Package evaluation of SyntacticModels on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T17:08:47.173 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.24s ################################################################################ # Installation # Installing SyntacticModels... Resolving package versions... ┌ Warning: tarball content does not match git-tree-sha1 └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:660 Cloning [227ef7b5-1206-438b-ac65-934d6da304b8] ACSets from https://github.com/AlgebraicJulia/ACSets.jl.git Installed ACSets ─ v0.2.21 Updating `~/.julia/environments/v1.10/Project.toml` [22bb929c] + SyntacticModels v0.2.0 Updating `~/.julia/environments/v1.10/Manifest.toml` [227ef7b5] + ACSets v0.2.21 [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.41 [79e6a3ab] + Adapt v4.2.0 [23cfdc9f] + AlgebraicInterfaces v0.1.4 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.18.0 [13072b0f] + AxisAlgorithms v1.1.0 [39de3d68] + AxisArrays v0.4.7 [e2ed5e7c] + Bijections v0.1.9 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [fa961155] + CEnum v0.5.0 [2a0fbf3d] + CPUSummary v0.2.6 [aafaddc9] + CatIndices v0.2.2 [134e5e36] + Catlab v0.16.19 [d360d2e6] + ChainRulesCore v1.25.1 [fb6a15b2] + CloseOpenIntervals v0.1.13 [aaaa29a8] + Clustering v0.15.8 [d3e213a1] + ColorSchemeTools v1.6.0 [35d6a980] + ColorSchemes v3.29.0 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌃ [c3611d14] + ColorVectorSpace v0.10.0 ⌅ [5ae59095] + Colors v0.12.11 [861a8166] + Combinatorics v1.0.2 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [0fb5dd42] + CompTime v0.1.2 [34da2185] + Compat v4.16.0 [a81c6b42] + Compose v0.9.5 [a33af91c] + CompositionsBase v0.1.2 [ed09eef8] + ComputationalResources v0.3.2 [187b0558] + ConstructionBase v1.5.8 [150eb455] + CoordinateTransformations v0.6.4 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [dc8bdbbb] + CustomUnitRanges v1.0.2 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [6f00c28b] + DiagrammaticEquations v0.1.8 [b4f34e82] + Distances v0.10.12 [ffbed154] + DocStringExtensions v0.9.3 [7c1d4256] + DynamicPolynomials v0.6.1 [e2ba6199] + ExprTools v0.1.10 [4f61f5a4] + FFTViews v0.3.2 [7a1cc6ca] + FFTW v1.8.1 [5789e2e9] + FileIO v1.16.6 [53c48c17] + FixedPointNumbers v0.8.5 ⌅ [f0ffcf3b] + GATlab v0.1.5 [6b9d7cbe] + GeneralizedGenerated v0.3.3 [a2bd30eb] + Graphics v1.1.3 [86223c79] + Graphs v1.12.0 [2c695a8d] + HistogramThresholding v0.3.1 [3e5b6fbb] + HostCPUFeatures v0.1.17 [615f187c] + IfElse v0.1.1 [2803e5a7] + ImageAxes v0.6.12 [c817782e] + ImageBase v0.1.7 [cbc4b850] + ImageBinarization v0.3.1 [f332f351] + ImageContrastAdjustment v0.3.12 [a09fc81d] + ImageCore v0.10.5 [89d5987c] + ImageCorners v0.1.3 [51556ac3] + ImageDistances v0.2.17 [6a3955dd] + ImageFiltering v0.7.9 [82e4d734] + ImageIO v0.6.9 [6218d12a] + ImageMagick v1.4.0 [bc367c6b] + ImageMetadata v0.9.10 [787d08f9] + ImageMorphology v0.4.5 [2996bd0c] + ImageQualityIndexes v0.3.7 [80713f31] + ImageSegmentation v1.8.4 [4e3cecfd] + ImageShow v0.3.8 [02fcd773] + ImageTransformations v0.10.1 [916415d5] + Images v0.26.2 [9b13fd28] + IndirectArrays v1.0.0 [d25df0c9] + Inflate v0.1.5 [1d092043] + IntegralArrays v0.1.6 [a98d9a8b] + Interpolations v0.15.1 [8197267c] + IntervalSets v0.7.10 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [033835bb] + JLD2 v0.4.54 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.1 [b835a17e] + JpegTurbo v0.1.5 [b14d175d] + JuliaVariables v0.2.4 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [8cdb02fc] + LazyModules v0.3.1 [9c8b4983] + LightXML v0.9.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.171 [d8e11817] + MLStyle v0.4.17 [1914dd2f] + MacroTools v0.5.15 [d125e4d3] + ManualMemory v0.1.8 [dbb5928d] + MappedArrays v0.4.2 [442fdcdd] + Measures v0.3.2 ⌃ [626554b9] + MetaGraphs v0.7.2 [e1d29d7a] + Missings v1.2.0 [e94cdb99] + MosaicViews v0.3.4 [102ac46a] + MultivariatePolynomials v0.5.7 [d8a4904e] + MutableArithmetics v1.6.4 [77ba4419] + NaNMath v1.1.2 [71a1bf82] + NameResolution v0.1.5 [b8a86587] + NearestNeighbors v0.4.21 [f09324ee] + Netpbm v1.1.1 [6fe1bfb0] + OffsetArrays v1.15.0 [52e1d378] + OpenEXR v0.3.3 [bac558e1] + OrderedCollections v1.8.0 [12d937ae] + PEG v1.0.2 [f57f5aa1] + PNGFiles v0.4.4 [5432bcbf] + PaddedViews v0.5.12 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.1 [2ae35dd2] + Permutations v0.4.23 [eebad327] + PkgVersion v0.3.3 [1d0040c9] + PolyesterWeave v0.2.2 [f27b6e38] + Polynomials v4.0.17 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [8162dcfd] + PrettyPrint v0.2.0 [08abe8d2] + PrettyTables v2.4.0 [92933f4c] + ProgressMeter v1.10.2 [43287f4e] + PtrArrays v1.3.0 [4b34888f] + QOI v1.0.1 [dca85d43] + QuartzImageIO v0.7.5 [94ee1d12] + Quaternions v0.7.6 [b3c3ace0] + RangeArrays v0.3.2 [c84ed2f1] + Ratios v0.4.5 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [dee08c22] + RegionTrees v0.3.2 [ae029012] + Requires v1.3.0 [6038ab10] + Rotations v1.7.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.13 [fdea26ae] + SIMD v3.7.1 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [efcf1570] + Setfield v1.1.1 [699a6c99] + SimpleTraits v0.9.4 [47aef6b3] + SimpleWeightedGraphs v1.4.0 [45858cf5] + Sixel v0.1.3 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [cae243ae] + StackViews v0.1.1 [aedffcd0] + Static v1.1.1 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.12 [1e83bf80] + StaticArraysCore v1.4.3 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [892a3eda] + StringManipulation v0.4.1 [6ec83bb0] + StructEquality v2.1.0 [856f2bd8] + StructTypes v1.11.0 [2efcf032] + SymbolicIndexingInterface v0.3.38 [d1185830] + SymbolicUtils v3.15.0 [22bb929c] + SyntacticModels v0.2.