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Running Models with Discrete Data documentation throws errors #267

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aditya-sengupta opened this issue Feb 21, 2024 · 6 comments
Closed

Running Models with Discrete Data documentation throws errors #267

aditya-sengupta opened this issue Feb 21, 2024 · 6 comments
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bug Something isn't working

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@aditya-sengupta
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aditya-sengupta commented Feb 21, 2024 •
edited
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Describe the bug 🐞

The Running Models with Discrete Data documentation page throws errors, and I'm not able to modify it to get to the correct output.

Expected behavior

The code should run and should insert ODE solutions for the problem with data1 and data2 in the variables sol1 and sol2 respectively. I tried to fix any bugs I could with minor modifications, but wasn't able to get past a certain point in trying to get this working; in particular I added @named to a few intermediate calls. I removed the @sync and @async at the end to get a clearer error message.

I wasn't able to do anything further to address the error: no method matching getindex(::Parameter{Float64}, ::Int64).

Minimal Reproducible Example 👇

using ModelingToolkit
using ModelingToolkitStandardLibrary.Blocks
using DataInterpolations
using OrdinaryDiffEq
using Test

@parameters t
D = Differential(t)

function System(f; name)
    @named src = TimeVaryingFunction(f)

    vars = @variables f(t)=0 x(t)=0 dx(t)=0 ddx(t)=0
    pars = @parameters m=10 k=1000 d=1

    eqs = [f ~ src.output.u
        ddx * 10 ~ k * x + d * dx + f
        D(x) ~ dx
        D(dx) ~ ddx]

    ODESystem(eqs, t, vars, pars; systems = [src], name)
end

dt = 4e-4
time = 0:dt:0.1
data = sin.(2 * pi * time * 100) # example data

f = LinearInterpolation(data, time)

@named system = System(f)
sys = structural_simplify(system)
prob = ODEProblem(sys, [], (0, time[end]))
sol = solve(prob, ImplicitEuler())

const rdata = Ref{Vector{Float64}}()

# Data Sets
data1 = sin.(2 * pi * time * 100)
data2 = cos.(2 * pi * time * 50)

function get_sampled_data(t)
    i = floor(Int, t / dt) + 1
    x = rdata[][i]

    return x
end

Symbolics.@register_symbolic get_sampled_data(t)

function System(; name)
    vars = @variables f(t)=0 x(t)=0 dx(t)=0 ddx(t)=0
    pars = @parameters m=10 k=1000 d=1

    eqs = [f ~ get_sampled_data(t)
        ddx * 10 ~ k * x + d * dx + f
        D(x) ~ dx
        D(dx) ~ ddx]

    ODESystem(eqs, t, vars, pars; name)
end

@named system = System()
sys = structural_simplify(system)
prob = ODEProblem(sys, [], (0, time[end]))

rdata[] = data1
sol1 = solve(prob, ImplicitEuler(); dt, adaptive = false)
ddx1 = sol1[sys.ddx]

rdata[] = data2
sol2 = solve(prob, ImplicitEuler(); dt, adaptive = false)
ddx2 = sol2[sys.ddx]

# the following test will fail
@test !all(ddx1 .== sol1[sys.ddx]) #returns false

function System(; name)
    @named src = SampledData(Float64, name=name)

    vars = @variables f(t)=0 x(t)=0 dx(t)=0 ddx(t)=0
    pars = @parameters m=10 k=1000 d=1

    eqs = [f ~ src.output.u
        ddx * 10 ~ k * x + d * dx + f
        D(x) ~ dx
        D(dx) ~ ddx]

    ODESystem(eqs, t, vars, pars; systems = [src], name)
end

@named system = System()
sys = structural_simplify(system)
s = complete(system)
prob = ODEProblem(sys, [], (0, time[end]); tofloat = false)
defs = ModelingToolkit.defaults(sys)

function get_prob(data)
    defs[s.src.buffer] = Parameter(data, dt)
    # ensure p is a uniform type of Vector{Parameter{Float64}} (converting from Vector{Any})
    p = Parameter.(ModelingToolkit.varmap_to_vars(defs, parameters(sys); tofloat = false))
    remake(prob; p)
end

prob1 = get_prob(data1)
prob2 = get_prob(data2)

sol1 = Ref{ODESolution}()
sol2 = Ref{ODESolution}()

sol1[] = solve(prob1, ImplicitEuler()) # errors
sol2[] = solve(prob2, ImplicitEuler())

