From 3d725b0f9aa946dbb21fb2a13b50460849396ea5 Mon Sep 17 00:00:00 2001 From: Jadon Clugston <34165782+jClugstor@users.noreply.github.com> Date: Fri, 24 May 2024 10:35:06 -0400 Subject: [PATCH] Update to use MTK v9 (#176) --- .github/workflows/ci-threaded.yaml | 2 +- Manifest.toml | 1239 +++++++++++++++------------- Project.toml | 4 +- src/SimulationService.jl | 2 +- src/model_parsers/RegNets.jl | 2 +- src/operations.jl | 16 +- test/runtests.jl | 20 +- 7 files changed, 707 insertions(+), 578 deletions(-) diff --git a/.github/workflows/ci-threaded.yaml b/.github/workflows/ci-threaded.yaml index ae1decd..916e4e8 100644 --- a/.github/workflows/ci-threaded.yaml +++ b/.github/workflows/ci-threaded.yaml @@ -16,7 +16,7 @@ - uses: actions/checkout@v2 - uses: julia-actions/setup-julia@v1 with: - version: '1.9' + version: '1.10' - uses: julia-actions/cache@v1 with: cache-compiled: "true" diff --git a/Manifest.toml b/Manifest.toml index 4d9ca8c..d629519 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,27 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.1" +julia_version = "1.10.2" manifest_format = "2.0" -project_hash = "16611c55e79d8854246798eb5a97f3abbbf54f1a" - -[[deps.ACSets]] -deps = ["AlgebraicInterfaces", "Base64", "CompTime", "DataStructures", "JSON3", "MLStyle", "OrderedCollections", "Permutations", "Pkg", "PrettyTables", "Random", "Reexport", "SHA", "StaticArrays", "StructEquality", "StructTypes", "Tables"] -git-tree-sha1 = "e1c46b1bd0a58238ddeae34b55b758635151d75b" -uuid = "227ef7b5-1206-438b-ac65-934d6da304b8" -version = "0.2.14" - - [deps.ACSets.extensions] - NautyACSetsExt = "nauty_jll" - XLSXACSetsExt = "XLSX" - - [deps.ACSets.weakdeps] - XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0" - nauty_jll = "55c6dc9b-343a-50ca-8ff2-b71adb3733d5" +project_hash = "af64ab2aca6e9cffe334c248c72b31908b66cf2a" [[deps.ADTypes]] -git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245" +git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.2.6" +version = "0.2.7" [[deps.AMQPClient]] deps = ["Logging", "MbedTLS", "Sockets"] @@ -29,18 +15,6 @@ git-tree-sha1 = "508457ed7a2afb432590247dc363fffc51f242fc" uuid = "79c8b4cd-a41a-55fa-907c-fab5288e1383" version = "0.5.1" -[[deps.ASL_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6252039f98492252f9e47c312c8ffda0e3b9e78d" -uuid = "ae81ac8f-d209-56e5-92de-9978fef736f9" -version = "0.1.3+0" - -[[deps.AbstractAlgebra]] -deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Preferences", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "d7832de8cf7af26abac741f10372080ac6cb73df" -uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.34.7" - [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" @@ -53,16 +27,16 @@ weakdeps = ["ChainRulesCore", "Test"] AbstractFFTsTestExt = "Test" [[deps.AbstractMCMC]] -deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] -git-tree-sha1 = "87e63dcb990029346b091b170252f3c416568afc" +deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] +git-tree-sha1 = "b0489adc45a7c8cf0d8e2ddf764f89c1c3decebd" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "4.4.2" +version = "5.2.0" [[deps.AbstractPPL]] -deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield"] +git-tree-sha1 = "9774889eac07c2e342e547b5c5c8ae5a2ce5c80b" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.7.1" [[deps.AbstractTrees]] git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" @@ -70,16 +44,17 @@ uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" [[deps.Accessors]] -deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Test"] -git-tree-sha1 = "cb96992f1bec110ad211b7e410e57ddf7944c16f" +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] +git-tree-sha1 = "c0d491ef0b135fd7d63cbc6404286bc633329425" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.35" +version = "0.1.36" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" AccessorsIntervalSetsExt = "IntervalSets" AccessorsStaticArraysExt = "StaticArrays" AccessorsStructArraysExt = "StructArrays" + AccessorsUnitfulExt = "Unitful" [deps.Accessors.weakdeps] AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" @@ -87,12 +62,13 @@ version = "0.1.35" Requires = "ae029012-a4dd-5104-9daa-d747884805df" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" +git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.7.2" +version = "4.0.4" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -100,9 +76,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "3bf24030e85b1d6d298e4f483f6aeff6f38462db" +git-tree-sha1 = "dfa0e3508fc3df81d28624b328f3b937c1df8bc2" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.4.6" +version = "0.6.1" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -116,9 +92,9 @@ version = "0.4.6" [[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"] -git-tree-sha1 = "b2a1602952739e589cf5e2daff1274a49f22c9a4" +git-tree-sha1 = "16589dbdd36c782ff01700908e962b303474f641" uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -version = "0.7.5" +version = "0.8.1" weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] [deps.AdvancedMH.extensions] @@ -127,37 +103,44 @@ weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] AdvancedMHStructArraysExt = "StructArrays" [[deps.AdvancedPS]] -deps = ["AbstractMCMC", "Distributions", "Libtask", "Random", "Random123", "StatsFuns"] -git-tree-sha1 = "4d73400b3583147b1b639794696c78202a226584" +deps = ["AbstractMCMC", "Distributions", "Random", "Random123", "Requires", "StatsFuns"] +git-tree-sha1 = "672f7ce648e06f93fceefde463c5855d77b6915a" uuid = "576499cb-2369-40b2-a588-c64705576edc" -version = "0.4.3" +version = "0.5.4" +weakdeps = ["Libtask"] + + [deps.AdvancedPS.extensions] + AdvancedPSLibtaskExt = "Libtask" [[deps.AdvancedVI]] -deps = ["Bijectors", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "67fcc7d46c26250e89fc62798fbe07b5ee264c6f" +deps = ["ADTypes", "Bijectors", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] +git-tree-sha1 = "187f67ab998f25208651262fee9539d845016b26" uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" -version = "0.1.6" +version = "0.2.5" -[[deps.AlgebraicInterfaces]] -git-tree-sha1 = "a81b76ea8d1801494562dd057315e4b7b25b8de1" -uuid = "23cfdc9f-0504-424a-be1f-4892b28e2f0c" -version = "0.1.1" + [deps.AdvancedVI.extensions] + AdvancedVIEnzymeExt = ["Enzyme"] + AdvancedVIFluxExt = ["Flux"] + AdvancedVIReverseDiffExt = ["ReverseDiff"] + AdvancedVIZygoteExt = ["Zygote"] + + [deps.AdvancedVI.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.AlgebraicPetri]] -deps = ["Catlab", "GeneralizedGenerated", "LabelledArrays"] -git-tree-sha1 = "25a196f3b0de6182f47769c79fc31260c0597977" +deps = ["Catlab", "DataStructures", "GeneralizedGenerated", "LabelledArrays", "LinearAlgebra", "Requires", "StatsBase"] +git-tree-sha1 = "7b07f05fec4e9649ebae8a40b60fbe12d7d004a3" uuid = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b" -version = "0.9.2" - - [deps.AlgebraicPetri.extensions] - AlgebraicPetriCatalystExt = "Catalyst" - AlgebraicPetriModelingToolkitExt = "ModelingToolkit" - AlgebraicPetriOrdinaryDiffEqExt = "OrdinaryDiffEq" +version = "0.8.10" - [deps.AlgebraicPetri.weakdeps] - Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83" - ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" - OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" +[[deps.AliasTables]] +deps = ["Random"] +git-tree-sha1 = "82b912bb5215792fd33df26f407d064d3602af98" +uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" +version = "1.1.2" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -170,21 +153,24 @@ version = "1.1.1" [[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] -git-tree-sha1 = "62e51b39331de8911e4a7ff6f5aaf38a5f4cc0ae" +git-tree-sha1 = "d57bd3762d308bded22c3b82d033bff85f6195c6" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" -version = "0.2.0" +version = "0.4.0" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c5aeb516a84459e0318a02507d2261edad97eb75" +deps = ["Adapt", "LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "133a240faec6e074e07c31ee75619c90544179cf" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.7.1" +version = "7.10.