697] ([johnomotani][https://github.com/johnomotani])
• Experimental CMake support [#1696][boutproject#1696] ([ZedThree][https://github.com/ZedThree])
• Convert Options::isSection() argument to lower case [#1695][boutproject#1695] ([johnomotani][https://github.com/johnomotani])
• Update required Jinja2 version to avoid CVE-2019-10906 [#1694][boutproject#1694] ([ZedThree][https://github.com/ZedThree])
• Move Gridfile::get implementations for Field3D/Field2D to .cxx [#1693][boutproject#1693] ([johnomotani][https://github.com/johnomotani])
• Warn about random failures in test [#1692][boutproject#1692] ([dschwoerer][https://github.com/dschwoerer])
• Use asynchronous communications in LaplaceMultigrid [#1691][boutproject#1691] ([johnomotani][https://github.com/johnomotani])
• Remove multiple printing of BOUTLOCALE to stderr [#1689][boutproject#1689] ([johnomotani][https://github.com/johnomotani])
• Fix elm pb example [#1688][boutproject#1688] ([bendudson][https://github.com/bendudson])
• Bugfix: bracket operator slowdown [#1686][boutproject#1686] ([johnomotani][https://github.com/johnomotani])
• Fix and reenable [#1684][boutproject#1684] ([dschwoerer][https://github.com/dschwoerer])
• call Finalise in test [#1683][boutproject#1683] ([dschwoerer][https://github.com/dschwoerer])
• Fix comparison of corner boundary cells in test-squash [#1682][boutproject#1682] ([johnomotani][https://github.com/johnomotani])
• Clear Field3D parallel slices in operator= [#1681][boutproject#1681] ([johnomotani][https://github.com/johnomotani])
• Ignore new meta-vars in test-squash [#1679][boutproject#1679] ([dschwoerer][https://github.com/dschwoerer])
• Fix examples [#1678][boutproject#1678] ([dschwoerer][https://github.com/dschwoerer])
• Add .BOUT.pid.* files to .gitignore [#1674][boutproject#1674] ([johnomotani][https://github.com/johnomotani])
• Runge-Kutta-Legendre stabilised explicit method [#1673][boutproject#1673] ([bendudson][https://github.com/bendudson])
• Unit tests and template-isation of where [#1672][boutproject#1672] ([ZedThree][https://github.com/ZedThree])
• Don't try to build documentation [#1671][boutproject#1671] ([dschwoerer][https://github.com/dschwoerer])
• Method for Laplace solvers to say whether they use 3D coefficients [#1669][boutproject#1669] ([johnomotani][https://github.com/johnomotani])
• Fix dereferencing null Coordinates in FieldFactory [#1667][boutproject#1667] ([ZedThree][https://github.com/ZedThree])
• Bugfix: return fields by reference [#1663][boutproject#1663] ([dschwoerer][https://github.com/dschwoerer])
• Allow clean exit in boutcore [#1662][boutproject#1662] ([dschwoerer][https://github.com/dschwoerer])
• Make mixed second-derivative operators more correct [#1661][boutproject#1661] ([johnomotani][https://github.com/johnomotani])
• Unit tests and various small refactorings of Solver [#1660][boutproject#1660] ([ZedThree][https://github.com/ZedThree])
• Under-relaxation for LaplaceNaulin [#1659][boutproject#1659] ([johnomotani][https://github.com/johnomotani])
• Counters for timers, makes them correct with multiple Timer objects [#1658][boutproject#1658] ([johnomotani][https://github.com/johnomotani])
• Generate FieldPerp arithmetic operators with jinja [#1655][boutproject#1655] ([johnomotani][https://github.com/johnomotani])
• LaplaceNaulin solver improvement, and more general coefficients for LaplaceCyclic [#1654][boutproject#1654] ([johnomotani][https://github.com/johnomotani])
• Options type and doc attributes [#1653][boutproject#1653] ([bendudson][https://github.com/bendudson])
• Fix mesh checks in Laplace implementation headers [#1652][boutproject#1652] ([johnomotani][https://github.com/johnomotani])
• Minor refactoring of BoutInitialise, BoutFinalise [#1651][boutproject#1651] ([ZedThree][https://github.com/ZedThree])
• Add name argument to Options::isSection to test for presence of subsection [#1650][boutproject#1650] ([johnomotani][https://github.com/johnomotani])
• Support SUNDIALS 4.1.0 [#1649][boutproject#1649] ([ZedThree][https://github.com/ZedThree])
• Make transforming Field3D inputs from field aligned optional [#1648][boutproject#1648] ([johnomotani][https://github.com/johnomotani])
• Hypnotoad: double precision and y-boundary guard cells [#1647][boutproject#1647] ([johnomotani][https://github.com/johnomotani])
• Fix y-boundaries of Coordinates fields [#1646][boutproject#1646] ([johnomotani][https://github.com/johnomotani])
• Add order-only dependency on gtest sentinel to unit test objects [#1643][boutproject#1643] ([ZedThree][https://github.com/ZedThree])
• Change variable names for output from staggered Coordinates [#1639][boutproject#1639] ([johnomotani][https://github.com/johnomotani])
• Hypnotoad: enable 'Detailed settings' for nonorthogonal grids [#1636][boutproject#1636] ([johnomotani][https://github.com/johnomotani])
• Make ParallelTransform location-aware [#1635][boutproject#1635] ([johnomotani][https://github.com/johnomotani])
• Replace ENUM_STRING functions with toString overloads [#1634][boutproject#1634] ([ZedThree][https://github.com/ZedThree])
• Last couple of master bugfixes into next [#1633][boutproject#1633] ([ZedThree][https://github.com/ZedThree])
• Write Field directions as attributes in output files [#1631][boutproject#1631] ([johnomotani][https://github.com/johnomotani])
• Some small improvements to unit tests [#1630][boutproject#1630] ([ZedThree][https://github.com/ZedThree])
• Loosen tolerance for CyclicReduce tests [#1628][boutproject#1628] ([ZedThree][https://github.com/ZedThree])
• Add some basic unit tests for CyclicReduce [#1625][boutproject#1625] ([ZedThree][https://github.com/ZedThree])
• Direction tagging and emptyFrom [#1624][boutproject#1624] ([johnomotani][https://github.com/johnomotani])
• Fix spatial advection 2 [#1623][boutproject#1623] ([dschwoerer][https://github.com/dschwoerer])
• set -e [#1622][boutproject#1622] ([dschwoerer][https://github.com/dschwoerer])
• Pin pip packages on Travis [#1621][boutproject#1621] ([ZedThree][https://github.com/ZedThree])
• Fix printf formats in Ncxx4/H5Format::setAttribute(..., BoutReal) [#1620][boutproject#1620] ([ZedThree][https://github.com/ZedThree])
• Use std::map::find to avoid double lookup in getCoordinates [#1618][boutproject#1618] ([johnomotani][https://github.com/johnomotani])
• Merge v4.2.2 into next [#1616][boutproject#1616] ([ZedThree][https://github.com/ZedThree])
• Add FDDX_U2 implementation, plus minor bugfixes [#1615][boutproject#1615] ([johnomotani][https://github.com/johnomotani])
• Unit tests for GridFromOptions [#1614][boutproject#1614] ([ZedThree][https://github.com/ZedThree])
• A few small unit test improvements [#1613][boutproject#1613] ([ZedThree][https://github.com/ZedThree])
• Initial profile tests and tidy [#1602][boutproject#1602] ([ZedThree][https://github.com/ZedThree])
• Some quality of life improvements for unit tests [#1601][boutproject#1601] ([ZedThree][https://github.com/ZedThree])
• FieldFactory and ExpressionParser tidy [#1597][boutproject#1597] ([ZedThree][https://github.com/ZedThree])
• Hypnotoad: more flexible transitions in nonorthogonal grid generation [#1596][boutproject#1596] ([johnomotani][https://github.com/johnomotani])
• Hypnotoad nonorthogonal fixes [#1593][boutproject#1593] ([johnomotani][https://github.com/johnomotani])
• More unit tests for derivatives [#1592][boutproject#1592] ([ZedThree][https://github.com/ZedThree])
• More Field* tests [#1591][boutproject#1591] ([ZedThree][https://github.com/ZedThree])
• InterpolationFactory tests [#1590][boutproject#1590] ([ZedThree][https://github.com/ZedThree])
• Timer tests and refactor [#1589][boutproject#1589] ([ZedThree][https://github.com/ZedThree])
• Check buffer length [#1586][boutproject#1586] ([dschwoerer][https://github.com/dschwoerer])
• getmpirun default [#1584][boutproject#1584] ([dschwoerer][https://github.com/dschwoerer])
• Spanish translation [#1579][boutproject#1579] ([bendudson][https://github.com/bendudson])
• Make application of INVERT_SET at outer boundary clearer in cyclic solver [#1578][boutproject#1578] ([johnomotani][https://github.com/johnomotani])
• Use Xenial on Travis [#1577][boutproject#1577] ([ZedThree][https://github.com/ZedThree])
• Tidy derivatives [#1576][boutproject#1576] ([d7919][https://github.com/d7919])
• Hypnotoad: output coordinate system labelling [#1575][boutproject#1575] ([johnomotani][https://github.com/johnomotani])
• Codecov tweaks [#1571][boutproject#1571] ([ZedThree][https://github.com/ZedThree])
• Avoid out-of-range access for invalid regions [#1570][boutproject#1570] ([dschwoerer][https://github.com/dschwoerer])
• Allow Coordinates on staggered grids to be read from grid files [#1564][boutproject#1564] ([johnomotani][https://github.com/johnomotani])
• Enable communications for simulations with no core, only divertor legs [#1563][boutproject#1563] ([johnomotani][https://github.com/johnomotani])
• Hypnotoad: add checkbox to output metrics for orthogonal coordinates [#1562][boutproject#1562] ([johnomotani][https://github.com/johnomotani])
• Hypnotoad: handle case when break of contour is very close to x-point [#1561][boutproject#1561] ([johnomotani][https://github.com/johnomotani])
• Inform about gettext's license [#1559][boutproject#1559] ([dschwoerer][https://github.com/dschwoerer])
• Prevent data corruption [#1558][boutproject#1558] ([dschwoerer][https://github.com/dschwoerer])
• Locale de [#1556][boutproject#1556] ([dschwoerer][https://github.com/dschwoerer])
• Fix expr.hxx [#1555][boutproject#1555] ([dschwoerer][https://github.com/dschwoerer])
• Update name of helper function [#1553][boutproject#1553] ([d7919][https://github.com/d7919])
• Remove old examples and change to use new options style [#1550][boutproject#1550] ([d7919][https://github.com/d7919])
• Replace IsField*Equal* predicates with templated versions [#1547][boutproject#1547] ([ZedThree][https://github.com/ZedThree])
• Fix bug in DST option for cyclic solve [#1546][boutproject#1546] ([bendudson][https://github.com/bendudson])
• More derivative tests [#1545][boutproject#1545] ([d7919][https://github.com/d7919])
• Improve make-script example [#1542][boutproject#1542] ([dschwoerer][https://github.com/dschwoerer])
• Pass by reference in makeField [#1541][boutproject#1541] ([ZedThree][https://github.com/ZedThree])
• Replace MMS/spatial/advection with simpler/more complete test [#1540][boutproject#1540] ([ZedThree][https://github.com/ZedThree])
• Fix time MMS [#1539][boutproject#1539] ([ZedThree][https://github.com/ZedThree])
• Minor improvments for boutcore [#1536][boutproject#1536] ([dschwoerer][https://github.com/dschwoerer])
• Remove setLocation() in Field3D::operator=(FieldPerp) [#1535][boutproject#1535] ([johnomotani][https://github.com/johnomotani])
• Derivative unit tests [#1534][boutproject#1534] ([ZedThree][https://github.com/ZedThree])
• Remove checkData from copy constructor and assignment operator in Fields [#1533][boutproject#1533] ([d7919][https://github.com/d7919])
• Merge v4.2.1 release into next [#1532][boutproject#1532] ([ZedThree][https://github.com/ZedThree])
• Write job execution information to dump file [#1531][boutproject#1531] ([JosephThomasParker][https://github.com/JosephThomasParker])
• Use third order B.C. in MMS/advection/weno3 test case. [#1528][boutproject#1528] ([d7919][https://github.com/d7919])
• Documentation for Scorep [#1525][boutproject#1525] ([JosephThomasParker][https://github.com/JosephThomasParker])
• Remove support for scipy/scientific netcdf libraries [#1524][boutproject#1524] ([d7919][https://github.com/d7919])
• Fix typo in petsc installation instructions [#1523][boutproject#1523] ([bshanahan][https://github.com/bshanahan])
• Move googletest into externalpackages [#1522][boutproject#1522] ([d7919][https://github.com/d7919])
• Comment out clang-format options that are not recognised [#1519][boutproject#1519] ([d7919][https://github.com/d7919])
• Fix assert in definition of FFT 2nd derivative [#1518][boutproject#1518] ([d7919][https://github.com/d7919])
• Delp2 test requires fftw [#1513][boutproject#1513] ([dschwoerer][https://github.com/dschwoerer])
• Two stage add coordinates [#1506][boutproject#1506] ([d7919][https://github.com/d7919])
• Show available options in Factory [#1497][boutproject#1497] ([dschwoerer][https://github.com/dschwoerer])
• FieldFactory: Separate parsing, looping stages in create{2,3}D [#1494][boutproject#1494] ([bendudson][https://github.com/bendudson])
• specify python package versions for Travis [#1493][boutproject#1493] ([d7919][https://github.com/d7919])
• Array flexible backing [#1492][boutproject#1492] ([d7919][https://github.com/d7919])
• Add Matrix/Tensor::reallocate; check Arrays are of positive size [#1491][boutproject#1491] ([ZedThree][https://github.com/ZedThree])
• Fix bug in fft Array interface when using odd-length signals [#1490][boutproject#1490] ([ZedThree][https://github.com/ZedThree])
• Add Array::resize [#1489][boutproject#1489] ([ZedThree][https://github.com/ZedThree])
• Move map and function definitions into source file for bout_types [#1486][boutproject#1486] ([d7919][https://github.com/d7919])
• Testing shiftedmetric [#1483][boutproject#1483] ([ZedThree][https://github.com/ZedThree])
• Fix location of Coordinates* in tridagCoefs [#1481][boutproject#1481] ([johnomotani][https://github.com/johnomotani])
• Make absence of fftw-wisdom non-fatal in configure [#1475][boutproject#1475] ([d7919][https://github.com/d7919])
• Use namespace for global variables 'mesh' and 'dump' [#1470][boutproject#1470] ([johnomotani][https://github.com/johnomotani])
• Use non-Fourier Delp2 in test-multigrid_laplace [#1469][boutproject#1469] ([johnomotani][https://github.com/johnomotani])
• Reduce code duplication in interp_to [#1467][boutproject#1467] ([d7919][https://github.com/d7919])
• Ensure the location is initialised in LaplaceXZ [#1466][boutproject#1466] ([d7919][https://github.com/d7919])
• Make most examples compilable [#1458][boutproject#1458] ([d7919][https://github.com/d7919])
• Deprecate invert_laplace() free functions [#1453][boutproject#1453] ([johnomotani][https://github.com/johnomotani])
• Remove const from bool return [#1450][boutproject#1450] ([bendudson][https://github.com/bendudson])
• Verbose output [#1447][boutproject#1447] ([ZedThree][https://github.com/ZedThree])
• Pass f_aligned to standardDerivative in DDY/D2DY2/D4DY4 [#1446][boutproject#1446] ([johnomotani][https://github.com/johnomotani])
• Make free interpolate use the Lagrange4pt class [#1445][boutproject#1445] ([d7919][https://github.com/d7919])
• Add FieldPerp location [#1441][boutproject#1441] ([d7919][https://github.com/d7919])
• Removes explicit request for timezone [#1440][boutproject#1440] ([d7919][https://github.com/d7919])
• Add tool for generic operator inversion [#1439][boutproject#1439] ([d7919][https://github.com/d7919])
• Be more explicit about how many threads to use in some tests. [#1438][boutproject#1438] ([d7919][https://github.com/d7919])
• Non-fourier delp2 [#1436][boutproject#1436] ([d7919][https://github.com/d7919])
• Fix FV::Div_par_K_Grad_par [#1434][boutproject#1434] ([johnomotani][https://github.com/johnomotani])
• Location checking in ShiftedMetric::shiftZ() [#1433][boutproject#1433] ([johnomotani][https://github.com/johnomotani])
• Add region arguments for toFieldAligned/fromFieldAligned [#1432][boutproject#1432] ([johnomotani][https://github.com/johnomotani])
• Remove result_fa from interp_to [#1427][boutproject#1427] ([johnomotani][https://github.com/johnomotani])
• Options use variant type (towards a DataFile replacement) [#1425][boutproject#1425] ([bendudson][https://github.com/bendudson])
• Adding toString specialisations [#1424][boutproject#1424] ([bendudson][https://github.com/bendudson])
• Start to introduce zstart and zend [#1423][boutproject#1423] ([d7919][https://github.com/d7919])
• Make FFTW an optional dependency [#1422][boutproject#1422] ([d7919][https://github.com/d7919])
• Warnings tidyup derivative overhaul mesh [#1420][boutproject#1420] ([d7919][https://github.com/d7919])
• Workaround for gcc ICE to do with binding class bound member with [#1419][boutproject#1419] ([d7919][https://github.com/d7919])
• Ensure we install cython for Travis before netcdf4 [#1417][boutproject#1417] ([d7919][https://github.com/d7919])
• Move index derivs out of mesh [#1416][boutproject#1416] ([d7919][https://github.com/d7919])
• Add a couple of sanity tests for ffts [#1415][boutproject#1415] ([ZedThree][https://github.com/ZedThree])
• Pass zShift to ShiftedMetric constructor (backwards compatible) [#1413][boutproject#1413] ([ZedThree][https://github.com/ZedThree])
• Split backtrace generation and prettification up [#1412][boutproject#1412] ([ZedThree][https://github.com/ZedThree])
• Add some missing autoconf macros needed to build configure [#1410][boutproject#1410] ([ZedThree][https://github.com/ZedThree])
• Fix MAYBE_UNUSED for some compilers [#1409][boutproject#1409] ([ZedThree][https://github.com/ZedThree])
• List OpenMP schedule options in configure help [#1408][boutproject#1408] ([JosephThomasParker][https://github.com/JosephThomasParker])
• Remove comm_group as not used anywhere [#1406][boutproject#1406] ([bendudson][https://github.com/bendudson])
• Remove restart.split python routine [#1405][boutproject#1405] ([bendudson][https://github.com/bendudson])
• Small user manual improvements [#1404][boutproject#1404] ([bendudson][https://github.com/bendudson])
• Remove even more warnings [#1403][boutproject#1403] ([ZedThree][https://github.com/ZedThree])
• "Dumb" constructor for Coordinates and Vector tests [#1402][boutproject#1402] ([ZedThree][https://github.com/ZedThree])
• Bugfix: new_location check in setLocation would always be false [#1401][boutproject#1401] ([ZedThree][https://github.com/ZedThree])
• Two small improvements to command line options [#1400][boutproject#1400] ([ZedThree][https://github.com/ZedThree])
• More fixes for invparderiv [#1399][boutproject#1399] ([d7919][https://github.com/d7919])
• Add implementation of make_unique [#1396][boutproject#1396] ([ZedThree][https://github.com/ZedThree])
• Replace deprecated C headers with C++ version [#1391][boutproject#1391] ([ZedThree][https://github.com/ZedThree])
• Replace abs with std abs [#1390][boutproject#1390] ([d7919][https://github.com/d7919])
• Adding simple integrated test to compile all example files [#1389][boutproject#1389] ([d7919][https://github.com/d7919])
• Fix examples so most compile [#1388][boutproject#1388] ([d7919][https://github.com/d7919])
• Use python unittest in runtests [#1386][boutproject#1386] ([ZedThree][https://github.com/ZedThree])
• Field* constructor tidy [#1385][boutproject#1385] ([ZedThree][https://github.com/ZedThree])
• Overhaul derivatives for vectorisation and user registration [#1384][boutproject#1384] ([d7919][https://github.com/d7919])
• Don't clobber command line short options when reading input file [#1382][boutproject#1382] ([ZedThree][https://github.com/ZedThree])
• Bc docs [#1381][boutproject#1381] ([dschwoerer][https://github.com/dschwoerer])
• Basic Vector support for boutcore [#1380][boutproject#1380] ([dschwoerer][https://github.com/dschwoerer])
• Fix:Escaping in makefile [#1379][boutproject#1379] ([dschwoerer][https://github.com/dschwoerer])
• Add documentation [#1376][boutproject#1376] ([dschwoerer][https://github.com/dschwoerer])
• Remove regeneration test [#1375][boutproject#1375] ([dschwoerer][https://github.com/dschwoerer])
• Print command line options to output_info [#1373][boutproject#1373] ([johnomotani][https://github.com/johnomotani])
• Remove uses of global 'mesh' from Laplacian solvers [#1371][boutproject#1371] ([johnomotani][https://github.com/johnomotani])
• Set location in LaplaceCyclic::solve() and DC() [#1367][boutproject#1367] ([johnomotani][https://github.com/johnomotani])
• Move the definition of __thefunc__ and add AUTO_TRACE [#1366][boutproject#1366] ([d7919][https://github.com/d7919])
• Optimisations to certain vector routines [#1363][boutproject#1363] ([d7919][https://github.com/d7919])
• Clean squashoutput.py [#1362][boutproject#1362] ([dschwoerer][https://github.com/dschwoerer])
• Fix path for locale files [#1360][boutproject#1360] ([dschwoerer][https://github.com/dschwoerer])
• Remove last DataIterator references/uses [#1358][boutproject#1358] ([ZedThree][https://github.com/ZedThree])
• Disable broken tests [#1356][boutproject#1356] ([dschwoerer][https://github.com/dschwoerer])
• Comment out clang-format directives that need clang-format >= 6 [#1353][boutproject#1353] ([ZedThree][https://github.com/ZedThree])
• Support BoutReal and file-level attributes for netCDF and HDF5 files [#1350][boutproject#1350] ([johnomotani][https://github.com/johnomotani])
• Delete dependency .mk files in clean target [#1348][boutproject#1348] ([bendudson][https://github.com/bendudson])
• Boundary keywords and bugfix [#1346][boutproject#1346] ([bendudson][https://github.com/bendudson])
• Add multiple parallel slices [#1345][boutproject#1345] ([ZedThree][https://github.com/ZedThree])
• Reuse fixture for creating/destroying FakeMesh [#1344][boutproject#1344] ([ZedThree][https://github.com/ZedThree])
• Clang format update [#1343][boutproject#1343] ([ZedThree][https://github.com/ZedThree])
• Fix FV::Div_Par_K_Grad_Par [#1341][boutproject#1341] ([johnomotani][https://github.com/johnomotani])
• Changing README example to use cross rather than ^ [#1340][boutproject#1340] ([bendudson][https://github.com/bendudson])
• Remove using std::string etc from headers [#1339][boutproject#1339] ([ZedThree][https://github.com/ZedThree])
• Boutexception backtrace tidy [#1338][boutproject#1338] ([ZedThree][https://github.com/ZedThree])
• A couple of small bugfixes for Zoidberg [#1337][boutproject#1337] ([ZedThree][https://github.com/ZedThree])
• Internationalisation with gettext [#1335][boutproject#1335] ([bendudson][https://github.com/bendudson])
• Expressions improvements: escape chars and unicode [#1333][boutproject#1333] ([bendudson][https://github.com/bendudson])
• Save run information to settings file [#1332][boutproject#1332] ([bendudson][https://github.com/bendudson])
• Remove more deprecated derivs boundaries [#1331][boutproject#1331] ([d7919][https://github.com/d7919])
• Add unary operator+ to fields [#1329][boutproject#1329] ([bendudson][https://github.com/bendudson])
• Add support for enum class [#1328][boutproject#1328] ([dschwoerer][https://github.com/dschwoerer])
• Remove deprecated routines [#1326][boutproject#1326] ([d7919][https://github.com/d7919])