Error & Stacktrace ⚠️

ERROR: MethodError: no method matching getindex(::Parameter{Float64}, ::Int64)
Stacktrace:
  [1] macro expansion
    @ ~/.julia/packages/SymbolicUtils/r1pzW/src/code.jl:375 [inlined]
  [2] macro expansion
    @ ~/.julia/packages/RuntimeGeneratedFunctions/Yo8zx/src/RuntimeGeneratedFunctions.jl:163 [inlined]
  [3] macro expansion
    @ ./none:0 [inlined]
  [4] generated_callfunc
    @ ./none:0 [inlined]
  [5] (::RuntimeGeneratedFunctions.RuntimeGeneratedFunction{…})(::Vector{…}, ::Vector{…}, ::Parameter{…}, ::Parameter{…}, ::Parameter{…}, ::Parameter{…}, ::Float64)
    @ RuntimeGeneratedFunctions ~/.julia/packages/RuntimeGeneratedFunctions/Yo8zx/src/RuntimeGeneratedFunctions.jl:150
  [6] g
    @ ~/.julia/packages/ModelingToolkit/Gpzyo/src/systems/diffeqs/abstractodesystem.jl:367 [inlined]
  [7] Void
    @ ~/.julia/packages/SciMLBase/wVDwN/src/utils.jl:481 [inlined]
  [8] (::FunctionWrappers.CallWrapper{…})(f::SciMLBase.Void{…}, arg1::Vector{…}, arg2::Vector{…}, arg3::Vector{…}, arg4::Float64)
    @ FunctionWrappers ~/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:65
  [9] macro expansion
    @ ~/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:137 [inlined]
 [10] do_ccall
    @ ~/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:125 [inlined]
 [11] FunctionWrapper
    @ ~/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:144 [inlined]
 [12] _call
    @ ~/.julia/packages/FunctionWrappersWrappers/9XR0m/src/FunctionWrappersWrappers.jl:12 [inlined]
 [13] FunctionWrappersWrapper
    @ ~/.julia/packages/FunctionWrappersWrappers/9XR0m/src/FunctionWrappersWrappers.jl:10 [inlined]
 [14] ODEFunction
    @ ~/.julia/packages/SciMLBase/wVDwN/src/scimlfunctions.jl:2196 [inlined]
 [15] initialize!(integrator::OrdinaryDiffEq.ODEIntegrator{…}, cache::OrdinaryDiffEq.ImplicitEulerCache{…})
    @ OrdinaryDiffEq ~/.julia/packages/OrdinaryDiffEq/5mSPQ/src/perform_step/sdirk_perform_step.jl:58
 [16] __init(prob::ODEProblem{…}, alg::ImplicitEuler{…}, timeseries_init::Tuple{}, ts_init::Tuple{}, ks_init::Tuple{}, recompile::Type{…}; saveat::Tuple{}, tstops::Tuple{}, d_discontinuities::Tuple{}, save_idxs::Nothing, save_everystep::Bool, save_on::Bool, save_start::Bool, save_end::Nothing, callback::Nothing, dense::Bool, calck::Bool, dt::Float64, dtmin::Float64, dtmax::Float64, force_dtmin::Bool, adaptive::Bool, gamma::Rational{…}, abstol::Nothing, reltol::Nothing, qmin::Rational{…}, qmax::Int64, qsteady_min::Int64, qsteady_max::Rational{…}, beta1::Nothing, beta2::Nothing, qoldinit::Rational{…}, controller::Nothing, fullnormalize::Bool, failfactor::Int64, maxiters::Int64, internalnorm::typeof(DiffEqBase.ODE_DEFAULT_NORM), internalopnorm::typeof(LinearAlgebra.opnorm), isoutofdomain::typeof(DiffEqBase.ODE_DEFAULT_ISOUTOFDOMAIN), unstable_check::typeof(DiffEqBase.ODE_DEFAULT_UNSTABLE_CHECK), verbose::Bool, timeseries_errors::Bool, dense_errors::Bool, advance_to_tstop::Bool, stop_at_next_tstop::Bool, initialize_save::Bool, progress::Bool, progress_steps::Int64, progress_name::String, progress_message::typeof(DiffEqBase.ODE_DEFAULT_PROG_MESSAGE), progress_id::Symbol, userdata::Nothing, allow_extrapolation::Bool, initialize_integrator::Bool, alias_u0::Bool, alias_du0::Bool, initializealg::OrdinaryDiffEq.DefaultInit, kwargs::@Kwargs{})
    @ OrdinaryDiffEq ~/.julia/packages/OrdinaryDiffEq/5mSPQ/src/solve.jl:512
 [17] __init (repeats 5 times)
    @ ~/.julia/packages/OrdinaryDiffEq/5mSPQ/src/solve.jl:10 [inlined]
 [18] __solve(::ODEProblem{…}, ::ImplicitEuler{…}; kwargs::@Kwargs{})
    @ OrdinaryDiffEq ~/.julia/packages/OrdinaryDiffEq/5mSPQ/src/solve.jl:5
 [19] __solve
    @ ~/.julia/packages/OrdinaryDiffEq/5mSPQ/src/solve.jl:1 [inlined]
 [20] #solve_call#34
    @ ~/.julia/packages/DiffEqBase/Sueu7/src/solve.jl:612 [inlined]
 [21] solve_call
    @ ~/.julia/packages/DiffEqBase/Sueu7/src/solve.jl:569 [inlined]
 [22] #solve_up#42
    @ ~/.julia/packages/DiffEqBase/Sueu7/src/solve.jl:1062 [inlined]
 [23] solve_up
    @ ~/.julia/packages/DiffEqBase/Sueu7/src/solve.jl:1048 [inlined]
 [24] #solve#40
    @ ~/.julia/packages/DiffEqBase/Sueu7/src/solve.jl:985 [inlined]
 [25] solve(prob::ODEProblem{…}, args::ImplicitEuler{…})
    @ DiffEqBase ~/.julia/packages/DiffEqBase/Sueu7/src/solve.jl:975
 [26] top-level scope
    @ ~/projects/test_mtk/run_docs.jl:110
Some type information was truncated. Use `show(err)` to see complete types.

