update

Author: TorkelE

ext/CatalystBifurcationKitExtension/bifurcation_kit_extension.jl

@@ -13,7 +13,7 @@ function BK.BifurcationProblem(rs::ReactionSystem, u0_bif, ps, bif_par, args...;
 
     # Creates NonlinearSystem.
     Catalyst.conservationlaw_errorcheck(rs, vcat(ps, u0))
-    nsys = convert(NonlinearSystem, rs; remove_conserved=true, defaults=Dict(u0))
+    nsys = complete(convert(NonlinearSystem, rs; remove_conserved=true, defaults=Dict(u0)))
 
     # Makes BifurcationProblem (this call goes through the ModelingToolkit-based BifurcationKit extension).
     return BK.BifurcationProblem(nsys, u0_bif, ps, bif_par, args...; plot_var=plot_var,

ext/CatalystHomotopyContinuationExtension/homotopy_continuation_extension.jl

@@ -45,7 +45,7 @@ end
 # For a given reaction system, parameter values, and initial conditions, find the polynomial that HC solves to find steady states.
 function steady_state_polynomial(rs::ReactionSystem, ps, u0)
     rs = Catalyst.expand_registered_functions(rs)
-    ns = convert(NonlinearSystem, rs; remove_conserved = true)
+    ns = complete(convert(NonlinearSystem, rs; remove_conserved = true))
     pre_varmap = [symmap_to_varmap(rs,u0)..., symmap_to_varmap(rs,ps)...]
     Catalyst.conservationlaw_errorcheck(rs, pre_varmap)
     p_vals = ModelingToolkit.varmap_to_vars(pre_varmap, parameters(ns); defaults = ModelingToolkit.defaults(ns))

src/spatial_reaction_systems/spatial_ODE_systems.jl

@@ -156,7 +156,7 @@ function build_odefunction(lrs::LatticeReactionSystem, vert_ps::Vector{Vector{T}
     transport_rates = make_sidxs_to_transrate_map(vert_ps, edge_ps, lrs)    
 
     # Prepares the Jacobian and forcing functions (depending on jacobian and sparsity selection).
-    osys = convert(ODESystem, lrs.rs; name, combinatoric_ratelaws, include_zero_odes, checks)
+    osys = complete(convert(ODESystem, lrs.rs; name, combinatoric_ratelaws, include_zero_odes, checks))
     if jac
         # `build_jac_prototype` currently assumes a sparse (non-spatial) Jacobian. Hence compute this.
         # `LatticeTransportODEjac` currently assumes a dense (non-spatial) Jacobian. Hence compute this.