Issues

• Nightly sanitizers: reports detected

  lanl/bngsim#1429 · Filter by author github-actions opened on Oct 31, 2026

• Leftovers from the #1353 review: a commuting pair on one instant is refused, and a dropped fire is not asked

  lanl/bngsim#1425 · Filter by author wshlavacek opened on Oct 31, 2026

• The interpreter reads a bracket after a call as a second statement: k*exp(-A)(B) is B, and k*exp(-A) is dropped without a word

  lanl/bngsim#1415 · Filter by author elyfmiller opened on Oct 30, 2026

• SUNDIALS: drop the #1301 carry once LLNL/sundials#1073 is merged and the pin moves past it

  gated
  lanl/bngsim#1410 · Filter by author wshlavacek opened on Oct 30, 2026

• cBNGL writer: the assignment-rule species refusal is right, but its reason is wrong (the rule IS carried; only the species' column freezes)

  lanl/bngsim#1400 · Filter by author wshlavacek opened on Oct 29, 2026

• A state-switch hold keeps CVODE's error log muted for the rest of a run that has a crossing stop

  lanl/bngsim#1389 · Filter by author Montana opened on Oct 29, 2026

• amici_sens nightly: BIOMD0000000457 compiles twice on some nights, tripping the wall alert

  testing
  lanl/bngsim#1386 · Filter by author wshlavacek opened on Oct 29, 2026

• SSA reports the wrong concentration after an event resizes a compartment: Result.species divides by the load-time size (exactly 2x after c: 2 -> 4)

  bugcorrectness concernfamily: variable volumes
  lanl/bngsim#1368 · Filter by author wshlavacek opened on Oct 28, 2026

• Evaluate from_bngl dropping post-generate_network actions: 14 of 103 benchmark BNGL models are benchmarked from seed state, not their authors' protocol

  questiontesting
  lanl/bngsim#1366 · Filter by author wshlavacek opened on Oct 28, 2026

• run_replicates / run_batch: ensembles from consecutive base seeds share almost every trajectory

  correctness concernenhancement
  lanl/bngsim#1365 · Filter by author wshlavacek opened on Oct 28, 2026

• Result.sse_gradient() documents observable-shaped data but silently scores it against species

  bugcorrectness concern
  lanl/bngsim#1363 · Filter by author wshlavacek opened on Oct 28, 2026

• Nightly parity: regressions detected

  lanl/bngsim#1355 · Filter by author github-actions opened on Oct 28, 2026
  4

• sbml: reversing listOfSpecies makes MODEL1812040005 fail (P below 0, a*P^z NaN) where the order written runs; RoadRunner runs both

  lanl/bngsim#1340 · Filter by author Montana opened on Oct 27, 2026

• A step across a pole of the right-hand side returns a trajectory where no solution exists

  correctness concern
  lanl/bngsim#1339 · Filter by author wshlavacek opened on Oct 27, 2026

• Performance: the step of the solvers' own difference quotients, and #1302's +4–36% wall on the fd path (Step 4 of #1002)

  family: steady stateperformance
  lanl/bngsim#1333 · Filter by author wshlavacek opened on Oct 27, 2026

• Forward sensitivity at a parameter that sits on a kink of a rate law returns one side's slope or neither (dX*/dq = 0 for ±47.6), with no error

  bugcorrectness concernfamily: sensitivity terms
  lanl/bngsim#1332 · Filter by author wshlavacek opened on Oct 27, 2026

• A run that slides along a moving threshold is wrong with no error on a differenced Jacobian (X(40) = 19.7 for 25), and times out on the closed form

  bugcorrectness concern
  lanl/bngsim#1331 · Filter by author wshlavacek opened on Oct 27, 2026

• A differenced Jacobian can be wrong at every step a check takes: take exact derivatives where there is no closed form (Step 3 of #1002)

  bugcorrectness concernfamily: steady state
  lanl/bngsim#1330 · Filter by author wshlavacek opened on Oct 27, 2026
  1

• A failed NFsim load leaves the host process in the XML's directory: create_system() changes the cwd and an exception from initializeFromXML skips the restore. The stream swap and global RNG reseed also need to be explicit and contained

  bug
  lanl/bngsim#1314 · Filter by author wshlavacek opened on Oct 27, 2026

• Typed exceptions for "no sparse Jacobian for KLU" and "codegen declined this model"

  enhancement
  lanl/bngsim#1313 · Filter by author wshlavacek opened on Oct 27, 2026

• BIOMD0000000338 and 339: KLU and the dense solver take different branches past a step-size collapse (Fg 311 on KLU, 0.73 on dense and libRoadRunner)

  bugcorrectness concern
  lanl/bngsim#1304 · Filter by author wshlavacek opened on Oct 27, 2026
  3

• A sensitivity run's state departs from a converged plain run by 0.9% on MODEL2001200002 (no events), and does not converge onto it at 100x tighter tolerances

  lanl/bngsim#1298 · Filter by author Montana opened on Oct 26, 2026
  1

• BIOMD0000000810 asked for 8x the output points returns 5.3e7 of its trajectory's peak off the converged run, with no error

  lanl/bngsim#1297 · Filter by author Montana opened on Oct 26, 2026
  2

• deps: move the uv.lock pins to antimony 3.2.1 and libroadrunner 2.11.0, after evaluating what each upgrade changes

  enhancementtesting
  lanl/bngsim#1288 · Filter by author wshlavacek opened on Oct 26, 2026

• A smooth narrow pulse (a Gaussian or sech² in a clock) is stepped over: Y = 0 for 2.212 at every tolerance, with no warning

  bugcorrectness concern
  lanl/bngsim#1286 · Filter by author wshlavacek opened on Oct 25, 2026
  1