Environment (please complete the following information):

  • Output of using Pkg; Pkg.status()
Status `~/projects/test_mtk/Project.toml`
  [82cc6244] DataInterpolations v4.6.0
  [961ee093] ModelingToolkit v8.75.0
  [16a59e39] ModelingToolkitStandardLibrary v2.3.4
  [1dea7af3] OrdinaryDiffEq v6.71.0
  [0c5d862f] Symbolics v5.19.1
  • Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
Status `~/projects/test_mtk/Manifest.toml`
  [47edcb42] ADTypes v0.2.6
  [1520ce14] AbstractTrees v0.4.5
  [79e6a3ab] Adapt v4.0.1
⌅ [ec485272] ArnoldiMethod v0.2.0
  [4fba245c] ArrayInterface v7.7.1
  [4c555306] ArrayLayouts v1.6.0
  [e2ed5e7c] Bijections v0.1.6
  [62783981] BitTwiddlingConvenienceFunctions v0.1.5
  [2a0fbf3d] CPUSummary v0.2.4
  [00ebfdb7] CSTParser v3.4.1
  [49dc2e85] Calculus v0.5.1
  [d360d2e6] ChainRulesCore v1.22.0
  [fb6a15b2] CloseOpenIntervals v0.1.12
  [861a8166] Combinatorics v1.0.2
  [a80b9123] CommonMark v0.8.12
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.0
  [34da2185] Compat v4.13.0
  [b152e2b5] CompositeTypes v0.1.3
  [2569d6c7] ConcreteStructs v0.2.3
  [187b0558] ConstructionBase v1.5.4
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [82cc6244] DataInterpolations v4.6.0
  [864edb3b] DataStructures v0.18.17
  [e2d170a0] DataValueInterfaces v1.0.0
  [2b5f629d] DiffEqBase v6.147.0
  [459566f4] DiffEqCallbacks v2.37.0
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [b4f34e82] Distances v0.10.11
  [31c24e10] Distributions v0.25.107
  [ffbed154] DocStringExtensions v0.9.3
⌅ [5b8099bc] DomainSets v0.6.7
  [fa6b7ba4] DualNumbers v0.6.8
  [7c1d4256] DynamicPolynomials v0.5.5
  [4e289a0a] EnumX v1.0.4
  [f151be2c] EnzymeCore v0.6.5
  [d4d017d3] ExponentialUtilities v1.26.1
  [e2ba6199] ExprTools v0.1.10
  [7034ab61] FastBroadcast v0.2.8
  [9aa1b823] FastClosures v0.3.2
  [29a986be] FastLapackInterface v2.0.1
  [1a297f60] FillArrays v1.9.3
  [6a86dc24] FiniteDiff v2.22.0
  [59287772] Formatting v0.4.2
  [f6369f11] ForwardDiff v0.10.36
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [d9f16b24] Functors v0.4.7
  [46192b85] GPUArraysCore v0.1.6
  [c145ed77] GenericSchur v0.5.3
  [c27321d9] Glob v1.3.1
  [86223c79] Graphs v1.9.0
  [3e5b6fbb] HostCPUFeatures v0.1.16
  [34004b35] HypergeometricFunctions v0.3.23
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.4
  [8197267c] IntervalSets v0.7.10
  [92d709cd] IrrationalConstants v0.2.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.5.0
  [682c06a0] JSON v0.21.4
  [98e50ef6] JuliaFormatter v1.0.50
  [ccbc3e58] JumpProcesses v9.10.1
  [ef3ab10e] KLU v0.5.0
  [ba0b0d4f] Krylov v0.9.5
  [b964fa9f] LaTeXStrings v1.3.1
  [2ee39098] LabelledArrays v1.15.1
  [984bce1d] LambertW v0.4.6
  [23fbe1c1] Latexify v0.16.1
  [10f19ff3] LayoutPointers v0.1.15
  [50d2b5c4] Lazy v0.15.1
  [5078a376] LazyArrays v1.8.3
  [d3d80556] LineSearches v7.2.0
  [7ed4a6bd] LinearSolve v2.23.4
  [2ab3a3ac] LogExpFunctions v0.3.27
  [bdcacae8] LoopVectorization v0.12.166
  [d8e11817] MLStyle v0.4.17
  [1914dd2f] MacroTools v0.5.13
  [d125e4d3] ManualMemory v0.1.8
  [a3b82374] MatrixFactorizations v2.1.0
  [bb5d69b7] MaybeInplace v0.1.1
  [e1d29d7a] Missings v1.1.0
  [961ee093] ModelingToolkit v8.75.0
  [16a59e39] ModelingToolkitStandardLibrary v2.3.4
  [46d2c3a1] MuladdMacro v0.2.4
  [102ac46a] MultivariatePolynomials v0.5.4
  [d8a4904e] MutableArithmetics v1.4.1
  [d41bc354] NLSolversBase v7.8.3
  [2774e3e8] NLsolve v4.5.1
  [77ba4419] NaNMath v1.0.2
