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I/O: Example of interface to IterableTables errors when trying to predefine column names #1020

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tomdstone opened this issue Mar 1, 2024 · 1 comment
Open

I/O: Example of interface to IterableTables errors when trying to predefine column names #1020

tomdstone opened this issue Mar 1, 2024 · 1 comment
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@AayushSabharwal
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@tomdstone
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Describe the bug 🐞

The example on https://docs.sciml.ai/DiffEqDocs/stable/features/io/ showing how to provide column names to DataFrame(::ODESolution) does not work, it errors when you provide either symbols or strings to the syms keyword, both cases it gives a method error on the getname function.

Expected behavior
The column names are [:a, :b, :c, :d]

Minimal Reproducible Example 👇

This is the example on the docs, I was also able to reproduce with my own toy example

using OrdinaryDiffEq, DataFrames
f_2dlinear = (du, u, p, t) -> du .= 1.01u;

f = ODEFunction(f_2dlinear, syms = [:a, :b, :c, :d])
prob = ODEProblem(f, rand(2, 2), (0.0, 1.0));
sol = solve(prob, Euler(); dt = 1 // 2^(4));
df = DataFrame(sol)

Error & Stacktrace ⚠️

ERROR: MethodError: no method matching getname(::Symbol)
Stacktrace:
 [1] (::SciMLBase.var"#611#614"{Vector{Symbol}})(i::Int64)
   @ SciMLBase ./essentials.jl:0
 [2] iterate(::Base.Generator{UnitRange{Int64}, SciMLBase.var"#611#614"{Vector{Symbol}}})
   @ Base ./generator.jl:47
 [3] rows
   @ ~/.julia/packages/SciMLBase/Dwomw/src/tabletraits.jl:31 [inlined]
 [4] columns
   @ ~/.julia/packages/SciMLBase/Dwomw/src/tabletraits.jl:2 [inlined]
 [5] DataFrame(x::ODESolution{…}; copycols::Nothing)
   @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/other/tables.jl:57
 [6] DataFrame(x::ODESolution{…})
   @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/other/tables.jl:48
 [7] top-level scope
   @ ~/Documents/pkpd_modeling/bug_report.jl:19
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 `~/.julia/environments/v1.10/Project.toml`
  [c7e460c6] ArgParse v1.1.5
  [ad839575] Blink v0.12.9
  [336ed68f] CSV v0.10.12
  [5ae59095] Colors v0.12.10
  [717857b8] DSP v0.7.9
  [a93c6f00] DataFrames v1.6.1
  [1313f7d8] DataFramesMeta v0.14.1
  [864edb3b] DataStructures v0.18.17
  [0c46a032] DifferentialEquations v7.12.0
  [31c24e10] Distributions v0.25.107
  [38e38edf] GLM v1.9.0
  [09f84164] HypothesisTests v0.11.0
  [c601a237] Interact v0.10.5
  [92481ed7] LinearRegression v0.2.1
  [1dea7af3] OrdinaryDiffEq v6.73.1
  [f0f68f2c] PlotlyJS v0.18.13
  [49802e3a] ProgressBars v1.5.1
  [6c5003b2] PyMNE v0.2.2
  [6f49c342] RCall v0.14.1
  [df47a6cb] RData v1.0.0
  [f2b01f46] Roots v2.1.2
  [276daf66] SpecialFunctions v2.3.1
  [2913bbd2] StatsBase v0.34.2
  [fdbf4ff8] XLSX v0.10.1
  [ade2ca70] Dates
  [37e2e46d] LinearAlgebra
  [10745b16] Statistics v1.10.0
  • Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
Status `~/.julia/environments/v1.10/Manifest.toml`
  [47edcb42] ADTypes v0.2.6
  [621f4979] AbstractFFTs v1.5.0
  [7d9f7c33] Accessors v0.1.35
  [79e6a3ab] Adapt v4.0.1
  [c7e460c6] ArgParse v1.1.5
⌅ [ec485272] ArnoldiMethod v0.2.0
  [4fba245c] ArrayInterface v7.7.1
  [4c555306] ArrayLayouts v1.6.0
  [bf4720bc] AssetRegistry v0.1.0
  [aae01518] BandedMatrices v1.5.0
  [6e4b80f9] BenchmarkTools v1.5.0
  [d1d4a3ce] BitFlags v0.1.8
  [62783981] BitTwiddlingConvenienceFunctions v0.1.5
  [ad839575] Blink v0.12.9
  [764a87c0] BoundaryValueDiffEq v5.6.3
  [fa961155] CEnum v0.5.0
  [2a0fbf3d] CPUSummary v0.2.4
  [70588ee8] CSSUtil v0.1.1
  [336ed68f] CSV v0.10.12
  [49dc2e85] Calculus v0.5.1
  [324d7699] CategoricalArrays v0.10.8
