SciML / Catalyst.jl

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
https://docs.sciml.ai/Catalyst/stable/
Other
460 stars 77 forks source link

DSL doesn't allow `@species` to be assigned default values and metadata when using `begin ... end` syntax #1054

Closed jonathanfischer97 closed 1 day ago

jonathanfischer97 commented 2 weeks ago

Can't assign default value AND include species metadata within @species begin block

Trying to define this reaction network, where

will generate the following error:

ERROR: syntax: misplaced assignment statement in "[#482#description = "Enzyme"]" around ~/.julia/packages/Catalyst/48wH3/src/dsl.jl:600
Stacktrace:
 [1] top-level scope

Combination of begin block, default species assignment, and extra metadata produce the error

It seems this is a problem with how the DSL is parsing the new begin block syntax.

Using this syntax and giving a default value, OR metadata, doesn't seem to produce an error. Only the combination of these two specie specifications within a begin block produces the error.

Additionally, it only affects the @species block, not @parameters

catalysis_sys = @reaction_network begin
    @species begin
        E(t), [description = "Enzyme"]
        Pᵢ(t) = 1.0
        Pₐ(t) = 0.0
    end
    @parameters begin
        k = 1.0, [description = "Catalysis rate"]
    end
    k*E, Pᵢ --> Pₐ
end

Environment (please complete the following information):