  [8913a72c] NonlinearSolve v3.6.0
  [6fe1bfb0] OffsetArrays v1.13.0
  [bac558e1] OrderedCollections v1.6.3
  [1dea7af3] OrdinaryDiffEq v6.71.0
  [90014a1f] PDMats v0.11.31
  [65ce6f38] PackageExtensionCompat v1.0.2
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.8.1
  [e409e4f3] PoissonRandom v0.4.4
  [f517fe37] Polyester v0.7.9
  [1d0040c9] PolyesterWeave v0.2.1
  [d236fae5] PreallocationTools v0.4.20
  [aea7be01] PrecompileTools v1.2.0
  [21216c6a] Preferences v1.4.1
  [08abe8d2] PrettyTables v2.3.1
  [1fd47b50] QuadGK v2.9.4
  [e6cf234a] RandomNumbers v1.5.3
  [3cdcf5f2] RecipesBase v1.3.4
  [731186ca] RecursiveArrayTools v3.8.1
  [f2c3362d] RecursiveFactorization v0.2.21
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [79098fc4] Rmath v0.7.1
  [7e49a35a] RuntimeGeneratedFunctions v0.5.12
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.42
  [0bca4576] SciMLBase v2.26.1
  [c0aeaf25] SciMLOperators v0.3.7
  [efcf1570] Setfield v1.1.1
  [727e6d20] SimpleNonlinearSolve v1.5.0
  [699a6c99] SimpleTraits v0.9.4
  [ce78b400] SimpleUnPack v1.1.0
  [a2af1166] SortingAlgorithms v1.2.1
  [47a9eef4] SparseDiffTools v2.17.0
  [e56a9233] Sparspak v0.3.9
  [276daf66] SpecialFunctions v2.3.1
  [aedffcd0] Static v0.8.10
  [0d7ed370] StaticArrayInterface v1.5.0
  [90137ffa] StaticArrays v1.9.2
  [1e83bf80] StaticArraysCore v1.4.2
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.2
  [4c63d2b9] StatsFuns v1.3.1
  [7792a7ef] StrideArraysCore v0.5.2
  [892a3eda] StringManipulation v0.3.4
  [2efcf032] SymbolicIndexingInterface v0.3.6
  [d1185830] SymbolicUtils v1.5.0
  [0c5d862f] Symbolics v5.19.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.11.1
  [8290d209] ThreadingUtilities v0.5.2
  [a759f4b9] TimerOutputs v0.5.23
  [0796e94c] Tokenize v0.5.28
  [d5829a12] TriangularSolve v0.1.20
  [410a4b4d] Tricks v0.1.8
  [781d530d] TruncatedStacktraces v1.4.0
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1986cc42] Unitful v1.19.0
  [a7c27f48] Unityper v0.1.6
  [3d5dd08c] VectorizationBase v0.21.65
  [19fa3120] VertexSafeGraphs v0.2.0
  [1d5cc7b8] IntelOpenMP_jll v2024.0.2+0
  [856f044c] MKL_jll v2024.0.0+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [f50d1b31] Rmath_jll v0.4.0+0
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.10.0
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.1.0+0
  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.6.4+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.23+4
  [05823500] OpenLibm_jll v0.8.1+2
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.8.0+1
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
  • Output of versioninfo()
Julia Version 1.10.1
Commit 7790d6f0641 (2024-02-13 20:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin22.4.0)
  CPU: 10 × Apple M1 Pro
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, apple-m1)
Threads: 8 default, 0 interactive, 4 GC (on 8 virtual cores)
Environment:
  JULIA_NUM_THREADS = 8
  LD_LIBRARY_PATH = :/Users/adityasengupta/scetre/DAOROOT/lib:/Users/adityasengupta/scetre/DAOROOT/lib64:/opt/homebrew/lib
  JULIA_EDITOR = code
@aditya-sengupta aditya-sengupta added the bug Something isn't working label Feb 21, 2024
@aditya-sengupta
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Undoing some of my changes in accordance with #253 so I can just use @named instead of passing around a kwarg and get closer to the expected behaviour. The substantial issue remains.