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [62fd8b95] + TensorCore v0.1.1 [8ea1fca8] + TermInterface v2.0.0 [8290d209] + ThreadingUtilities v0.5.2 [731e570b] + TiffImages v0.11.3 [06e1c1a7] + TiledIteration v0.5.0 [a759f4b9] + TimerOutputs v0.5.27 [3bb67fe8] + TranscodingStreams v0.11.3 [3a884ed6] + UnPack v1.0.2 [a7c27f48] + Unityper v0.1.6 [3d5dd08c] + VectorizationBase v0.21.71 [897b6980] + WeakValueDicts v0.1.0 [e3aaa7dc] + WebP v0.1.3 [efce3f68] + WoodburyMatrices v1.0.0 [f5851436] + FFTW_jll v3.3.10+3 [61579ee1] + Ghostscript_jll v9.55.0+4 [59f7168a] + Giflib_jll v5.2.3+0 [c73af94c] + ImageMagick_jll v7.1.1+1 [905a6f67] + Imath_jll v3.1.11+0 [1d5cc7b8] + IntelOpenMP_jll v2025.0.4+0 [aacddb02] + JpegTurbo_jll v3.1.1+0 ⌅ [88015f11] + LERC_jll v3.0.0+1 [d4300ac3] + Libgcrypt_jll v1.11.0+0 [7e76a0d4] + Libglvnd_jll v1.7.0+0 [7add5ba3] + Libgpg_error_jll v1.51.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 ⌅ [89763e89] + Libtiff_jll v4.4.0+0 ⌃ [d3a379c0] + LittleCMS_jll v2.12.0+0 [856f044c] + MKL_jll v2025.0.1+1 [18a262bb] + OpenEXR_jll v3.2.4+0 ⌃ [643b3616] + OpenJpeg_jll v2.4.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [02c8fc9c] + XML2_jll v2.13.6+1 [aed1982a] + XSLT_jll v1.1.42+0 [4f6342f7] + Xorg_libX11_jll v1.8.6+3 [0c0b7dd1] + Xorg_libXau_jll v1.0.12+0 [a3789734] + Xorg_libXdmcp_jll v1.1.5+0 [1082639a] + Xorg_libXext_jll v1.3.6+3 [14d82f49] + Xorg_libpthread_stubs_jll v0.1.2+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.0+3 [c5fb5394] + Xorg_xtrans_jll v1.5.1+0 [3161d3a3] + Zstd_jll v1.5.7+1 [b53b4c65] + libpng_jll v1.6.46+0 [075b6546] + libsixel_jll v1.10.5+0 ⌃ [c5f90fcd] + libwebp_jll v1.4.0+0 [1317d2d5] + oneTBB_jll v2022.0.0+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 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+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+4 [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 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` Installation completed after 9.26s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 909.96s ################################################################################ # Testing # Testing SyntacticModels Status `/tmp/jl_YNJkth/Project.toml` [227ef7b5] ACSets v0.2.21 [134e5e36] Catlab v0.16.19 [6f00c28b] DiagrammaticEquations v0.1.8 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.1 [d8e11817] MLStyle v0.4.17 [189a3867] Reexport v1.2.2 [856f2bd8] StructTypes v1.11.0 [22bb929c] SyntacticModels v0.2.0 [8dfed614] Test Status `/tmp/jl_YNJkth/Manifest.toml` [227ef7b5] ACSets v0.2.21 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.41 [79e6a3ab] Adapt v4.2.0 [23cfdc9f] AlgebraicInterfaces v0.1.4 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.18.0 [13072b0f] AxisAlgorithms v1.1.0 [39de3d68] AxisArrays v0.4.7 [e2ed5e7c] Bijections v0.1.9 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [fa961155] CEnum v0.5.0 [2a0fbf3d] CPUSummary v0.2.6 [aafaddc9] CatIndices v0.2.2 [134e5e36] Catlab v0.16.19 [d360d2e6] ChainRulesCore v1.25.1 [fb6a15b2] CloseOpenIntervals v0.1.13 [aaaa29a8] Clustering v0.15.8 [d3e213a1] ColorSchemeTools v1.6.0 [35d6a980] ColorSchemes v3.29.0 ⌅ [3da002f7] ColorTypes v0.11.5 ⌃ [c3611d14] ColorVectorSpace v0.10.0 ⌅ [5ae59095] Colors v0.12.11 [861a8166] Combinatorics v1.0.2 [f70d9fcc] CommonWorldInvalidations v1.0.0 [0fb5dd42] CompTime v0.1.2 [34da2185] Compat v4.16.0 [a81c6b42] Compose v0.9.5 [a33af91c] CompositionsBase v0.1.2 [ed09eef8] ComputationalResources v0.3.2 [187b0558] ConstructionBase v1.5.8 [150eb455] CoordinateTransformations v0.6.4 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [dc8bdbbb] CustomUnitRanges v1.0.2 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.20 [e2d170a0] DataValueInterfaces v1.0.0 [6f00c28b] DiagrammaticEquations v0.1.8 [b4f34e82] Distances v0.10.12 [ffbed154] DocStringExtensions v0.9.3 [7c1d4256] DynamicPolynomials v0.6.1 [e2ba6199] ExprTools v0.1.10 [4f61f5a4] FFTViews v0.3.2 [7a1cc6ca] FFTW v1.8.1 [5789e2e9] FileIO v1.16.6 [53c48c17] FixedPointNumbers v0.8.5 ⌅ [f0ffcf3b] GATlab v0.1.5 [6b9d7cbe] GeneralizedGenerated v0.3.3 [a2bd30eb] Graphics v1.1.3 [86223c79] Graphs v1.12.0 [2c695a8d] HistogramThresholding v0.3.1 [3e5b6fbb] HostCPUFeatures v0.1.17 [615f187c] IfElse v0.1.1 [2803e5a7] ImageAxes v0.6.12 [c817782e] ImageBase v0.1.7 [cbc4b850] ImageBinarization v0.3.1 [f332f351] ImageContrastAdjustment v0.3.12 [a09fc81d] ImageCore v0.10.5 [89d5987c] ImageCorners v0.1.3 [51556ac3] ImageDistances v0.2.17 [6a3955dd] ImageFiltering v0.7.9 [82e4d734] ImageIO v0.6.9 [6218d12a] ImageMagick v1.4.0 [bc367c6b] ImageMetadata v0.9.10 [787d08f9] ImageMorphology v0.4.5 [2996bd0c] ImageQualityIndexes v0.3.7 [80713f31] ImageSegmentation v1.8.4 [4e3cecfd] ImageShow v0.3.8 [02fcd773] ImageTransformations v0.10.1 [916415d5] Images v0.26.2 [9b13fd28] IndirectArrays v1.0.0 [d25df0c9] Inflate v0.1.5 [1d092043] IntegralArrays v0.1.6 [a98d9a8b] Interpolations v0.15.1 [8197267c] IntervalSets v0.7.10 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.4 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 ⌅ [033835bb] JLD2 v0.4.54 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.1 [b835a17e] JpegTurbo v0.1.5 [b14d175d] JuliaVariables v0.2.4 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 [8cdb02fc] LazyModules v0.3.1 [9c8b4983] LightXML v0.9.1 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.171 [d8e11817] MLStyle v0.4.17 [1914dd2f] MacroTools v0.5.15 [d125e4d3] ManualMemory v0.1.8 [dbb5928d] MappedArrays v0.4.2 [442fdcdd] Measures v0.3.2 ⌃ [626554b9] MetaGraphs v0.7.2 [e1d29d7a] Missings v1.2.0 [e94cdb99] MosaicViews v0.3.4 [102ac46a] MultivariatePolynomials v0.5.7 [d8a4904e] MutableArithmetics v1.6.4 [77ba4419] NaNMath v1.1.2 [71a1bf82] NameResolution v0.1.5 [b8a86587] NearestNeighbors v0.4.21 [f09324ee] Netpbm v1.1.1 [6fe1bfb0] OffsetArrays v1.15.0 [52e1d378] OpenEXR v0.3.3 [bac558e1] OrderedCollections v1.8.0 [12d937ae] PEG v1.0.2 [f57f5aa1] PNGFiles v0.4.4 [5432bcbf] PaddedViews v0.5.12 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.1 [2ae35dd2] Permutations v0.4.23 [eebad327] PkgVersion v0.3.3 [1d0040c9] PolyesterWeave v0.2.2 [f27b6e38] Polynomials v4.0.17 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [8162dcfd] PrettyPrint v0.2.0 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.2 [43287f4e] PtrArrays v1.3.0 [4b34888f] QOI v1.0.1 [dca85d43] QuartzImageIO v0.7.5 [94ee1d12] Quaternions v0.7.6 [b3c3ace0] RangeArrays v0.3.2 [c84ed2f1] Ratios v0.4.5 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [dee08c22] RegionTrees v0.3.2 [ae029012] Requires v1.3.0 [6038ab10] Rotations v1.7.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.13 [fdea26ae] SIMD v3.7.1 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.43 [efcf1570] Setfield v1.1.1 [699a6c99] SimpleTraits v0.9.4 [47aef6b3] SimpleWeightedGraphs v1.4.0 [45858cf5] Sixel v0.1.3 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [cae243ae] StackViews v0.1.1 [aedffcd0] Static v1.1.1 [0d7ed370] StaticArrayInterface v1.8.0 [90137ffa] StaticArrays v1.9.12 [1e83bf80] StaticArraysCore v1.4.3 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [892a3eda] StringManipulation v0.4.1 [6ec83bb0] StructEquality v2.1.0 [856f2bd8] StructTypes v1.11.0 [2efcf032] SymbolicIndexingInterface v0.3.38 [d1185830] SymbolicUtils v3.15.0 [22bb929c] SyntacticModels v0.2.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [62fd8b95] TensorCore v0.1.1 [8ea1fca8] TermInterface v2.0.0 [8290d209] ThreadingUtilities v0.5.2 [731e570b] TiffImages v0.11.3 [06e1c1a7] TiledIteration v0.5.0 [a759f4b9] TimerOutputs v0.5.27 [3bb67fe8] TranscodingStreams v0.11.3 [3a884ed6] UnPack v1.0.2 [a7c27f48] Unityper v0.1.6 [3d5dd08c] VectorizationBase v0.21.71 [897b6980] WeakValueDicts v0.1.0 [e3aaa7dc] WebP v0.1.3 [efce3f68] WoodburyMatrices v1.0.0 [f5851436] FFTW_jll v3.3.10+3 [61579ee1] Ghostscript_jll v9.55.0+4 [59f7168a] Giflib_jll v5.2.3+0 [c73af94c] ImageMagick_jll v7.1.1+1 [905a6f67] Imath_jll v3.1.11+0 [1d5cc7b8] IntelOpenMP_jll v2025.0.4+0 [aacddb02] JpegTurbo_jll v3.1.1+0 ⌅ [88015f11] LERC_jll v3.0.0+1 [d4300ac3] Libgcrypt_jll v1.11.0+0 [7e76a0d4] Libglvnd_jll v1.7.0+0 [7add5ba3] Libgpg_error_jll v1.51.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 ⌅ [89763e89] Libtiff_jll v4.4.0+0 ⌃ [d3a379c0] LittleCMS_jll v2.12.0+0 [856f044c] MKL_jll v2025.0.1+1 [18a262bb] OpenEXR_jll v3.2.4+0 ⌃ [643b3616] OpenJpeg_jll v2.4.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [02c8fc9c] XML2_jll v2.13.6+1 [aed1982a] XSLT_jll v1.1.42+0 [4f6342f7] Xorg_libX11_jll v1.8.6+3 [0c0b7dd1] Xorg_libXau_jll v1.0.12+0 [a3789734] Xorg_libXdmcp_jll v1.1.5+0 [1082639a] Xorg_libXext_jll v1.3.6+3 [14d82f49] Xorg_libpthread_stubs_jll v0.1.2+0 [c7cfdc94] Xorg_libxcb_jll v1.17.0+3 [c5fb5394] Xorg_xtrans_jll v1.5.1+0 [3161d3a3] Zstd_jll v1.5.7+1 [b53b4c65] libpng_jll v1.6.46+0 [075b6546] libsixel_jll v1.10.5+0 ⌃ [c5f90fcd] libwebp_jll v1.4.0+0 [1317d2d5] oneTBB_jll v2022.0.0+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 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+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+4 [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 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... WARNING: Method definition (::Type{StructTypes.StructType})(Type{DiagrammaticEquations.decapodes.Equation}) in module decapodes at /home/pkgeval/.julia/packages/ACSets/7LOk7/src/intertypes/julia.jl:450 overwritten in module ASKEMDecapodes at /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/decapodes.jl:46. ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. WARNING: Method definition (::Type{StructTypes.StructType})(Type{DiagrammaticEquations.decapodes.Equation}) in module decapodes at /home/pkgeval/.julia/packages/ACSets/7LOk7/src/intertypes/julia.jl:450 overwritten in module ASKEMDecapodes at /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/decapodes.jl:46. WARNING: Method definition subtypekey(Type{DiagrammaticEquations.decapodes.Equation}) in module decapodes at /home/pkgeval/.julia/packages/ACSets/7LOk7/src/intertypes/julia.jl:452 overwritten in module ASKEMDecapodes at /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/decapodes.jl:47. WARNING: Method definition subtypes(Type{DiagrammaticEquations.decapodes.Equation}) in module decapodes at /home/pkgeval/.julia/packages/ACSets/7LOk7/src/intertypes/julia.jl:453 overwritten in module ASKEMDecapodes at /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/decapodes.jl:48. WARNING: Method definition (::Type{StructTypes.StructType})(Type{DiagrammaticEquations.decapodes.Term}) in module decapodes at /home/pkgeval/.julia/packages/ACSets/7LOk7/src/intertypes/julia.jl:450 overwritten in module ASKEMDecapodes at /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/decapodes.jl:50. WARNING: Method definition subtypekey(Type{DiagrammaticEquations.decapodes.Term}) in module decapodes at /home/pkgeval/.julia/packages/ACSets/7LOk7/src/intertypes/julia.jl:452 overwritten in module ASKEMDecapodes at /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/decapodes.jl:51. WARNING: Method definition subtypes(Type{DiagrammaticEquations.decapodes.Term}) in