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceReverseDiffExt = "ReverseDiff" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -192,15 +178,18 @@ version = "7.7.1" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "64d582bcb9c93ac741234789eeb4f16812413efb" +git-tree-sha1 = "33207a8be6267bc389d0701e97a9bce6a4de68eb" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.6.0" +version = "1.9.2" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -229,9 +218,9 @@ version = "0.4.7" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "0b816941273b5b162be122a6c94d706e3b3125ca" +git-tree-sha1 = "30b7ea34abc4fe816eb1a5f434a43da804836163" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "0.17.38" +version = "1.7.0" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] @@ -265,22 +254,38 @@ git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" -[[deps.BenchmarkTools]] -deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "f1dff6729bc61f4d49e140da1af55dcd1ac97b2f" -uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.5.0" - [[deps.Bijections]] git-tree-sha1 = "c9b163bd832e023571e86d0b90d9de92a9879088" uuid = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04" version = "0.1.6" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "1234b03e94938e6f2b14834dfd3ef45698d5e14f" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "c12f0e123d21091546d11164d2665e70558a32b3" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.10.8" +version = "0.13.11" + + [deps.Bijectors.extensions] + BijectorsDistributionsADExt = "DistributionsAD" + BijectorsForwardDiffExt = "ForwardDiff" + BijectorsLazyArraysExt = "LazyArrays" + BijectorsReverseDiffExt = "ReverseDiff" + BijectorsTrackerExt = "Tracker" + BijectorsZygoteExt = "Zygote" + + [deps.Bijectors.weakdeps] + DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.BinaryProvider]] +deps = ["Libdl", "Logging", "SHA"] +git-tree-sha1 = "ecdec412a9abc8db54c0efc5548c64dfce072058" +uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232" +version = "0.5.10" [[deps.BitFlags]] git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" @@ -304,10 +309,16 @@ weakdeps = ["HTTP", "Sockets"] BlackBoxOptimRealtimePlotServerExt = ["HTTP", "Sockets"] [[deps.BoundaryValueDiffEq]] -deps = ["ArrayInterface", "BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NonlinearSolve", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "TruncatedStacktraces", "UnPack"] -git-tree-sha1 = "f7392ce20e6dafa8fee406142b1764de7d7cd911" +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "005b55fa2eebaa4d7bf3cfb8097807f47116175f" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "4.0.1" +version = "5.7.1" + + [deps.BoundaryValueDiffEq.extensions] + BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" + + [deps.BoundaryValueDiffEq.weakdeps] + ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -322,9 +333,9 @@ version = "0.5.0" [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] -git-tree-sha1 = "601f7e7b3d36f18790e2caf83a882d88e9b71ff1" +git-tree-sha1 = "585a387a490f1c4bd88be67eea15b93da5e85db7" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.2.4" +version = "0.2.5" [[deps.CPUTime]] git-tree-sha1 = "2dcc50ea6a0a1ef6440d6eecd0fe3813e5671f45" @@ -333,21 +344,21 @@ version = "1.0.0" [[deps.CSTParser]] deps = ["Tokenize"] -git-tree-sha1 = "b1d309487c04e92253b55c1f803b1d6f0e136920" +git-tree-sha1 = "0157e592151e39fa570645e2b2debcdfb8a0f112" uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f" -version = "3.4.1" +version = "3.4.3" [[deps.CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "679e69c611fff422038e9e21e270c4197d49d918" +git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.12" +version = "0.10.14" [[deps.Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" +deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "a4c43f59baa34011e303e76f5c8c91bf58415aaf" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.16.1+1" +version = "1.18.0+1" [[deps.Calculus]] deps = ["LinearAlgebra"] @@ -356,40 +367,22 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.Catlab]] -deps = ["ACSets", "Colors", "CompTime", "Compose", "DataStructures", "GeneralizedGenerated", "JSON", "LightXML", "LinearAlgebra", "Logging", "MLStyle", "PrettyTables", "Random", "Reexport", "SparseArrays", "StaticArrays", "Statistics", "StructEquality", "Tables"] -git-tree-sha1 = "33715b4addaa1f6cacd5a6f6fd0b6a93b8e80478" +deps = ["Colors", "CompTime", "Compose", "DataStructures", "GeneralizedGenerated", "JSON", "LightXML", "LinearAlgebra", "Logging", "MLStyle", "Pkg", "PrettyTables", "Random", "Reexport", "Requires", "SparseArrays", "StaticArrays", "Statistics", "StructEquality", "Tables"] +git-tree-sha1 = "821d6dcf331981e7c1d6377a6baee112a79a1021" uuid = "134e5e36-593f-5add-ad60-77f754baafbe" -version = "0.15.5" - - [deps.Catlab.extensions] - CatlabConvexExt = "Convex" - CatlabDataFramesExt = "DataFrames" - CatlabGraphsExt = "Graphs" - CatlabGraphvizExt = "Graphviz_jll" - CatlabMetaGraphsExt = "MetaGraphs" - CatlabSCSExt = "SCS" - CatlabTikzPicturesExt = "TikzPictures" - - [deps.Catlab.weakdeps] - Convex = "f65535da-76fb-5f13-bab9-19810c17039a" - DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" - Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6" - Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85" - MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5" - SCS = "c946c3f1-0d1f-5ce8-9dea-7daa1f7e2d13" - TikzPictures = "37f6aa50-8035-52d0-81c2-5a1d08754b2d" +version = "0.14.17" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "4e42872be98fa3343c4f8458cbda8c5c6a6fa97c" +git-tree-sha1 = "291821c1251486504f6bae435227907d734e94d2" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.63.0" +version = "1.66.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "aef70bb349b20aa81a82a19704c3ef339d4ee494" +git-tree-sha1 = "575cd02e080939a33b6df6c5853d14924c08e35b" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.22.1" +version = "1.23.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -423,12 +416,6 @@ git-tree-sha1 = "c0216e792f518b39b22212127d4a84dc31e4e386" uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" version = "1.3.5" -[[deps.CodecBzip2]] -deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] -git-tree-sha1 = "9b1ca1aa6ce3f71b3d1840c538a8210a043625eb" -uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.8.2" - [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73" @@ -437,15 +424,15 @@ version = "0.7.4" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "67c1f244b991cad9b0aa4b7540fb758c2488b129" +git-tree-sha1 = "4b270d6465eb21ae89b732182c20dc165f8bf9f2" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.24.0" +version = "3.25.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" +git-tree-sha1 = "b10d0b65641d57b8b4d5e234446582de5047050d" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.4" +version = "0.11.5" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] @@ -459,9 +446,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" +git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.10" +version = "0.12.11" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -493,9 +480,9 @@ version = "0.1.2" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "c955881e3c981181362ae4088b35995446298b80" +git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.14.0" +version = "4.15.