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Type piracy by DataFrames.jl causes error during SDE simplification #2965

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MasonProtter opened this issue Aug 14, 2024 · 0 comments · Fixed by #2966
Closed

Type piracy by DataFrames.jl causes error during SDE simplification #2965

MasonProtter opened this issue Aug 14, 2024 · 0 comments · Fixed by #2966
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@MasonProtter
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MasonProtter commented Aug 14, 2024 •
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Describe the bug 🐞

DataFrames.jl pirates reduce(vcat, ::Vector{Union{}}), which ModelingToolkit can hit during the structural simplification of an SDE (not sure if it's intentional, but 🤷), and this causes complete to error out:

Minimal Reproducible Example 👇

Setup:

using  DataFrames # only errors if this line is here
using ModelingToolkit
using ModelingToolkit: t_nounits as t, D_nounits as D

# Define some variables
@parameters σ ρ β
@variables x(t) y(t) z(t)
@brownian a
eqs = [D(x) ~ σ * (y - x) + 0.1a * x,
    D(y) ~ x * (ρ - z) - y + 0.1a * y,
    D(z) ~ x * y - β * z + 0.1a * z]

@mtkbuild de = System(eqs, t)

Error & Stacktrace ⚠️

julia> @mtkbuild de = System(eqs, t)
ERROR: TypeError: in keyword argument init, expected AbstractDataFrame, got a value of type Vector{Equation}
Stacktrace:
 [1] parameter_dependencies(sys::SDESystem)
   @ ModelingToolkit ~/.julia/packages/ModelingToolkit/SjwiH/src/systems/abstractsystem.jl:1348
 [2] ModelingToolkit.IndexCache(sys::SDESystem)
   @ ModelingToolkit ~/.julia/packages/ModelingToolkit/SjwiH/src/systems/index_cache.jl:319
 [3] macro expansion
   @ ~/.julia/packages/Setfield/PdKfV/src/sugar.jl:197 [inlined]
 [4] complete(sys::SDESystem; split::Bool)
   @ ModelingToolkit ~/.julia/packages/ModelingToolkit/SjwiH/src/systems/abstractsystem.jl:864
 [5] structural_simplify(sys::ODESystem, io::Nothing; simplify::Bool, split::Bool, allow_symbolic::Bool, allow_parameter::Bool, conservative::Bool, fully_determined::Bool, kwargs::@Kwargs{})
   @ ModelingToolkit ~/.julia/packages/ModelingToolkit/SjwiH/src/systems/systems.jl:43
 [6] structural_simplify
   @ ~/.julia/packages/ModelingToolkit/SjwiH/src/systems/systems.jl:20 [inlined]
 [7] structural_simplify(sys::ODESystem)
   @ ModelingToolkit ~/.julia/packages/ModelingToolkit/SjwiH/src/systems/systems.jl:20
 [8] top-level scope
   @ ~/.julia/packages/ModelingToolkit/SjwiH/src/systems/abstractsystem.jl:2121

Environment (please complete the following information):

