Issues

• Nightly parity: regressions detected

  lanl/bngsim#1153 · Filter by author github-actions opened on Oct 20, 2026
  1

• Bend roots restart CVODE at crossings where their guarded if() branch is off (half of #1089's guard crossings do no work)

  performance
  lanl/bngsim#1147 · Filter by author wshlavacek opened on Oct 19, 2026

• A pulse written with the % operator gets no stop and no root, so it is stepped over: Y = 0 for 3.9347, with no error (the mod() spelling is caught)

  bugcorrectness concernfamily: expression semantics
  lanl/bngsim#1127 · Filter by author wshlavacek opened on Oct 19, 2026

• A sensitivity run on a min()/max()/abs() pulse over state is on the difference quotient: the clock-rate column is off by up to 6x and does not converge (Y and dY/dkx are right)

  bugcorrectness concernfamily: sensitivity terms
  lanl/bngsim#1126 · Filter by author wshlavacek opened on Oct 19, 2026

• Leftovers from clearing the variable-volume family (#787): 3 edge-case wrong answers, 4 slow paths, 3 over-refusals

  correctness concernfamily: variable volumesperformancetracking
  lanl/bngsim#1124 · Filter by author wshlavacek opened on Oct 19, 2026
  3

• nightly: re-baseline rr_ode and amici_sens on the full BioModels corpus (follow-up to #807)

  enhancement
  lanl/bngsim#1098 · Filter by author wshlavacek opened on Oct 18, 2026

• SBML loader registers a condition twice when it is reached through a function definition with a call argument such as time(): (time()) vs time() (harmless extra roots)

  enhancementlow priority
  lanl/bngsim#1082 · Filter by author wshlavacek opened on Oct 18, 2026

• Lift NFsim's refusal of compartment models once its compartment defects are fixed upstream and vendored

  gated
  lanl/bngsim#1067 · Filter by author wshlavacek opened on Oct 16, 2026

• The restart test for a state-switch root is not scale-invariant: if(Sobs*H<H,1,-1) steps differently and logs CVodeGetDky errors once H > ~3.5e21

  bug
  lanl/bngsim#1064 · Filter by author wshlavacek opened on Oct 16, 2026

• rm: run a model that reads the clock on elapsed time with time() offset by t_start, so a late start keeps its waiting times (#1059)

  bugcorrectness concernfamily: SSA exactness
  lanl/bngsim#1063 · Filter by author wshlavacek opened on Oct 16, 2026

• Lift NFsim's refusal of local functions that read an observable outside their argument once RuleWorld/nfsim#104 is fixed and vendored

  gated
  lanl/bngsim#1062 · Filter by author wshlavacek opened on Oct 15, 2026

• NFsim: a set_param on a compartment-size parameter never reaches the model (gated on BioNetGen and NFsim fixes)

  gated
  lanl/bngsim#1061 · Filter by author wshlavacek opened on Oct 15, 2026

• SSA, and rm on a model that reads the clock, lose waiting times to rounding at a large absolute t_start (z = -287 at 1e12, silent)

  bugcorrectness concernfamily: SSA exactness
  lanl/bngsim#1059 · Filter by author wshlavacek opened on Oct 15, 2026
  1

• Lift method='rm''s refusal of Arrhenius rules RuleMonkey misreads, once richardposner/RuleMonkey#109 is fixed and vendored

  gated
  lanl/bngsim#1058 · Filter by author wshlavacek opened on Oct 15, 2026

• Lift NFsim's refusal of Arrhenius rate laws once RuleWorld/nfsim#102 is fixed and vendored

  gated
  lanl/bngsim#1057 · Filter by author wshlavacek opened on Oct 15, 2026

• The #945 refusal holds at the tolerance its test pins and not around it: a state switch 2e-5 after an event returns dW/dtau = -1.05 for -3.15 at rtol 5e-7 to 2e-6, with no error

  bugcorrectness concernfamily: sensitivity terms
  lanl/bngsim#1025 · Filter by author wshlavacek opened on Oct 12, 2026

• Read a rate law on a far-offset line tread by tread, so that what #1015 refuses or leaves without stops gets them

  correctness concernenhancement
  lanl/bngsim#1018 · Filter by author wshlavacek opened on Oct 12, 2026
  1

• The differenced state Jacobian steps every species by 1.5e-8 of the largest concentration: dY_ss/dp with jacobian="fd" is 7% off beside an unrelated species at 1e7 and 44% at 1e8, with no error

  bugcorrectness concernfamily: steady state
  lanl/bngsim#1002 · Filter by author wshlavacek opened on Oct 9, 2026
  2

• steady_state() accepts a state by an absolute residual: a model in small units, or a slow one, is returned far from its steady state with converged=True (x = 0.89 for 1 at 1e-9; BIOMD0000000407 one step from where it starts)

  bugcorrectness concernfamily: steady statehigh priority
  lanl/bngsim#1001 · Filter by author wshlavacek opened on Oct 9, 2026
  1

• An ODE run with a stop on every wrap of a remainder of a far clock stops adding to X after about 72 stops, with no error (100*mod(1e12 + time(), 0.125): 0.72 of the integral over 100 periods)

  bugcorrectness concern
  lanl/bngsim#998 · Filter by author wshlavacek opened on Oct 9, 2026
  1

• Tracking: forward-sensitivity runs that are refused where a derivative exists (refusals to lift)

  enhancementfamily: sensitivity termstracking
  lanl/bngsim#961 · Filter by author wshlavacek opened on Oct 1, 2026
  2

• Process: fix review findings in the PR, and refuse forward sensitivities outside a supported envelope

  tracking
  lanl/bngsim#960 · Filter by author wshlavacek opened on Oct 1, 2026

• Events on time >= tau and time > tau fire as one batch or in sequence depending on the rounding of tau (X ends at 0.50 or 0.15)

  bugcorrectness concernfamily: ODE events
  lanl/bngsim#947 · Filter by author wshlavacek opened on Oct 1, 2026
  1

• differentiable_solve repeats structure-only work every call since routing through Simulator (up to 6x on a 300-species primal)

  enhancementperformance
  lanl/bngsim#919 · Filter by author wshlavacek opened on Sep 30, 2026

• A state window a restart would catch is still stepped over when #903's restart test calls the crossing unresolved (16-point sampling, 10·√N band)

  bugcorrectness concern
  lanl/bngsim#907 · Filter by author wshlavacek opened on Sep 30, 2026