module decapodes at /home/pkgeval/.julia/packages/ACSets/7LOk7/src/intertypes/julia.jl:453 overwritten in module ASKEMDecapodes at /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/decapodes.jl:52. """ ASKE Model Representation: SIR0.2 :: petrinet amr-schemas:petri_schema.json The SIR Model of disease """ Model = begin LabelledPetriNet{Symbol} begin S(label=:S) S(label=:I) S(label=:R) T(label=:inf) T(label=:rec) I(is=:S,it=:inf) I(is=:I,it=:inf) I(is=:I,it=:rec) O(os=:I,it=:inf) O(os=:I,it=:inf) O(os=:R,it=:rec) end end ODE_Record = begin inf::Rate = S*I*β rec::Rate = I*γ S::Initial = S₀ I::Initial = I₀ R::Initial = R₀ # β-- the beta parameter β::Parameter{1/(persons^2*day)} = 0.01 ~ U(0.001,0.02) # γ-- the gama parameter γ::Parameter{1/(persons*day)} = 3.0 ~ U(1,200.0) # S₀-- the initial susceptible population S₀::Parameter{persons} = 3.0e8 ~ U(1.0e6,4.0e6) # I₀-- the initial infected population I₀::Parameter{persons} = 1.0 ~ U(1,1) # R₀-- the initial recovered population R₀::Parameter{persons} = 0.0 ~ U(0,4) t::Time{day} end """ ASKE Model Representation: SIR0.2 :: petrinet amr-schemas:petri_schema.json The SIR Model of disease """ Model = begin LabelledPetriNet{Symbol} begin S(label=:S) S(label=:I) S(label=:R) T(label=:inf) T(label=:rec) I(is=:S,it=:inf) I(is=:I,it=:inf) I(is=:I,it=:rec) O(os=:I,it=:inf) O(os=:I,it=:inf) O(os=:R,it=:rec) end end ODE_Equations = begin t::Time{day} # β-- the beta parameter β::Parameter{1/(persons^2*day)} = 0.01 ~ U(0.001,0.02) inf::Rate = S*I*β # γ-- the gama parameter γ::Parameter{1/(persons*day)} = 3.0 ~ U(1,200.0) rec::Rate = I*γ # S₀-- the initial susceptible population S₀::Parameter{persons} = 3.0e8 ~ U(1.0e6,4.0e6) S₀::Initial = S₀ # I₀-- the initial infected population I₀::Parameter{persons} = 1.0 ~ U(1,1) I₀::Initial = I₀ # R₀-- the initial recovered population R₀::Parameter{persons} = 0.0 ~ U(0,4) R₀::Initial = R₀ end Typing = begin Model = begin LabelledPetriNet{Symbol} begin S(label=:Pop) T(label=:inf) T(label=:disease) T(label=:strata) I(is=:Pop,it=:inf) I(is=:Pop,it=:inf) I(is=:Pop,it=:disease) I(is=:Pop,it=:strata) O(os=:Pop,it=:inf) O(os=:Pop,it=:inf) O(os=:Pop,it=:disease) O(os=:Pop,it=:strata) end end TypeMap = [ S => Pop, I => Pop, R => Pop, inf => inf, rec => disease,] end begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:182 =# @doc "ASKE Model Representation: SIR0.2 :: petrinet \n amr-schemas:petri_schema.json\n\nThe SIR Model of disease" #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:191 =# Model = begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:184 =# begin #= none:2 =# S(label = :S) #= none:3 =# S(label = :I) #= none:4 =# S(label = :R) #= none:5 =# T(label = :inf) #= none:6 =# T(label = :rec) #= none:7 =# I(is = :S, it = :inf) #= none:8 =# I(is = :I, it = :inf) #= none:9 =# I(is = :I, it = :rec) #= none:10 =# O(os = :I, it = :inf) #= none:11 =# O(os = :I, it = :inf) #= none:12 =# O(os = :R, it = :rec) end end #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:191 =# begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:161 =# ODE_Record = (rates = begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:161 =# inf::Rate = "S*I*β" rec::Rate = "I*γ" end, initials = begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:161 =# S::Initial = "S₀" I::Initial = "I₀" R::Initial = "R₀" end, parameters = begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:161 =# #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "β-- the beta parameter" β::Parameter{"1/(persons^2*day)"} = (0.01 ~ U(0.001, 0.02)) #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "γ-- the gama parameter" γ::Parameter{"1/(persons*day)"} = (3.0 ~ U(1, 200.0)) #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "S₀-- the initial susceptible population" S₀::Parameter{"persons"} = (3.0e8 ~ U(1.0e6, 4.0e6)) #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "I₀-- the initial infected population" I₀::Parameter{"persons"} = (1.0 ~ U(1, 1)) #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "R₀-- the initial recovered population" R₀::Parameter{"persons"} = (0.0 ~ U(0, 4)) end, time = !time) end end #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:182 =# @doc "ASKE Model Representation: SIR0.2 :: petrinet \n amr-schemas:petri_schema.json\n\nThe SIR Model of disease" Model = begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:184 =# begin #= none:2 =# S(label = :S) #= none:3 =# S(label = :I) #= none:4 =# S(label = :R) #= none:5 =# T(label = :inf) #= none:6 =# T(label = :rec) #= none:7 =# I(is = :S, it = :inf) #= none:8 =# I(is = :I, it = :inf) #= none:9 =# I(is = :I, it = :rec) #= none:10 =# O(os = :I, it = :inf) #= none:11 =# O(os = :I, it = :inf) #= none:12 =# O(os = :R, it = :rec) end end #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:161 =# t::Time{"day"} #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "β-- the beta parameter" β::Parameter{"1/(persons^2*day)"} = (0.01 ~ U(0.001, 0.02)) inf::Rate = "S*I*β" #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "γ-- the gama parameter" γ::Parameter{"1/(persons*day)"} = (3.0 ~ U(1, 200.0)) rec::Rate = "I*γ" #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "S₀-- the initial susceptible population" S₀::Parameter{"persons"} = (3.0e8 ~ U(1.0e6, 4.0e6)) S₀::Initial = "S₀" #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "I₀-- the initial infected population" I₀::Parameter{"persons"} = (1.0 ~ U(1, 1)) I₀::Initial = "I₀" #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "R₀-- the initial recovered population" R₀::Parameter{"persons"} = (0.0 ~ U(0, 4)) R₀::Initial = "R₀" begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:182 =# @doc "ASKE Model Representation: SIR0.2 :: petrinet \n amr-schemas:petri_schema.json\n\nThe SIR Model of disease" #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:191 =# Model = begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:184 =# begin #= none:2 =# S(label = :S) #= none:3 =# S(label = :I) #= none:4 =# S(label = :R) #= none:5 =# T(label = :inf) #= none:6 =# T(label = :rec) #= none:7 =# I(is = :S, it = :inf) #= none:8 =# I(is = :I, it = :inf) #= none:9 =# I(is = :I, it = :rec) #= none:10 =# O(os = :I, it = :inf) #= none:11 =# O(os = :I, it = :inf) #= none:12 =# O(os = :R, it = :rec) end end #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:191 =# begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:161 =# ODE_Equations = begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:161 =# t::Time{"day"} #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "β-- the beta parameter" β::Parameter{"1/(persons^2*day)"} = (0.01 ~ U(0.001, 0.02)) inf::Rate = "S*I*β" #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "γ-- the gama parameter" γ::Parameter{"1/(persons*day)"} = (3.0 ~ U(1, 200.0)) rec::Rate = "I*γ" #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "S₀-- the initial susceptible population" S₀::Parameter{"persons"} = (3.0e8 ~ U(1.0e6, 4.0e6)) S₀::Initial = "S₀" #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "I₀-- the initial infected population" I₀::Parameter{"persons"} = (1.0 ~ U(1, 1)) I₀::Initial = "I₀" #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:183 =# @doc "R₀-- the initial recovered population" R₀::Parameter{"persons"} = (0.0 ~ U(0, 4)) R₀::Initial = "R₀" end begin Typing = (Model = begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:184 =# begin #= none:2 =# S(label = :Pop) #= none:3 =# T(label = :inf) #= none:4 =# T(label = :disease) #= none:5 =# T(label = :strata) #= none:6 =# I(is = :Pop, it = :inf) #= none:7 =# I(is = :Pop, it = :inf) #= none:8 =# I(is = :Pop, it = :disease) #= none:9 =# I(is = :Pop, it = :strata) #= none:10 =# O(os = :Pop, it = :inf) #= none:11 =# O(os = :Pop, it = :inf) #= none:12 =# O(os = :Pop, it = :disease) #= none:13 =# O(os = :Pop, it = :strata) end end) #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:190 =# TypeMap = begin #= /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/src/amr.jl:161 =# :S => :Pop :I => :Pop :R => :Pop :inf => :inf :rec => :disease end end end end AMRPetriNet begin S(id=S,name=Susceptible,units=person) S(id=I,name=Infected,units=person) S(id=R,name=Recovered,units=person) T(id=inf,name=Infection,desc=Infective process between individuals) T(id=rec,name=Recovery,desc=Recovery process of a infected individual) I(is=S,it=inf) I(is=I,it=inf) I(is=I,it=rec) O(os=I,ot=inf) O(os=I,ot=inf) O(os=R,ot=rec) end semantics_dict = Dict{String, Any}("ode" => Dict{String, Any}("initials" => Any[Dict{String, Any}("expression" => "S0", "expression_mathml" => "S0", "target" => "S"), Dict{String, Any}("expression" => "I0", "expression_mathml" => "I0", "target" => "I"), Dict{String, Any}("expression" => "R0", "expression_mathml" => "R0", "target" => "R")], "parameters" => Any[Dict{String, Any}("units" => Dict{String, Any}("expression" => "1/(person*day)", "expression_mathml" => "1personday"), "name" => "β", "id" => "beta", "distribution" => Dict{String, Any}("parameters" => Dict{String, Any}("minimum" => 2.6e-7, "maximum" => 2.8e-7), "type" => "StandardUniform1"), "value" => 2.7e-7, "description" => "infection rate"), Dict{String, Any}("units" => Dict{String, Any}("expression" => "1/day", "expression_mathml" => "1day"), "name" => "γ", "id" => "gamma", "grounding" => Dict{String, Any}("identifiers" => Dict{String, Any}("askemo" => "0000013")), "distribution" => Dict{String, Any}("parameters" => Dict{String, Any}("minimum" => 0.1, "maximum" => 0.18), "type" => "StandardUniform1"), "value" => 0.14, "description" => "recovery rate"), Dict{String, Any}("name" => "S₀", "id" => "S0", "value" => 1000, "description" => "Total susceptible population at timestep 0"), Dict{String, Any}("name" => "I₀", "id" => "I0", "value" => 1, "description" => "Total infected population at timestep 0"), Dict{String, Any}("name" => "R₀", "id" => "R0", "value" => 0, "description" => "Total recovered population at timestep 0")], "rates" => Any[Dict{String, Any}("expression" => "S*I*beta", "expression_mathml" => "SIbeta", "target" => "inf"), Dict{String, Any}("expression" => "I*gamma", "expression_mathml" => "Igamma", "target" => "rec")], "time" => Dict{String, Any}("units" => Dict{String, Any}("expression" => "day", "expression_mathml" => "day"), "id" => "t"), "observables" => Any[Dict{String, Any}("name" => "Non-infectious", "expression" => "S+R", "expression_mathml" => "SR", "id" => "noninf", "states" => Any["S", "R"])])) ODE_Record = begin inf::Rate = S*I*beta rec::Rate = I*gamma S::Initial = S0 I::Initial = I0 R::Initial = R0 # β-- infection rate beta::Parameter{1/(person*day)} = 2.7e-7 ~ U(0,1) # γ-- recovery rate gamma::Parameter{1/day} = 0.14 ~ U(0,1) # S₀-- Total susceptible population at timestep 0 S0::Parameter{} = 1000.0 ~ δ(missing) # I₀-- Total infected population at timestep 0 I0::Parameter{} = 1.0 ~ δ(missing) # R₀-- Total recovered population at timestep 0 R0::Parameter{} = 0.0 ~ δ(missing) t::Time{day} end Any[Dict{String, Any}("units" => Dict{String, Any}("expression" => "person", "expression_mathml" => "person"), "name" => "Susceptible", "id" => "S", "grounding" => Dict{String, Any}("identifiers" => Dict{String, Any}("ido" => "0000514")), "description" => "Number