Issues

• Chen_MSB2009: the reference log-likelihood of the benchmark test is stale

  AMICI-dev/AMICI#3503 · Filter by author matthiaskoenig opened on Nov 2, 2026

• PEtab v2: check for timepoint-specific overrides in ExperimentManager.apply_parameters never fires

  Bug

  AMICI-dev/AMICI#3476 · Filter by author dweindl opened on Oct 24, 2026

• Data race on skipThrough in run_simulations

  Bug

  AMICI-dev/AMICI#3475 · Filter by author dweindl opened on Oct 24, 2026

• ExpData.__repr__ misreports state reinitialization

  Bug

  AMICI-dev/AMICI#3474 · Filter by author dweindl opened on Oct 24, 2026

• ExpData(model) ignores Model.t0()

  Bug

  AMICI-dev/AMICI#3473 · Filter by author dweindl opened on Oct 24, 2026

• ReturnDataView.by_id fails for x0, x_ss and sllh

  Bug

  AMICI-dev/AMICI#3472 · Filter by author dweindl opened on Oct 24, 2026

• DAE: sensitivity error control is disabled after the first event with forward sensitivities

  Bug

  AMICI-dev/AMICI#3464 · Filter by author dweindl opened on Oct 24, 2026

• DAE: adjoint steady-state sensitivities by simulation fail

  adjointDAEsteady state
  Bug

  AMICI-dev/AMICI#3461 · Filter by author dweindl opened on Oct 24, 2026

• ExpData(model) drops the model's state reinitialization at the start of presimulation

  steady state
  Bug

  AMICI-dev/AMICI#3458 · Filter by author dweindl opened on Oct 24, 2026
  

• Switch reverted and event executed spuriously right after a root, depending on output timepoints

  eventspiecewise
  Bug

  AMICI-dev/AMICI#3444 · Filter by author dweindl opened on Oct 23, 2026
  

• Event at the last output timepoint executes all other events; post-equilibration with event outputs crashes

  event observableseventssteady state
  Bug

  AMICI-dev/AMICI#3438 · Filter by author dweindl opened on Oct 22, 2026

• DAE: wrong sensitivities if an event reads an algebraic state that an earlier event at the same time changed

  adjointDAEevents
  Bug

  AMICI-dev/AMICI#3437 · Filter by author dweindl opened on Oct 21, 2026
  

• JAX: Heaviside variables flipped by event assignments are not updated

  eventsJAXpiecewise
  Bug

  AMICI-dev/AMICI#3435 · Filter by author dweindl opened on Oct 21, 2026

• Wrong piecewise branch after an event moves the state back across a switch that crossed at the same time

  eventspiecewise
  Bug

  AMICI-dev/AMICI#3425 · Filter by author dweindl opened on Oct 19, 2026
  1

  

• Splines in event assignments don't compile

  code generationevents
  Bug

  AMICI-dev/AMICI#3424 · Filter by author dweindl opened on Oct 19, 2026
  

• Event output sensitivities are zero for events triggered by event assignments

  event observablesevents
  Bug

  AMICI-dev/AMICI#3422 · Filter by author dweindl opened on Oct 19, 2026
  

• Wrong adjoint sensitivities if an event moves the state back across a piecewise switch

  adjointeventspiecewise
  Bug

  AMICI-dev/AMICI#3415 · Filter by author dweindl opened on Oct 15, 2026

• Adjoint sensitivities with event outputs and pre-simulation crash; pre-equilibration adds event likelihood derivatives twice

  adjointevent observablesevents
  Bug

  AMICI-dev/AMICI#3413 · Filter by author dweindl opened on Oct 15, 2026
  1

• DAE event handling: Heaviside flipped back after events, adjoint sensitivities ignore event outputs of algebraic states, IDAGetQuadB failure

  adjointDAEevents
  Bug

  AMICI-dev/AMICI#3411 · Filter by author dweindl opened on Oct 15, 2026

• JAX: piecewise switch not updated when an event assignment moves its trigger across the current time

  eventsJAXpiecewise
  AMICI-dev/AMICI#3410 · Filter by author FFroehlich opened on Oct 15, 2026

• Introduce static expressions (ws) as a first-class model quantity to simplify SBML entity classification

  SBML
  AMICI-dev/AMICI#3409 · Filter by author dweindl opened on Oct 15, 2026
  

• Store non-integer stoichiometry attributes as exact rationals

  conservation lawspythonSBML
  AMICI-dev/AMICI#3402 · Filter by author dweindl opened on Oct 15, 2026

• Enable conservation laws for non-constant species by default

  conservation lawspythonSBML
  AMICI-dev/AMICI#3401 · Filter by author dweindl opened on Oct 15, 2026

• Remove or deprecate the De Martino algorithm for conservation law detection

  conservation lawsmaintenancepythonSBML
  AMICI-dev/AMICI#3400 · Filter by author dweindl opened on Oct 15, 2026
  

• Wrong forward sensitivities of event outputs

  event observablesevents
  Bug

  AMICI-dev/AMICI#3361 · Filter by author dweindl opened on Oct 14, 2026
  1