  [c7e460c6] ArgParse v1.2.0
  [6e4b80f9] BenchmarkTools v1.5.0
⌃ [0f109fa4] BifurcationKit v0.3.6
  [336ed68f] CSV v0.10.14
  [13f3f980] CairoMakie v0.12.11
  [479239e8] Catalyst v14.4.1
  [324d7699] CategoricalArrays v0.10.8
  [aaaa29a8] Clustering v0.15.7
  [35d6a980] ColorSchemes v3.26.0
  [5ae59095] Colors v0.12.11
  [b0b7db55] ComponentArrays v0.15.17
  [f68482b8] Cthulhu v2.15.0
  [a93c6f00] DataFrames v1.6.1
  [1313f7d8] DataFramesMeta v0.15.3
  [85a47980] Dictionaries v0.4.2
  [459566f4] DiffEqCallbacks v3.9.1
  [0c46a032] DifferentialEquations v7.14.0
  [0703355e] DimensionalData v0.28.0
  [b4f34e82] Distances v0.10.11
  [31c24e10] Distributions v0.25.111
  [634d3b9d] DrWatson v2.16.0
  [7c1d4256] DynamicPolynomials v0.6.0
  [06fc5a27] DynamicQuantities v1.0.0
  [61744808] DynamicalSystems v3.3.20
  [86b6b26d] Evolutionary v0.11.2 `~/.julia/dev/Evolutionary`
  [7a1cc6ca] FFTW v1.8.0
  [f6369f11] ForwardDiff v0.10.36
  [e9467ef8] GLMakie v0.10.11
  [f213a82b] HomotopyContinuation v2.11.0
  [5903a43b] Infiltrator v1.8.3
  [b964fa9f] LaTeXStrings v1.3.1
  [2ee39098] LabelledArrays v1.16.0
  [23fbe1c1] Latexify v0.16.5
  [33e6dc65] MKL v0.7.0
  [ee78f7c6] Makie v0.21.11
  [961ee093] ModelingToolkit v9.40.0
  [6f286f6a] MultivariateStats v0.10.3
  [b8a86587] NearestNeighbors v0.4.18
  [8913a72c] NonlinearSolve v3.14.0
  [510215fc] Observables v0.5.5
  [5fb14364] OhMyREPL v0.5.28
  [67456a42] OhMyThreads v0.6.0
  [1dea7af3] OrdinaryDiffEq v6.89.0
  [91a5bcdd] Plots v1.40.8
  [c3e4b0f8] Pluto v0.19.46
  [2dfb63ee] PooledArrays v1.4.3
  [08abe8d2] PrettyTables v2.3.2
  [92933f4c] ProgressMeter v1.10.2
  [1e97bd63] ReachabilityAnalysis v0.26.1
  [295af30f] Revise v3.5.18
  [7e49a35a] RuntimeGeneratedFunctions v0.5.13
  [efcf1570] Setfield v1.1.1
  [f1835b91] SpeedMapping v0.3.0
  [90137ffa] StaticArrays v1.9.7
  [2913bbd2] StatsBase v0.34.3
  [f3b207a7] StatsPlots v0.15.7
  [9672c7b4] SteadyStateDiffEq v2.4.0
  [2efcf032] SymbolicIndexingInterface v0.3.30
  [d1185830] SymbolicUtils v3.7.0
  [0c5d862f] Symbolics v6.11.0
  [22787eb5] Term v2.0.6
  [811555cd] ThreadPinning v1.0.2
  [b8865327] UnicodePlots v3.6.4
  [276b4fcb] WGLMakie v0.10.11
  [fdbf4ff8] XLSX v0.10.3
  [8ba89e20] Distributed
  [b77e0a4c] InteractiveUtils
  [37e2e46d] LinearAlgebra
  [9a3f8284] Random
  [10745b16] Statistics v1.10.0
  [47edcb42] ADTypes v1.8.0
  [a4c015fc] ANSIColoredPrinters v0.0.1
  [621f4979] AbstractFFTs v1.5.0
  [398f06c4] AbstractLattices v0.3.1
  [1520ce14] AbstractTrees v0.4.5
  [7d9f7c33] Accessors v0.1.38
  [22286c92] AccurateArithmetic v0.3.8
  [79e6a3ab] Adapt v4.0.4
  [35492f91] AdaptivePredicates v1.2.0
  [66dad0bd] AliasTables v1.1.3
  [27a7e980] Animations v0.4.1
  [fb37089c] Arblib v1.2.1
  [dce04be8] ArgCheck v2.3.0
  [c7e460c6] ArgParse v1.2.0
  [ec485272] ArnoldiMethod v0.4.0
⌅ [7d9fca2a] Arpack v0.5.3
  [4fba245c] ArrayInterface v7.16.0
  [4c555306] ArrayLayouts v1.10.3
  [f3fd9213] Attractors v1.19.4
  [67c07d97] Automa v1.0.4
  [13072b0f] AxisAlgorithms v1.1.0
  [39de3d68] AxisArrays v0.4.7
  [aae01518] BandedMatrices v1.7.5
  [198e06fe] BangBang v0.4.3
  [6e4b80f9] BenchmarkTools v1.5.0
⌃ [0f109fa4] BifurcationKit v0.3.6
  [e2ed5e7c] Bijections v0.1.9
  [d1d4a3ce] BitFlags v0.1.9
  [62783981] BitTwiddlingConvenienceFunctions v0.1.6
  [a134a8b2] BlackBoxOptim v0.6.3
  [8e7c35d0] BlockArrays v1.1.1
  [824d6782] Bonito v3.2.0
  [764a87c0] BoundaryValueDiffEq v5.10.0
  [fa961155] CEnum v0.5.0
  [2a0fbf3d] CPUSummary v0.2.6
  [a9c8d775] CPUTime v1.0.0
  [96374032] CRlibm v1.0.1
  [00ebfdb7] CSTParser v3.4.3
  [336ed68f] CSV v0.10.14
  [159f3aea] Cairo v1.1.0
  [13f3f980] CairoMakie v0.12.11
  [49dc2e85] Calculus v0.5.1
⌅ [4803f6b2] CarlemanLinearization v0.3.4
  [479239e8] Catalyst v14.4.1
  [324d7699] CategoricalArrays v0.10.8
  [8be319e6] Chain v0.6.0
  [d360d2e6] ChainRulesCore v1.24.0