v4 known bugs

See #2154.

v4.4.2 (2021-12-15)

Full Changelog

Merged pull requests:

• 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)

v4.4.1 (2021-12-15)

Full Changelog

Merged pull requests:

• Back-port beuler/snes improvements to master #2459 (bendudson)
• Update "Running BOUT++" documentation #2475 (ZedThree)
• Raise more descriptive error if converting Option fails #2474 (ZedThree)
• Print correct CMake build directory in configure message #2473 (ZedThree)
• CMake: Fix using the build directory directly #2464 (ZedThree)
• Add bout::utils:: prefix to visit #2463 (ZedThree)
• Fix SUNDIALS download git tag #2462 (ZedThree)
• Fix permission of shared objects #2433 (dschwoerer)
• Fix BOUT_OVERRIDE_DEFAULT_OPTION() #2417 (johnomotani)
• Ensure MPI is initialised before writing #2409 (dschwoerer)
• Remove <optional> include from uuid (v4.4.1) #2407 (ZedThree)
• Fix make install #2401 (dschwoerer)
• Fix soname #2400 (dschwoerer)

v4.4.0 (2021-07-30)

Full Changelog

Merged pull requests:

• Add ability to use FieldPerp in Options (v.4.4) #2395 (ZedThree)
• Fix some HDF5 related issues and add Mesh::getLocal{X,Y,Z}Index (v4.4) #2394 (ZedThree)
• Add Mesh::getRegion for use in generic code (v4.4) #2393 (ZedThree)
• Adding an adaptive, arbitrary order, Adams-Bashforth solver (v4.4) #2392 (ZedThree)
• Allow PETSc options to be passed from BOUT.inp (v4.4) #2391 (ZedThree)
• Add new contributors #2386 (dschwoerer)
• Update locale #2385 (dschwoerer)
• Fix RTD #2384 (dschwoerer)
• Rename max_nonlinear_it to max_nonlinear_iterations #2339 (johnomotani)
• CVODE constraints and max_noinlinear_iterations options (4.4) #2304 (johnomotani)
• Fix some Solvers not always using user preconditioner/Jacobian (v4.4) #2284 (ZedThree)
• Fix formatting strings for pre-fmt in beuler solver #2278 (bendudson)
• Backport of Backward Euler solver to v4.4 #2265 (bendudson)
• Fix use of uninitialised value in Delp2 (4.4) #2263 (johnomotani)
• Save provenance tracking info from grid file (4.4) #2231 (johnomotani)
• Generate random run ID, track restarts (4.4) #2224 (johnomotani)
• Generate report for Timers (4.4) #2216 (johnomotani)
• Replace boutdata and boututils directories with submodules (v4.4) #2198 (johnomotani)
• Use bout_type="string" for strings in H5Format (4.4) #2194 (johnomotani)
• Write descriptions for std::vector and std::string variables #2191 (johnomotani)
• Fix reading of char* in Ncxx4 (4.4) #2189 (johnomotani)
• Merge master into v4.4.0-alpha #2174 (ZedThree)
• I/O for std::vector and std::string (4.4) #2155 (johnomotani)
• Check DataFile grid sizes match those in existing mesh (v4.4) #2148 (johnomotani)
• Call checkData() before returning result in Laplace inversions (v4.4) #2134 (johnomotani)
• Allow setting FFTW_EXHAUSTIVE (v4.4) #2132 (johnomotani)
• Make example relocatable #2127 (dschwoerer)
• Merge master into v4.4.0-alpha #2121 (ZedThree)
• Handle FieldPerps in Datafile::varAdded() and Datafile::varPtr() (v4.4.0) #2094 (johnomotani)
• Staggered grids in InvertPar (v4.4.0) #2088 (johnomotani)
• Allow descriptions of output variables; save some diagnostics for solvers (v4.4) #2086 (johnomotani)
• Correct Grad2_par2 implementation in InvertParCR (v4.4.0) #2077 (johnomotani)
• Enable staggered versions of SplitFluxDerivativeType (4.4) #2059 (johnomotani)
• Merge master into v4.4.0-alpha #1998 (ZedThree)
• LaplaceXY: finite difference option (v4.4) #1924 (johnomotani)
• Backport of Laplace performance test #1910 (JosephThomasParker)
• Macro for creating enum classes (v4.4) #1895 (johnomotani)
• Implement toFieldAligned and fromFieldAligned for Vector3D (v4.4) #1878 (johnomotani)
• Remove 3-element list indexers for collect() #1862 (johnomotani)
• Allow user to override library option defaults (v4.4) #1849 (johnomotani)

