Symbolic remaking of jump problem errors

[gaurav-arya]

MWE:

using Catalyst
using JumpProcesses

rn = @reaction_network begin
    k, X --> ∅
end

@unpack k = rn # NB: if I use rn.k directly below, I get a different error even in construction which I don't understand, but that's probably a separate issue.

op = ODEProblem(rn, [1.0], (0.0, 1.0), [k => 1.0])
remake(op; p = [k => 3.0]) # works fine

dp = DiscreteProblem(rn, [1.0], (0.0, 1.0), [k => 1.0])
jp = JumpProblem(rn, dp, Direct())
remake(jp; p = [k => 3.0]) # error

Version info:

  [479239e8] Catalyst v13.5.1
  [ccbc3e58] JumpProcesses v9.10.1

Error:

ERROR: MethodError: Cannot `convert` an object of type Pair{Num, Float64} to an object of type Float64

Closest candidates are:
  convert(::Type{T}, ::DualNumbers.Dual) where T<:Union{Real, Complex}
   @ DualNumbers ~/.julia/packages/DualNumbers/5knFX/src/dual.jl:24
  convert(::Type{T}, ::VectorizationBase.AbstractSIMD) where T<:Union{Bool, Float16, Float32, Float64, Int16, Int32, Int64, Int8, UInt16, UInt32, UInt64, UInt8, SIMDTypes.Bit}
   @ VectorizationBase ~/.julia/packages/VectorizationBase/xE5Tx/src/base_defs.jl:201
  convert(::Type{T}, ::Union{Static.StaticBool{N}, Static.StaticFloat64{N}, Static.StaticInt{N}} where N) where T<:Number
   @ Static ~/.julia/packages/Static/dLrtk/src/Static.jl:414
  ...

Stacktrace:
 [1] setindex!(h::Dict{…}, v0::Pair{…}, key::SymbolicUtils.BasicSymbolic{…})
   @ Base ./dict.jl:376
 [2] updateparams!(ratemap::ModelingToolkit.JumpSysMajParamMapper{Vector{…}, Vector{…}, Float64}, params::Vector{Pair{…}})
   @ ModelingToolkit ~/.julia/packages/ModelingToolkit/arrCl/src/systems/jumps/jumpsystem.jl:479
 [3] (::ModelingToolkit.JumpSysMajParamMapper{…})(maj::MassActionJump{…}, newparams::Vector{…}; scale_rates::Bool, kwargs::@Kwargs{…})
   @ ModelingToolkit ~/.julia/packages/ModelingToolkit/arrCl/src/systems/jumps/jumpsystem.jl:506
 [4] JumpSysMajParamMapper
   @ ~/.julia/packages/ModelingToolkit/arrCl/src/systems/jumps/jumpsystem.jl:502 [inlined]
 [5] #update_parameters!#14
   @ ~/.julia/packages/JumpProcesses/HPjOl/src/jumps.jl:450 [inlined]
 [6] update_parameters!
   @ ~/.julia/packages/JumpProcesses/HPjOl/src/jumps.jl:447 [inlined]
 [7] remake(thing::JumpProblem{…}; kwargs::@Kwargs{…})
   @ JumpProcesses ~/.julia/packages/JumpProcesses/HPjOl/src/problem.jl:104

[isaacsas]

This is from some bugs introduced when SciMLBase switched the symbolic indexing backend. You can see what @TorkelE reported there at https://github.com/SciML/SciMLBase.jl/issues/581

They should hopefully get fixed soon in SciMLbase and this should work again, but in the meantime I’d suggest manually adding and downgrading SciMLBase.

[gabo-di]

maybe you can add the following code into ~/.julia/packages/ModelingToolkit/arrCl/src/systems/jumps/jumpsystem.jl around line 479

function updateparams!(ratemap::JumpSysMajParamMapper{U, V, W},
    params::Vector{Pair{Num,T}}) where {U <: AbstractArray, V <: AbstractArray, W, T}
    for (i, p) in enumerate(params)
        sympar = ratemap.sympars[i]
        ratemap.subdict[sympar] = Dict(p)[sympar]
    end
    nothing
end

just for the moment

[isaacsas]

This is fixed on the V14 branch via changes to SciMLBase and SymbolicIndexingInterface.