  [608a59af] ChaosTools v3.1.2
  [ae650224] ChunkSplitters v2.4.5
  [fb6a15b2] CloseOpenIntervals v0.1.13
  [aaaa29a8] Clustering v0.15.7
  [da1fd8a2] CodeTracking v1.3.6
  [523fee87] CodecBzip2 v0.8.4
  [6309b1aa] CodecInflate64 v0.1.3
  [944b1d66] CodecZlib v0.7.6
  [a2cac450] ColorBrewer v0.4.0
  [35d6a980] ColorSchemes v3.26.0
  [3da002f7] ColorTypes v0.11.5
  [c3611d14] ColorVectorSpace v0.10.0
  [5ae59095] Colors v0.12.11
  [861a8166] Combinatorics v1.0.2
  [a80b9123] CommonMark v0.8.12
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.1
  [f70d9fcc] CommonWorldInvalidations v1.0.0
  [34da2185] Compat v4.16.0
  [ab4b797d] ComplexityMeasures v3.6.6
  [b0b7db55] ComponentArrays v0.15.17
  [b152e2b5] CompositeTypes v0.1.4
  [a33af91c] CompositionsBase v0.1.2
  [2569d6c7] ConcreteStructs v0.2.3
  [f0e56b4a] ConcurrentUtilities v2.4.2
  [5218b696] Configurations v0.17.6
  [187b0558] ConstructionBase v1.5.8
  [d38c429a] Contour v0.6.3
  [a2441757] Coverage v1.6.1
  [c36e975a] CoverageTools v1.3.2
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [f68482b8] Cthulhu v2.15.0
  [717857b8] DSP v0.7.9
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.6.1
  [1313f7d8] DataFramesMeta v0.15.3
  [864edb3b] DataStructures v0.18.20
  [e2d170a0] DataValueInterfaces v1.0.0
  [927a84f5] DelaunayTriangulation v1.4.0
  [bcd4f6db] DelayDiffEq v5.48.1
  [5732040d] DelayEmbeddings v2.7.4
  [8bb1440f] DelimitedFiles v1.9.1
  [85a47980] Dictionaries v0.4.2
  [2b5f629d] DiffEqBase v6.155.1
  [459566f4] DiffEqCallbacks v3.9.1
  [77a26b50] DiffEqNoiseProcess v5.23.0
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [0c46a032] DifferentialEquations v7.14.0
  [a0c0ee7d] DifferentiationInterface v0.5.17
  [0703355e] DimensionalData v0.28.0
  [8d63f2c5] DispatchDoctor v0.4.14
  [b4f34e82] Distances v0.10.11
  [31c24e10] Distributions v0.25.111
  [ffbed154] DocStringExtensions v0.9.3
  [e30172f5] Documenter v1.7.0
  [35a29f4d] DocumenterTools v0.1.19
  [5b8099bc] DomainSets v0.7.14
  [634d3b9d] DrWatson v2.16.0
  [7c1d4256] DynamicPolynomials v0.6.0
  [06fc5a27] DynamicQuantities v1.0.0
  [61744808] DynamicalSystems v3.3.20
  [6e36e845] DynamicalSystemsBase v3.9.1
  [fdbdab4c] ElasticArrays v1.2.12
  [4e289a0a] EnumX v1.0.4
  [f151be2c] EnzymeCore v0.7.8
  [90fa49ef] ErrorfreeArithmetic v0.5.2
  [6912e4f1] Espresso v0.6.3
  [86b6b26d] Evolutionary v0.11.2 `~/.julia/dev/Evolutionary`
⌃ [429591f6] ExactPredicates v2.2.5
  [460bff9d] ExceptionUnwrapping v0.1.10
  [d4d017d3] ExponentialUtilities v1.26.1
  [e2ba6199] ExprTools v0.1.10
  [21656369] ExpressionExplorer v1.0.4
⌅ [6b7a57c9] Expronicon v0.8.5
  [55351af7] ExproniconLite v0.10.13
  [411431e0] Extents v0.1.4
  [8f5d6c58] EzXML v1.2.0
  [c87230d0] FFMPEG v0.4.1
  [7a1cc6ca] FFTW v1.8.0
  [9d29842c] FastAlmostBandedMatrices v0.1.3
  [7034ab61] FastBroadcast v0.3.5
  [9aa1b823] FastClosures v0.3.2
  [442a2c76] FastGaussQuadrature v1.0.2
  [29a986be] FastLapackInterface v2.0.4
  [fa42c844] FastRounding v0.3.1
  [5789e2e9] FileIO v1.16.3
  [8fc22ac5] FilePaths v0.8.3
  [48062228] FilePathsBase v0.9.22
  [1a297f60] FillArrays v1.13.0
  [64ca27bc] FindFirstFunctions v1.4.1
  [6a86dc24] FiniteDiff v2.24.0
  [53c48c17] FixedPointNumbers v0.8.5
  [1eca21be] FoldingTrees v1.2.1
  [1fa38f19] Format v1.3.7
  [f6369f11] ForwardDiff v0.10.36
  [4665ce21] FractalDimensions v1.8.1
  [b38be410] FreeType v4.1.1
  [663a7486] FreeTypeAbstraction v0.10.3
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [d9f16b24] Functors v0.4.12
⌅ [fb4132e2] FuzzyCompletions v0.5.4
  [f7f18e0c] GLFW v3.4.3
  [e9467ef8] GLMakie v0.10.11
  [60bf3e95] GLPK v1.2.1
  [46192b85] GPUArraysCore v0.1.6
⌃ [28b8d3ca] GR v0.73.5
  [c145ed77] GenericSchur v0.5.4
  [68eda718] GeoFormatTypes v0.4.2
  [cf35fbd7] GeoInterface v1.3.6
  [5c1252a2] GeometryBasics v0.4.11
⌃ [d7ba0133] Git v1.3.0
  [c27321d9] Glob v1.3.1