of individuals that are 'susceptible' to a disease infection"), Dict{String, Any}("units" => Dict{String, Any}("expression" => "person", "expression_mathml" => "person"), "name" => "Infected", "id" => "I", "grounding" => Dict{String, Any}("identifiers" => Dict{String, Any}("ido" => "0000511")), "description" => "Number of individuals that are 'infected' by a disease"), Dict{String, Any}("units" => Dict{String, Any}("expression" => "person", "expression_mathml" => "person"), "name" => "Recovered", "id" => "R", "grounding" => Dict{String, Any}("identifiers" => Dict{String, Any}("ido" => "0000592")), "description" => "Number of individuals that have 'recovered' from a disease infection")]""" ASKE Model Representation: SIR Model0.1 :: petrinet https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json SIR model """ Model = begin AMRPetriNet begin S(id=S,name=Susceptible,units=person) S(id=I,name=Infected,units=person) S(id=R,name=Recovered,units=person) T(id=inf,name=Infection,desc=Infective process between individuals) T(id=rec,name=Recovery,desc=Recovery process of a infected individual) I(is=S,it=inf) I(is=I,it=inf) I(is=I,it=rec) O(os=I,ot=inf) O(os=I,ot=inf) O(os=R,ot=rec) end end ODE_Record = begin inf::Rate = S*I*beta rec::Rate = I*gamma S::Initial = S0 I::Initial = I0 R::Initial = R0 # β-- infection rate beta::Parameter{1/(person*day)} = 2.7e-7 ~ U(2.6e-7,2.8e-7) # γ-- recovery rate gamma::Parameter{1/day} = 0.14 ~ U(0.1,0.18) # S₀-- Total susceptible population at timestep 0 S0::Parameter{} = 1000.0 ~ δ(missing) # I₀-- Total infected population at timestep 0 I0::Parameter{} = 1.0 ~ δ(missing) # R₀-- Total recovered population at timestep 0 R0::Parameter{} = 0.0 ~ δ(missing) t::Time{day} end m = Any[Any["S", "Pop"], Any["I", "Pop"], Any["R", "Pop"], Any["inf", "Infect"], Any["rec", "Disease"]] Typing = begin Model = begin AMRPetriNet begin S(id=Pop,name=Pop,units=nothing) S(id=Vaccine,name=Vaccine,units=nothing) T(id=Infect,name=Infect,desc=2-to-2 process that represents infectious contact between two human individuals) T(id=Disease,name=Disease,desc=1-to-1 process that represents a change in th edisease status of a human individual.) T(id=Strata,name=Strata,desc=1-to-1 process that represents a change in the demographic division of a human individual.) T(id=Vaccinate,name=Vaccinate,desc=2-to-1 process that represents an human individual receiving a vaccine dose.) T(id=Produce_Vaccine,name=Produce Vaccine,desc=0-to-1 process that represents the production of a single vaccine dose.) I(is=Pop,it=Infect) I(is=Pop,it=Infect) I(is=Pop,it=Disease) I(is=Pop,it=Strata) I(is=Pop,it=Vaccinate) I(is=Vaccine,it=Vaccinate) O(os=Pop,ot=Infect) O(os=Pop,ot=Infect) O(os=Pop,ot=Disease) O(os=Pop,ot=Strata) O(os=Pop,ot=Vaccinate) O(os=Vaccine,ot=Produce_Vaccine) end end TypeMap = [ S => Pop, I => Pop, R => Pop, inf => Infect, rec => Disease,] end m = Any[Any["S", "Pop"], Any["I", "Pop"], Any["R", "Pop"], Any["inf", "Infect"], Any["rec", "Disease"]] """ ASKE Model Representation: SIR Model0.1 :: petrinet https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json Typed SIR model created by Nelson, derived from the one by Ben, Micah, Brandon """ Model = begin AMRPetriNet begin S(id=S,name=Susceptible,units=nothing) S(id=I,name=Infected,units=nothing) S(id=R,name=Recovered,units=nothing) T(id=inf,name=Infection,desc=Infective process between individuals) T(id=rec,name=Recovery,desc=Recovery process of a infected individual) I(is=S,it=inf) I(is=I,it=inf) I(is=I,it=rec) O(os=I,ot=inf) O(os=I,ot=inf) O(os=R,ot=rec) end end ODE_Record = begin inf::Rate = S*I*beta rec::Rate = I*gamma S::Initial = S0 I::Initial = I0 R::Initial = R0 # β-- infection rate beta::Parameter{} = 0.027 ~ U(0.026,0.028) # γ-- recovery rate gamma::Parameter{} = 0.14 ~ U(0.1,0.18) # S₀-- Total susceptible population at timestep 0 S0::Parameter{} = 1000.0 ~ δ(missing) # I₀-- Total infected population at timestep 0 I0::Parameter{} = 1.0 ~ δ(missing) # R₀-- Total recovered population at timestep 0 R0::Parameter{} = 0.0 ~ δ(missing) t::Time{} end Typing = begin Model = begin AMRPetriNet begin S(id=Pop,name=Pop,units=nothing) S(id=Vaccine,name=Vaccine,units=nothing) T(id=Infect,name=Infect,desc=2-to-2 process that represents infectious contact between two human individuals) T(id=Disease,name=Disease,desc=1-to-1 process that represents a change in th edisease status of a human individual.) T(id=Strata,name=Strata,desc=1-to-1 process that represents a change in the demographic division of a human individual.) T(id=Vaccinate,name=Vaccinate,desc=2-to-1 process that represents an human individual receiving a vaccine dose.) T(id=Produce_Vaccine,name=Produce Vaccine,desc=0-to-1 process that represents the production of a single vaccine dose.) I(is=Pop,it=Infect) I(is=Pop,it=Infect) I(is=Pop,it=Disease) I(is=Pop,it=Strata) I(is=Pop,it=Vaccinate) I(is=Vaccine,it=Vaccinate) O(os=Pop,ot=Infect) O(os=Pop,ot=Infect) O(os=Pop,ot=Disease) O(os=Pop,ot=Strata) O(os=Pop,ot=Vaccinate) O(os=Vaccine,ot=Produce_Vaccine) end end TypeMap = [ S => Pop, I => Pop, R => Pop, inf => Infect, rec => Disease,] end ODE_Equations = begin inf::Rate = S * I * beta rec::Rate = I * gamma # β-- infection rate beta::Parameter{} = 0.027 ~ U(0,1) # γ-- recovery rate gamma::Parameter{} = 0.14 ~ U(0,1) # S₀-- Total susceptible population at timestep 0 S0::Parameter{} = 1000.0 ~ δ(missing) # I₀-- Total infected population at timestep 0 I0::Parameter{} = 1.0 ~ δ(missing) # R₀-- Total recovered population at timestep 0 R0::Parameter{} = 0.0 ~ δ(missing) t::Time{day} end begin """ ASKE Model