⌅ [8be319e6] Chain v0.5.0
  [d360d2e6] ChainRulesCore v1.22.1
  [fb6a15b2] CloseOpenIntervals v0.1.12
  [523fee87] CodecBzip2 v0.8.2
  [944b1d66] CodecZlib v0.7.4
  [35d6a980] ColorSchemes v3.24.0
  [3da002f7] ColorTypes v0.11.4
  [c3611d14] ColorVectorSpace v0.10.0
  [5ae59095] Colors v0.12.10
  [861a8166] Combinatorics v1.0.2
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.0
⌃ [34da2185] Compat v4.13.0
  [a33af91c] CompositionsBase v0.1.2
  [2569d6c7] ConcreteStructs v0.2.3
  [f0e56b4a] ConcurrentUtilities v2.3.1
  [8f4d0f93] Conda v1.10.0
  [992eb4ea] CondaPkg v0.2.22
  [187b0558] ConstructionBase v1.5.4
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [717857b8] DSP v0.7.9
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.6.1
  [1313f7d8] DataFramesMeta v0.14.1
  [864edb3b] DataStructures v0.18.17
  [e2d170a0] DataValueInterfaces v1.0.0
  [bcd4f6db] DelayDiffEq v5.47.0
  [8bb1440f] DelimitedFiles v1.9.1
  [2b5f629d] DiffEqBase v6.147.2
⌅ [459566f4] DiffEqCallbacks v2.37.0
  [77a26b50] DiffEqNoiseProcess v5.20.1
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [0c46a032] DifferentialEquations v7.12.0
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⌃ [f151be2c] EnzymeCore v0.6.5
  [460bff9d] ExceptionUnwrapping v0.1.10
  [d4d017d3] ExponentialUtilities v1.26.1
  [e2ba6199] ExprTools v0.1.10
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  [9aa1b823] FastClosures v0.3.2
  [29a986be] FastLapackInterface v2.0.2
  [5789e2e9] FileIO v1.16.2
  [48062228] FilePathsBase v0.9.21
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  [6a86dc24] FiniteDiff v2.22.0
  [53c48c17] FixedPointNumbers v0.8.4
  [f6369f11] ForwardDiff v0.10.36
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [de31a74c] FunctionalCollections v0.5.0
  [d9f16b24] Functors v0.4.7
  [38e38edf] GLM v1.9.0
  [46192b85] GPUArraysCore v0.1.6
  [c145ed77] GenericSchur v0.5.3
  [86223c79] Graphs v1.9.0
  [cd3eb016] HTTP v1.10.2
  [9fb69e20] Hiccup v0.2.2
  [3e5b6fbb] HostCPUFeatures v0.1.16
  [34004b35] HypergeometricFunctions v0.3.23
  [09f84164] HypothesisTests v0.11.0
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.4
  [842dd82b] InlineStrings v1.4.0
  [c601a237] Interact v0.10.5
  [d3863d7c] InteractBase v0.10.10
  [3587e190] InverseFunctions v0.1.12
  [41ab1584] InvertedIndices v1.3.0
  [92d709cd] IrrationalConstants v0.2.2
  [c8e1da08] IterTools v1.10.0
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.5.0
  [97c1335a] JSExpr v0.5.4
  [682c06a0] JSON v0.21.4
  [0f8b85d8] JSON3 v1.14.0
  [ccbc3e58] JumpProcesses v9.10.1
  [ef3ab10e] KLU v0.6.0
  [bcebb21b] Knockout v0.2.6
  [ba0b0d4f] Krylov v0.9.5
  [b964fa9f] LaTeXStrings v1.3.1
  [10f19ff3] LayoutPointers v0.1.15
  [50d2b5c4] Lazy v0.15.1
  [5078a376] LazyArrays v1.8.3
  [2d8b4e74] LevyArea v1.0.0
  [d3d80556] LineSearches v7.2.0
  [92481ed7] LinearRegression v0.2.1
  [7ed4a6bd] LinearSolve v2.26.0
  [2ab3a3ac] LogExpFunctions v0.3.27
  [e6f89c97] LoggingExtras v1.0.3
  [bdcacae8] LoopVectorization v0.12.166
  [1914dd2f] MacroTools v0.5.13
  [d125e4d3] ManualMemory v0.1.8
  [b8f27783] MathOptInterface v1.27.0
  [a3b82374] MatrixFactorizations v2.1.0
  [bb5d69b7] MaybeInplace v0.1.1
  [739be429] MbedTLS v1.1.9
  [442fdcdd] Measures v0.3.2
  [0b3b1443] MicroMamba v0.1.14
  [e1d29d7a] Missings v1.1.0
  [78c3b35d] Mocking v0.7.7
  [46d2c3a1] MuladdMacro v0.2.4
  [ffc61752] Mustache v1.0.19
  [d8a4904e] MutableArithmetics v1.4.1
  [a975b10e] Mux v1.0.1
  [d41bc354] NLSolversBase v7.8.3
  [2774e3e8] NLsolve v4.5.1
  [77ba4419] NaNMath v1.0.2
  [8913a72c] NonlinearSolve v3.7.3
  [510215fc] Observables v0.5.5
  [6fe1bfb0] OffsetArrays v1.13.0
  [4d8831e6] OpenSSL v1.4.1
  [429524aa] Optim v1.9.2
  [bac558e1] OrderedCollections v1.6.3
  [1dea7af3] OrdinaryDiffEq v6.73.1
