AMICI v0.23.0

Features

• SBML InitialAssignment are no longer absorbed into other model expressions, but are available as parameters or expressions (w) in the amici model
  by @dweindl in #2304, #2305, #2345, #2359

• Upgraded to SuiteSparse 7.6
  by @dweindl in #2316

• Model expressions w are now split into static and dynamic expressions, and only evaluated as needed
  by @dweindl in #2303

• Exposed additional solver settings:

  • Solver.setMaxConvFails(): maximum number of non-linear solver convergence failures
  • Solver.setMaxNonlinIters(): maximum number of non-linear solver iterations
  • Solver.setMaxStepSize(): maximum step size
  • Solver.setConstraints(): for setting (non)negativity/positivity constraints on state variables

  by @dweindl in #2335, #2360, #2340

• Improved output for debugging simulation failures:
  ReturnData.{xdot,J} now contain the respective values from the timepoint of failure, not the last output timepoint. NaN/Inf warnings now always include the timepoint at which the issue occurred. Note that C++ stacktraces are now only logged for debug builds.
  by @dweindl in #2349, #2347, #2366

• Updated dataframes import/export to include parameter values and scales
  by @FFroehlich in #2351

Fixes

• CMake: Updated BLAS detection and some minor fixes
  by @dweindl in #2318 and #2357
• Deterministic ordering of source files in generated CMakeLists.txt
  by @dweindl in #2322
• Fixed size check in Model::setStateIsNonNegative
  by @dweindl in #2332
• Fixed uncaught C++ exception in runAmiciSimulation that may crash Python in case of invalid values for standard deviations
  by @dweindl in #2338
• Fixed missing import in amici/petab/petab_import.py
  by @plakrisenko in #2342
• Fixed ReturnDataView AttributeError: messages
  by @dweindl in #2341
• Added a missing return code constant LSETUP_FAIL
  by @dweindl in #2353
• Fixed in-place building of model wheels
  by @dweindl in #2352
• Made is-zero-checks compatible with the upcoming sympy>1.12
  by @dweindl in #2350
• Fixed issues with paths containing blanks for sundials
  by @dweindl in #2361
• Added amici.petab.conditions to the API documentation
  by @PaulJonasJost in #2364
• Improved type annotations in swig-wrappers
  by @dweindl in #2344, #2365

Full Changelog: v0.22.0...v0.23.0