  [a2bd30eb] Graphics v1.1.2
  [86223c79] Graphs v1.11.2
  [3955a311] GridLayoutBase v0.11.0
  [42e2da0e] Grisu v1.0.2
  [708ec375] Gumbo v0.8.2
  [cd3eb016] HTTP v1.10.8
  [eafb193a] Highlights v0.5.3
  [f213a82b] HomotopyContinuation v2.11.0
  [3e5b6fbb] HostCPUFeatures v0.1.17
  [0e44f5e4] Hwloc v3.3.0
  [2207ec0c] HybridSystems v0.4.3
  [34004b35] HypergeometricFunctions v0.3.24
  [47d2ed2b] Hyperscript v0.0.5
  [ac1192a8] HypertextLiteral v0.9.5
  [09f84164] HypothesisTests v0.11.2
  [b5f81e59] IOCapture v0.2.5
  [615f187c] IfElse v0.1.1
  [2803e5a7] ImageAxes v0.6.11
  [c817782e] ImageBase v0.1.7
  [a09fc81d] ImageCore v0.10.2
  [82e4d734] ImageIO v0.6.8
  [bc367c6b] ImageMetadata v0.9.9
  [313cdc1a] Indexing v1.1.1
  [9b13fd28] IndirectArrays v1.0.0
  [5903a43b] Infiltrator v1.8.3
  [d25df0c9] Inflate v0.1.5
  [22cec73e] InitialValues v0.3.1
  [842dd82b] InlineStrings v1.4.2
  [0c81fc1b] InputBuffers v1.0.0
  [18e54dd8] IntegerMathUtils v0.1.2
  [85a1e053] Interfaces v0.3.2
  [a98d9a8b] Interpolations v0.15.1
⌅ [d1acc4aa] IntervalArithmetic v0.20.9
⌅ [5c1f47dc] IntervalMatrices v0.10.0
  [d2bf35a9] IntervalRootFinding v0.5.11
  [8197267c] IntervalSets v0.7.10
  [524e6230] IntervalTrees v1.1.0
  [3587e190] InverseFunctions v0.1.16
  [41ab1584] InvertedIndices v1.3.0
  [92d709cd] IrrationalConstants v0.2.2
  [f1662d9f] Isoband v0.1.1
  [c8e1da08] IterTools v1.10.0
  [42fd0dbc] IterativeSolvers v0.9.4
  [82899510] IteratorInterfaceExtensions v1.0.0
⌅ [033835bb] JLD2 v0.4.53
  [1019f520] JLFzf v0.1.8
  [692b3bcd] JLLWrappers v1.6.0
  [682c06a0] JSON v0.21.4
  [b835a17e] JpegTurbo v0.1.5
⌃ [4076af6c] JuMP v1.13.0
  [98e50ef6] JuliaFormatter v1.0.60
  [aa1ae85d] JuliaInterpreter v0.9.36
  [70703baa] JuliaSyntax v0.4.10
  [ccbc3e58] JumpProcesses v9.13.7
  [ef3ab10e] KLU v0.6.0
  [5ab0869b] KernelDensity v0.6.9
  [ba0b0d4f] Krylov v0.9.6
  [0b1a1467] KrylovKit v0.8.1
  [8ac3fa9e] LRUCache v1.6.1
  [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
  [0e77f7df] LazilyInitializedFields v1.2.2
  [5078a376] LazyArrays v2.2.1
  [8cdb02fc] LazyModules v0.3.1
  [b4f0291d] LazySets v2.14.2
  [2d8b4e74] LevyArea v1.0.0
  [9c8b4983] LightXML v0.9.1
  [d3d80556] LineSearches v7.3.0
  [9b3f67b0] LinearAlgebraX v0.2.10
  [7a12625a] LinearMaps v3.11.3
  [7ed4a6bd] LinearSolve v2.34.0
  [2ab3a3ac] LogExpFunctions v0.3.28
  [e6f89c97] LoggingExtras v1.0.3
  [fc60dff9] LombScargle v1.0.3
  [bdcacae8] LoopVectorization v0.12.171
  [6f1432cf] LoweredCodeUtils v3.0.2
  [6c6e2e6c] MIMEs v0.1.4
  [33e6dc65] MKL v0.7.0
  [d8e11817] MLStyle v0.4.17
  [1914dd2f] MacroTools v0.5.13
  [ee78f7c6] Makie v0.21.11
  [20f20a25] MakieCore v0.8.8
  [36869731] Malt v1.1.1
  [d125e4d3] ManualMemory v0.1.8
  [dbb5928d] MappedArrays v0.4.2
  [299715c1] MarchingCubes v0.1.9
  [d0879d2d] MarkdownAST v0.1.2
  [b8f27783] MathOptInterface v1.31.2
  [0a4f8689] MathTeXEngine v0.6.1
  [d14a8603] MathematicalSystems v0.13.6
  [a3b82374] MatrixFactorizations v3.0.1
  [bb5d69b7] MaybeInplace v0.1.4
  [739be429] MbedTLS v1.1.9
  [eff96d63] Measurements v2.11.0
  [442fdcdd] Measures v0.3.2
  [7269a6da] MeshIO v0.4.12
  [e1d29d7a] Missings v1.2.0
  [291d046c] MixedSubdivisions v1.1.4
  [961ee093] ModelingToolkit v9.40.0
  [66fc600b] ModernGL v1.1.7
  [7475f97c] Mods v2.2.5
  [e94cdb99] MosaicViews v0.3.4
  [99f44e22] MsgPack v1.2.1
  [46d2c3a1] MuladdMacro v0.2.4
  [3b2b4ff1] Multisets v0.4.5
  [102ac46a] MultivariatePolynomials v0.5.6
  [6f286f6a] MultivariateStats v0.10.3
  [d8a4904e] MutableArithmetics v1.4.6
  [1c23619d] MyterialColors v0.3.0
  [d41bc354] NLSolversBase v7.8.3
  [2774e3e8] NLsolve v4.5.1
  [77ba4419] NaNMath v1.0.2
  [b8a86587] NearestNeighbors v0.4.18
  [645ca80c] Neighborhood v0.2.4
  [f09324ee] Netpbm v1.1.1
  [8913a72c] NonlinearSolve v3.14.0
  [510215fc] Observables v0.5.5
  [6fe1bfb0] OffsetArrays v1.14.1