  • Output of using Pkg; Pkg.status()
julia> using Pkg; Pkg.status()
Project SDESystemRepro v0.1.0
Status `~/SDESystemRepro/Project.toml`
  [a93c6f00] DataFrames v1.6.1
  [961ee093] ModelingToolkit v9.33.0
  • Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
julia> using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
Project SDESystemRepro v0.1.0
Status `~/SDESystemRepro/Manifest.toml`
  [47edcb42] ADTypes v1.7.1
  [1520ce14] AbstractTrees v0.4.5
  [7d9f7c33] Accessors v0.1.37
  [79e6a3ab] Adapt v4.0.4
  [66dad0bd] AliasTables v1.1.3
  [ec485272] ArnoldiMethod v0.4.0
  [4fba245c] ArrayInterface v7.15.0
  [4c555306] ArrayLayouts v1.10.2
  [e2ed5e7c] Bijections v0.1.7
  [62783981] BitTwiddlingConvenienceFunctions v0.1.6
  [2a0fbf3d] CPUSummary v0.2.6
  [00ebfdb7] CSTParser v3.4.3
  [d360d2e6] ChainRulesCore v1.24.0
  [fb6a15b2] CloseOpenIntervals v0.1.13
  [861a8166] Combinatorics v1.0.2
  [3709ef60] CommonEq v0.2.1
  [a80b9123] CommonMark v0.8.12
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.0
  [f70d9fcc] CommonWorldInvalidations v1.0.0
  [34da2185] Compat v4.16.0
  [b152e2b5] CompositeTypes v0.1.4
  [a33af91c] CompositionsBase v0.1.2
  [2569d6c7] ConcreteStructs v0.2.3
  [187b0558] ConstructionBase v1.5.6
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.6.1
  [864edb3b] DataStructures v0.18.20
  [e2d170a0] DataValueInterfaces v1.0.0
  [2b5f629d] DiffEqBase v6.152.2
  [459566f4] DiffEqCallbacks v3.7.0
  [77a26b50] DiffEqNoiseProcess v5.23.0
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [31c24e10] Distributions v0.25.110
  [ffbed154] DocStringExtensions v0.9.3
  [5b8099bc] DomainSets v0.7.14
⌅ [7c1d4256] DynamicPolynomials v0.5.7
⌅ [06fc5a27] DynamicQuantities v0.13.2
  [4e289a0a] EnumX v1.0.4
  [f151be2c] EnzymeCore v0.7.8
  [e2ba6199] ExprTools v0.1.10
⌅ [6b7a57c9] Expronicon v0.8.5
  [7034ab61] FastBroadcast v0.3.5
  [9aa1b823] FastClosures v0.3.2
  [29a986be] FastLapackInterface v2.0.4
  [1a297f60] FillArrays v1.11.0
  [64ca27bc] FindFirstFunctions v1.3.0
  [6a86dc24] FiniteDiff v2.24.0
  [1fa38f19] Format v1.3.7
  [f6369f11] ForwardDiff v0.10.36
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [d9f16b24] Functors v0.4.12
  [46192b85] GPUArraysCore v0.1.6
  [c27321d9] Glob v1.3.1
  [86223c79] Graphs v1.11.2
  [3e5b6fbb] HostCPUFeatures v0.1.17
  [34004b35] HypergeometricFunctions v0.3.24
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.5
  [842dd82b] InlineStrings v1.4.2
  [8197267c] IntervalSets v0.7.10
  [3587e190] InverseFunctions v0.1.16
  [41ab1584] InvertedIndices v1.3.0
  [92d709cd] IrrationalConstants v0.2.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.5.0
  [682c06a0] JSON v0.21.4
  [98e50ef6] JuliaFormatter v1.0.59
  [ccbc3e58] JumpProcesses v9.13.3
  [ef3ab10e] KLU v0.6.0
  [ba0b0d4f] Krylov v0.9.6
  [b964fa9f] LaTeXStrings v1.3.1
  [2ee39098] LabelledArrays v1.16.0
  [984bce1d] LambertW v0.4.6
  [23fbe1c1] Latexify v0.16.5
  [10f19ff3] LayoutPointers v0.1.17
  [5078a376] LazyArrays v2.2.0
  [d3d80556] LineSearches v7.3.0
  [7ed4a6bd] LinearSolve v2.32.0
  [2ab3a3ac] LogExpFunctions v0.3.28
  [bdcacae8] LoopVectorization v0.12.171
  [d8e11817] MLStyle v0.4.17
  [1914dd2f] MacroTools v0.5.13
  [d125e4d3] ManualMemory v0.1.8
  [bb5d69b7] MaybeInplace v0.1.3
  [e1d29d7a] Missings v1.2.0
  [961ee093] ModelingToolkit v9.33.0
  [46d2c3a1] MuladdMacro v0.2.4
  [102ac46a] MultivariatePolynomials v0.5.6
  [d8a4904e] MutableArithmetics v1.4.6
  [d41bc354] NLSolversBase v7.8.3
  [77ba4419] NaNMath v1.0.2
  [8913a72c] NonlinearSolve v3.14.0
  [6fe1bfb0] OffsetArrays v1.14.1
  [429524aa] Optim v1.9.4
