AMICI v0.34.0

The amici 0.34.0 release contains a number of bug fixes and new features.

Note that this will probably be the last release to include the MATLAB interface.

Fixes

• Breaking changes Events are now also handled during pre-equilibration, presimulation, and post-equilibration.
  This may be a breaking change, as it may lead to different results for models with events that may trigger during these periods. This change is considered a bugfix, as it was not intended to ignore events during these periods.
  (by @dweindl in #2777, #2780, #2859, #2881, #2889, #2920, #2921, #2925)
• Fixed various issues related to adjoint sensitivity analysis for models with events.
  While many cases are now supported, it is still highly recommended to check the ASA results for models with events against forward sensitivities or finite differences.
  • Adjoint sensitivities for Python-imported models with events (by @paulstapor & @dweindl in #1539)
  • Fix Model::addAdjointQuadratureEventUpdate (by @dweindl in #2787)
  • Fix indexing errors for adjoint quadratures during event updates (by @dweindl in #2796)
  • Fix deltaxB dimensions (by @dweindl in #2803)
  • Fix (some) ASA event handling (by @dweindl in #2797)
• Fixed a number of issues related to the handling of events or discontinuities in general:
  • Fixed import of DAE models with events (by @dweindl in #2897)
  • Fixed root functions for events with initialValue=trigger=false (by @dweindl in #2910)
  • Fixed check for sign change, fix Heaviside update (by @dweindl in #2927)
• Fixed sign of residuals (by @dweindl in #2896)
• Updated the steady state notebook to match the current implementation (by @plakrisenko & @dweindl in #2891)
• Improved sigma<=0 error reporting (by @FFroehlich in #2829)
• Fixed sensitivities for the total abundances of conservation laws (only relevant if AMICI_EXPERIMENTAL_SBML_NONCONST_CLS is enabled) (by @dweindl in #2782)
• Fix sensitivities w.r.t. unused log-scaled NaN parameters (by @dweindl in #2903)

Features

• AMICI should now be pip-installable without pre-installing SWIG or BLAS (by @dweindl in #2774, #2772)
• Event/discontinuity handling for JAX models
  • Track discontinuities in JAX & fix gradient for models with parameter dependent roots (by @FFroehlich in #2815)
  • Improve JAX event integration (by @FFroehlich in #2841)
  • mask event functions in jax (by @FFroehlich in #2863)
• Handle state-independent, parameter-dependent event triggers without root-finding (by @dweindl in #2913)
• Presimulation is now also supported in combination with adjoint sensitivities (by @dweindl in #2786)
• It is now possible to set a separate $t_0$ for pre-equilibration and main simulation (by @dweindl in #2793)
• Sensitivity analysis for AlgebraicRule / DAE models is now also supported for Python-imported models
  (by @dweindl in #2101)
• An optional random generator seed can now be passed to ExpData::ExpData(ReturnData const&, ...) when generating synthetic measurements (by @dweindl in #2802)
• Added ReturnData::plist (by @dweindl in #2874)

... and extended tests, documentation, and many changes under the hood.

Full Changelog: v0.33.0...v0.34.0