The following were backported from v5.0.0 in #2389:

• Add remaining integrated tests to CMake build #1833 (ZedThree)
• Fixes for Windows #1874 (ZedThree)
• CMake: fix FindSlepc for non-make generators #1881 (ZedThree)
• CMake: enable using external mpark.variant #1900 (ZedThree)
• Cmake fixes #1909 (dschwoerer)
• CMake: find package fixes #1912 (ZedThree)
• Fix runtest for non-make generators #1952 (ZedThree)
• CMake: Generate Field arithmetic operators #2119 (dschwoerer)
• CMake: Add option to download and build netCDF C++ API #2138 (ZedThree)
• Fix CMake config file following change to netCDF cmake module #2162 (ZedThree)
• Make input Options case sensitive and error on unused Options #2210 (ZedThree)
• Next CMake fixes #2275 (bendudson)
• Add MMS tests to CMake build #2286 (ZedThree)
• CMake: Build documentation #2300 (ZedThree)
• Fix for FindPETSc not being reentrant if pkg-config used (next) #2318 (ZedThree)
• CMake: Fix a few minor issues, generate bout-config #2328 (ZedThree)
• CMake: Add option to download SUNDIALS at configure time #2331 (ZedThree)
• CMake rename PACKAGE_TESTS to BOUT_TESTS #2347 (bendudson)
• CMake: Add SOVERSION; fix FindSUNDIALS #2358 (dschwoerer)
• Faster recompile #2294 (dschwoerer)

v4.3.3 (2021-07-28)

Full Changelog

Merged pull requests:

• Fix documentation for examples/wave-slab #2369 (ZedThree)
• Make include optional #2360 (dschwoerer)
• Fix ReadTheDocs (master) #2319 (ZedThree)
• Fix for FindPETSc not being reentrant if pkg-config used #2317 (ZedThree)
• Add missing snb.cxx to CMakeLists.txt #2315 (bendudson)
• Add notes on installing SUNDIALS #2311 (bendudson)
• Make blob2d example self contained #2288 (dschwoerer)
• Fix some Solvers not always using user preconditioner/Jacobian #2283 (ZedThree)
• Bump jinja2 from 2.10.1 to 2.11.3 #2266 (dependabot[bot])
• Fix use of uninitialised value in Delp2 #2262 (johnomotani)
• Add requirements to boutcore/print test #2175 (ZedThree)
• Update docs on supported PETSc versions #2171 (johnomotani)
• Convert Travis to Github Actions (master) #2170 (ZedThree)
• Boutcore improvements #2166 (dschwoerer)
• Fix shiftOutput (master) #2158 (johnomotani)
• Fix test-restart-io and FieldPerp writes #2154 (johnomotani)
• Ignore more test data #2125 (dschwoerer)
• Fix links to open-mpi.org and lam-mpi.org #2122 (tobyjamez)

v4.3.2 (2020-10-19)

Full Changelog

Merged pull requests:

• Make output nicer + add info about timeout'ed tests #2120 (dschwoerer)
• Add timeout to tests #2118 (ZedThree)
• Fix reading/writing std::string attributes when using HDF5 #2116 (ZedThree)
• Rename death tests according to gtest recommendations #2115 (ZedThree)
• Update breathe for readthedocs #2114 (ZedThree)
• Fix Div_par when using more than one y guard cell #2113 (ZedThree)
• Update documentation on processor splitting and advanced installation #2109 (ZedThree)
• Soname v4.3.2 #2108 (dschwoerer)
• Add configure option to use system mpark.variant #2107 (dschwoerer)
• CI: Turn off patch coverage check #2103 (ZedThree)
• Make examples relocatable #2100 (dschwoerer)
• Handle FieldPerps in Datafile::varAdded() and Datafile::varPtr() #2093 (johnomotani)
• Correct Grad2_par2 implementation in InvertParCR #2076 (johnomotani)
• Enable staggered versions of SplitFluxDerivativeType #2058 (johnomotani)
• Fixes for tokamak-2fluid example #2043 (johnomotani)
• Add location checks to Div_par_K_Grad_par #2039 (bshanahan)
• Add clang-format bot command for pull requests #2032 (ZedThree)
• Update the staggered grids section of the manual #2029 (johnomotani)
• Make dz in boutcore a property #2024 (dschwoerer)
• Prevent deadlock in downloading mpark #2017 (dschwoerer)

v4.3.1 (2020-03-27)

Full Changelog

Merged pull requests:

• Fix examples/make-script #1995 (ZedThree)
• Travis: Update pinned pip packages #1994 (ZedThree)
• Remove unused VERSIONS file #1993 (ZedThree)
• Minor Travis fixes and job names (master) #1990 (ZedThree)
• conditionally add -Og for non-gcc #1987 (dschwoerer)
• fix test-laplace-petsc3d #1985 (dschwoerer)
• Use '==' to compare to literals in Python #1980 (ZedThree)
• Read staggered J and Bxy from grid if present (master) #1975 (johnomotani)
• Remove reference to deleted test in documentation #1973 (ZedThree)
• Remove -Og from debug flags #1972 (ZedThree)
• Fix documented requirements #1971 (ZedThree)
• Compat make.config for make 4.3 #1970 (dschwoerer)
• Install make.config with header files #1969 (dschwoerer)
• Translations 4.3.1 #1968 (dschwoerer)
• Fix collect when given similar name #1966 (bendudson)
• Fix deprecated initialisation and boundary options #1956 (ZedThree)
• make README.md readabile #1953 (dschwoerer)
• Fix lapd_drift input files #1950 (bendudson)
• Remove FieldData::setBoundary #1949 (bendudson)
• Fixes for staggering in lapd-drift example (master) #1928 (johnomotani)
• Fix segfaults from PvodeSolver (master) #1927 (johnomotani)
• pkg-config petsc (master) #1913 (dschwoerer)
• Fix hypnotoad #1911 (johnomotani)
• complete instructions for archlinux #1892 (dschwoerer)
• Petsc interface generalisation #1889 (cmacmackin)
• fix citation #1888 (dschwoerer)
• If variable is added to Datafile twice, do not write twice #1876 (johnomotani)
• Fix loss of restart files caused by crash during initialisation #1875 (johnomotani)
• Do not include if is released #1871 (dschwoerer)
• Easier instructions for Fedora #1870 (dschwoerer)
• Basic lock for mpark.variant #1869 (dschwoerer)
• Add BOUT_REVISION (git hash of compiled version) to dump files #1867 (johnomotani)
• Mesh requires Option to stay around. #1860 (dschwoerer)
• Try to prevent race condition while building. #1856 (dschwoerer)
• Address needs to be aligned #1855 (dschwoerer)
• set OMPI_MCA_rmaps_base_oversubscribe=yes for tests #1854 (dschwoerer)
• Loosen tolerance for other arches #1853 (dschwoerer)
• Bugfix: $MPIRUN should include -np #1851 (dschwoerer)
• Add some documentation on setting locales #1845 (bendudson)
• Fix typo in initialisation of rgn_outer_x #1838 (ZedThree)

v4.3.0 (2019-10-24)

Full Changelog

Merged pull requests:

• Micro optimise some common routines for v4.3.0-rc #1824 (d7919)
• Automagically checkout mpark.variant submodule #1823 (ZedThree)
• Deprecate CtoL and LtoC differential operators #1822 (johnomotani)
• Bugfix add missing include and update configure #1819 (d7919)
• Performance fixes: ShiftedMetric and VDDY #1816 (ZedThree)
• Save all commonly used geometry variables #1815 (johnomotani)
• Make interp_to and finite-volume parallel operators return result in the same space as the input #1813 (johnomotani)
• Ensure parallel_transform is only read from grid files, not from options #1812 (johnomotani)
• Bugfixes for writing Vector2D and Vector3D #1809 (johnomotani)
• Bugfix: result of InvertParCR::solve tagged in wrong y space #1806 (ZedThree)
• Remove some superfluous location checks in Laplacian #1804 (ZedThree)
• Fix for Intel enabling -Wnull-dereference despite not accepting it #1801 (ZedThree)
• Fix assignment instead of comparison in ASSERTs #1800 (ZedThree)
• Fix y-extrapolation in BoundaryDirichlet::apply(Field2D&) #1799 (johnomotani)
• Fix typo in ternary in InvertableOperator #1798 (ZedThree)
• Fix in-place Region methods returning new instances #1797 (ZedThree)
• Make CELL_LOC strongly typed #1796 (johnomotani)
• Allow NYPE to be given instead of NXPE in input files #1794 (johnomotani)
• Implement boundary conditions for CELL_ZLOW fields #1793 (johnomotani)
• Fix initial conditions not being transformed correctly #1791 (ZedThree)
• Add manual section on xlC compiler #1790 (bendudson)
• Remove checks in Laplace that fail if outloc==CELL_DEFAULT #1788 (johnomotani)
• Implement the INVERT_ZERO_DC flag in LaplaceCyclic #1786 (johnomotani)
• Add macro for Scorep instrumentation of a user-defined code region #1784 (JosephThomasParker)
• Fix some issues in hypnotoad #1783 (friva000)
• Remove redundant 'allocate()' calls #1782 (johnomotani)
• Correct manual - default for 'floats' is true for dump files too #1780 (johnomotani)
• Support bool variables in file I/O #1779 (johnomotani)
• Scripts cleanup #1778 (dschwoerer)
• File open error messages #1777 (johnomotani)
• Don't ignore $MPIRUN #1776 (dschwoerer)
• Update performance/iterator-offsets example #1775 (dschwoerer)
• Bout4to5 script #1774 (bendudson)
• Consistent global indices #1770 (johnomotani)
• Add processor indices to dump files #1769 (johnomotani)
• Try GitHub url for SUNDIALS if LLNL url fails #1768 (ZedThree)
• Fix reading of zShift_ylow #1767 (johnomotani)
• Fixes for Python DataFile class #1766 (johnomotani)
• Fix y-boundary cells of phi in conducting-wall-mode example #1765 (johnomotani)
• Add mesh options for extrapolate_{x,y} #1760 (bendudson)
• Deprecate Laplacian::setFlags() #1758 (johnomotani)
• Fix advection MMS tests #1757 (ZedThree)
• Rename 'coordinates_type' gridfile attribute to 'parallel_transform' #1756 (ZedThree)
• More clang-tidy fixes #1755 (ZedThree)
• Add default value to Mesh::get for ints #1754 (JosephThomasParker)
• Remove FIXME comment from interp_to #1752 (johnomotani)
• Build pdf manual #1751 (johnomotani)
• Bug fix, test and tidy SLEPc solver #1749 (ZedThree)
• SNB nonlocal heat flux model #1748 (bendudson)
• Pin packages in requirements.txt for Sphinx docs #1746 (ZedThree)
• Don't mark Coordinates::zShift as const, can't be output #1745 (ZedThree)
• Laplacian: FFT include dfdz term, plus manual updates #1744 (johnomotani)
• Fix interpolation of staggered zShift #1743 (johnomotani)
• Correct calculation of Bxy when interpolating from CELL_CENTRE #1741 (johnomotani)
• Only call checkPositive(g) for grid cells #1739 (johnomotani)
• Output ParallelTransform variables #1736 (johnomotani)
• Fix BoutMesh decomposition on single processor #1735 (ZedThree)
• Deprecate some unused methods #1734 (ZedThree)
• make sure values() returns valid pointer #1733 (dschwoerer)
• Twistshift for field-aligned variables #1732 (johnomotani)
• Add bout::utils::is_Field and variants #1730 (ZedThree)
• Deprecate Karniadakis solver #1727 (ZedThree)
• Make MsgStack and BoutException unit tests more flexible #1726 (ZedThree)
• Bugfix: use region in Coordinates::calcCovariant/calcContravariant #1725 (ZedThree)
• Hardcode all variables for test-solver; remove input file #1724 (ZedThree)
• Remove Laplace3D #1723 (ZedThree)
• Add function_traits template and replace SUNDIALS int type macros #1722 (ZedThree)
• fix nc-format #1721 (dschwoerer)
• Templated Field functions and deprecate REGION enum arguments #1720 (johnomotani)
• More robust staggered Jacobian and RGN_NOCORNERS #1719 (johnomotani)
• Handle attributes for missing variables #1718 (bendudson)
• Revert "Hypnotoad: 'H' is derivative of integral" #1717 (johnomotani)
• Remove deprecated invert_laplace from gyro_average #1716 (ZedThree)
• Lots of small clang-tidy fixes #1715 (ZedThree)
• Tidy up direction-type setters #1712 (johnomotani)
• Add implementation of Field2D::applyBoundary(BoutReal time) #1711 (ZedThree)
• Fix BoutMesh boundary regions #1710 (ZedThree)
• Don't run tests that use FFTW if not compiled with it #1709 (ZedThree)
• Fixes for FV::Div_a_Laplace_perp #1707 (bendudson)
• Set y-direction of FieldPerp results in ParallelTransformIdentity #1704 (johnomotani)
• Do not calculate parallel slices for field-aligned fields #1703 (johnomotani)
• Allow default value of Options to be set from another Options object #1702 (johnomotani)
• Fieldperp I/O #1699 (johnomotani)
• Set y-direction of results in ParallelTransformIdentity #1698 (johnomotani)
• Add support for shifting a FieldPerp toFieldAligned/fromFieldAligned #1697 (johnomotani)
• Experimental CMake support #1696 (ZedThree)
• Convert Options::isSection() argument to lower case #1695 (johnomotani)
• Update required Jinja2 version to avoid CVE-2019-10906 #1694 (ZedThree)
• Move Gridfile::get implementations for Field3D/Field2D to .cxx #1693 (johnomotani)
• Warn about random failures in test #1692 (dschwoerer)
• Use asynchronous communications in LaplaceMultigrid #1691 (johnomotani)
• Remove multiple printing of BOUTLOCALE to stderr #1689 (johnomotani)
• Fix elm pb example #1688 (bendudson)
• Bugfix: bracket operator slowdown #1686 (johnomotani)
• Fix and reenable #1684 (dschwoerer)
• call Finalise in test #1683 (dschwoerer)
• Fix comparison of corner boundary cells in test-squash #1682 (johnomotani)
• Clear Field3D parallel slices in operator= #1681 (johnomotani)
• Ignore new meta-vars in test-squash #1679 (dschwoerer)
• Fix examples #1678 (dschwoerer)
• Add .BOUT.pid.* files to .gitignore #1674 (johnomotani)
• Runge-Kutta-Legendre stabilised explicit method #1673 (bendudson)
• Unit tests and template-isation of where #1672 (ZedThree)
• Don't try to build documentation #1671 (dschwoerer)
• Method for Laplace solvers to say whether they use 3D coefficients #1669 (johnomotani)
• Fix dereferencing null Coordinates in FieldFactory #1667 (ZedThree)
• Bugfix: return fields by reference #1663 (dschwoerer)
• Allow clean exit in boutcore #1662 (dschwoerer)
• Make mixed second-derivative operators more correct #1661 (johnomotani)
• Unit tests and various small refactorings of Solver #1660 (ZedThree)
• Under-relaxation for LaplaceNaulin #1659 (johnomotani)
• Counters for timers, makes them correct with multiple Timer objects #1658 (johnomotani)
• Generate FieldPerp arithmetic operators with jinja #1655 (johnomotani)
• LaplaceNaulin solver improvement, and more general coefficients for LaplaceCyclic #1654 (johnomotani)
• Options type and doc attributes #1653 (bendudson)
• Fix mesh checks in Laplace implementation headers #1652 (johnomotani)
• Minor refactoring of BoutInitialise, BoutFinalise #1651 (ZedThree)
• Add name argument to Options::isSection to test for presence of subsection #1650 (johnomotani)
• Support SUNDIALS 4.1.0 #1649 (ZedThree)
• Make transforming Field3D inputs from field aligned optional #1648 (johnomotani)
• Hypnotoad: double precision and y-boundary guard cells #1647 (johnomotani)
• Fix y-boundaries of Coordinates fields #1646 (johnomotani)
• Add order-only dependency on gtest sentinel to unit test objects #1643 (ZedThree)
• Change variable names for output from staggered Coordinates #1639 (johnomotani)
• Hypnotoad: enable 'Detailed settings' for nonorthogonal grids #1636 (johnomotani)
• Make ParallelTransform location-aware #1635 (johnomotani)
• Replace ENUM\ss_STRING functions with toString overloads #1634 (ZedThree)
• Last couple of master bugfixes into next #1633 (ZedThree)
• Write Field directions as attributes in output files #1631 (johnomotani)
• Some small improvements to unit tests #1630 (ZedThree)
• Loosen tolerance for CyclicReduce tests #1628 (ZedThree)
• Add some basic unit tests for CyclicReduce #1625 (ZedThree)
• Direction tagging and emptyFrom #1624 (johnomotani)
• Fix spatial advection 2 #1623 (dschwoerer)
• set -e #1622 (dschwoerer)
• Pin pip packages on Travis #1621 (ZedThree)
• Fix printf formats in Ncxx4/H5Format::setAttribute(..., BoutReal) #1620 (ZedThree)
• Use std::map::find to avoid double lookup in getCoordinates #1618 (johnomotani)
• Merge v4.2.2 into next #1616 (ZedThree)
• Add FDDX_U2 implementation, plus minor bugfixes #1615 (johnomotani)
• Unit tests for GridFromOptions #1614 (ZedThree)
• A few small unit test improvements #1613 (ZedThree)
• Initial profile tests and tidy #1602 (ZedThree)
• Some quality of life improvements for unit tests #1601 (ZedThree)
• FieldFactory and ExpressionParser tidy #1597 (ZedThree)
• Hypnotoad: more flexible transitions in nonorthogonal grid generation #1596 (johnomotani)
• Hypnotoad nonorthogonal fixes #1593 (johnomotani)
• More unit tests for derivatives #1592 (ZedThree)
• More Field* tests #1591 (ZedThree)
• InterpolationFactory tests #1590 (ZedThree)
• Timer tests and refactor #1589 (ZedThree)
• Check buffer length #1586 (dschwoerer)
• getmpirun default #1584 (dschwoerer)
• Spanish translation #1579 (bendudson)
• Make application of INVERT_SET at outer boundary clearer in cyclic solver #1578 (johnomotani)
• Use Xenial on Travis #1577 (ZedThree)
• Tidy derivatives #1576 (d7919)
• Hypnotoad: output coordinate system labelling #1575 (johnomotani)
• Codecov tweaks #1571 (ZedThree)
• Avoid out-of-range access for invalid regions #1570 (dschwoerer)
• Allow Coordinates on staggered grids to be read from grid files #1564 (johnomotani)
• Enable communications for simulations with no core, only divertor legs #1563 (johnomotani)
• Hypnotoad: add checkbox to output metrics for orthogonal coordinates #1562 (johnomotani)
• Hypnotoad: handle case when break of contour is very close to x-point #1561 (johnomotani)
• Prevent data corruption #1558 (dschwoerer)
• Locale de #1556 (dschwoerer)
• Fix expr.hxx #1555 (dschwoerer)
• Update name of helper function #1553 (d7919)
• Remove old examples and change to use new options style #1550 (d7919)
• Replace IsField\Equal\ predicates with templated versions #1547 (ZedThree)
• Fix bug in DST option for cyclic solve #1546 (bendudson)
• More derivative tests #1545 (d7919)
• Improve make-script example #1542 (dschwoerer)
• Pass by reference in makeField #1541 (ZedThree)
• Replace MMS/spatial/advection with simpler/more complete test #1540 (ZedThree)
• Fix time MMS #1539 (ZedThree)
• Minor improvments for boutcore #1536 (dschwoerer)
• Remove setLocation() in Field3D::operator=(FieldPerp) #1535 (johnomotani)
• Derivative unit tests #1534 (ZedThree)
• Remove checkData from copy constructor and assignment operator in Fields #1533 (d7919)
• Merge v4.2.1 release into next #1532 (ZedThree)
• Write job execution information to dump file #1531 (JosephThomasParker)
• Use third order B.C. in MMS/advection/weno3 test case. #1528 (d7919)
• Documentation for Scorep #1525 (JosephThomasParker)
• Remove support for scipy/scientific netcdf libraries #1524 (d7919)
• Fix typo in petsc installation instructions #1523 (bshanahan)
• Move googletest into externalpackages #1522 (d7919)
• Comment out clang-format options that are not recognised #1519 (d7919)
• Fix assert in definition of FFT 2nd derivative #1518 (d7919)
• Delp2 test requires fftw #1513 (dschwoerer)
• Two stage add coordinates #1506 (d7919)
• Show available options in Factory #1497 (dschwoerer)
• FieldFactory: Separate parsing, looping stages in create{2,3}D #1494 (bendudson)
• specify python package versions for Travis #1493 (d7919)
• Array flexible backing #1492 (d7919)
• Add Matrix/Tensor::reallocate; check Arrays are of positive size #1491 (ZedThree)
• Fix bug in fft Array interface when using odd-length signals #1490 (ZedThree)
• Add Array::resize #1489 (ZedThree)
• Move map and function definitions into source file for bout_types #1486 (d7919)
• Testing shiftedmetric #1483 (ZedThree)
• Fix location of Coordinates* in tridagCoefs #1481 (johnomotani)
• Make absence of fftw-wisdom non-fatal in configure #1475 (d7919)
• Use namespace for global variables 'mesh' and 'dump' #1470 (johnomotani)
• Use non-Fourier Delp2 in test-multigrid_laplace #1469 (johnomotani)
• Reduce code duplication in interp_to #1467 (d7919)
• Ensure the location is initialised in LaplaceXZ #1466 (d7919)
• Make most examples compilable #1458 (d7919)
• Deprecate invert_laplace() free functions #1453 (johnomotani)
• Remove const from bool return #1450 (bendudson)
• Verbose output #1447 (ZedThree)
• Pass f_aligned to standardDerivative in DDY/D2DY2/D4DY4 #1446 (johnomotani)
• Make free interpolate use the Lagrange4pt class #1445 (d7919)
• Add FieldPerp location #1441 (d7919)
• Removes explicit request for timezone #1440 (d7919)
• Add tool for generic operator inversion #1439 (d7919)
• Be more explicit about how many threads to use in some tests. #1438 (d7919)
• Non-fourier delp2 #1436 (d7919)
• Fix FV::Div_par_K_Grad_par #1434 (johnomotani)
• Location checking in ShiftedMetric::shiftZ() #1433 (johnomotani)
• Add region arguments for toFieldAligned/fromFieldAligned #1432 (johnomotani)
• Remove result_fa from interp_to #1427 (johnomotani)
• Options use variant type (towards a DataFile replacement) #1425 (bendudson)
• Adding toString specialisations #1424 (bendudson)
• Start to introduce zstart and zend #1423 (d7919)
• Make FFTW an optional dependency #1422 (d7919)
• Warnings tidyup derivative overhaul mesh #1420 (d7919)
• Workaround for gcc ICE to do with binding class bound member with #1419 (d7919)
• Ensure we install cython for Travis before netcdf4 #1417 (d7919)
• Move index derivs out of mesh #1416 (d7919)
• Add a couple of sanity tests for ffts #1415 (ZedThree)
• Pass zShift to ShiftedMetric constructor (backwards compatible) #1413 (ZedThree)
• Split backtrace generation and prettification up #1412 (ZedThree)
• Add some missing autoconf macros needed to build configure #1410 (ZedThree)
• Fix MAYBE_UNUSED for some compilers #1409 (ZedThree)
• List OpenMP schedule options in configure help #1408 (JosephThomasParker)
• Remove comm_group as not used anywhere #1406 (bendudson)
• Remove restart.split python routine #1405 (bendudson)
• Small user manual improvements #1404 (bendudson)
• Remove even more warnings #1403 (ZedThree)
• "Dumb" constructor for Coordinates and Vector tests #1402 (ZedThree)
• Bugfix: new_location check in setLocation would always be false #1401 (ZedThree)
• Two small improvements to command line options #1400 (ZedThree)
• More fixes for invparderiv #1399 (d7919)
• Add implementation of make_unique #1396 (ZedThree)
• Replace deprecated C headers with C++ version #1391 (ZedThree)
• Replace abs with std abs #1390 (d7919)
• Adding simple integrated test to compile all example files #1389 (d7919)
• Fix examples so most compile #1388 (d7919)
• Use python unittest in runtests #1386 (ZedThree)
• Field* constructor tidy #1385 (ZedThree)
• Overhaul derivatives for vectorisation and user registration #1384 (d7919)
• Don't clobber command line short options when reading input file #1382 (ZedThree)
• Bc docs #1381 (dschwoerer)
• Basic Vector support for boutcore #1380 (dschwoerer)
• Fix:Escaping in makefile #1379 (dschwoerer)
• Add documentation #1376 (dschwoerer)
• Remove regeneration test #1375 (dschwoerer)
• Print command line options to output_info #1373 (johnomotani)
• Remove uses of global 'mesh' from Laplacian solvers #1371 (johnomotani)
• Set location in LaplaceCyclic::solve() and DC() #1367 (johnomotani)
• Move the definition of \_\_thefunc\_\_ and add AUTO_TRACE #1366 (d7919)
• Optimisations to certain vector routines #1363 (d7919)
• Clean squashoutput.py #1362 (dschwoerer)
• Fix path for locale files #1360 (dschwoerer)
• Remove last DataIterator references/uses #1358 (ZedThree)
• Disable broken tests #1356 (dschwoerer)
• Comment out clang-format directives that need clang-format >= 6 #1353 (ZedThree)
• Support BoutReal and file-level attributes for netCDF and HDF5 files #1350 (johnomotani)
• Delete dependency .mk files in clean target #1348 (bendudson)
• Boundary keywords and bugfix #1346 (bendudson)
• Add multiple parallel slices #1345 (ZedThree)
• Reuse fixture for creating/destroying FakeMesh #1344 (ZedThree)
• Clang format update #1343 (ZedThree)
• Fix FV::Div_Par_K_Grad_Par #1341 (johnomotani)
• Changing README example to use cross rather than ^ #1340 (bendudson)
• Remove using std::string etc from headers #1339 (ZedThree)
• Boutexception backtrace tidy #1338 (ZedThree)
• A couple of small bugfixes for Zoidberg #1337 (ZedThree)
• Internationalisation with gettext #1335 (bendudson)
• Expressions improvements: escape chars and unicode #1333 (bendudson)
• Save run information to settings file #1332 (bendudson)
• Remove more deprecated derivs boundaries #1331 (d7919)
• Add unary operator+ to fields #1329 (bendudson)
• Add support for enum class #1328 (dschwoerer)
• Remove deprecated routines #1326 (d7919)

v4.2.3 (2019-10-23)

Full Changelog

Merged pull requests:

• Add counters to Timers to avoid double-counting sections #1817 (ZedThree)
• Bugfix: cyclic parallel derivative inversion done in wrong space #1807 (ZedThree)
• Add instructions for Ubuntu 16.04 #1690 (dschwoerer)
• Allow relative paths to be followed when making #1670 (johnomotani)
• Update examples/staggered_grid for v4.2 #1645 (johnomotani)
• Add EXTRA_LIBS to LIBS when searching for libraries #1632 (ZedThree)
• Recent fixes/improvements for Travis into master #1627 (ZedThree)
• Bug in calculation of ShiftAngle (qloop) #1626 (bendudson)

v4.2.2 (2019-02-27)

Full Changelog

Merged pull requests:

• Fix some clang-tidy warnings #1612 (ZedThree)
• Check if we need to link against libdl for dladdr #1611 (ZedThree)
• Fix unclean exit #1610 (dschwoerer)
• Fix a couple of small(ish) bugs in FV::Div_par_K_Grad_par #1609 (bendudson)
• Fix FV::Div_a_Laplace_perp and FV::Div_par_K_Grad_par #1606 (bendudson)
• Bugfix laplacexz #1605 (bendudson)
• Initialise some mesh variables to sensible defaults #1604 (ZedThree)
• Fix prototype Div(v2d, f2d) in header #1603 (bendudson)
• Hypnotoad version numbering #1595 (johnomotani)
• Provide formatting string #1588 (dschwoerer)
• Fix bug in FCI: missed last point in Z for corner displacements #1587 (ZedThree)
• use MPIRUN if set #1585 (dschwoerer)
• Prevent failures on parallel, clean build #1583 (dschwoerer)
• More printf #1581 (dschwoerer)
• Provide argument for printf #1580 (dschwoerer)
• Ensure Coordinates is a complete type when trying to swap #1574 (ZedThree)
• Compile with BOUT_FLAGS #1573 (dschwoerer)
• Swap coordinates when adding - to master #1549 (johnomotani)

v4.2.1 (2019-01-23)

Full Changelog

Merged pull requests:

• Fix MAYBE_UNUSED for some compilers #1520 (ZedThree)
• Try to provide some thread safety to msg_stack #1517 (d7919)
• Fix listing available derivative methods #1515 (ZedThree)
• Initialize Coordinates objects in BoutMesh::load() #1509 (johnomotani)
• Use localmesh for d2x and d2y, and interpolate them to location #1496 (johnomotani)
• Hypnotoad fixes #1487 (bendudson)
• Silence remaining warnings on master #1485 (ZedThree)
• Documentation for making releases #1482 (ZedThree)
• Silence gcc warning about unrecognised option Wno-cast-function-type #1480 (ZedThree)
• Fix bugs in boututils.calculus.deriv2D #1479 (bendudson)
• Fix failure of collect() with integer slice argument #1421 (johnomotani)
• Fix setCoefs in InvertPar #1398 (arkabokshi)
• Support BoutOutputs caching option in boutcore *.fromBoutOutputs #1397 (johnomotani)
• Hypnotoad: fix unstable integration method used to calculate zShift #1387 (johnomotani)
• Check for nullptr in NcFormat::get/setAttribute #1374 (johnomotani)
• Set location in LaplaceCyclic::solve() and DC() #1368 (johnomotani)
• Changing README example to use cross rather than ^ #1357 (dschwoerer)

v4.2.0 (2018-10-16)

Full Changelog

Merged pull requests:

• Check TwistShift==true in ShiftedMetric with no changes to Mesh #1323 (johnomotani)
• Derivatives more tidyup #1318 (johnomotani)
• Use std::map::emplace to avoid naming complicated type with insert #1317 (ZedThree)
• Provide getRegion method on Fields #1316 (d7919)
• Throw error messages for non-python collect routines #1312 (ZedThree)
• Rename Mesh::coordinates -> Mesh::getCoordinates; deprecate old name #1310 (ZedThree)
• Vecops consistent cell default add more checking on location #1308 (d7919)
• Include caveats on OpenMP parallelisation in documentation #1307 (ZedThree)
• Bugfixes from shiftedmetric-update #1306 (johnomotani)
• Squash test #1303 (dschwoerer)
• Derivatives bugfixes #1302 (johnomotani)
• Set 'non_uniform' to true by default #1301 (johnomotani)
• Stagger derivatives fixes #1297 (dschwoerer)
• Documentation for marconi #1296 (dschwoerer)
• Use checkData instead of ASSERT(finite()) in test-petsc-laplace #1295 (ZedThree)
• Use input field/vector location for CELL_DEFAULT in vecops #1293 (ZedThree)
• Options with empty strings #1292 (bendudson)
• Change Solver::add to take std::string #1291 (bendudson)
• Add back "user" as a synonym for "shell" PETSc PCTYPE #1289 (ZedThree)
• Add MACRO_FOR_EACH for variadic macros #1285 (bendudson)
• More consistent CELL\_DEFAULT handling #1284 (d7919)
• Remove unused local variable #1282 (ZedThree)
• Add fromBoutOutputs method to boutcore.Field3D #1281 (johnomotani)
• Bugfix for linking boutcore when $ldflags is empty #1280 (johnomotani)
• Add location checking for generated field ops involving Field2Ds #1278 (d7919)
• Pour some sugar on Options #1277 (bendudson)
• Adding OMP parallelisation for loops in rkgeneric solver #1272 (d7919)
• Tidyup coordinates field fix #1271 (d7919)
• Simplifying interchange instability test #1270 (bendudson)
• Don't overwrite local mesh with global one #1269 (d7919)
• Add checks in case Mesh::source is nullptr and try to do sensible things #1268 (d7919)
• Field{2,3}D::applyBoundary(string,string) throw #1265 (bendudson)
• hypnotoad: make dpsi in PF region continuous at separatrix #1264 (johnomotani)
• Less confusing error message #1262 (dschwoerer)
• Support for old install #1261 (dschwoerer)
• Fix return type #1260 (dschwoerer)
• Deprecate Field::getName/setName #1257 (bendudson)
• Fix warnings with default configure #1256 (ZedThree)
• Morecommands #1255 (dschwoerer)
• Cyclic Laplace solve(Field3D) #1253 (bendudson)
• Field2D and Coordinates for boutcore #1251 (johnomotani)
• Respect 'enabled' option in Datafile::add #1250 (johnomotani)
• More omp cyclic laplace #1249 (d7919)
• Fix for h5py bug #1248 (dschwoerer)
• Add -Wall -Wextra to default configure #1246 (ZedThree)
• Monitor frequency fix #1244 (johnomotani)
• DataFile return self from __enter__ #1243 (johnomotani)
• Reduce memory usage of squashoutput #1241 (dschwoerer)
• Faster arakawa with bout for #1239 (d7919)
• More consistent/stringent pre/postconditions on Field* functions #1238 (ZedThree)
• Check int arguments to *ind in collect #1235 (johnomotani)
• Make pow(Field3D, FieldPerp) return FieldPerp #1234 (ZedThree)
• Fix includes for region.hxx #1232 (ZedThree)
• Fix constructors for BoundaryRegion classes #1231 (ZedThree)
• isSet returns false if set via default #1227 (dschwoerer)
• Fix interpolation boundaries #1226 (dschwoerer)
• Summarise test-include test in the end #1225 (dschwoerer)
• Improve comments for Mesh::?GLOBAL #1224 (dschwoerer)
• Add 'Laplace()' operator in boutcore #1223 (johnomotani)
• Add ind perp to region support #1222 (d7919)
• Squashoutput #1220 (dschwoerer)
• Collect: Fix if a list containing zero, one or three elements #1219 (dschwoerer)
• Expose the setCoef* methods of Laplacian in boutcore #1216 (johnomotani)
• Check for None explicitly in collect #1215 (johnomotani)
• Template SpecificInd to allow strong typedef like Ind2D and Ind3D #1214 (d7919)
• Matrix tensor size type #1212 (d7919)
• Add offsetting to Region and Ind2D/Ind3D #1211 (ZedThree)
• Towards stencil deprecation #1210 (d7919)
• New region block loop macro #1209 (ZedThree)
• Stencil small tweak to aid vectorisation #1208 (d7919)
• Manual instructions on Docker image #1207 (bendudson)
• Improved VDDX_U2_stag #1205 (johnomotani)
• Add SUNDIALS_EXTRA_LIBS linker flag #1204 (bendudson)
• Extend Ubuntu installation instructions #1203 (dschwoerer)
• Make Monitor::timestep settable #1202 (johnomotani)
• Search for expressions as whole words when evaluating options #1201 (johnomotani)
• Set coordinates location #1200 (johnomotani)
• Don't use global mesh in BoundaryRegion #1199 (johnomotani)
• Coordinates location #1198 (johnomotani)
• Cython linking #1197 (dschwoerer)
• Speedup travis by removing jobs #1196 (d7919)
• Write attributes to file only once #1195 (johnomotani)
• Block region describe #1194 (d7919)
• Attributes for scalars #1193 (johnomotani)
• MMS fixes #1190 (dschwoerer)
• Escape variable names for expression parsing in BoutOptions/BoutOptionsFile #1188 (johnomotani)
• Fix check for post_processing_function in bout_runners #1185 (ZedThree)
• Manual operator typo #1184 (ZedThree)
• Change 'auto i' to 'const auto &i' in for loops #1182 (johnomotani)
• Expose applyBoundary to boutcore #1180 (dschwoerer)
• Fix documentation #1172 (dschwoerer)
• Various modernise fixes #1171 (ZedThree)
• Codacy tweaks #1169 (d7919)
• Add support for multiple Options #1168 (dschwoerer)
• Avoid throwing a copy of existing exception #1167 (d7919)
• Rethrow exceptions without copying #1165 (d7919)
• Replace shared_ptr<?>(new ?()) with make_shared #1164 (d7919)
• Fix various unused warnings #1159 (ZedThree)
• Modernise MsgStack #1156 (ZedThree)
• More unit tests fields #1155 (d7919)
• More unit tests include files #1154 (d7919)
• More robust tests for Array, plus C++11 idioms #1153 (ZedThree)
• More unit tests expressionparser #1151 (d7919)
• More unit tests msg stack #1150 (d7919)
• More unit tests for optionsreader #1148 (d7919)
• Slepc configure update #1145 (d7919)
• Use Array<BoutReal> in imex-bdf2 #1144 (ZedThree)
• Fix some sign comparison warnings #1143 (ZedThree)
• Remove some unused variables #1142 (ZedThree)
• Fix memory leak in laplacexy #1140 (ZedThree)
• Restore coordinate documentation #1139 (ZedThree)
• Allows rkgeneric to reset for use with SLEPc #1138 (d7919)
• Fix showdata error when plotting 0. #1137 (johnomotani)
• The simple version does not work. #1135 (dschwoerer)
• Extend support for 1D simulation #1130 (dschwoerer)
• Silence Options unit test #1129 (ZedThree)
• Use nullptr everywhere possible in library #1128 (ZedThree)
• Add implementation of 'Naulin' Laplacian solver #1127 (johnomotani)
• Use character overload of string::find_first/last_of #1125 (ZedThree)
• Set result location in Delp2 from incoming field #1124 (AdamD94)
• Bugfixes for non-zero Neumann boundary conditions in tridagMatrix #1122 (johnomotani)
• clang-tidy: avoid copies #1121 (ZedThree)
• Fix deprecated warning in vecops Div #1120 (ZedThree)
• Don't set/delete MMS_err for Vectors #1118 (ZedThree)
• Add monotonic Hermite spline interpolator #1116 (bendudson)
• Fix bug in FCI area integration #1115 (bendudson)
• Guard against double-frees of PETSc objects #1112 (ZedThree)
• Fix wrong function signature in ArkodeSolver #1111 (ZedThree)
• pol_slice tidy and simplify #1110 (ZedThree)
• Simplify some bout_type <-> dimensions tuple handling #1109 (ZedThree)
• Monkey patch old versions of scipy.io.netcdf #1108 (ZedThree)
• Add write method to BoutOptionsFile and update showdata #1107 (johnomotani)
• Additions to Python tools #1106 (johnomotani)
• More SI constants #1105 (dschwoerer)
• Add option for setting the window title in showdata #1104 (johnomotani)
• Python DataFile 64-bit offsets #1103 (bendudson)
• Python numpy #1102 (dschwoerer)
• Take parameter by const-reference in SQ #1101 (ZedThree)
• Fix some memory leaks in multigrid #1100 (ZedThree)
• Zoidberg large grids #1099 (bendudson)
• Monitor tidy #1098 (ZedThree)
• fix D2DXDY: include x boundary #1097 (dschwoerer)
• Sub Libs most likely depend on BOUT++ #1096 (dschwoerer)
• Check field location in solver #1095 (dschwoerer)
• fix isMultiple #1094 (dschwoerer)
• ExpressionParser throw ParseException rather than returning null #1091 (bendudson)
• Fix typo in collect #1089 (johnomotani)
• Fix copy constructor bug #1088 (d7919)
• Evaluate expressions from input files in BoutOptions/BoutOptionsFile #1087 (johnomotani)
• Fix exit status of quiet script #1086 (dschwoerer)
• Remove MPICH from Travis build #1084 (ZedThree)
• rhs counters are reset by Solver #1083 (dschwoerer)
• Improve scripts in bin #1082 (dschwoerer)
• FCI divergence operators #1081 (bendudson)
• Fix various 'import' related issues in python #1080 (ZedThree)
• Allow number of x-boundary points to change in FFT Laplace solvers #1078 (johnomotani)
• Fix order of arguments in call to tridagMatrix in LaplaceSPT #1077 (johnomotani)
• Fix zoidberg with ny=1 #1075 (bendudson)
• Fixes pol_slice by adding np. in appropriate places #1074 (d7919)
• Python numpydocs #1073 (ZedThree)
• Bring back progress spinner and ETA estimate #1072 (ZedThree)
• Remove our own error messages on ImportError #1070 (ZedThree)
• Remove BoutComm::cleanup() call from exception catch in BoutInitialise() #1069 (johnomotani)
• Boutoptionsfile update #1066 (johnomotani)
• Ny interp pol slice #1063 (d7919)
• Workarounds to get boutcore Cython module to work with OpenMPI #1059 (johnomotani)
• Add readme for boutcore tests #1058 (dschwoerer)
• Bugfix for BoutOutputs when not caching open DataFiles #1057 (johnomotani)
• Bracket mms #1055 (dschwoerer)
• Make unit tests less verbose #1052 (dschwoerer)
• Add missing fromFieldAligned() in interp_to() #1051 (johnomotani)
• Cleanup PETSc interface #1050 (ZedThree)
• Fix missing braces in interp_to #1046 (johnomotani)
• Enable formatting of single numbers #1045 (dschwoerer)
• Disable pnetcdf configure by default #1044 (bendudson)
• Save field cell location attributes #1042 (bendudson)
• Deprecate ^ operator as cross product #1041 (dschwoerer)
• D2dy2 bugfix test2 #1040 (dschwoerer)
• Expose forceset #1038 (dschwoerer)
• Fix compiling for petsc 3.9 #1035 (dschwoerer)
• Simlify and extend Function lookup #1034 (dschwoerer)
• Add installation instruction for fedora #1033 (dschwoerer)
• Make Solvers discoverable #1032 (ZedThree)
• Remove header file changes tracking #1031 (dschwoerer)
• netCDF-cxx library needed for Ubuntu #1030 (jenuis)
• Use POSIX-compliant syntax for file redirects #1028 (johnomotani)
• jyseps checking update #1027 (johnomotani)
• Increase the precision of stored BoutReals in Options #1026 (ZedThree)
• jyseps* checking #1025 (johnomotani)
• Fix elm-pb case with compressional effects #1023 (bendudson)
• Throw if options is changed #1021 (dschwoerer)
• Cleanup calculus.py #1020 (dschwoerer)
• Even more manual improvements #1019 (ZedThree)
• Print names first in tests #1016 (dschwoerer)
• += is not supported by dash #1015 (dschwoerer)
• Warn if object files remain after cleaning #1014 (dschwoerer)
• Add explanaiton for test and disable by default #1012 (dschwoerer)
• Remove test-ballooning #1005 (dschwoerer)
• Make sure DataIterator.zp() is not used with negative numbers #1002 (dschwoerer)
• Avoid exception if no implementation found #1000 (dschwoerer)
• Redistribute dmp files #996 (johnomotani)
• Fix multigrid openmp collapse loops #995 (JosephThomasParker)
• Check result location in derivatives #994 (johnomotani)
• Enable configuring for fedoras installed PETSc #993 (dschwoerer)
• Fix test-petsc_laplace_MAST-grid #992 (dschwoerer)
• Fix test-fieldgroupComm #991 (dschwoerer)
• Fix hdf5 test #990 (dschwoerer)
• Slow tests #989 (dschwoerer)
• Prevent issues with parallel documentation build #982 (dschwoerer)
• Improve manual #981 (bendudson)
• Basic version of test requirement scripts #980 (bendudson)
• Prevent shadowing #978 (dschwoerer)
• Suppress multigrid diagnostic output #977 (johnomotani)
• Include fixes #976 (dschwoerer)
• Prefer passing nullptr #975 (dschwoerer)
• Indent make messages more consistently #974 (dschwoerer)
• Update documentation of integer expressions #973 (bendudson)
• Rangeiterator to region in Solver #972 (bendudson)
• Fix test-dataiterator #971 (dschwoerer)
• Prevent issues with parallel clean builds #970 (dschwoerer)
• OpenMP cyclic-reduce solver; add ensureUnique to Matrix,Tensor #969 (bendudson)
• Add DataFile shiftInput option #968 (bendudson)
• Documentation - local build #967 (dschwoerer)
• Backtrace fixes #966 (dschwoerer)
• Correcting documentation #965 (dschwoerer)
• Fix assignment in assert #964 (ZedThree)
• Exception by ref test #963 (dschwoerer)
• Fix order of HDF5 flags #962 (ZedThree)
• Ensure nullptr checks come before dereferences #960 (ZedThree)
• Fix reorder warning in DataIterator ctor #959 (ZedThree)
• Catch all exceptions by reference #958 (ZedThree)
• Cleanup makefiles #955 (dschwoerer)
• Configure faster #954 (dschwoerer)
• Track Headerfile changes for rebuild #953 (dschwoerer)
• Extend differencing type checking slightly to be more rigorous in checking #948 (d7919)
• Various configure fixes and improvements #944 (ZedThree)
• Don't ignore CELL_LOC #942 (dschwoerer)
• Interp to fixes #940 (dschwoerer)
• Add override to region in Fields #939 (d7919)
• Tweak travis script #938 (dschwoerer)
• Speed up Travis and refactor config #936 (d7919)
• Remove copy on write from matrix/tensor #935 (d7919)
• Fieldops region 2d-3d special treatment #934 (d7919)
• Update field2d.cxx #929 (d7919)
• Allow runtime control of maximum size of contiguous block to use in Region #927 (d7919)
• Add performance/arithmetic_3d2d case #926 (d7919)
• More region arguments #920 (johnomotani)
• More unit tests #918 (d7919)
• Remove deprecated code #917 (d7919)
• Extend field perp #916 (d7919)
• Use web service for tracking unit test coverage #915 (ZedThree)
• Fix use of old restarting in slepc solver #911 (ZedThree)
• Update region.hxx #910 (d7919)
• Block region iterator field ops #908 (d7919)
• Build API documentation on Readthedocs #907 (ZedThree)
• Clean comments on removed files #906 (dschwoerer)
• Multigrid bugfixes and test #903 (johnomotani)
• Replace new with array #902 (d7919)
• Remove matrix remainder #901 (d7919)
• Replace matrix with Matrix in various cyclic inversions #900 (d7919)
• Fixes issue in cyclic and adds comments #899 (bendudson)
• Add ASSERT3 checks to Array indexing to check bounds #896 (d7919)
• Ensure Matrix/Tensor data block unique before modification #894 (d7919)
• Replace matrix with Matrix in serial_tri #891 (d7919)
• Manual build #890 (dschwoerer)
• Avoid potentially slow locate #889 (dschwoerer)
• Fix some minor warnings #887 (ZedThree)
• Add OpenMP dataiterator test to unit tests #886 (dschwoerer)
• More region arguments #885 (johnomotani)
• Remove lapack replacement code #884 (bendudson)
• Replace gaussj with direct invert 3x3 #883 (d7919)
• Download googletest on make build-check #882 (dschwoerer)
• Exclude guard cells when checking finite values in field functions #881 (johnomotani)
• Report if Lapack is available in this build #880 (d7919)
• Finish Fieldgroup tests #879 (ZedThree)
• Better matrices/tensors #878 (d7919)
• Has openmp #877 (dschwoerer)
• Extend Region class #875 (d7919)
• Fix two potential bugs: out-of-bounds access and use-after-scope #872 (ZedThree)
• Invalidate guards #871 (d7919)
• Change LaplaceXZ-PETSc to Dirichlet boundary conditions by default. #868 (bshanahan)
• Bug fix for build without checks #867 (d7919)
• Fixes for 2D interpolation (for FCI) #866 (ZedThree)
• Allow checkData to take a region #863 (d7919)
• Create decent stacktrace with PIE code #862 (dschwoerer)
• Pylib dimensions #861 (dschwoerer)
• Improve subdir target #860 (dschwoerer)
• Configure options should be preferred in manual #859 (dschwoerer)
• Replace one more mesh with localmesh #858 (dschwoerer)
• Remove unused variables/lambda from FCI #856 (ZedThree)
• Remove PETSc type string comparisons #855 (bendudson)
• Fix local build of manual PDF #854 (ZedThree)
• Make function match signature in ncxx4 #853 (dschwoerer)
• Localmesh fixes #851 (dschwoerer)
• Improve build of autogenerated text files #848 (dschwoerer)
• Fix missing overrides #847 (d7919)
• Fix prefix operator in RangeIterator header #845 (d7919)
• small cleanup #843 (dschwoerer)
• make performance/arithmetic more reliable #842 (dschwoerer)
• Block region iterating #841 (d7919)
• More region #839 (dschwoerer)
• increase constants accuracy #838 (dschwoerer)
• Update constants.hxx #836 (d7919)
• Performance iterator update #835 (d7919)
• Update array.hxx #832 (d7919)
• Avoid macro name clash in bout++.cxx #831 (d7919)
• Allow specification of number of OMP threads in job launcher #830 (d7919)
• Petsc3.7 compatibility #828 (johnomotani)
• fix sign error in FDDX_U1 #827 (dschwoerer)
• ignore vectorization reports and temporary files #826 (dschwoerer)
• prevent some issues with -Ofast #825 (dschwoerer)
• Dataiterator improvements #824 (dschwoerer)
• Python tools minor upgrades #822 (johnomotani)
• Change default for include_yguards in Laplace inversion to false #821 (johnomotani)
• Remove shifted grids from test-interchange-instability #819 (ZedThree)
• Use Jinja2 to generate code for Field* arithmetic operators #818 (ZedThree)
• Update Travis miniconda setup for speed. #817 (d7919)
• Allow no openmp for pvode #816 (d7919)
• Unify derivative function signatures #815 (dschwoerer)
• remove exit calls #813 (dschwoerer)
• Improve makefile: #812 (dschwoerer)
• Add overload for checkData(BoutReal) #809 (ZedThree)
• Consistently return fields from index derivs functions #808 (ZedThree)
• Set location of fields only if StaggerGrids is enabled #807 (ZedThree)
• make sure units test link against lib pthread #806 (dschwoerer)
• Next remove bindex #804 (JosephThomasParker)
• Fix BoundaryRegion link #803 (d7919)
• Remove old configuration files for specific machines #802 (d7919)
• Minor documentation fixes #800 (d7919)
• Travis update gcc6 to gcc7 #797 (d7919)
• Update makefile to put back removed @ #796 (d7919)
• Bug Fix : Add one level of indirection to stringify #795 (d7919)
• NPES bugfix #794 (loeiten)
• Lots of documentation fixes #793 (ZedThree)
• Next remove bindex #792 (johnomotani)
• Use specialised output object for warnings/errors/info #791 (ZedThree)
• use python3 rather then default python #790 (dschwoerer)
• assert lhs and rhs are on the same location in pow #788 (dschwoerer)
• set and check location in CtoL and LtoC routines #787 (dschwoerer)
• merge ./test_suite and be more verbose to prevent timeouts #786 (dschwoerer)
• Tests verbose on fail #785 (dschwoerer)
• Zoidberg generates grids for tokamaks #782 (bendudson)
• Lazy backtrace #781 (dschwoerer)
• allow to build tests with make build-check #780 (dschwoerer)
• add interface to mesh to ask whether it is possible to transform. #779 (dschwoerer)
• .so support #778 (dschwoerer)
• Default to not building with scorep #777 (ZedThree)
• Some small tests for Field2D/3D #776 (ZedThree)
• Report the value of BOUT_FLAGS used to compile. #774 (d7919)
• Array with shared ptrs #773 (d7919)
• Remove unused mesh routines #772 (d7919)
• Adding support for attributes (NetCDF only) #770 (bendudson)
• Fix off by one error in FFT based DDZ loop #769 (d7919)
• Optimise omp fftw #767 (d7919)
• make sure time derivative are at proper location #766 (dschwoerer)
• Finite volume methods #760 (bendudson)
• Make Field2/3D arthimetic operators return non-const value #756 (ZedThree)
• Fix bug in infinite recursion in configure when netcdf not found #754 (ZedThree)
• disable plotting in test-fci-slab #753 (dschwoerer)
• Global mesh #752 (dschwoerer)
• Adding -l,--log command-line argument #751 (bendudson)
• Adding restart.addvar routine for Python #750 (bendudson)
• Nonuniform single option #740 (bendudson)
• Delete boundary regions in test_vector?d when tearing down test #738 (ZedThree)
• Removing genZMode from initial_profiles.cxx #735 (bendudson)
• allow collect to suceed if not all writes to the files have finished #732 (dschwoerer)
• Avoid unknown omp pragma warnings #726 (d7919)
• Update showdata #725 (AdamD94)
• FFT derivs for staggered meshes seem to be broken for Z #723 (dschwoerer)
• Adding Vector applyboundary(string) #716 (bendudson)
• Cython #641 (dschwoerer)