  [bac558e1] OrderedCollections v1.6.3
  [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 v0.7.16
  [1d0040c9] PolyesterWeave v0.2.2
  [2dfb63ee] PooledArrays v1.4.3
  [85a6dd25] PositiveFactorizations v0.2.4
  [d236fae5] PreallocationTools v0.4.23
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [08abe8d2] PrettyTables v2.3.2
  [43287f4e] PtrArrays v1.2.0
  [1fd47b50] QuadGK v2.10.1
  [74087812] Random123 v1.7.0
  [e6cf234a] RandomNumbers v1.6.0
  [3cdcf5f2] RecipesBase v1.3.4
  [731186ca] RecursiveArrayTools v3.27.0
  [f2c3362d] RecursiveFactorization v0.2.23
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [ae5879a3] ResettableStacks v1.1.1
  [79098fc4] Rmath v0.7.1
  [7e49a35a] RuntimeGeneratedFunctions v0.5.13
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.43
  [0bca4576] SciMLBase v2.48.1
  [c0aeaf25] SciMLOperators v0.3.9
  [53ae85a6] SciMLStructures v1.4.2
  [91c51154] SentinelArrays v1.4.5
  [efcf1570] Setfield v1.1.1
⌃ [727e6d20] SimpleNonlinearSolve v1.8.1
  [699a6c99] SimpleTraits v0.9.4
  [a2af1166] SortingAlgorithms v1.2.1
  [47a9eef4] SparseDiffTools v2.20.0
  [e56a9233] Sparspak v0.3.9
  [276daf66] SpecialFunctions v2.4.0
  [aedffcd0] Static v1.1.1
  [0d7ed370] StaticArrayInterface v1.8.0
  [90137ffa] StaticArrays v1.9.7
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.3
  [4c63d2b9] StatsFuns v1.3.1
  [7792a7ef] StrideArraysCore v0.5.7
  [892a3eda] StringManipulation v0.3.4
  [458b697b] SymPyCore v0.2.5
  [2efcf032] SymbolicIndexingInterface v0.3.28
  [19f23fe9] SymbolicLimits v0.2.2
  [d1185830] SymbolicUtils v3.1.2
  [0c5d862f] Symbolics v6.0.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [8ea1fca8] TermInterface v2.0.0
  [8290d209] ThreadingUtilities v0.5.2
  [a759f4b9] TimerOutputs v0.5.24
  [0796e94c] Tokenize v0.5.29
  [d5829a12] TriangularSolve v0.2.1
  [410a4b4d] Tricks v0.1.9
  [781d530d] TruncatedStacktraces v1.4.0
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1986cc42] Unitful v1.21.0
  [a7c27f48] Unityper v0.1.6
  [3d5dd08c] VectorizationBase v0.21.70
  [19fa3120] VertexSafeGraphs v0.2.0
  [1d5cc7b8] IntelOpenMP_jll v2024.2.0+0
  [856f044c] MKL_jll v2024.2.0+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
⌅ [f50d1b31] Rmath_jll v0.4.3+0
  [1317d2d5] oneTBB_jll v2021.12.0+0
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [4af54fe1] LazyArtifacts v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.11.0
  [de0858da] Printf v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [1a1011a3] SharedArrays v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays v1.11.0
  [f489334b] StyledStrings v1.11.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.7.2+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [4536629a] OpenBLAS_jll v0.3.27+1
  [05823500] OpenLibm_jll v0.8.1+2
  [bea87d4a] SuiteSparse_jll v7.7.0+0
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.10.1+0
  [8e850ede] nghttp2_jll v1.59.0+0
  [3f19e933] p7zip_jll v17.4.0+2
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
  • Output of versioninfo()
julia> versioninfo()
Julia Version 1.11.0-rc2
Commit 34c3a63147b (2024-07-29 06:24 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 12 × AMD Ryzen 5 5600X 6-Core Processor
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
Threads: 6 default, 0 interactive, 3 GC (on 12 virtual cores)
Environment:
  JULIA_NUM_THREADS = 6

(I also tested and reproduced this on v1.10)

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Hotfix to avoid DataFrames.jl piracy MasonProtter/ModelingToolkit.jl
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@MasonProtter