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -513,9 +500,9 @@ uuid = "a81c6b42-2e10-5240-aca2-a61377ecd94b" version = "0.9.5" [[deps.CompositeTypes]] -git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" +git-tree-sha1 = "bce26c3dab336582805503bed209faab1c279768" uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" -version = "0.1.3" +version = "0.1.4" [[deps.CompositionsBase]] git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" @@ -533,9 +520,9 @@ version = "0.2.3" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "9c4708e3ed2b799e6124b5673a712dda0b596a9b" +git-tree-sha1 = "6cbbd4d241d7e6579ab354737f4dd95ca43946e1" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.3.1" +version = "2.4.1" [[deps.ConsoleProgressMonitor]] deps = ["Logging", "ProgressMeter"] @@ -545,9 +532,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" +git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.4" +version = "1.5.5" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -555,15 +542,15 @@ weakdeps = ["IntervalSets", "StaticArrays"] ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.Contour]] -git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" +git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.6.2" +version = "0.6.3" [[deps.Copulas]] -deps = ["Combinatorics", "Cubature", "Distributions", "ForwardDiff", "InteractiveUtils", "LogExpFunctions", "MvNormalCDF", "PrecompileTools", "QuadGK", "Random", "Roots", "SpecialFunctions", "StatsBase", "TaylorSeries", "WilliamsonTransforms"] -git-tree-sha1 = "16dc275bbc11b104f38241925a9b677f06801e02" +deps = ["Combinatorics", "Cubature", "Distributions", "ForwardDiff", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MvNormalCDF", "PrecompileTools", "QuadGK", "Random", "Roots", "SpecialFunctions", "StatsBase", "TaylorSeries", "WilliamsonTransforms"] +git-tree-sha1 = "1e62e3debe3268f5f1a22f7808207a1d16f8572b" uuid = "ae264745-0b69-425e-9d9d-cf662c5eec93" -version = "0.1.21" +version = "0.1.23" [[deps.CpuId]] deps = ["Markdown"] @@ -601,9 +588,9 @@ version = "1.6.1" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "1fb174f0d48fe7d142e1109a10636bc1d14f5ac2" +git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.17" +version = "0.18.20" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -621,9 +608,9 @@ version = "0.1.2" [[deps.DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack"] -git-tree-sha1 = "e40378efd2af7658d0a0579aa9e15b17137368f4" +git-tree-sha1 = "5959ae76ebd198f70e9af81153644543da0cfaf2" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.44.0" +version = "5.47.3" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -638,13 +625,15 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "0d9982e8dee851d519145857e79a17ee33ede154" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] +git-tree-sha1 = "c8b0bdee28a1addddb7ab939365fe6543d7d2d0d" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.130.0" +version = "6.149.2" [deps.DiffEqBase.extensions] + DiffEqBaseChainRulesCoreExt = "ChainRulesCore" DiffEqBaseDistributionsExt = "Distributions" + DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" DiffEqBaseMPIExt = "MPI" DiffEqBaseMeasurementsExt = "Measurements" @@ -652,10 +641,11 @@ version = "6.130.0" DiffEqBaseReverseDiffExt = "ReverseDiff" DiffEqBaseTrackerExt = "Tracker" DiffEqBaseUnitfulExt = "Unitful" - DiffEqBaseZygoteExt = "Zygote" [deps.DiffEqBase.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" @@ -663,20 +653,19 @@ version = "6.130.0" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "9c7d3a84264d935f6981504388b202a770113faa" +deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NonlinearSolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "c959cfd2657d16beada157a74d52269e8556500e" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.29.1" +version = "3.6.2" weakdeps = ["OrdinaryDiffEq", "Sundials"] [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "3d440ee25f48e5c7b08af71f2997daca45bf6856" +git-tree-sha1 = "65cbbe1450ced323b4b17228ccd96349d96795a7" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.20.1" +version = "5.21.0" [deps.DiffEqNoiseProcess.extensions] DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" @@ -698,9 +687,9 @@ version = "1.15.1" [[deps.DifferentialEquations]] deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] -git-tree-sha1 = "96a19f498504e4a3b39524196b73eb60ccef30e9" +git-tree-sha1 = "81042254a307980b8ab5b67033aca26c2e157ebb" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.10.0" +version = "7.13.0" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] @@ -718,10 +707,10 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "7c302d7a5fec5214eb8a5a4c466dcf7a51fcf169" +deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "22c595ca4146c07b16bcf9c8bea86f731f7109d2" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.107" +version = "0.25.108" weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [deps.Distributions.extensions] @@ -731,9 +720,9 @@ weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [[deps.DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "Distributions", "FillArrays", "LinearAlgebra", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsFuns", "ZygoteRules"] -git-tree-sha1 = "060a19f3f879773399a7011676eb273ccc265241" +git-tree-sha1 = "f4dd7727b07b4b7fff5ff4149118ee06e83dfab7" uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c" -version = "0.6.54" +version = "0.6.55" [deps.DistributionsAD.extensions] DistributionsADForwardDiffExt = "ForwardDiff" @@ -754,10 +743,16 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.9.3" [[deps.DomainSets]] -deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays", "Statistics"] -git-tree-sha1 = "51b4b84d33ec5e0955b55ff4b748b99ce2c3faa9" +deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "Random", "StaticArrays"] +git-tree-sha1 = "f300614d950439b5501e4198b0440c7e8b511894" uuid = "5b8099bc-c8ec-5219-889f-1d9e522a28bf" -version = "0.6.7" +version = "0.7.13" + + [deps.DomainSets.extensions] + DomainSetsMakieExt = "Makie" + + [deps.DomainSets.weakdeps] + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -771,28 +766,62 @@ uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" version = "0.6.8" [[deps.DynamicPPL]] -deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "932f5f977b04db019cc72ebd1f4161a6e7bded14" +deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Setfield", "Test"] +git-tree-sha1 = "839b5a5257047c2fe47946e84a706e37d9cfee27" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.21.6" +version = "0.24.11" + + [deps.DynamicPPL.extensions] + DynamicPPLChainRulesCoreExt = ["ChainRulesCore"] + DynamicPPLEnzymeCoreExt = ["EnzymeCore"] + DynamicPPLForwardDiffExt = ["ForwardDiff"] + DynamicPPLMCMCChainsExt = ["MCMCChains"] + DynamicPPLReverseDiffExt = ["ReverseDiff"] + DynamicPPLZygoteRulesExt = ["ZygoteRules"] + + [deps.DynamicPPL.