  [5fb14364] OhMyREPL v0.5.28
  [67456a42] OhMyThreads v0.6.0
  [52e1d378] OpenEXR v0.3.2
  [4d8831e6] OpenSSL v1.4.3
  [429524aa] Optim v1.9.4
  [bac558e1] OrderedCollections v1.6.3
  [1dea7af3] OrdinaryDiffEq v6.89.0
  [89bda076] OrdinaryDiffEqAdamsBashforthMoulton v1.1.0
  [6ad6398a] OrdinaryDiffEqBDF v1.1.2
  [bbf590c4] OrdinaryDiffEqCore v1.6.0
  [50262376] OrdinaryDiffEqDefault v1.1.0
  [4302a76b] OrdinaryDiffEqDifferentiation v1.1.0
  [9286f039] OrdinaryDiffEqExplicitRK v1.1.0
  [e0540318] OrdinaryDiffEqExponentialRK v1.1.0
  [becaefa8] OrdinaryDiffEqExtrapolation v1.1.0
  [5960d6e9] OrdinaryDiffEqFIRK v1.1.1
  [101fe9f7] OrdinaryDiffEqFeagin v1.1.0
  [d3585ca7] OrdinaryDiffEqFunctionMap v1.1.1
  [d28bc4f8] OrdinaryDiffEqHighOrderRK v1.1.0
  [9f002381] OrdinaryDiffEqIMEXMultistep v1.1.0
  [521117fe] OrdinaryDiffEqLinear v1.1.0
  [1344f307] OrdinaryDiffEqLowOrderRK v1.2.0
  [b0944070] OrdinaryDiffEqLowStorageRK v1.2.1
  [127b3ac7] OrdinaryDiffEqNonlinearSolve v1.2.1
  [c9986a66] OrdinaryDiffEqNordsieck v1.1.0
  [5dd0a6cf] OrdinaryDiffEqPDIRK v1.1.0
  [5b33eab2] OrdinaryDiffEqPRK v1.1.0
  [04162be5] OrdinaryDiffEqQPRK v1.1.0
  [af6ede74] OrdinaryDiffEqRKN v1.1.0
  [43230ef6] OrdinaryDiffEqRosenbrock v1.2.0
  [2d112036] OrdinaryDiffEqSDIRK v1.1.0
  [669c94d9] OrdinaryDiffEqSSPRK v1.2.0
  [e3e12d00] OrdinaryDiffEqStabilizedIRK v1.1.0
  [358294b1] OrdinaryDiffEqStabilizedRK v1.1.0
  [fa646aed] OrdinaryDiffEqSymplecticRK v1.1.0
  [b1df2697] OrdinaryDiffEqTsit5 v1.1.0
  [79d7bb75] OrdinaryDiffEqVerner v1.1.1
  [90014a1f] PDMats v0.11.31
  [f57f5aa1] PNGFiles v0.4.3
  [65ce6f38] PackageExtensionCompat v1.0.2
  [19eb6ba3] Packing v0.5.0
  [5432bcbf] PaddedViews v0.5.12
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.8.1
  [2ae35dd2] Permutations v0.4.22
  [b98c9c47] Pipe v1.3.0
  [eebad327] PkgVersion v0.3.3
  [ccf2f8ad] PlotThemes v3.2.0
  [995b91a9] PlotUtils v1.4.1
  [91a5bcdd] Plots v1.40.8
  [c3e4b0f8] Pluto v0.19.46
  [72656b73] PlutoDependencyExplorer v1.0.4
  [e409e4f3] PoissonRandom v0.4.4
  [f517fe37] Polyester v0.7.16
  [1d0040c9] PolyesterWeave v0.2.2
  [647866c9] PolygonOps v0.1.2
⌅ [f27b6e38] Polynomials v3.2.4
  [2dfb63ee] PooledArrays v1.4.3
  [85a6dd25] PositiveFactorizations v0.2.4
  [d236fae5] PreallocationTools v0.4.24
  [91cefc8d] PrecompileSignatures v3.0.3
  [aea7be01] PrecompileTools v1.2.1
  [31e2f376] PredefinedDynamicalSystems v1.2.0
  [21216c6a] Preferences v1.4.3
  [08abe8d2] PrettyTables v2.3.2
  [27ebfcd6] Primes v0.5.6
  [33c8b6b6] ProgressLogging v0.1.4
  [92933f4c] ProgressMeter v1.10.2
  [01f381cc] ProjectiveVectors v1.1.4
  [43287f4e] PtrArrays v1.2.1
  [4b34888f] QOI v1.0.0
  [1fd47b50] QuadGK v2.11.0
  [74087812] Random123 v1.7.0
  [e6cf234a] RandomNumbers v1.6.0
  [b3c3ace0] RangeArrays v0.3.2
  [c84ed2f1] Ratios v0.4.5
  [1e97bd63] ReachabilityAnalysis v0.26.1
  [379f33d0] ReachabilityBase v0.3.1
  [3cdcf5f2] RecipesBase v1.3.4
  [01d81517] RecipesPipeline v0.6.12
  [639c3291] RecurrenceAnalysis v2.0.8
  [731186ca] RecursiveArrayTools v3.27.0
  [f2c3362d] RecursiveFactorization v0.2.23
  [189a3867] Reexport v1.2.2
  [2792f1a3] RegistryInstances v0.1.0
  [05181044] RelocatableFolders v1.0.1
  [ae029012] Requires v1.3.0
  [ae5879a3] ResettableStacks v1.1.1
  [295af30f] Revise v3.5.18
  [286e9d63] RingLists v0.2.9
  [79098fc4] Rmath v0.8.0
  [f2b01f46] Roots v2.2.1
  [5eaf0fd0] RoundingEmulator v0.2.1
  [7e49a35a] RuntimeGeneratedFunctions v0.5.13
  [fdea26ae] SIMD v3.5.0
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.43
  [322a6be2] Sass v0.2.0
  [0bca4576] SciMLBase v2.53.1
  [c0aeaf25] SciMLOperators v0.3.10
  [53ae85a6] SciMLStructures v1.5.0
  [6c6a2e73] Scratch v1.2.1
  [8e049039] SemialgebraicSets v0.3.3
  [91c51154] SentinelArrays v1.4.5
  [3cc68bcd] SetRounding v0.2.1
  [efcf1570] Setfield v1.1.1
  [65257c39] ShaderAbstractions v0.4.1
  [992d4aef] Showoff v1.0.3