  [90014a1f] PDMats v0.11.31
  [65ce6f38] PackageExtensionCompat v1.0.2
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.8.1
  [fa939f87] Pidfile v1.3.0
  [a03496cd] PlotlyBase v0.8.19
  [f0f68f2c] PlotlyJS v0.18.13
  [f2990250] PlotlyKaleido v2.2.2
  [e409e4f3] PoissonRandom v0.4.4
  [f517fe37] Polyester v0.7.9
  [1d0040c9] PolyesterWeave v0.2.1
  [f27b6e38] Polynomials v4.0.6
  [2dfb63ee] PooledArrays v1.4.3
  [85a6dd25] PositiveFactorizations v0.2.4
  [d236fae5] PreallocationTools v0.4.20
  [aea7be01] PrecompileTools v1.2.0
⌃ [21216c6a] Preferences v1.4.1
  [08abe8d2] PrettyTables v2.3.1
  [49802e3a] ProgressBars v1.5.1
  [6c5003b2] PyMNE v0.2.2
  [6099a3de] PythonCall v0.9.15
  [1fd47b50] QuadGK v2.9.4
  [6f49c342] RCall v0.14.1
  [df47a6cb] RData v1.0.0
  [74087812] Random123 v1.7.0
  [e6cf234a] RandomNumbers v1.5.3
  [3cdcf5f2] RecipesBase v1.3.4
  [731186ca] RecursiveArrayTools v3.10.1
  [f2c3362d] RecursiveFactorization v0.2.21
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [ae5879a3] ResettableStacks v1.1.1
  [79098fc4] Rmath v0.7.1
  [f2b01f46] Roots v2.1.2
  [7e49a35a] RuntimeGeneratedFunctions v0.5.12
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.42
  [0bca4576] SciMLBase v2.29.0
  [c0aeaf25] SciMLOperators v0.3.8
  [6c6a2e73] Scratch v1.2.1
  [91c51154] SentinelArrays v1.4.1
  [efcf1570] Setfield v1.1.1
  [1277b4bf] ShiftedArrays v2.0.0
  [777ac1f9] SimpleBufferStream v1.1.0
  [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 v1.9.3
  [1e83bf80] StaticArraysCore v1.4.2
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.2
  [4c63d2b9] StatsFuns v1.3.1
  [3eaba693] StatsModels v0.7.3
  [9672c7b4] SteadyStateDiffEq v2.0.1
  [789caeaf] StochasticDiffEq v6.65.1
  [7792a7ef] StrideArraysCore v0.5.2
  [892a3eda] StringManipulation v0.3.4
  [856f2bd8] StructTypes v1.10.0
  [c3572dad] Sundials v4.24.0
  [2efcf032] SymbolicIndexingInterface v0.3.8
  [dc5dba14] TZJData v1.1.0+2023d
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.11.1
  [62fd8b95] TensorCore v0.1.1
  [b718987f] TextWrap v1.0.1
  [8290d209] ThreadingUtilities v0.5.2
  [f269a46b] TimeZones v1.13.0
  [a759f4b9] TimerOutputs v0.5.23
  [3bb67fe8] TranscodingStreams v0.10.3
  [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
  [e17b2a0c] UnsafePointers v1.0.0
  [3d5dd08c] VectorizationBase v0.21.65
  [81def892] VersionParsing v1.3.0
  [19fa3120] VertexSafeGraphs v0.2.0
  [ea10d353] WeakRefStrings v1.4.2
  [0f1e0344] WebIO v0.8.21
  [104b5d7c] WebSockets v1.6.0
  [cc8bc4a8] Widgets v0.6.6
  [1b915085] WinReg v1.0.0
  [76eceee3] WorkerUtilities v1.6.1
  [fdbf4ff8] XLSX v0.10.1
  [a5390f91] ZipFile v0.10.1
  [6e34b625] Bzip2_jll v1.0.8+1
  [f5851436] FFTW_jll v3.3.10+0
  [1d5cc7b8] IntelOpenMP_jll v2024.0.2+0
  [f7e6163d] Kaleido_jll v0.2.1+0
  [94ce4f54] Libiconv_jll v1.17.0+0
  [856f044c] MKL_jll v2024.0.0+0
  [458c3c95] OpenSSL_jll v3.0.13+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [f50d1b31] Rmath_jll v0.4.0+0
⌅ [fb77eaff] Sundials_jll v5.2.2+0
⌃ [02c8fc9c] XML2_jll v2.12.2+0
  [f8abcde7] micromamba_jll v1.4.9+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
  [9abbd945] Profile
  [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 ⌃ 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 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: 12 × Apple M2 Pro
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, apple-m1)
Threads: 1 default, 0 interactive, 1 GC (on 8 virtual cores)
Environment:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS =
@tomdstone tomdstone added the bug label Mar 1, 2024
@ChrisRackauckas
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@AayushSabharwal I think this broke with the SII changes.

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