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444" [[deps.DynamicPolynomials]] deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Pkg", "Reexport", "Test"] -git-tree-sha1 = "0bb0a6f812213ecc8fbbcf472f4a993036858971" +git-tree-sha1 = "30a1848c4f4fc35d1d4bbbd125650f6a11b5bc6c" uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07" -version = "0.5.5" +version = "0.5.7" + +[[deps.DynamicQuantities]] +deps = ["Compat", "PackageExtensionCompat", "Tricks"] +git-tree-sha1 = "412b25c7d99ec6b06967d315c7b29bb8e484f092" +uuid = "06fc5a27-2a28-4c7c-a15d-362465fb6821" +version = "0.13.2" + + [deps.DynamicQuantities.extensions] + DynamicQuantitiesLinearAlgebraExt = "LinearAlgebra" + DynamicQuantitiesMeasurementsExt = "Measurements" + DynamicQuantitiesScientificTypesExt = "ScientificTypes" + DynamicQuantitiesUnitfulExt = "Unitful" + + [deps.DynamicQuantities.weakdeps] + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + ScientificTypes = "321657f4-b219-11e9-178b-2701a2544e81" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.EasyModelAnalysis]] -deps = ["DifferentialEquations", "Distributions", "GlobalSensitivity", "LinearAlgebra", "ModelingToolkit", "NLopt", "Optimization", "OptimizationBBO", "OptimizationMOI", "OptimizationNLopt", "Plots", "Reexport", "SciMLBase", "SciMLExpectations", "Turing"] -git-tree-sha1 = "ec1d97f9afe42fc6d4ea19190e8d0b82ad80512a" +deps = ["DifferentialEquations", "Distributions", "GlobalSensitivity", "LinearAlgebra", "ModelingToolkit", "NLopt", "Optimization", "OptimizationBBO", "OptimizationNLopt", "Plots", "Reexport", "SciMLBase", "SciMLExpectations", "Turing"] +git-tree-sha1 = "c434bce643e1f851c914d349c10307b6ae7ff8fd" uuid = "ef4b24a4-a090-4686-a932-e7e56a5a83bd" -version = "0.1.13" +version = "1.0.0" [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] -git-tree-sha1 = "973b4927d112559dc737f55d6bf06503a5b3fc14" +git-tree-sha1 = "e611b7fdfbfb5b18d5e98776c30daede41b44542" uuid = "cad2338a-1db2-11e9-3401-43bc07c9ede2" -version = "1.1.0" +version = "2.0.0" [[deps.EnumX]] git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" @@ -800,9 +829,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -git-tree-sha1 = "59c44d8fbc651c0395d8a6eda64b05ce316f58b4" +git-tree-sha1 = "18394bc78ac2814ff38fe5e0c9dc2cd171e2810c" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.6.5" +version = "0.7.2" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -822,9 +851,9 @@ version = "0.1.10" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c" +git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.5.0+0" +version = "2.6.2+0" [[deps.ExponentialUtilities]] deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] @@ -844,16 +873,16 @@ uuid = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615" version = "1.2.0" [[deps.FFMPEG]] -deps = ["FFMPEG_jll"] -git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" +deps = ["BinaryProvider", "Libdl"] +git-tree-sha1 = "9143266ba77d3313a4cf61d8333a1970e8c5d8b6" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.1" +version = "0.2.4" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e" +git-tree-sha1 = "ab3f7e1819dba9434a3a5126510c8fda3a4e7000" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.4+1" +version = "6.1.1+0" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] @@ -867,6 +896,12 @@ git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" version = "3.3.10+0" +[[deps.FastAlmostBandedMatrices]] +deps = ["ArrayInterface", "ArrayLayouts", "BandedMatrices", "ConcreteStructs", "LazyArrays", "LinearAlgebra", "MatrixFactorizations", "PrecompileTools", "Reexport"] +git-tree-sha1 = "9dc913faf8552fd09b92a0d7fcc25f1d5609d795" +uuid = "9d29842c-ecb8-4973-b1e9-a27b1157504e" +version = "0.1.1" + [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] git-tree-sha1 = "a6e756a880fc419c8b41592010aebe6a5ce09136" @@ -880,15 +915,15 @@ version = "0.3.2" [[deps.FastLapackInterface]] deps = ["LinearAlgebra"] -git-tree-sha1 = "0a59c7d1002f3131de53dc4568a47d15a44daef7" +git-tree-sha1 = "f4102aab9c7df8691ed09f9c42e34f5ab5458ab9" uuid = "29a986be-02c6-4525-aec4-84b980013641" -version = "2.0.2" +version = "2.0.3" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "c5c28c245101bd59154f649e19b038d15901b5dc" +git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.2" +version = "1.16.3" [[deps.FilePathsBase]] deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] @@ -900,10 +935,10 @@ version = "0.9.21" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random"] -git-tree-sha1 = "5b93957f6dcd33fc343044af3d48c215be2562f1" +deps = ["LinearAlgebra"] +git-tree-sha1 = "0653c0a2396a6da5bc4766c43041ef5fd3efbe57" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.9.3" +version = "1.11.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -911,11 +946,16 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysSparseArraysExt = "SparseArrays" FillArraysStatisticsExt = "Statistics" +[[deps.FindFirstFunctions]] +git-tree-sha1 = "e90fef90f7d75e6a5b435b0fd65609759f99717a" +uuid = "64ca27bc-2ba2-4a57-88aa-44e436879224" +version = "1.2.0" + [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] -git-tree-sha1 = "73d1214fec245096717847c62d389a5d2ac86504" +git-tree-sha1 = "2de436b72c3422940cbe1367611d137008af7ec3" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.22.0" +version = "2.23.1" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" @@ -929,21 +969,20 @@ version = "2.22.0" [[deps.FixedPointNumbers]] deps = ["Statistics"] -git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" +git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172" uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" -version = "0.8.4" +version = "0.8.5" [[deps.Fontconfig_jll]] -deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" +deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] +git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.93+0" +version = "2.13.96+0" -[[deps.Formatting]] -deps = ["Logging", "Printf"] -git-tree-sha1 = "fb409abab2caf118986fc597ba84b50cbaf00b87" -uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" -version = "0.4.3" +[[deps.Format]] +git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" +uuid = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8" +version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] @@ -962,10 +1001,10 @@ uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" version = "2.13.1+0" [[deps.FriBidi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.10+0" +version = "1.0.14+0" [[deps.FunctionWrappers]] git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" @@ -980,9 +1019,9 @@ version = "0.1.3" [[deps.Functors]] deps = ["LinearAlgebra"] -git-tree-sha1 = "a2657dd0f3e8a61dbe70fc7c122038bd33790af5" +git-tree-sha1 = "d3e63d9fa13f8eaa2f06f64949e2afc593ff52c2" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.3.0" +version = "0.4.10" [[deps.Future]] deps = ["Random"] @@ -1002,27 +1041,27 @@ version = "3.3.9+0" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "85d7fb51afb3def5dcb85ad31c3707795c8bccc1" +git-tree-sha1 = "68e8ff56a4a355a85d2784b94614491f8c900cde" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "9.1.0" +version = "10.1.0" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" +git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.5" +version = "0.1.6" [[deps.GR]] -deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "3458564589be207fa6a77dbbf8b97674c9836aab" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] +git-tree-sha1 = "ddda044ca260ee324c5fc07edb6d7cf3f0b9c350" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.2" +version = "0.73.5" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "77f81da2964cc9fa7c0127f941e8bce37f7f1d70" +git-tree-sha1 = "278e5e0f820178e8a26df3184fcb2280717c79b1" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.2+0" +version = "0.73.5+0" [[deps.GeneralizedGenerated]] deps = ["DataStructures", "JuliaVariables", "MLStyle", "Serialization"] @@ -1032,9 +1071,9 @@ version = "0.3.3" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] -git-tree-sha1 = "fb69b2a645fa69ba5f474af09221b9308b160ce6" +git-tree-sha1 = "af49a0851f8113fcfae2ef5027c6d49d0acec39b" uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" -version = "0.5.3" +version = "0.5.4" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -1044,9 +1083,9 @@ version = "0.21.0+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" +git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.76.5+0" +version = "2.80.2+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -1055,9 +1094,9 @@ version = "1.3.1" [[deps.GlobalSensitivity]] deps = ["Combinatorics", "Copulas", "Distributions", "FFTW", "ForwardDiff", "KernelDensity", "LinearAlgebra", "Parameters", "QuasiMonteCarlo", "Random", "RecursiveArrayTools", "Statistics", "StatsBase", "ThreadsX", "Trapz"] -git-tree-sha1 = "75c048c5657d890d75696a14e9dcff752d4f5bea" +git-tree-sha1 = "c8791c355322050eba036d31e7c64881f67592c5" uuid = "af5da776-676b-467e-8baf-acd8249e4f0f" -version = "2.3.0" +version = "2.6.1" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1067,27 +1106,15 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "899050ace26649433ef1af25bc17a815b3db52b7" +git-tree-sha1 = "4f2b57488ac7ee16124396de4f2bbdd51b2602ad" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.9.0" +version = "1.11.