v4.1.2 (2017-12-01)

Full Changelog

Fixed bugs:

• ./configure deadlock #744
• Typo in unit test makefile? #730
• Laplacian Serial_tri incorrect operation #727
• memory leak in pylib/boututils/showdata #231
• Fix minor typo in unit test makefile #731 (d7919)

Closed issues:

• Test fci-slab #748
• BOUT.log is hardcoded #745
• FFT for DDZ hard coded parameters #647
• genZMode no longer used? #645
• Vector applyBoundary #584

Merged pull requests:

• Bug fix bout runners #758 (loeiten)
• Fix bug in infinite recursion in configure when netcdf not found #754 (ZedThree)
• disable plotting in test-fci-slab #753 (dschwoerer)
• Fixing bug in calculation of non-uniform correction #739 (bendudson)
• Laplacexy examples fix #733 (bendudson)
• Small fixes for serial_tri Laplace solver #729 (bendudson)
• Adding missing __setitem__ and keys() functions #728 (bendudson)
• Manual fix #721 (dschwoerer)

v4.1.1 (2017-10-18)

Full Changelog

Fixed bugs:

• Generalise the "boundaries" section of Delp2 for Field3D #708 (d7919)
• Cleanup array :: cleanup all at end of sim #706 (d7919)
• Ensure VarStr entries are initialised in all cases #705 (d7919)
• Initialise covar for all VarStr instances #704 (d7919)
• Removing Field3D move constructor #699 (bendudson)
• Field3D default move constructor leading to segfaults #698
• Unit test seg fault (Output::cleanup) -- order dependent #693
• test-fci-slab fix: Don't show plot by default #692 (d7919)

Closed issues:

• Integrated tests don't all compile and not all used #701
• PYTHONPATH in tests #695
• Dynamic casts in ConditionalOutput #691
• Segfault when increasing verbosity #690
• v4.1 release candidate #640
• -DCHECK changes memory layout #594
• nx and ny constant for different processors #560
• release notes #504
• y initial conditions always at CELL_YLOW #484
• Free boundaries #429
• Adding TRACE and BoutException to monitors #355
• indexDDZ (staggered) #335
• Reducing compiler warnings #322
• Derivatives: free boundary - Issues if MXG not 2 #250

Merged pull requests:

• Fix broken links, code blocks and tables in documentation #722 (ZedThree)
• Small bug fixes for Options/OptionsReader and their tests #718 (ZedThree)
• Update user manual: --enable-checks is the configure option for checking #717 (JosephThomasParker)
• Make sure link flags apply correctly to unit tests #715 (ZedThree)
• throw exception if staggererd deriv in z direction #714 (dschwoerer)
• Set PYTHONPATH for tests #713 (ZedThree)
• A few small fixes and tests for Output/ConditionalOutput #712 (ZedThree)
• Output message if NetCDF4 support is enabled #711 (ZedThree)
• Make bout_test_main.o depend on source file #710 (ZedThree)
• Make shiftedmetric use const refs when possible #703 (d7919)
• Some fixes to the integrated tests #702 (bendudson)
• Add an option "ddz:fft_filter" to control filtering in DDZ #700 (bendudson)
• Multigrid solver memory leak bugfix #696 (johnomotani)
• Bugfix: Checkout googletest if not available #694 (bendudson)

v4.1.0 (2017-09-20)