  [73760f76] SignedDistanceFields v0.4.0
  [777ac1f9] SimpleBufferStream v1.1.0
  [55797a34] SimpleGraphs v0.8.6
  [727e6d20] SimpleNonlinearSolve v1.12.1
  [ec83eff0] SimplePartitions v0.3.3
  [cc47b68c] SimplePolynomials v0.2.18
  [a6525b86] SimpleRandom v0.3.2
  [699a6c99] SimpleTraits v0.9.4
  [ce78b400] SimpleUnPack v1.1.0
  [45858cf5] Sixel v0.1.3
  [66db9d55] SnoopPrecompile v1.0.3
  [a2af1166] SortingAlgorithms v1.2.1
  [47a9eef4] SparseDiffTools v2.20.0
  [0a514795] SparseMatrixColorings v0.4.0
  [e56a9233] Sparspak v0.3.9
  [d4ead438] SpatialIndexing v0.1.6
  [276daf66] SpecialFunctions v2.4.0
  [f1835b91] SpeedMapping v0.3.0
  [91464d47] StableTasks v0.1.5
  [cae243ae] StackViews v0.1.1
  [40b095a5] StateSpaceSets v1.5.0
  [aedffcd0] Static v1.1.1
  [0d7ed370] StaticArrayInterface v1.8.0
  [90137ffa] StaticArrays v1.9.7
  [1e83bf80] StaticArraysCore v1.4.3
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.3
  [4c63d2b9] StatsFuns v1.3.2
  [f3b207a7] StatsPlots v0.15.7
  [9672c7b4] SteadyStateDiffEq v2.4.0
  [789caeaf] StochasticDiffEq v6.69.0
  [7792a7ef] StrideArraysCore v0.5.7
  [892a3eda] StringManipulation v0.3.4
  [09ab397b] StructArrays v0.6.18
  [c3572dad] Sundials v4.25.0
  [2efcf032] SymbolicIndexingInterface v0.3.30
  [19f23fe9] SymbolicLimits v0.2.2
  [d1185830] SymbolicUtils v3.7.0
  [0c5d862f] Symbolics v6.11.0
  [90a7ee08] SysInfo v0.3.0
  [9ce81f87] TableMetadataTools v0.1.0
  [ab02a1b2] TableOperations v1.2.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [ed4db957] TaskLocalValues v0.1.1
⌅ [92b13dbe] TaylorIntegration v0.15.2
  [314ce334] TaylorModels v0.7.1
⌅ [6aa5eb33] TaylorSeries v0.17.8
  [62fd8b95] TensorCore v0.1.1
  [22787eb5] Term v2.0.6
  [8ea1fca8] TermInterface v2.0.0
  [1c621080] TestItems v1.0.0
  [b718987f] TextWrap v1.0.2
  [811555cd] ThreadPinning v1.0.2
  [6f48bc29] ThreadPinningCore v0.4.5
  [b189fb0b] ThreadPools v2.1.1
  [8290d209] ThreadingUtilities v0.5.2
  [731e570b] TiffImages v0.10.0
  [a759f4b9] TimerOutputs v0.5.24
  [c804724b] TimeseriesSurrogates v2.7.1
  [0796e94c] Tokenize v0.5.29
  [3bb67fe8] TranscodingStreams v0.11.2
  [a2a6695c] TreeViews v0.3.0
  [d5829a12] TriangularSolve v0.2.1
  [410a4b4d] Tricks v0.1.9
  [981d1d27] TriplotBase v0.1.0
  [781d530d] TruncatedStacktraces v1.4.0
  [d265eb64] TypedSyntax v1.4.1
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1cfade01] UnicodeFun v0.4.1
  [b8865327] UnicodePlots v3.6.4
  [1986cc42] Unitful v1.21.0
  [45397f5d] UnitfulLatexify v1.6.4
  [a7c27f48] Unityper v0.1.6
  [41fe7b60] Unzip v0.2.0
  [409d34a3] VectorInterface v0.4.6
  [3d5dd08c] VectorizationBase v0.21.70
  [19fa3120] VertexSafeGraphs v0.2.0
  [276b4fcb] WGLMakie v0.10.11
  [29a6e085] Wavelets v0.10.0
  [ea10d353] WeakRefStrings v1.4.2
  [cc8bc4a8] Widgets v0.6.6
  [eead4739] WidgetsBase v0.1.4
  [b8c1c048] WidthLimitedIO v1.0.1
  [efce3f68] WoodburyMatrices v1.0.0
  [76eceee3] WorkerUtilities v1.6.1
  [fdbf4ff8] XLSX v0.10.3
  [49080126] ZipArchives v2.3.0
  [a5390f91] ZipFile v0.10.1
⌅ [68821587] Arpack_jll v3.5.1+1
  [6e34b625] Bzip2_jll v1.0.8+1
  [4e9b3aee] CRlibm_jll v1.0.1+0
  [83423d85] Cairo_jll v1.18.0+2
  [ee1fde0b] Dbus_jll v1.14.10+0
  [04572ae6] Deno_jll v1.33.4+0
  [5ae413db] EarCut_jll v2.2.4+0
  [2702e6a9] EpollShim_jll v0.0.20230411+0
  [2e619515] Expat_jll v2.6.2+0
⌅ [b22a6f82] FFMPEG_jll v4.4.2+2
  [f5851436] FFTW_jll v3.3.10+0
  [e134572f] FLINT_jll v300.100.300+0
  [a3f928ae] Fontconfig_jll v2.13.96+0
  [d7e528f0] FreeType2_jll v2.13.2+0
  [559328eb] FriBidi_jll v1.0.14+0
  [0656b61e] GLFW_jll v3.4.0+1
  [e8aa6df9] GLPK_jll v5.0.1+0
⌅ [d2c73de3] GR_jll v0.73.5+0
  [78b55507] Gettext_jll v0.21.0+0
⌃ [f8c6e375] Git_jll v2.36.1+2
  [7746bdde] Glib_jll v2.80.2+0
  [3b182d85] Graphite2_jll v1.3.14+0
  [528830af] Gumbo_jll v0.10.2+0
  [2e76f6c2] HarfBuzz_jll v8.3.1+0
  [e33a78d0] Hwloc_jll v2.11.1+0