@aditya-sengupta
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Found a workaround, but I don't know if this is idiomatic for MTK; it uses some awkward type mixing.

@named system = System()
sys = structural_simplify(system)
prob = ODEProblem(sys, [], (0, time[end]); tofloat = false)

function get_prob(data)
    remake(prob; p=[prob.p[1], [Parameter(data, dt)]])
end

prob1 = get_prob(data1)
prob2 = get_prob(data2)

sol1 = Ref{ODESolution}()
sol2 = Ref{ODESolution}()

sol1[] = solve(prob1, ImplicitEuler())
sol2[] = solve(prob2, ImplicitEuler())

@langestefan
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langestefan commented May 20, 2024 •
edited
Loading

Hi @aditya-sengupta unfortunately the examples are still broken. Have you found a way to get the TimeVaryingFunction Component sample (the top one) to work? I fixed the issue with the name (@named src = TimeVaryingFunction(f)) but the example still doesn't run, throwing:

MethodError: objects of type Vector{Float64} are not callable
Use square brackets [] for indexing an Array.

Edit:
If anyone comes across this issue, I was able to solve it by updating DataInterpolations v4.8.0 ⇒ v5.0.0.

@aditya-sengupta
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aditya-sengupta commented May 20, 2024 via email

@langestefan
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I managed to get it running by upgrading datainterpolations.jl

@ChrisRackauckas
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Yes DataInterpolations v5 should have fixed this, and I can see from this issue that it was opened with v4

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@ChrisRackauckas @aditya-sengupta @langestefan