Representation: SIR Model@0.1 :: petrinet https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json Typed SIR model created by Nelson, derived from the one by Ben, Micah, Brandon """ Model = begin AMRPetriNet = begin S(id=S,name=Susceptible,units=nothing) S(id=I,name=Infected,units=nothing) S(id=R,name=Recovered,units=nothing) T(id=inf,name=Infection,desc="Infective process between individuals") T(id=rec,name=Recovery,desc="Recovery process of a infected individual") I(is=S,it=inf) I(is=I,it=inf) I(is=I,it=rec) O(os=I,ot=inf) O(os=I,ot=inf) O(os=R,ot=rec) end end ODE_Record = begin inf::Rate = S*I*beta rec::Rate = I*gamma S::Initial = S0 I::Initial = I0 R::Initial = R0 """ β -- infection rate """ beta::Parameter{} = 0.027 ~ U(0,1) """ γ -- recovery rate """ gamma::Parameter{} = 0.14 ~ U(0,1) """ S₀ -- Total susceptible population at timestep 0 """ S0::Parameter{} = 1000.0 ~ δ(missing) """ I₀ -- Total infected population at timestep 0""" I0::Parameter{} = 1.0 ~ δ(missing) """ R₀ -- Total recovered population at timestep 0""" R0::Parameter{} = 0.0 ~ δ(missing) t::Time{day} end Typing = begin Model = begin AMRPetriNet = begin S(id=Pop,name=Pop,units=nothing) S(id=Vaccine,name=Vaccine,units=nothing) T(id=Infect,name=Infect,desc="2-to-2 process that represents infectious contact between two human individuals.") T(id=Disease,name=Disease,desc="1-to-1 process that represents a change in th edisease status of a human individual.") T(id=Strata,name=Strata,desc="1-to-1 process that represents a change in the demographic division of a human individual.") T(id=Vaccinate,name=Vaccinate,desc="2-to-1 process that represents an human individual receiving a vaccine dose.") T(id=Produce_Vaccine,name="Produce Vaccine",desc="0-to-1 process that represents the production of a single vaccine dose.") I(is=Pop,it=Infect) I(is=Pop,it=Infect) I(is=Pop,it=Disease) I(is=Pop,it=Strata) I(is=Pop,it=Vaccinate) I(is=Vaccine,it=Vaccinate) O(os=Pop,ot=Infect) O(os=Pop,ot=Infect) O(os=Pop,ot=Disease) O(os=Pop,ot=Strata) O(os=Pop,ot=Vaccinate) O(os=Vaccine,ot=Produce_Vaccine) end end TypeMap = [ S => Pop, I => Pop, R => Pop, inf => Infect, rec => Disease,] end end """ ASKE Model Representation: SIR Model0.1 :: petrinet https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json Typed SIR model created by Nelson, derived from the one by Ben, Micah, Brandon """ Model = begin AMRPetriNet begin S(id=S,name=Susceptible,units=nothing) S(id=I,name=Infected,units=nothing) S(id=R,name=Recovered,units=nothing) T(id=inf,name=Infection,desc=Infective process between individuals) T(id=rec,name=Recovery,desc=Recovery process of a infected individual) I(is=S,it=inf) I(is=I,it=inf) I(is=I,it=rec) O(os=I,ot=inf) O(os=I,ot=inf) O(os=R,ot=rec) end end ODE_Equations = begin inf::Rate = S * I * beta rec::Rate = I * gamma # β-- infection rate beta::Parameter{} = 0.027 ~ U(0,1) # γ-- recovery rate gamma::Parameter{} = 0.14 ~ U(0,1) # S₀-- Total susceptible population at timestep 0 S0::Parameter{} = 1000.0 ~ δ(missing) # I₀-- Total infected population at timestep 0 I0::Parameter{} = 1.0 ~ δ(missing) # R₀-- Total recovered population at timestep 0 R0::Parameter{} = 0.0 ~ δ(missing) t::Time{day} end Typing = begin Model = begin AMRPetriNet begin S(id=Pop,name=Pop,units=nothing) S(id=Vaccine,name=Vaccine,units=nothing) T(id=Infect,name=Infect,desc=2-to-2 process that represents infectious contact between two human individuals.) T(id=Disease,name=Disease,desc=1-to-1 process that represents a change in th edisease status of a human individual.) T(id=Strata,name=Strata,desc=1-to-1 process that represents a change in the demographic division of a human individual.) T(id=Vaccinate,name=Vaccinate,desc=2-to-1 process that represents an human individual receiving a vaccine dose.) T(id=Produce_Vaccine,name=Produce Vaccine,desc=0-to-1 process that represents the production of a single vaccine dose.) I(is=Pop,it=Infect) I(is=Pop,it=Infect) I(is=Pop,it=Disease) I(is=Pop,it=Strata) I(is=Pop,it=Vaccinate) I(is=Vaccine,it=Vaccinate) O(os=Pop,ot=Infect) O(os=Pop,ot=Infect) O(os=Pop,ot=Disease) O(os=Pop,ot=Strata) O(os=Pop,ot=Vaccinate) O(os=Vaccine,ot=Produce_Vaccine) end end TypeMap = [ S => Pop, I => Pop, R => Pop, inf => Infect, rec => Disease,] end Test Summary: | Pass Broken Total Time AMR Examples | 28 1 29 30.1s Test Summary: | Pass Total Time Decapodes Examples | 2 2 1m25.9s Catlab.Programs.RelationalPrograms.TypedUnnamedRelationDiagram{Symbol, Symbol, Symbol} {Box:3, Port:7, OuterPort:2, Junction:4, Type:0, Name:0, VarName:0} ┌─────┬──────┐ │ Box │ name │ ├─────┼──────┤ │ 1 │ R │ │ 2 │ S │ │ 3 │ T │ └─────┴──────┘ ┌──────┬─────┬──────────┬───────────┐ │ Port │ box │ junction │ port_type │ ├──────┼─────┼──────────┼───────────┤ │ 1 │ 1 │ 1 │ X │ │ 2 │ 1 │ 3 │ Y │ │ 3 │ 2 │ 3 │ Y │ │ 4 │ 2 │ 2 │ Z │ │ 5 │ 3 │ 2 │ Z │ │ 6 │ 3 │ 3 │ Y │ │ 7 │ 3 │ 4 │ untyped │ └──────┴─────┴──────────┴───────────┘ ┌───────────┬────────────────┬─────────────────┐ │ OuterPort │ outer_junction │ outer_port_type │ ├───────────┼────────────────┼─────────────────┤ │ 1 │ 1 │ x │ │ 2 │ 2 │ z │ └───────────┴────────────────┴─────────────────┘ ┌──────────┬───────────────┬──────────┐ │ Junction │ junction_type │ variable │ ├──────────┼───────────────┼──────────┤ │ 1 │ X │ x │ │ 2 │ Z │ z │ │ 3 │ Y │ y │ │ 4 │ untyped │ u │ └──────────┴───────────────┴──────────┘ Test Summary: | Pass Total Time UWD Examples | 13 13 41.3s SummationDecapode{Any, Any, Symbol} {Var:14, TVar:3, Op1:4, Op2:4, Σ:1, Summand:2, Type:0, Operator:0, Name:0} ┌─────┬───────────┬───────────────────┐ │ Var │ type │ name │ ├─────┼───────────┼───────────────────┤ │ 1 │ Form0 │ X │ │ 2 │ Form0 │ V │ │ 3 │ Constant │ oscillator_k │ │ 4 │ infer │ oscillator_mult_1 │ │ 5 │ infer │ oscillator_V̇ │ │ 6 │ Literal │ -1 │ │ 7 │ Form0 │ Q │ │ 8 │ Constant │ heating_κ │ │ 9 │ Constant │ heating_λ │ │ 10 │ Parameter │ heating_Q₀ │ │ 11 │ infer │ heating_Q̇ │ │ 12 │ infer │ heating_•2 │ │ 13 │ infer │ heating_•3 │ │ 14 │ infer │ heating_•4 │ └─────┴───────────┴───────────────────┘ ┌──────┬──────┐ │ TVar │ incl │ ├──────┼──────┤ │ 1 │ 2 │ │ 2 │ 5 │ │ 3 │ 11 │ └──────┴──────┘ ┌─────┬─────┬─────┬─────┐ │ Op1 │ src │ tgt │ op1 │ ├─────┼─────┼─────┼─────┤ │ 1 │ 1 │ 2 │ ∂ₜ │ │ 2 │ 2 │ 5 │ ∂ₜ │ │ 3 │ 7 │ 11 │ ∂ₜ │ │ 4 │ 14 │ 13 │ λ │ └─────┴─────┴─────┴─────┘ ┌─────┬───────┬───────┬─────┬─────┐ │ Op2 │ proj1 │ proj2 │ res │ op2 │ ├─────┼───────┼───────┼─────┼─────┤ │ 1 │ 6 │ 3 │ 4 │ * │ │ 2 │ 4 │ 1 │ 5 │ * │ │ 3 │ 8 │ 2 │ 12 │ * │ │ 4 │ 7 │ 10 │ 14 │ - │ └─────┴───────┴───────┴─────┴─────┘ ┌───┬─────┐ │ Σ │ sum │ ├───┼─────┤ │ 1 │ 11 │ └───┴─────┘ ┌─────────┬─────────┬───────────┐ │ Summand │ summand │ summation │ ├─────────┼─────────┼───────────┤ │ 1 │ 12 │ 1 │ │ 2 │ 13 │ 1 │ └─────────┴─────────┴───────────┘ Test Summary: | Pass Total Time Composite Model Examples | 1 1 2m20.2s {"a":{"a":{"s":"x"},"b":{"x":3.2}},"b":{"a":{"s":"y"},"b":{"x":5.4}}} {"left":{"left":{"name":"x","head":"Var"},"right":{"value":"3.2","head":"Val"},"head":"Plus"},"right":{"left":{"name":"y","head":"Var"},"right":{"value":"5.4","head":"Val"},"head":"Plus"},"head":"Times"} {"a":{"a":{"s":"x"},"b":{"x":3.2}},"b":{"a":{"s":"y"},"b":{"x":5.4}}} Serialization Minimum Working Example: Error During Test at /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/test/runtests.jl:48 Got exception outside of a @test LoadError: ArgumentError: type does not have a definite number of fields Stacktrace: [1] fieldcount(t::Any) @ Base ./reflection.jl:895 [2] read(::StructTypes.UnorderedStruct, buf::Base.CodeUnits{UInt8, String}, pos::Int64, len::Int64, b::UInt8, ::Type{Number}; kw::@Kwargs{}) @ JSON3 ~/.julia/packages/JSON3/ntJon/src/structs.jl:562 [3] read(::StructTypes.UnorderedStruct, buf::Base.CodeUnits{UInt8, String}, pos::Int64, len::Int64, b::UInt8, ::Type{Number}) @ JSON3 ~/.julia/packages/JSON3/ntJon/src/structs.jl:561 [4] #_#49 @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:555 [inlined] [5] StructClosure @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:553 [inlined] [6] applyfield @ ~/.julia/packages/StructTypes/PaLwj/src/StructTypes.jl:875 [inlined] [7] read(::StructTypes.UnorderedStruct, buf::Base.CodeUnits{UInt8, String}, pos::Int64, len::Int64, b::UInt8, ::Type{Main.SerializationTest.Val}; kw::@Kwargs{}) @ JSON3 ~/.julia/packages/JSON3/ntJon/src/structs.jl:612 [8] read(::StructTypes.UnorderedStruct, buf::Base.CodeUnits{UInt8, String}, pos::Int64, len::Int64, b::UInt8, ::Type{Main.SerializationTest.Val}) @ JSON3 ~/.julia/packages/JSON3/ntJon/src/structs.jl:561 [9] #_read#54 @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:799 [inlined] [10] _read @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:743 [inlined] [11] #read#53 @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:740 [inlined] [12] read @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:734 [inlined] [13] #_#49 @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:555 [inlined] [14] StructClosure @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:553 [inlined] [15] applyfield @ ~/.julia/packages/StructTypes/PaLwj/src/StructTypes.jl:875 [inlined] [16] read(::StructTypes.UnorderedStruct, buf::Base.CodeUnits{UInt8, String}, pos::Int64, len::Int64, b::UInt8, ::Type{Main.SerializationTest.Plus}; kw::@Kwargs{}) @ JSON3 ~/.julia/packages/JSON3/ntJon/src/structs.jl:612 [17] read(::StructTypes.UnorderedStruct, buf::Base.CodeUnits{UInt8, String}, pos::Int64, len::Int64, b::UInt8, ::Type{Main.SerializationTest.Plus}) @ JSON3 ~/.julia/packages/JSON3/ntJon/src/structs.jl:561 [18] #_read#54 @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:799 [inlined] [19] _read @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:743 [inlined] [20] #read#53 @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:740 [inlined] [21] read @ ~/.julia/packages/JSON3/ntJon/src/structs.jl:734 [inlined] [22] read(str::String, ::Type{Main.SerializationTest.Formula}; jsonlines::Bool, kw::@Kwargs{}) @ JSON3 ~/.julia/packages/JSON3/ntJon/src/structs.jl:41 [23] read(str::String, ::Type{Main.SerializationTest.Formula}) @ JSON3 ~/.julia/packages/JSON3/ntJon/src/structs.jl:33 [24] top-level scope @ ~/.julia/packages/SyntacticModels/i2tmh/test/serialization_mwe.jl:73 [25] include(fname::String) @ Base.MainInclude ./client.jl:494 [26] macro expansion @ ~/.julia/packages/SyntacticModels/i2tmh/test/runtests.jl:49 [inlined] [27] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] [28] top-level scope @ ~/.julia/packages/SyntacticModels/i2tmh/test/runtests.jl:49 [29] include(fname::String) @ Base.MainInclude ./client.jl:494 [30] top-level scope @ none:6 [31] eval @ ./boot.jl:385 [inlined] [32] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [33] _start() @ Base ./client.jl:557 in expression starting at /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/test/serialization_mwe.jl:1 Test Summary: | Error Total Time Serialization Minimum Working Example | 1 1 28.0s ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/SyntacticModels/i2tmh/test/runtests.jl:48 Testing failed after 427.26s ERROR: LoadError: Package SyntacticModels errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1442.21s: illegal method overwrites during precompilation