AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models

Breaking changes

• Changed the default steady-state method to integrationOnly (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2574)

  The default mode for computing steady states and sensitivities at steady state was changed to integrationOnly (from previously integrateIfNewtonFails).

  This was done for a more robust default behavior. For example, the evaluation in https://doi.org/10.1371/journal.pone.0312148 shows that - at least for some models - Newton's method may easily lead to physically impossible solutions.

  To keep the previous behavior, use:

  amici_model.setSteadyStateComputationMode(amici.SteadyStateComputationMode.integrateIfNewtonFails)
  amici_model.setSteadyStateSensitivityMode(amici.SteadyStateSensitivityMode.integrateIfNewtonFails)
  

Fixes

• PEtab import: Fixed potentially incorrect sensitivities with observable/state-dependent sigmas. This was fixed for all cases amici can handle, others cases will now result in ValueErrors (https://github.com/AMICI-dev/AMICI/pull/2563).

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2562

• Fixed potentially incorrect disabling of Newton's method

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2576

• Fixed ModelStateDerived copy ctor, where previously dangling pointers could lead to crashes in some situations

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2583

• Added missing simulation status codes

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2560

• Check for unsupported observable IDs in sigma expressions

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2563

Features

• Optional warning in fill_in_parameters

  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2578

Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.27.0...v0.28.0