Full Changelog

Fixed bugs:

• Boundary non-staggered dirichlet with Field3D #651
• Ensure doneComms always defined in field\_data #618 (d7919)
• Consistency of CHECK usage #569
• Making PhysicsModel's destructor virtual #552 (bendudson)
• Various test fails #551
• Error message is not informative when specifying a non existing directory on command line -d #526
• Communication of vectors gives segfault in BOUT++ 4 #522
• Getters for BoutMesh nx and ny now return ints #497 (JensMadsen)
• Rebuild incomplete #453
• BoutMesh ignores non-available differentiation-options #419
• Calculating Christoffel symbols crashes if MYG=0 #376
• D2DX2_C4_stag is only 2nd order #352
• DataIterator::offset() #278
• No dmp files when appending #199

Closed issues:

• v4.0.1 #676
• Bugfixes available - but not in 4.1.0 #675
• LaplaceXZcyclic::setCoefs is ambiguous #663
• Use of floats in Coordinates::gaussj #656
• Unused source files #653
• Extra boundary files #646
• Building Manual #639
• Options:set() #620
• get/set?array in Field/Field2D #610
• BOUT.log files too noisy #608
• Derivatives - why global mesh? #596
• Laplacian maxmode limits #589
• Separating examples and tests #588
• Trying to avoiding branch misprediction #583
• ASSERT0 in "per element" functions #580
• Collect on Marconi-Fusion #579
• Expanding the capability of TRACE #573
• python2 compatible? #547
• FieldGroup adding const fields #540
• nype is not written to log #539
• Parallel transforms are not documented #503
• getters for nx, ny and nz #498
• MYG and MXG not read from gridfile #493
• Restart files should include MXSUB such that boutdata.collect can read them #483
• Should mergeYupYdown check for ydown_field too? #474
• Increase verbosity of option reader #451
• User defined flush frequency #449
• Restart should be moved from the solvers #439
• RangeIterator created by mesh->iterateBndryLowerY() return wrong indices when nxpe!=0 #435
• laplacexz should exit when g13 \neq 0 #425
• Mesh::getXcomm() #416
• Deprecate functions #405
• v4.0.0-RC branch takes forever to compile #382
• Datafile copy constructor #367
• getName/setName only available for -DTRACK #362
• Monitors rewrite #346
• Compilation of BOUT++ on ARCHER and batch jobs #282
• ShiftInitial compatibility in next #266
• MXG and MYG saved to the restart files #212
• Check that the manuals are building #159
• Testcases #152

Merged pull requests:

• Release 4.1 #688 (ZedThree)
• Update version to 4.0.1 #687 (dschwoerer)
• showdata call cla() for contour plots #686 (bendudson)
• rename runtest that are not tests #685 (dschwoerer)
• Fix for BOUT_ADDPATH_CHECK_LIB and BOUT_ADDPATH_CHECK_HEADER #682 (bendudson)
• Fci slab poloidal grids #681 (bshanahan)
• Quick patch to try to ensure only one processor #680 (d7919)
• Removing files associated with old style unit tests #679 (d7919)
• Remove unused options from configure #678 (d7919)
• Throw in petsc solver if following invalid path. #677 (d7919)
• Documentation #674 (bendudson)
• Convert old-style casts to static_cast #673 (ZedThree)
• Remove header files associated with files removed earlier #672 (d7919)
• Remove lots of commented-out code #671 (ZedThree)
• Remove unused files associated with mesh impls #670 (d7919)
• Add inline to prototypes where inline on implementation #669 (d7919)
• Travis include externals #667 (d7919)
• Travis testing gcc6 #666 (d7919)
• Update petsc-3.4.cxx #665 (d7919)
• V4.1 Intel warnings/remarks fixes #664 (ZedThree)
• Travis tweak parallel build #659 (d7919)
• make install and uninstall targets #658 (bendudson)
• Remove unused files #654 (d7919)
• Remove unused boundary files and small bug fix in Dirichlet non-staggered #652 (d7919)
• Making integrated test suite quiet by default #650 (bendudson)
• Delete free boundary in diffs #649 (d7919)
• Fix various warnings in v4.1-RC #643 (ZedThree)
• Remove deprecated get/setdata from fields #642 (ZedThree)
• Overhaul testing framework #637 (ZedThree)
• Reinstate newline accidentally removed in #615 #636 (d7919)
• SUNDIALS shared libraries #635 (bendudson)
• Operators with dataiterator arg #634 (bendudson)
• Replacing old stencils with DataIterator loops in index_derivs #633 (bendudson)
• Memory tidy #631 (bendudson)
• Add color to output #630 (bendudson)
• Dschwoerer verbosity #629 (bendudson)
• Lapd drift example #628 (bendudson)
• Fixes mapping of profiles in gridgen #627 (bendudson)
• Zoidberg poloidal grids #626 (bendudson)
• Optimise pack_data/unpack_data #622 (d7919)
• Options::cleanCache() #621 (dschwoerer)
• Tidying BoutException #619 (bendudson)
• Adding symmetric keyword to griddata.gridcontourf #617 (bendudson)
• Options logging #615 (bendudson)
• Deprecate get set xyz array #614 (d7919)
• Delete more of the variables allocated with new and related #613 (d7919)
• Field3d shift fix and const auto loops, Field2D/3D consistency #609 (d7919)
• Make finite(Field2D), finite(Field3D) behave identically #607 (ZedThree)
• Warnings squash #606 (bendudson)
• Scorep wrapper #605 (d7919)
• make sure input file is not overwritten #601 (dschwoerer)
• getName always available #599 (dschwoerer)
• add fieldmesh and make derivatives default to fieldmesh #598 (dschwoerer)
• fix typos in bout-config #595 (dschwoerer)
• Laplacian maxmode fix #592 (d7919)
• Replacing modulus operation with ternary #591 (d7919)
• Small optimisations for rfft/irfft #590 (d7919)
• Small typo fix in Zoidberg #586 (bshanahan)
• Improve arakawa performance #585 (d7919)
• fix typo #582 (dschwoerer)
• allow to disable some checks #581 (dschwoerer)
• Fix typo in griddata.gridcontourf plotting routine #578 (bendudson)
• Replacing all \#ifdef CHECK lines with \#if CHECK \> 0 #577 (d7919)
• Updating documentation referring to TRACE/msg_stack #576 (d7919)
• Replace msg_stack with TRACE everywhere #575 (d7919)
• Let trace do formatting #574 (d7919)
• Test subdir new #570 (dschwoerer)
• Next feature user defined flush freq #568 (d7919)
• Adding build-aux to PVODE for make on *BSD #567 (bendudson)
• Freebsd compile fixes #565 (bendudson)
• Adding example of 1D advection with boundaries #564 (bendudson)
• Modify the IDL_PATH suggested by configure #562 (bendudson)
• Changing mesh:symmetricGlobalY to true by default #561 (bendudson)
• print NXPE/NYPE and localNX more clearly #559 (dschwoerer)
• rename examples #558 (dschwoerer)
• FieldGroup catch incorrect types at compile time #557 (bendudson)
• Next merge #556 (dschwoerer)
• Making ExpressionParser::LexInfo chars signed #553 (bendudson)
• add documentation for bout.m4 #549 (dschwoerer)
• cleanup of tools/pylib #548 (dschwoerer)
• Fixes to examples #545 (bendudson)
• Remove deprecated warnings from core library #537 (bendudson)
• Test subdir #536 (dschwoerer)
• Move restart logic from Solver to PhysicsModel #535 (bendudson)
• Target check #532 (dschwoerer)
• make build faster #531 (dschwoerer)
• Hypnotoad: Improving handling of boundaries and X-points #530 (bendudson)
• fix issue with makedir #529 (dschwoerer)
• cleanup test_suite #528 (dschwoerer)
• check data_dir exists #527 (dschwoerer)
• Adding documentation to manual #525 (bendudson)
• add basic test for vector communication #524 (dschwoerer)
• Supplements to bout_3to4.py #519 (loeiten)
• Important bugfix: Read dz from input #517 (bendudson)
• optionparser: only print source if not used #515 (dschwoerer)
• fix for datafile #514 (dschwoerer)
• Added checks for small g13 in LaplaceXZ #513 (bendudson)
• Output settings to file #512 (bendudson)
• Consolidating compressible gas examples #511 (bendudson)
• Allow wider stencil in parallel direction if yup/ydown is not used #510 (dschwoerer)
• Solver adds Mesh variables to restart files #508 (bendudson)
• Changes to PetscOptions in PETSc 3.7 #507 (bendudson)
• Simplify boutmain.hxx for legacy physics models #506 (bendudson)
• Adding boltzman constant to constants.hxx #505 (JensMadsen)
• delete filename in destructor #501 (dschwoerer)
• Removing IS_MYPROC #500 (loeiten)
• Petsc slepsc bug fixes #495 (loeiten)
• MXG and MYG read from grid files #494 (bendudson)
• Next examples tidy #491 (bendudson)
• Added an option to python gridcontourf #490 (bendudson)
• remove using namespace std; #489 (dschwoerer)
• use unique_ptr for dataformat in datafile #487 (dschwoerer)
• Inner outer mesh iterators #486 (dschwoerer)
• Allow no bndry #485 (dschwoerer)
• throw if diffmethod is unknown #481 (dschwoerer)
• MergeYupYdown() also checks status of ydown #480 (bshanahan)
• Support of reading Field2D from gridfiles which have values at ghost points #479 (JensMadsen)
• Adding error recovery to IMEX-BDF2 #476 (bendudson)
• Travis matrix (new) #473 (dschwoerer)
• fix return value of operator= #472 (dschwoerer)
• Catch BoutExceptions as references #470 (ZedThree)
• Fix rare double free with BoutException #469 (ZedThree)
• Alt fix for use with intel compilers without openmp. (more const) #468 (dschwoerer)
• Bug fix py boutdata #467 (ZedThree)
• Bug fixes and improvements for Zoidberg #465 (ZedThree)
• More gridinfo output #460 (JensMadsen)
• clean datafile from mem leaks #456 (dschwoerer)
• ensure target is rebuild if libbout++.a changes #454 (dschwoerer)
• Next multi timestep monitor #364 (dschwoerer)
• signal based user requested exit #343 (dschwoerer)
• User requested exit #321 (d7919)
• A "Z-folder" testing the D2DZ2 operator was added to examples/MMS/diffusion2. #314 (JensMadsen)

v4.0.1 (2017-09-02)

Full Changelog

Fixed bugs:

• Make sure to use c++ compiler with extern c declarations in configure #684 (dschwoerer)
• elm-pb option nogradparj is used without initialisation #571 (bendudson)
• small pyGridGen fixes #566 (HarukiST)
• fix test-initial to allow more precise calculation #555 (dschwoerer)
• fix drift-instability for python3 #554 (dschwoerer)
• Add support for installing bout #550 (dschwoerer)
• Cherry picked fixes to master #546 (ZedThree)
• Bugfix: FieldGroup handles Vectors #533 (dschwoerer)
• Changed ng@ to LocalN@ in the sphinx documentation #523 (loeiten)
• Bugfix bout_runners #521 (loeiten)
• Important bugfix: Read dz from input #518 (bendudson)
• Bout runners fix immutable and documentation #516 (loeiten)
• 2nd derivative staggered diffoperator is only 2nd order #482 (dschwoerer)
• reorder licenses, so github shows the license correctly #475 (dschwoerer)
• Fix small typo in make.config.in #471 (d7919)
• Bug fix for python BoutData #464 (bendudson)

v4.0.0 (2017-02-03)

Full Changelog

Fixed bugs:

• applyBoundary on Fields with background set #430
• Covariant metric tensor is calculated from contravariant metric tensor even if g_ij is given in gridfile #386
• test-initial ignores boundaries #360
• Building next with PETSc #356
• Vector3D DDZ not calculated correctly #123
• Bug fix for genRand in Mixmode field generator #399 (d7919)

Closed issues:

• test-invpar has high tolerance #422
• How to pass BoutReal #402
• Inital conditions test #400
• Merge Policy #395
• Version for BOUT++ 4.0 #383
• Metric tensor components (g_13) in b0xGrad_dot_Grad #377
• PVODE fails to build in next #369
• Enable -DCHECK to get trace doesn't work #353
• Replace all instances of MsgStackItem with TRACE macro #350
• Remove PDB file format #349
• Deprecate FieldXX::{get,set}Data #348
• FieldPerp doesn't have it's own mesh #347
• Final call for PRs for BOUT++ 4.0-RC #344
• double free or corruption #342
• Boundaries: check sufficient points available #305
• field::applyBoundary #300
• test-initial should be rewritten #297
• Boundary modifiers don't pass on time (master and next) #294
• vsprintf should be replaced by vsnprintf #286
• Delete the dirichlet and neuman boundary operators #256
• test-gyro fails with gcc 6.1 #236
• commandline options not recognized should halt program execution #233
• inconsistency in apply{X,Y,Z}diff #170
• Initial conditions test case #110
• Memleak in dump.writeVAR() #45
• output:floats default value #34
• NetCDF file format support #26

Merged pull requests:

• Update next to v4.0.0 #462 (ZedThree)
• Release v4.0.0 #461 (ZedThree)
• fix the dataiterator z-offset for abitrary offsets #457 (dschwoerer)
• exit if the first call to the monitor fails #455 (dschwoerer)
• Sphinx/readthedocs documentation #450 (ZedThree)
• Deprecate background #448 (ZedThree)
• Y derivatives transform toFieldAligned if no yup/down #447 (bendudson)
• Deprecate writeVar #446 (ZedThree)
• Fixes python restart.resizeY to handle Field2D, scalars (v4) #445 (bendudson)
• Remove abandoned diagnos class #442 (ZedThree)
• V4 manual updates #441 (ZedThree)
• Boutdata/restart fix new nz #440 (JensMadsen)
• Cache the value of localN #438 (bendudson)
• Added more diagnostics to CVODE #433 (bendudson)
• Small fix for configure NetCDF #432 (bendudson)
• Stop setting the corner of fields to zero during applyBoundary #431 (ZedThree)
• Doxygen comments #428 (bendudson)
• Dschwoerer issue 402 #427 (bendudson)
• Lovely lovely documentations #423 (ZedThree)
• remove quilt mesh #421 (dschwoerer)
• Doxygen comments #418 (bendudson)
• Remove unsupported quiltmesh implementation #417 (ZedThree)
• Fix several warnings in v4 #415 (ZedThree)
• Fix for multigrid: wrap #include omp.h in #ifdef _OPENMP #414 (ZedThree)
• Short laplace3d dc fix #413 (bshanahan)
• add test-minmax to test suite #410 (dschwoerer)
• use matching flags for ar #408 (dschwoerer)
• make test-initial more strict #407 (dschwoerer)
• set default output format to double #404 (dschwoerer)
• Changing rmatrix and cmatrix to matrix<> #403 (bendudson)
• Documentation and some tidying #398 (bendudson)
• Bug in Div_par fixed. Missing second argument in Grad_par 'metric' w… #397 (JensMadsen)
• More Doxygen documentation #391 (bendudson)
• Doxygen documentation additions #388 (bendudson)
• Doxygened documentation from a previous commit #387 (loeiten)
• Added Div_Par(f, metric) to mms.py. Calculates the parallel divergence. #381 (JensMadsen)
• fixing test staggered grid #379 (dschwoerer)
• small improvement for collect #373 (dschwoerer)
• use msg trace only if available #368 (dschwoerer)
• Next fix vsnprintf #365 (dschwoerer)
• Zoidberg - python grid generator for FCI #361 (ZedThree)
• utils for next #359 (dschwoerer)
• Various fixes and improvements to configure #358 (ZedThree)
• Add 0D ints as vars not attrs #357 (ZedThree)
• Remove support for PDB files #354 (ZedThree)
• Rewrite test-initial #345 (ZedThree)
• More warning fixes #341 (ZedThree)
• Potential bug fix: Ensure result location set #327 (d7919)
• Fix ddz of vector #316 (loeiten)
• include -fno-inline in debug mode #272 (dschwoerer)
• Make sure people notice this bug ... #253 (dschwoerer)
• Fast non-OpenMP DataIterator #186 (dschwoerer)

v3.1 (2016-10-28)

Full Changelog

Fixed bugs:

• Debugging broken after commit 2ba639c99460a9f7272da0959cdcfa948bd65ded #176
• Segmentation fault since 3a0c34be01c94303beb6c403a93e60581a8e3aeb #138
• ./configure can no longer find libfftw3.a #103

Closed issues:

• VDDX_stag broken #324
• Cannot make install on ubuntu 16.04 #308
• mask.hxx:73 - missing return statement (next) #299
• Datafile grow #287
• Failure to open output file is ignored #285
• next is broken with -DCHECK=3 #268
• Error in user_manual. no field twistshift #258
• OpenMPI does not exit reliably if BOUT crashes #255
• All:scale not passed to evolved variables in next #242
• Max/Min returning different values with next compared to master. #241
• Globalny set in boutmesh defaults to ny + 4 #230
• Field3D and Vector3D (probably field2D as well) do not allocate memory when variables defined #220
• BOUT version number #192
• Evaluation of nonlinear brackets #179
• Bug in applyYStencil? #155
• copy of unintialised field fails at run time #145
• Travis says test is successfull, even if it fails #141
• zeroComponent(int) and getData(int) #136
• error on flags: INVERT_AC_IN_GRAD & INVERT_AC_OUT_GRAD #134
• Repeated references in FieldGroup leads to incorrect behaviour when TwistShift=True #129
• Tagged releases #122
• PETSc version #119
• Remove mesh->zlength #114
• Grid generation from geqdsk with NaNs #113
• FieldGenerators error: ‘BoutException’ was not declared in this scope #108
• FCI generate.py should be generalised #101
• "Missing MXSUB variable" error for conduction NetCDF file #100
• Brackets operator [3D,2D] /= -[2D,3D] #94
• MMS-ing auxiliary variables using RK4 solver #84
• Arithmetic support for all variables in BOUT.inp #72
• Clean up __init__.py #68
• CVODE number of preconditioner calls #61
• Differing nrhs with changing processor count #48
• Minor: setLocation twice in spt inversion #41
• ^ exponentation operator in Field3d not working #33
• Exit code if boundary assignment is not succesfull #29
• function evaluation in "global" part of BOUT.inp #28
• Remove ngz-1 #19
• complex number class #17
• Restart file error message #16

Merged pull requests:

• Add macro to silence unused-parameter warning #337 (ZedThree)
• Use miniconda to install python packages in Travis #336 (ZedThree)
• Optimise next shift z #334 (d7919)
• Fix bug in bilinear interpolation #333 (ZedThree)
• improve boutexception #332 (dschwoerer)
• Ensure shiftOutput is set to an initial value #331 (d7919)
• Warnings fix merged #330 (d7919)
• Ensure physics model attached monitor can report state #328 (d7919)
• Check points for boundary #323 (d7919)
• FormatFactory throws exception if format not recognised #320 (bendudson)
• Small fix to mask.hxx #318 (bendudson)
• Bugfix in collect: don't use f.read #317 (ZedThree)
• Small bugfix bout_runners+improved doc of examples #315 (loeiten)
• Updated the user manual field initialisation #313 (bendudson)
• Added checks when reading netcdf files #310 (bendudson)
• Ensure a new line after exception #307 (dschwoerer)
• Ensure a new line after exception #306 (d7919)
• Modifying VDDX operators in index_derivs #303 (bendudson)
• Next gbs mmstest add comms and fix MYG #302 (d7919)
• Passing time through boundary modifiers #301 (d7919)
• Fixing tokamak mms test #298 (d7919)
• Changing yup() and ydown() to nullptr #296 (bendudson)
• datafile: replace returns with throw, if neccessary #295 (dschwoerer)
• Replace vsprintf with vsnprintf #291 (bendudson)
• Adding two new boundary modifiers #290 (d7919)
• replace int in datafile`s add to bool #289 (dschwoerer)
• Ignore boundaries when checking data is finite. #288 (d7919)
• Elm pb fixes #284 (d7919)
• Filter and lowpass fix #283 (d7919)
• missing y-derivative in coordinates.tex section B.5.1 line 5 modified: coordinates.tex #281 (JensMadsen)
• Hard coded MXG in MMS gridfile generator made flexible modified: mms.py #280 (JensMadsen)
• Removing hanging bracket #276 (d7919)
• Next shift output #275 (d7919)
• Next example fixes #273 (ZedThree)
• Next fix check3 #271 (dschwoerer)
• Backtrace for next #270 (dschwoerer)
• Add tool to help with updating files from v3 to v4 #269 (ZedThree)
• Bug fix for IMEX-BDF2 scheme for PETSc < 3.4 #267 (ZedThree)
• Fix numpy FutureWarning about comparison to None in pylib #264 (ZedThree)
• Added implementation of D2DXDY #263 (bendudson)
• Added Include library example in: make_subdir/fuu/fuu.cxx #261 (JensMadsen)
• Fixed erroneous reference to "twistshift[nx]" in section 11 usermanual. #260 (JensMadsen)
• Call MPI_Abort if physics_init returns non-zero exit code. #257 (dschwoerer)
• New test #254 (dschwoerer)
• fixing field.hxx #249 (dschwoerer)
• allocate time deriv in field2d if it is not allocated #248 (dschwoerer)
• Fixing min behaviour in field2d #247 (d7919)
• in case scale or function is not available for field, fallback to all… #246 (dschwoerer)
• ignoring extra point in z so dataiterator test doesn't fail #245 (dschwoerer)
• Adding missing newline to message #244 (d7919)
• fixing min max behaviour in field2d #243 (dschwoerer)
• Update make.config.in to support subdirs #240 (dschwoerer)
• Fixing the DALF3 example #238 (bendudson)
• Fix for Laplacian inversion when IncIntShear=true #237 (bendudson)
• Bout runners chaining #234 (loeiten)
• Add 0D ints as variables instead of attributes #219 (ZedThree)
• BoutMesh throws error if ShiftAngle not found #216 (bendudson)
• Changing non_uniform to default true #210 (bendudson)
• Updated version of multigrid solver. #209 (JosephThomasParker)
• Improved Arakawa bracket evaluation #205 (JosephThomasParker)
• Added neumann_o4 to boundaries #203 (loeiten)
• Bugfix of configure #202 (loeiten)
• Adding bout-sonnet script #201 (bendudson)
• Adding boutdata.data classes #200 (bendudson)
• DataFile throws exception for missing fields #197 (bendudson)
• Renamed ngx,ngy,ngz to LocalN* #194 (bendudson)
• check git revision at compile time #193 (dschwoerer)
• fix field2d #191 (dschwoerer)
• add FieldPerp::operator(int,int) #188 (dschwoerer)
• Fix array.cxx #187 (dschwoerer)
• fix typo in configure.ac #184 (dschwoerer)
• Updating Field2D #183 (bendudson)
• Fix fiedperp #181 (dschwoerer)
• Multigrid solver #178 (JosephThomasParker)
• OpenMP #177 (dschwoerer)
• Adding boundary conditions to LaplaceXY cyclic #174 (bendudson)
• D2DZ2 update #173 (loeiten)
• make travis output more verbose if configure fails #172 (dschwoerer)
• adding MPI flags for travis #171 (dschwoerer)
• PETSc 3.6 #168 (bendudson)
• D Schwoerer's configure improvements #166 (bendudson)
• Changing the way bracket [2d,3d] handels not implemented methods. #165 (dschwoerer)
• Improved reading of contravariant metrics #164 (loeiten)
• Coloring #160 (bendudson)
• Boundary condition laplace xz #158 (loeiten)
• Removing unused ioSupport functions #156 (bendudson)
• fix sign error #154 (dschwoerer)
• Added PETSC_VERSION_GE macro #153 (bendudson)
• Manual update #151 (loeiten)
• fixed/extended some tests #150 (dschwoerer)
• Configure optimize #144 (dschwoerer)
• added sys.exit(1) to test_suite, that failed test are detected by travis #142 (dschwoerer)
• typo in field2d.cxx #137 (dschwoerer)
• fixed missing track in copy constructor #135 (dschwoerer)
• Gridgen fixes #131 (bendudson)
• Unique field group #130 (d7919)
• Fix of conduction example #128 (loeiten)
• added strict flag for collect function #127 (dschwoerer)
• throw exception if given boundray is not found #126 (dschwoerer)
• Imex solver updates #120 (bendudson)
• Changed mesh->zlength to a function #118 (bendudson)
• Added the erf function and a hat function to the FieldFactory class #117 (loeiten)
• Added possibility to read covariant metric tensor from gridfile #116 (loeiten)
• Laplacian solvers #115 (bendudson)
• Clean up init #112 (loeiten)
• Arithmetic support for all options #107 (bendudson)
• Adding calls to run_rhs() to RK4, Euler and RK3-SSP solvers #105 (bendudson)
• Don't use missing CollectError #99 (erikgrinaker)
• Small clean-up #98 (loeiten)
• Added staggered 3rd order WENO scheme #31 (nick-walkden)

v3.0 (2015-09-17)

Full Changelog

Fixed bugs:

• collect when 'variable not found' broken #77
• "with" broken in the new datafile.py #76
• Some options in certain sections cannot be changed from the command #36

Closed issues:

• libhdf5 link failure on OS X #95
• Problems with building PETSc as described in user_manual #90
• configure file present #83
• Possible bug in call to tridagMatrix in serial_tri and cycl_laplace #71
• Arithmetic in input file when variable is specified on command line #62
• Boundaries not properly set when using a function as a boundary argument in BOUT.inp #54
• Laplacian Flags invert_set, invert_rhs implementation #52
• ffmpeg_path specified in showdata.py #47
• Obsolete files? #44
• Mesh::get fails if field is unallocated #43
• BoutInitialise failure #39
• Obsolete communicator in reference.pdf #32
• HDF5 file support #27
• Z domain size in input file, and non-FFT 3D fields #22

Merged pull requests:

• Commenting laplacian #97 (loeiten)
• Fix for libhdf path #96 (dschwoerer)
• Remove stray .svn/ directories #93 (erikgrinaker)
• Clean up and improve .gitignore #92 (erikgrinaker)
• Travis CI #86 (ZedThree)
• configure searches for libraries in lib64 and lib directories #85 (dschwoerer)
• DataFile raises exception not return None #82 (bendudson)
• README updates #81 (peternaylor)
• Basic vagrant config #80 (kevinpetersavage)
• Manual #79 (loeiten)
• Fixed tridagMatrix calls #78 (loeiten)
• Bout runners #75 (loeiten)
• IMEX-BDF2 and SNES time solvers #74 (bendudson)
• Adding HDF5 support #73 (bendudson)
• Added comments in the laplace solvers #70 (loeiten)
• Help message fix #69 (d7919)
• Python3 compatible #65 (loeiten)
• Add staggered field support to initial_profile #63 (johnomotani)
• Topology manual update #59 (nick-walkden)
• Enable C1 and C2 coefficients in Laplacian solvers #57 (johnomotani)
• Redistribute restarts #55 (johnomotani)
• Laplace invert set fix #53 (johnomotani)
• Implementation of ARKode solver #51 (nick-walkden)
• Output initial state when restarting #49 (johnomotani)
• Help message #38 (ZedThree)
• Fixed optimizer flag for debugging #30 (loeiten)
• Updated version of python tools #23 (brey)

v2.1 (2014-09-10)

Full Changelog

Merged pull requests:

• Bad behaviour fix for FieldGroup operator overload #11 (d7919)
• Adding + and += operators to FieldGroup class to allow FieldGroups to be... #10 (d7919)
• Introduce the python post processing routines and some scripts for analysis in elm-pb folder #9 (brey)
• Update import_data_netcdf.m #8 (sanatkrtiwari86)
• Inner radial bndry #7 (lukeeasy)
• Python modules for BOUT++ pre-processing #4 (brey)
• Timestep monitor #3 (bendudson)
• Improved python showdata routine to allow animation of multiple plots si... #2 (lukeeasy)

v2.0 (2013-09-23)

Full Changelog

v1.0 (2011-08-26)

* This Changelog was automatically generated by github_changelog_generator