chore(main): release 0.0.6

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🤖 I have created a release beep boop

0.0.6 (2025-12-27)

Features

• raw output type added to output device array copies with no processing (22cef9f)
• add time logging to cellml import (#257) (6a220f8)
• Additional summary output metrics added (#212) (daccbae)
• Buffer indexing, sizing, and locating now consolidated into a BufferSettings object (480df1a)
• Buffer memory locations on GPU now user-selectable (between local and shared) (480df1a)
• build_grid() surfaced to user API (#338) (45cfa90)
• CellML to Cubie adapter layer added (#221) (b8f448e)
• CUDAFactory.update() now updates nested dicts and attrs classes (480df1a)
• device buffers are now togglable (local, shared, local persistent) and managed centrally by buffer_registry (39107a9)
• Global stores now have cache write-through hints, closes #291 (480df1a)
• load_from_cellml updated to parse complicated models (#238) (50341f6)
• newton and linear solvers now fully-functional CUDAFactory subclasses (39107a9)
• optional configuration parameters are no longer explicit in inits, they are filtered and collected in kwargs (39107a9)
• py39 compatibility removed due to a Numba update. (480df1a)
• Solver API now skips extra memory and grid-building work when possible (#324) (5f225a0)
• summary metrics combined (eg. extrema, [mean, std, rms]) to reduce buffer space (daccbae)
• summary metrics now respect numerical precision (daccbae)
• Sympy inputs from CellML now go Sympy->Sympy instead of through strings (#259) (23e201d)
• time logging added to parsing, codegen, and CUDA compilation (#256) (5d8f75b)
• Trajectories with errors (nonzero status codes) now return NaNs in solveresult (#333) (6068ebc)
• update() methods now unpack settings dicts provided to them (#332) (f016e4d)
• Warp-friendly FSAL caching implented, redundant accumulation removed (#211) (96a9dd0)

Bug Fixes

• _ensure_context() method added to avoid segfaults in CI (#265) (60acecc)
• shift value in standard deviation calcs now updates after each save. (073d406)
• Adaptive step controllers now sum errors correctly, closes #302 (480df1a)
• add set_stride_order method for access from solver (e4b80d3)
• All algorithms now exit when the next save time is > end time (480df1a)
• buffer aliasing logic now child-location-agnostic (377ad10)
• Compile-timing kernels now use device arrays (16bf1d6)
• consolidate timing parameter sets for fewer fixture builds (#350) (4698e9e)
• contiguous arrays now marked as such for the compiler to do its grim work (#276) (fe97291)
• Controller-algorithm compatibility enforced (4ab0230)
• correct FIRK algorithm implementation (#408) (39107a9)
• correct fsal warp-vote implementation (60448f1)
• Counters array added to ERK signature (99db833)
• CUDA-breaking simsafe 'local' module adapter removed (d205979)
• CUDAFactories now only precompile if timelogging is on (836da2a)
• dead code and duplications pruned from codegenned device functions (#266) (de0dda8)
• default precision types have been removed from all but entry points (39107a9)
• fast path through batchgridbuilder for arrays provided verbatim added (080ab66)
• FIRK no longer does an extra f(x) calculation after performing its nonlinear solve (39107a9)
• Fixed steppers now use a slower but more sensible save time incrementing technique (480df1a)
• FSAL warp test now doesn't break everything (2e68692)
• gustafsson controller prev error ratio flipped, various test edits for GPU runs (3e04438)
• host arrays now pinned to facilitate asynchronous transfers (480df1a)
• infinite loops in adaptive steppers under dummy compile now finite (b0547fd)
• lineinfo toggle for CUDA compilation now conditional on CUDASIM status (#280) (6d5bf57)
• Loop iterators now 32-bit (480df1a)
• loops now accumulate time in f64, no longer get stuck when dt < 1e-7 * time (#281) (480df1a), closes #272
• make shape validator np.int compatible in BaseArrayManager.py (e77d800)
• make stage_increment buffer persistent in rosenbrock (#411) (4b0b6bc)
• Missing iteration_counters type added to device signature in BatchSolverKernel (6eefd67)
• move stream sync function to after chunked queue (e4b80d3)
• n_saves calculation now includes start time, closes #282 (480df1a)
• numeric literals now wrapped with precision() or int32 in CUDA code generation (#258) (21850f2)
• partially update cuda signatures with contiguity (8754661)
• reduced nonlinear solver memory footprint (3n → 2n buffers) (#224) (c4d95d4)
• Remaining hard-coded buffers now managed by buffer_registry (#412) (92e9313)
• remove redundant overwrite of initial values host array until #76 is implemented in device code (bc39fbb)
• Replace PEP 604 union syntax with Union[] for Python 3.8 compatibility (#236) (ea1e1fb)
• shared and local memory requirement names now consistent across package. (39107a9)
• size-1 runs no longer break Cubie (closes #142) (39107a9)
• steps now own solvers, and newton_krylov solver now owns it's internal krylov solver (39107a9)
• Tableau-driven algorithm loop indexing reorganised to give the compiler an easier job (480df1a)
• tsit5 tableau corrected (480df1a)
• types corrected in all step algorithms and solvers to run in 'precision' only (39107a9)
• update all-in-one rosenbrock function to use updated prod format (fa32a16)
• update placeholder parameters to not hide exception (8754661)
• updating a solverkernel with new outputtypes now correctly changes buffer and output array sizes. (39107a9)
• Use a warp-vote for FSAL caching, otherwise there is no benefit and potential divergence (d0334a2)
• Vern7 tableau corrected to match source (e6b900a)

Performance Improvements

• DIRK function profiled and streamlined (#355) (fd1f639)
• firk rewirked for a large speedup (39107a9)
• newton and linear solver branching and predication removed for a reasonable speedup (39107a9)
• rosenbrock function reworked for a moderate speedup (39107a9)

Documentation

• cubie_internal_structure.md filled with agent reference (#177) (02738e0)

Miscellaneous Chores

• Release 0.0.6 (baa2523)

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🤖 Created releases:

• v0.0.6

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