  [905a6f67] Imath_jll v3.1.11+0
  [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0
  [aacddb02] JpegTurbo_jll v3.0.3+0
  [c1c5ebd0] LAME_jll v3.100.2+0
⌅ [88015f11] LERC_jll v3.0.0+1
  [1d63c593] LLVMOpenMP_jll v18.1.7+0
  [dd4b983a] LZO_jll v2.10.2+0
⌅ [e9f186c6] Libffi_jll v3.2.2+1
  [d4300ac3] Libgcrypt_jll v1.8.11+0
  [7e76a0d4] Libglvnd_jll v1.6.0+0
  [7add5ba3] Libgpg_error_jll v1.49.0+0
  [94ce4f54] Libiconv_jll v1.17.0+0
  [4b2f31a3] Libmount_jll v2.40.1+0
⌅ [89763e89] Libtiff_jll v4.5.1+1
  [38a345b3] Libuuid_jll v2.40.1+0
  [856f044c] MKL_jll v2024.2.0+0
  [2ce0c516] MPC_jll v1.2.1+0
  [e7412a2a] Ogg_jll v1.3.5+1
⌅ [656ef2d0] OpenBLAS32_jll v0.3.24+0
  [18a262bb] OpenEXR_jll v3.2.4+0
⌅ [9bd350c2] OpenSSH_jll v8.9.0+1
⌅ [458c3c95] OpenSSL_jll v1.1.23+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [91d4177d] Opus_jll v1.3.3+0
  [36c8627f] Pango_jll v1.54.1+0
  [30392449] Pixman_jll v0.43.4+0
⌅ [c0090381] Qt6Base_jll v6.5.2+2
  [f50d1b31] Rmath_jll v0.5.1+0
⌅ [fb77eaff] Sundials_jll v5.2.2+0
⌅ [3428059b] SymEngine_jll v0.9.0+1
  [a44049a8] Vulkan_Loader_jll v1.3.243+0
  [a2964d1f] Wayland_jll v1.21.0+1
  [2381bf8a] Wayland_protocols_jll v1.31.0+0
  [02c8fc9c] XML2_jll v2.13.3+0
  [aed1982a] XSLT_jll v1.1.41+0
  [ffd25f8a] XZ_jll v5.4.6+0
  [f67eecfb] Xorg_libICE_jll v1.1.1+0
  [c834827a] Xorg_libSM_jll v1.2.4+0
  [4f6342f7] Xorg_libX11_jll v1.8.6+0
  [0c0b7dd1] Xorg_libXau_jll v1.0.11+0
  [935fb764] Xorg_libXcursor_jll v1.2.0+4
  [a3789734] Xorg_libXdmcp_jll v1.1.4+0
  [1082639a] Xorg_libXext_jll v1.3.6+0
  [d091e8ba] Xorg_libXfixes_jll v5.0.3+4
  [a51aa0fd] Xorg_libXi_jll v1.7.10+4
  [d1454406] Xorg_libXinerama_jll v1.1.4+4
  [ec84b674] Xorg_libXrandr_jll v1.5.2+4
  [ea2f1a96] Xorg_libXrender_jll v0.9.11+0
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.1+0
  [c7cfdc94] Xorg_libxcb_jll v1.17.0+0
  [cc61e674] Xorg_libxkbfile_jll v1.1.2+0
  [e920d4aa] Xorg_xcb_util_cursor_jll v0.1.4+0
  [12413925] Xorg_xcb_util_image_jll v0.4.0+1
  [2def613f] Xorg_xcb_util_jll v0.4.0+1
  [975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
  [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
  [c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
  [35661453] Xorg_xkbcomp_jll v1.4.6+0
  [33bec58e] Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] Xorg_xtrans_jll v1.5.0+0
  [3161d3a3] Zstd_jll v1.5.6+0
  [35ca27e7] eudev_jll v3.2.9+0
  [214eeab7] fzf_jll v0.53.0+0
  [1a1c6b14] gperf_jll v3.1.1+0
  [9a68df92] isoband_jll v0.2.3+0
  [a4ae2306] libaom_jll v3.9.0+0
  [0ac62f75] libass_jll v0.15.2+0
  [1183f4f0] libdecor_jll v0.2.2+0
  [2db6ffa8] libevdev_jll v1.11.0+0
  [f638f0a6] libfdk_aac_jll v2.0.3+0
  [36db933b] libinput_jll v1.18.0+0
  [b53b4c65] libpng_jll v1.6.43+1
  [47bcb7c8] libsass_jll v3.6.6+0
  [075b6546] libsixel_jll v1.10.3+0
  [f27f6e37] libvorbis_jll v1.3.7+2
  [009596ad] mtdev_jll v1.1.6+0
  [1317d2d5] oneTBB_jll v2021.12.0+0
⌅ [1270edf5] x264_jll v2021.5.5+0
⌅ [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+1
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [8bf52ea8] CRC32c
  [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 v1.1.1+0
  [781609d7] GMP_jll v6.2.1+6
  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.6.4+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [3a97d323] MPFR_jll v4.2.0+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
  [efcefdf7] PCRE2_jll v10.42.0+1
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2
Julia Version 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 36 × Intel(R) Core(TM) i9-10980XE CPU @ 3.00GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, cascadelake)
Threads: 18 default, 0 interactive, 9 GC (on 36 virtual cores)
Environment:
  LD_LIBRARY_PATH = /tmp/.mount_cursor0DmoQI/usr/lib:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS = 18
isaacsas commented 1 week ago

