For context: I am building a model using ModellingToolkit that has layers of connections as each component within the overall ODE will be built at runtime from symbolics equations etc.
I have built this model with the minimal requirements and when I go to structural_simply the final ODE it doesn’t work and produces the error I have attached beneath the MWE. This is being created as an issue from a Julia discourse: https://discourse.julialang.org/t/structural-simplify-not-working-on-tiered-model/114428

Here is the MWE:

using ModelingToolkit,DifferentialEquations,Symbolics,Latexify,LaTeXStrings
using ModelingToolkit: t_nounits as t, D_nounits as D 

function dX(;name)
    @parameters c
    @variables x(t) y(t) s(t)

    eqs = D(x) ~ -c*(x-y) + s

    ODESystem(eqs,t;name)
end

function dY(;name)
    @parameters c
    @variables x(t) y(t)

    eqs = D(y) ~ c*(x-y)

    ODESystem(eqs,t;name)
end

function symboliceq()
    @parameters a b
    s = sqrt(4*log(2)/pi)*a*exp(-(t-b))
    return s
end

function x_factory(;name)
    @named DX = dX()
    symbolic=symboliceq()
    connections=[DX.s~symbolic]
    compose(ODESystem(connections,t;name),DX)
end

function main()
    @named x_eq = x_factory()
    @named y_eq = dY()
    connections = [x_eq.DX.y ~ y_eq.y,
                   y_eq.x ~ x_eq.DX.x,
                   x_eq.DX.c ~ y_eq.c]
    connected = compose(ODESystem(connections,t,name=:connected),x_eq,y_eq)
    connected_simp = structural_simplify(connected)
end

main()

And the error message

ERROR: BoundsError: attempt to access 7-element Vector{Vector{Int64}} at index [8] Stacktrace: [1] getindex @ .\essentials.jl:13 [inlined] [2] 𝑑neighbors @ C:\Users\u5522838\.julia\packages\ModelingToolkit\w72sG\src\bipartite_graph.jl:369 [inlined] [3] 𝑑neighbors @ C:\Users\u5522838\.julia\packages\ModelingToolkit\w72sG\src\bipartite_graph.jl:368 [inlined] [4] check_consistency(state::TearingState{ODESystem}, orig_inputs::Set{Any}) @ ModelingToolkit.StructuralTransformations C:\Users\u5522838\.julia\packages\ModelingToolkit\w72sG\src\structural_transformation\utils.jl:96 [5] _structural_simplify!(state::TearingState{…}, io::Nothing; simplify::Bool, check_consistency::Bool, fully_determined::Bool, warn_initialize_determined::Bool, dummy_derivative::Bool, kwargs::@Kwargs{}) @ ModelingToolkit C:\Users\u5522838\.julia\packages\ModelingToolkit\w72sG\src\systems\systemstructure.jl:689 [6] structural_simplify!(state::TearingState{…}, io::Nothing; simplify::Bool, check_consistency::Bool, fully_determined::Bool, warn_initialize_determined::Bool, kwargs::@Kwargs{}) @ ModelingToolkit C:\Users\u5522838\.julia\packages\ModelingToolkit\w72sG\src\systems\systemstructure.jl:635 [7] __structural_simplify(sys::ODESystem, io::Nothing; simplify::Bool, kwargs::@Kwargs{}) @ ModelingToolkit C:\Users\u5522838\.julia\packages\ModelingToolkit\w72sG\src\systems\systems.jl:74 [8] __structural_simplify @ C:\Users\u5522838\.julia\packages\ModelingToolkit\w72sG\src\systems\systems.jl:55 [inlined] [9] structural_simplify(sys::ODESystem, io::Nothing; simplify::Bool, split::Bool, kwargs::@Kwargs{}) @ ModelingToolkit C:\Users\u5522838\.julia\packages\ModelingToolkit\w72sG\src\systems\systems.jl:22 [10] structural_simplify (repeats 2 times) @ C:\Users\u5522838\.julia\packages\ModelingToolkit\w72sG\src\systems\systems.jl:19 [inlined] [11] main() @ Main .\Untitled-1:42 [12] top-level scope @ Untitled-1:45 Some type information was truncated. Use show(err) to see complete types.