Issues

• PySB import with named sigma expression fails: duplicate SigmaY

  PySB
  Bug

  AMICI-dev/AMICI#3538 · Filter by author dweindl opened on Nov 13, 2026
  

• AmiVectorArray: assigning to an element leaves a dangling N_Vector pointer

  Bug

  AMICI-dev/AMICI#3534 · Filter by author dweindl opened on Nov 13, 2026

• amici.sim.sundials logger is set to DEBUG on import, so CVODES messages are printed on stderr by default

  AMICI-dev/AMICI#3517 · Filter by author matthiaskoenig opened on Nov 4, 2026

• SBML import: an event trigger with a negated comparison, !(X <= 3), fails to import

  AMICI-dev/AMICI#3516 · Filter by author matthiaskoenig opened on Nov 4, 2026
  

• A piecewise condition exactly at its threshold at t0 keeps its initial value for the whole simulation

  c++eventspiecewise
  Bug

  AMICI-dev/AMICI#3515 · Filter by author matthiaskoenig opened on Nov 4, 2026
  1

  

• Explicit trigger times are rounded to about 8 significant digits: sp.solve rationalizes floats

  AMICI-dev/AMICI#3514 · Filter by author matthiaskoenig opened on Nov 4, 2026

• Output timepoint within rounding of the previous timepoint or of an event time is NaN, with status AMICI_SUCCESS

  AMICI-dev/AMICI#3513 · Filter by author matthiaskoenig opened on Nov 4, 2026

• A root function that is 0 at t0 for a whole simulation stays inactive in the next simulation with the same solver: a crossing in its first step is missed

  c++events
  Bug

  AMICI-dev/AMICI#3512 · Filter by author matthiaskoenig opened on Nov 4, 2026
  

• DoubleVector[i] and IntVector[i] raise a TypeError after import amici: libsbml is loaded before the extension and its SWIG types win

  AMICI-dev/AMICI#3511 · Filter by author matthiaskoenig opened on Nov 4, 2026
  

• stdVec2ndarray segfaults: the SWIG wrapper releases the GIL around a function which creates a numpy array

  AMICI-dev/AMICI#3509 · Filter by author matthiaskoenig opened on Nov 4, 2026
  

• Strict event triggers (>, <) are true when both sides are equal: lost or spurious events at t0, output at the trigger time after the event

  AMICI-dev/AMICI#3508 · Filter by author matthiaskoenig opened on Nov 4, 2026
  1

• Feature request: continue a simulation from a custom t0 and state with the trigger states of the previous run

  AMICI-dev/AMICI#3507 · Filter by author matthiaskoenig opened on Nov 4, 2026

• SBML import: a parameter whose initial assignment reads an event-assigned parameter follows it after the event

  AMICI-dev/AMICI#3506 · Filter by author matthiaskoenig opened on Nov 4, 2026
  

• Model build fails with "Required command 'ninja' not found" when the environment is not activated, although cmake and ninja are installed in it

  AMICI-dev/AMICI#3505 · Filter by author matthiaskoenig opened on Nov 4, 2026

• SBML import: model with rateOf in an initial assignment fails to compile ('A_' was not declared in this scope in x0.cpp)

  SBML
  Bug

  AMICI-dev/AMICI#3504 · Filter by author matthiaskoenig opened on Nov 4, 2026
  1

  

• 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

• 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