This seems to actually be a Symbolics.jl bug. These work:

using ModelingToolkit
t = ModelingToolkit.t_nounits
@variables u(t)=1 [input = true, disturbance = true]
@variables begin
    u(t) = 1 
end
@parameters  begin
    a = 1
end
@parameters  begin
           a = 1, [input = true, description = "true"]
end

but this errors

julia> @variables begin
           u(t) = 1, [input = true]
       end
ERROR: syntax: misplaced assignment statement in "[input = true]" around REPL[37]:1
Stacktrace:
 [1] top-level scope
   @ REPL[37]:1

as does

julia> @parameters begin
                  u(t)=1, [input=true]
              end
ERROR: syntax: misplaced assignment statement in "[input = true]" around REPL[61]:1
Stacktrace:
 [1] top-level scope
   @ REPL[61]:1
isaacsas commented 1 week ago

This requires someone to update _parse_vars in Symbolics.jl I think. See https://github.com/JuliaSymbolics/Symbolics.jl/issues/1280

isaacsas commented 3 days ago

@jonathanfischer97 these seem fixed if you use ModelingToolkit master now. Can you double check on your end?

isaacsas commented 1 day ago

This now works for me using the latest Catalyst, MTK, and Symbolics releases, so I am going to close this. Feel free to reopen if that is not the case for you.

jonathanfischer97 commented 1 day ago

Thank you guys!