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" -[[deps.Groebner]] -deps = ["AbstractAlgebra", "Combinatorics", "ExprTools", "Logging", "MultivariatePolynomials", "PrecompileTools", "PrettyTables", "Primes", "Printf", "Random", "SIMD", "TimerOutputs"] -git-tree-sha1 = "6b505ef15e55bdc5bb3ddbcfebdff1c9e67081e8" -uuid = "0b43b601-686d-58a3-8a1c-6623616c7cd4" -version = "0.5.1" - -[[deps.GroupsCore]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "6df9cd6ee79fc59feab33f63a1b3c9e95e2461d5" -uuid = "d5909c97-4eac-4ecc-a3dc-fdd0858a4120" -version = "0.4.2" - [[deps.HCubature]] deps = ["Combinatorics", "DataStructures", "LinearAlgebra", "QuadGK", "StaticArrays"] git-tree-sha1 = "10f37537bbd83e52c63abf6393f209dbd641fedc" @@ -1096,9 +1123,9 @@ version = "1.6.0" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "ac7b73d562b8f4287c3b67b4c66a5395a19c1ae8" +git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.2" +version = "1.10.8" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -1125,10 +1152,10 @@ uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" version = "0.3.23" [[deps.IRTools]] -deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "5d8c5713f38f7bc029e26627b687710ba406d0dd" +deps = ["InteractiveUtils", "MacroTools"] +git-tree-sha1 = "950c3717af761bc3ff906c2e8e52bd83390b6ec2" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.12" +version = "0.4.14" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -1163,27 +1190,35 @@ uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" version = "0.1.2" [[deps.Integrals]] -deps = ["CommonSolve", "HCubature", "LinearAlgebra", "MonteCarloIntegration", "QuadGK", "Reexport", "Requires", "SciMLBase"] -git-tree-sha1 = "44dd71130586e1776fde9041bd81f2e0db15db10" +deps = ["CommonSolve", "HCubature", "LinearAlgebra", "MonteCarloIntegration", "QuadGK", "Reexport", "SciMLBase"] +git-tree-sha1 = "ebf5737d823873add85809f2b52e20e3eae71997" uuid = "de52edbc-65ea-441a-8357-d3a637375a31" -version = "3.9.0" +version = "4.4.1" [deps.Integrals.extensions] + IntegralsArblibExt = "Arblib" + IntegralsCubaExt = "Cuba" + IntegralsCubatureExt = "Cubature" IntegralsFastGaussQuadratureExt = "FastGaussQuadrature" IntegralsForwardDiffExt = "ForwardDiff" + IntegralsMCIntegrationExt = "MCIntegration" IntegralsZygoteExt = ["Zygote", "ChainRulesCore"] [deps.Integrals.weakdeps] + Arblib = "fb37089c-8514-4489-9461-98f9c8763369" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Cuba = "8a292aeb-7a57-582c-b821-06e4c11590b1" + Cubature = "667455a9-e2ce-5579-9412-b964f529a492" FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + MCIntegration = "ea1e2de9-7db7-4b42-91ee-0cd1bf6df167" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "5fdf2fe6724d8caabf43b557b84ce53f3b7e2f6b" +git-tree-sha1 = "be50fe8df3acbffa0274a744f1a99d29c45a57f4" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.0.2+0" +version = "2024.1.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -1212,21 +1247,19 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "68772f49f54b479fa88ace904f6127f0a3bb2e46" +git-tree-sha1 = "e7cbed5032c4c397a6ac23d1493f3289e01231c4" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.12" +version = "0.1.14" +weakdeps = ["Dates"] + + [deps.InverseFunctions.extensions] + DatesExt = "Dates" [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" version = "1.3.0" -[[deps.Ipopt_jll]] -deps = ["ASL_jll", "Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "MUMPS_seq_jll", "OpenBLAS32_jll", "Pkg"] -git-tree-sha1 = "e3e202237d93f18856b6ff1016166b0f172a49a8" -uuid = "9cc047cb-c261-5740-88fc-0cf96f7bdcc7" -version = "300.1400.400+0" - [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" @@ -1244,9 +1277,9 @@ version = "1.0.0" [[deps.JLD2]] deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "PrecompileTools", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "5ea6acdd53a51d897672edb694e3cc2912f3f8a7" +git-tree-sha1 = "dca9ff5abdf5fab4456876bc93f80c59a37b81df" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.46" +version = "0.4.47" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] @@ -1286,21 +1319,21 @@ version = "1.3.0" [[deps.JobSchedulers]] deps = ["Dates", "JLD2", "JSON", "Logging", "OrderedCollections", "Pipelines", "PrecompileTools", "PrettyTables", "Printf", "Reexport", "Term", "Terming", "Test"] -git-tree-sha1 = "9d90afe270e087d1f9be1f11800d3fe6467ca405" +git-tree-sha1 = "c53f137acf715e7347f1291cf3de7ae0af6a44b8" uuid = "eeff360b-c02d-44d3-ab26-4013c616a17e" -version = "0.8.4" +version = "0.9.0" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3336abae9a713d2210bb57ab484b1e065edd7d23" +git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.2+0" +version = "3.0.3+0" [[deps.JuliaFormatter]] -deps = ["CSTParser", "Combinatorics", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] -git-tree-sha1 = "fde717f9e3fe6ffb0336bcc2142cfa71dd9df1f5" +deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] +git-tree-sha1 = "1c4880cb70a5c6c87ea36deccc3d7f9e7969c18c" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.50" +version = "1.0.56" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1309,10 +1342,10 @@ uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" [[deps.JumpProcesses]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "UnPack"] -git-tree-sha1 = "c451feb97251965a9fe40bacd62551a72cc5902c" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] +git-tree-sha1 = "ed08d89318be7d625613f3c435d1f6678fba4850" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.10.1" +version = "9.11.1" weakdeps = ["FastBroadcast"] [deps.JumpProcesses.extensions] @@ -1320,15 +1353,15 @@ weakdeps = ["FastBroadcast"] [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] -git-tree-sha1 = "884c2968c2e8e7e6bf5956af88cb46aa745c854b" +git-tree-sha1 = "07649c499349dad9f08dde4243a4c597064663e9" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" -version = "0.4.1" +version = "0.6.0" [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "c7753cc3febe006708ce6798482004241f7d890b" +git-tree-sha1 = "db02395e4c374030c53dc28f3c1d33dec35f7272" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.17" +version = "0.9.19" weakdeps = ["EnzymeCore"] [deps.KernelAbstractions.extensions] @@ -1336,21 +1369,27 @@ weakdeps = ["EnzymeCore"] [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] -git-tree-sha1 = "fee018a29b60733876eb557804b5b109dd3dd8a7" +git-tree-sha1 = "7d703202e65efa1369de1279c162b915e245eed1" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.8" +version = "0.6.9" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "8a6837ec02fe5fb3def1abc907bb802ef11a0729" +git-tree-sha1 = "267dad6b4b7b5d529c76d40ff48d33f7e94cb834" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.5" +version = "0.9.6" [[deps.LAME_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.1+0" +version = "3.100.2+0" + +[[deps.LBFGSB]] +deps = ["L_BFGS_B_jll"] +git-tree-sha1 = "e2e6f53ee20605d0ea2be473480b7480bd5091b5" +uuid = "5be7bae1-8223-5378-bac3-9e7378a2f6e6" +version = "0.4.1" [[deps.LERC_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1360,9 +1399,9 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] -git-tree-sha1 = "ddab4d40513bce53c8e3157825e245224f74fae7" +git-tree-sha1 = "839c82932db86740ae729779e610f07a1640be9a" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.6.0" +version = "6.6.3" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1392,10 +1431,16 @@ weakdeps = ["Serialization"] SerializationExt = ["Serialization"] [[deps.LZO_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.1+0" +version = "2.10.2+0" + +[[deps.L_BFGS_B_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "77feda930ed3f04b2b0fbb5bea89e69d3677c6b0" +uuid = "81d17ec3-03a1-5e46-b53e-bddc35a13473" +version = "3.0.1+0" [[deps.LaTeXStrings]] git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" @@ -1404,9 +1449,9 @@ version = "1.3.1" [[deps.LabelledArrays]] deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "LinearAlgebra", "MacroTools", "PreallocationTools", "RecursiveArrayTools", "StaticArrays"] -git-tree-sha1 = "d1f981fba6eb3ec393eede4821bca3f2b7592cd4" +git-tree-sha1 = "e459fda6b68ea8684b3fcd513d2fd1e5130c4402" uuid = "2ee39098-c373-598a-b85f-a56591580800" -version = "1.15.1" +version = "1.16.0" [[deps.LambertW]] git-tree-sha1 = "c5ffc834de5d61d00d2b0e18c96267cffc21f648" @@ -1414,10 +1459,10 @@ uuid = "984bce1d-4616-540c-a9ee-88d1112d94c9" version = "0.4.6" [[deps.Latexify]] -deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] -git-tree-sha1 = "f428ae552340899a935973270b8d98e5a31c49fe" +deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] +git-tree-sha1 = "e0b5cd21dc1b44ec6e64f351976f961e6f31d6c4" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.1" +version = "0.16.3" [deps.Latexify.extensions] DataFramesExt = "DataFrames" @@ -1439,6 +1484,16 @@ git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" version = "0.1.15" +[[deps.LazyArrays]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays"] +git-tree-sha1 = "35079a6a869eecace778bcda8641f9a54ca3a828" +uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" +version = "1.10.0" +weakdeps = ["StaticArrays"] + + [deps.LazyArrays.extensions] + LazyArraysStaticArraysExt = "StaticArrays" + [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" @@ -1489,10 +1544,10 @@ uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" version = "3.2.2+1" [[deps.Libgcrypt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] -git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] +git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.7+0" +version = "1.8.11+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -1501,10 +1556,10 @@ uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" version = "1.6.0+0" [[deps.Libgpg_error_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.42.0+0" +version = "1.49.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1513,16 +1568,16 @@ uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" version = "1.17.0+0" [[deps.Libmount_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.35.0+0" +version = "2.40.1+0" [[deps.Libtask]] deps = ["FunctionWrappers", "LRUCache", "LinearAlgebra", "Statistics"] -git-tree-sha1 = "345a40c746404dd9cb1bbc368715856838ab96f2" +git-tree-sha1 = "ed1f362b3fd13f00b65e61d98669c652c17663ab" uuid = "6f1fad26-d15e-5dc8-ae53-837a1d7b8c9f" -version = "0.8.6" +version = "0.8.7" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] @@ -1531,10 +1586,10 @@ uuid = "89763e89-9b03-5906-acba-b20f662cd828" version = "4.5.1+1" [[deps.Libuuid_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.36.0+0" +version = "2.40.1+0" [[deps.LightXML]] deps = ["Libdl", "XML2_jll"] @@ -1553,32 +1608,41 @@ deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] -deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "EnzymeCore", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] -git-tree-sha1 = "9f27ba34f5821a0495efb09ea3a465c31326495a" +deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "efd815eaa56c0ffdf86581df5aaefb7e901323a0" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.10.0" +version = "2.30.0" [deps.LinearSolve.extensions] + LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" - LinearSolveEnzymeExt = "Enzyme" + LinearSolveCUDSSExt = "CUDSS" + LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] + LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" LinearSolveKrylovKitExt = "KrylovKit" LinearSolveMetalExt = "Metal" LinearSolvePardisoExt = "Pardiso" + LinearSolveRecursiveArrayToolsExt = "RecursiveArrayTools" [deps.LinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" + RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" [[deps.LogDensityProblems]] deps = ["ArgCheck", "DocStringExtensions", "Random"] @@ -1588,9 +1652,9 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "9c50732cd0f188766b6217ed6a2ebbdaf9890029" +git-tree-sha1 = "98cad2db1c46f2fff70a5e305fb42c97a251422a" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.7.0" +version = "1.9.0" [deps.LogDensityProblemsAD.extensions] LogDensityProblemsADADTypesExt = "ADTypes" @@ -1635,9 +1699,9 @@ version = "1.0.3" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "0f5648fbae0d015e3abe5867bca2b362f67a5894" +git-tree-sha1 = "8f6786d8b2b3248d79db3ad359ce95382d5a6df8" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.166" +version = "0.12.170" weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] @@ -1645,10 +1709,10 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] SpecialFunctionsExt = "SpecialFunctions" [[deps.MCMCChains]] -deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] -git-tree-sha1 = "d0ce57aa5ebbdb456bac3bc5a2ca15cd06ec5f1b" +deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] +git-tree-sha1 = "d28056379864318172ff4b7958710cfddd709339" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "6.0.5" +version = "6.0.6" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] @@ -1656,40 +1720,28 @@ git-tree-sha1 = "8ba8b1840d3ab5b38e7c71c23c3193bb5cbc02b5" uuid = "be115224-59cd-429b-ad48-344e309966f0" version = "0.3.10" -[[deps.METIS_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "1fd0a97409e418b78c53fac671cf4622efdf0f21" -uuid = "d00139f3-1899-568f-a2f0-47f597d42d70" -version = "5.1.2+0" - [[deps.MIMEs]] git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" version = "0.1.4" [[deps.MKL_jll]] -deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl"] -git-tree-sha1 = "72dc3cf284559eb8f53aa593fe62cb33f83ed0c0" +deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] +git-tree-sha1 = "80b2833b56d466b3858d565adcd16a4a05f2089b" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2024.0.0+0" +version = "2024.1.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "14bd8088cf7cd1676aa83a57004f8d23d43cd81e" +git-tree-sha1 = "d2a45e1b5998ba3fdfb6cfe0c81096d4c7fb40e7" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.9.5" +version = "1.9.6" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" uuid = "d8e11817-5142-5d16-987a-aa16d5891078" version = "0.4.17" -[[deps.MUMPS_seq_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "METIS_jll", "OpenBLAS32_jll", "Pkg"] -git-tree-sha1 = "29de2841fa5aefe615dea179fcde48bb87b58f57" -uuid = "d7ed1dd3-d0ae-5e8e-bfb4-87a502085b8d" -version = "5.4.1+0" - [[deps.MacroTools]] deps = ["Markdown", "Random"] git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" @@ -1716,17 +1768,17 @@ git-tree-sha1 = "12b0736d966c45d8621e895671266f05c881dda1" uuid = "abcecc63-2b08-419c-80c4-c63dca6fa478" version = "0.1.15" -[[deps.MathOptInterface]] -deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] -git-tree-sha1 = "e8b98c868029d007102dc5f98986c81f33b0ec37" -uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "1.26.0" +[[deps.MatrixFactorizations]] +deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] +git-tree-sha1 = "6731e0574fa5ee21c02733e397beb133df90de35" +uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" +version = "2.2.0" -[[deps.MathProgBase]] -deps = ["LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "9abbe463a1e9fc507f12a69e7f29346c2cdc472c" -uuid = "fdba3010-5040-5b88-9595-932c9decdf73" -version = "0.7.8" +[[deps.MaybeInplace]] +deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "SparseArrays"] +git-tree-sha1 = "b1f2f92feb0bc201e91c155ef575bcc7d9cc3526" +uuid = "bb5d69b7-63fc-4a16-80bd-7e42200c7bdb" +version = "0.1.2" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -1752,36 +1804,38 @@ version = "0.1.4" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" +git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.1.0" +version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.Mocking]] deps = ["Compat", "ExprTools"] -git-tree-sha1 = "4cc0c5a83933648b615c36c2b956d94fda70641e" +git-tree-sha1 = "bf17d9cb4f0d2882351dfad030598f64286e5936" uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" -version = "0.7.7" +version = "0.7.8" [[deps.ModelingToolkit]] -deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "IfElse", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "MacroTools", "NaNMath", "OrdinaryDiffEq", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] -git-tree-sha1 = "87a45c453295c1640a1fd011a85e42fda7a78d15" +deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "FindFirstFunctions", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "OrderedCollections", "OrdinaryDiffEq", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] +git-tree-sha1 = "84a6705e5379c3bd6b6cde4f54b2391337e5d0da" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "8.70.0" +version = "9.13.0" [deps.ModelingToolkit.extensions] + MTKBifurcationKitExt = "BifurcationKit" MTKDeepDiffsExt = "DeepDiffs" [deps.ModelingToolkit.weakdeps] + BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665" DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6" [[deps.MonteCarloIntegration]] -deps = ["Distributions", "Random"] -git-tree-sha1 = "3f78ebce296c927d5c854e83cccdb5dcb1845629" +deps = ["Distributions", "QuasiMonteCarlo", "Random"] +git-tree-sha1 = "722ad522068d31954b4a976b66a26aeccbf509ed" uuid = "4886b29c-78c9-11e9-0a6e-41e1f4161f7b" -version = "0.0.3" +version = "0.2.0" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" @@ -1794,21 +1848,21 @@ version = "0.2.4" [[deps.MultivariatePolynomials]] deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] -git-tree-sha1 = "769c9175942d91ed9b83fa929eee4fe6a1d128ad" +git-tree-sha1 = "dad7be0c92b688bf8f24af170825ccedc104b116" uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3" -version = "0.5.4" +version = "0.5.5" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "302fd161eb1c439e4115b51ae456da4e9984f130" +git-tree-sha1 = "a3589efe0005fc4718775d8641b2de9060d23f73" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.1" +version = "1.4.4" [[deps.MvNormalCDF]] deps = ["Distributions", "FillArrays", "LinearAlgebra", "Primes", "Random", "StatsBase"] -git-tree-sha1 = "3d1e8f8e683e506d6fcd41104b3d791aa25d4286" +git-tree-sha1 = "87ce0f8162ba3a9f1b6410d2180be4f04c0baac1" uuid = "37188c8d-bc69-4638-b057-733e744175ec" -version = "0.3.0" +version = "0.3.2" [[deps.MyterialColors]] git-tree-sha1 = "01d8466fb449436348999d7c6ad740f8f853a579" @@ -1822,10 +1876,16 @@ uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" version = "7.8.3" [[deps.NLopt]] -deps = ["MathOptInterface", "MathProgBase", "NLopt_jll"] -git-tree-sha1 = "5a7e32c569200a8a03c3d55d286254b0321cd262" +deps = ["NLopt_jll"] +git-tree-sha1 = "3b887e2ef56be3309e68d2546c6178e2d2fa9a60" uuid = "76087f3c-5699-56af-9a33-bf431cd00edd" -version = "0.6.5" +version = "1.0.2" + + [deps.NLopt.extensions] + NLoptMathOptInterfaceExt = ["MathOptInterface"] + + [deps.NLopt.weakdeps] + MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" [[deps.NLopt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1841,9 +1901,9 @@ version = "4.5.1" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "877f15c331337d54cf24c797d5bcb2e48ce21221" +git-tree-sha1 = "e0cea7ec219ada9ac80ec2e82e374ab2f154ae05" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.12" +version = "0.9.16" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1871,9 +1931,9 @@ version = "0.1.5" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "0ae91efac93c3859f5c812a24c9468bb9e50b028" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.1" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1885,15 +1945,41 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "e10debcea868cd6e51249e8eeaf191c25f68a640" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "dc0d78eeed89323526203b8a11a4fa6cdbe25cd6" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "1.10.1" +version = "3.11.0" + + [deps.NonlinearSolve.extensions] + NonlinearSolveBandedMatricesExt = "BandedMatrices" + NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" + NonlinearSolveFixedPointAccelerationExt = "FixedPointAcceleration" + NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" + NonlinearSolveMINPACKExt = "MINPACK" + NonlinearSolveNLSolversExt = "NLSolvers" + NonlinearSolveNLsolveExt = "NLsolve" + NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" + NonlinearSolveSpeedMappingExt = "SpeedMapping" + NonlinearSolveSymbolicsExt = "Symbolics" + NonlinearSolveZygoteExt = "Zygote" + + [deps.NonlinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce" + FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176" + LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" + MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9" + NLSolvers = "337daf1e-9722-11e9-073e-8b9effe078ba" + NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" + SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4" + SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.OffsetArrays]] -git-tree-sha1 = "6a731f2b5c03157418a20c12195eb4b74c8f8621" +git-tree-sha1 = "e64b4f5ea6b7389f6f046d13d4896a8f9c1ba71e" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.13.0" +version = "1.14.0" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -1907,15 +1993,9 @@ version = "1.3.5+1" [[deps.OpenAPI]] deps = ["Base64", "Dates", "Downloads", "HTTP", "JSON", "LibCURL", "MIMEs", "MbedTLS", "TimeZones", "URIs"] -git-tree-sha1 = "5e48ceeca7de91dc5ae0d3fe2c5d1c6defca474b" +git-tree-sha1 = "752a12cbf4234b48c3ea664a389b05b82151fa1b" uuid = "d5e62ea6-ddf3-4d43-8e4c-ad5e6c8bfd7d" -version = "0.1.21" - -[[deps.OpenBLAS32_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6065c4cff8fee6c6770b277af45d5082baacdba1" -uuid = "656ef2d0-ae68-5445-9ca0-591084a874a2" -version = "0.3.24+0" +version = "0.1.22" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] @@ -1929,15 +2009,15 @@ version = "0.8.1+2" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "51901a49222b09e3743c65b8847687ae5fc78eb2" +git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.4.1" +version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "60e3045590bd104a16fefb12836c00c0ef8c7f8c" +git-tree-sha1 = "3da7367955dcc5c54c1ba4d402ccdc09a1a3e046" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.13+0" +version = "3.0.13+1" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1946,24 +2026,42 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" [[deps.Optim]] -deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "MathOptInterface", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "d024bfb56144d947d4fafcd9cb5cafbe3410b133" +deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] +git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.9.2" +version = "1.9.4" + + [deps.Optim.extensions] + OptimMOIExt = "MathOptInterface" + + [deps.Optim.weakdeps] + MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "e5a1825d3d53aa4ad4fb42bd4927011ad4a78c3d" +git-tree-sha1 = "6572fe0c5b74431aaeb0b18a4aa5ef03c84678be" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.15" +version = "0.3.3" [[deps.Optimization]] -deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LinearAlgebra", "Logging", "LoggingExtras", "Pkg", "Printf", "ProgressLogging", "Reexport", "Requires", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "1aa7ffea6e171167e9cae620d749e16d5874414a" +deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Pkg", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] +git-tree-sha1 = "ff78e9cada1349a0fb64995db7325949cb34b67b" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "3.19.3" +version = "3.25.0" + +[[deps.OptimizationBBO]] +deps = ["BlackBoxOptim", "Optimization", "Reexport"] +git-tree-sha1 = "ae0742c7c4e17271fc713ce4c61c10c9ccdb15a4" +uuid = "3e6eede4-6085-4f62-9a71-46d9bc1eb92b" +version = "0.2.1" + +[[deps.OptimizationBase]] +deps = ["ADTypes", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "Reexport", "Requires", "SciMLBase", "SparseArrays"] +git-tree-sha1 = "d44c297c3103b1a733304eeb0f70c43eede5ee60" +uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb" +version = "0.0.7" - [deps.Optimization.extensions] + [deps.OptimizationBase.extensions] OptimizationEnzymeExt = "Enzyme" OptimizationFiniteDiffExt = "FiniteDiff" OptimizationForwardDiffExt = "ForwardDiff" @@ -1973,7 +2071,7 @@ version = "3.19.3" OptimizationTrackerExt = "Tracker" OptimizationZygoteExt = "Zygote" - [deps.Optimization.weakdeps] + [deps.OptimizationBase.weakdeps] Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" @@ -1984,23 +2082,11 @@ version = "3.19.3" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" -[[deps.OptimizationBBO]] -deps = ["BlackBoxOptim", "Optimization", "Reexport"] -git-tree-sha1 = "939b19f2c213901aa544d1fd50e5f0065e66127c" -uuid = "3e6eede4-6085-4f62-9a71-46d9bc1eb92b" -version = "0.1.5" - -[[deps.OptimizationMOI]] -deps = ["Ipopt_jll", "MathOptInterface", "ModelingToolkit", "Optimization", "Reexport", "SparseArrays", "Symbolics"] -git-tree-sha1 = "4fcaa63de3f8154d4ab164c0a2a0c488c6be8814" -uuid = "fd9f6733-72f4-499f-8506-86b2bdd0dea1" -version = "0.1.16" - [[deps.OptimizationNLopt]] deps = ["NLopt", "Optimization", "Reexport"] -git-tree-sha1 = "dc1b76eae7c47ae77560803587911d4d219af531" +git-tree-sha1 = "745df99f24c30787886b7b941553e513ffeccc8e" uuid = "4e6fcdb7-1186-4e1f-a706-475e75c168bb" -version = "0.1.8" +version = "0.2.0" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -2014,16 +2100,16 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.3" [[deps.OrdinaryDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "f0f43037c0ba045e96f32d65858eb825a211b817" +deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "cd8c4fb1cc88e65e27f92c7e714afc430cd1debc" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.58.2" +version = "6.75.0" [[deps.Oxygen]] -deps = ["DataStructures", "Dates", "HTTP", "JSON3", "MIMEs", "Reexport", "RelocatableFolders", "Requires", "Sockets", "Statistics"] -git-tree-sha1 = "5c069e6a5b01f48d2dea0849218388803725ef8d" +deps = ["DataStructures", "Dates", "HTTP", "JSON3", "MIMEs", "Reexport", "RelocatableFolders", "Requires", "Sockets", "Statistics", "StructTypes"] +git-tree-sha1 = "edc978d60d435abfc674b3f9f31d74a7ec4740d8" uuid = "df9a0d86-3283-4920-82dc-4555fc0d1d8b" -version = "1.5.0" +version = "1.5.8" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -2060,12 +2146,6 @@ git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" version = "2.8.1" -[[deps.Permutations]] -deps = ["Combinatorics", "LinearAlgebra", "Random"] -git-tree-sha1 = "eb3f9df2457819bf0a9019bd93cc451697a0751e" -uuid = "2ae35dd2-176d-5d53-8349-f30d82d94d4f" -version = "0.4.20" - [[deps.Pipe]] git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" @@ -2073,15 +2153,15 @@ version = "1.3.0" [[deps.Pipelines]] deps = ["Dates", "FilePathsBase", "Logging", "OrderedCollections", "Printf", "Reexport", "Test", "UUIDs"] -git-tree-sha1 = "45e0a70f4974fb1b7f1d2714bc68bffb8fdfe598" +git-tree-sha1 = "02c75655459f2a27cf583dea9ed51a6250079f6b" uuid = "ef544631-5c6f-4e9b-994c-12e7a4cd724c" -version = "0.10.5" +version = "0.10.6" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] -git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87" +git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.42.2+0" +version = "0.43.4+0" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] @@ -2096,9 +2176,9 @@ version = "3.1.0" [[deps.PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "862942baf5663da528f66d24996eb6da85218e76" +git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.0" +version = "1.4.1" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] @@ -2128,9 +2208,9 @@ version = "0.4.4" [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "fca25670784a1ae44546bcb17288218310af2778" +git-tree-sha1 = "2ba5f33cbb51a85ef58a850749492b08f9bf2193" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.7.9" +version = "0.7.13" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] @@ -2152,9 +2232,9 @@ version = "0.2.4" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "b6665214f2d0739f2d09a17474dd443b9139784a" +git-tree-sha1 = "a660e9daab5db07adf3dedfe09b435cc530d855e" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.20" +version = "0.4.21" [deps.PreallocationTools.extensions] PreallocationToolsReverseDiffExt = "ReverseDiff" @@ -2164,15 +2244,15 @@ version = "0.4.20" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" +git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.2.0" +version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "00805cd429dcb4870060ff49ef443486c262e38e" +git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.1" +version = "1.4.3" [[deps.PrettyPrint]] git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" @@ -2195,10 +2275,6 @@ version = "0.5.6" deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -[[deps.Profile]] -deps = ["Printf"] -uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" - [[deps.ProgressLogging]] deps = ["Logging", "SHA", "UUIDs"] git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539" @@ -2207,9 +2283,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "00099623ffee15972c16111bcf84c58a0051257c" +git-tree-sha1 = "763a8ceb07833dd51bb9e3bbca372de32c0605ad" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.9.0" +version = "1.10.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"] @@ -2247,12 +2323,6 @@ git-tree-sha1 = "4743b43e5a9c4a2ede372de7061eed81795b12e7" uuid = "74087812-796a-5b5d-8853-05524746bad3" version = "1.7.0" -[[deps.RandomExtensions]] -deps = ["Random", "SparseArrays"] -git-tree-sha1 = "b8a399e95663485820000f26b6a43c794e166a49" -uuid = "fb686558-2515-59ef-acaa-46db3789a887" -version = "0.4.4" - [[deps.RandomNumbers]] deps = ["Random", "Requires"] git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" @@ -2293,28 +2363,34 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "d7087c013e8a496ff396bae843b1e16d9a30ede8" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "f599a896fb28043dd63a4d372231dfcbdd117394" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.10" +version = "3.16.0" [deps.RecursiveArrayTools.extensions] + RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" + RecursiveArrayToolsForwardDiffExt = "ForwardDiff" RecursiveArrayToolsMeasurementsExt = "Measurements" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" + RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" [deps.RecursiveArrayTools.weakdeps] + FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "PrecompileTools", "StrideArraysCore", "TriangularSolve"] -git-tree-sha1 = "8bc86c78c7d8e2a5fe559e3721c0f9c9e303b2ed" +git-tree-sha1 = "6db1a75507051bc18bfa131fbc7c3f169cc4b2f6" uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.2.21" +version = "0.2.23" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -2329,9 +2405,9 @@ version = "0.1.3" [[deps.RegNets]] deps = ["AlgebraicPetri", "Catlab", "JSON"] -git-tree-sha1 = "6932d3bdd29b040a1138ffc261dc2c4d7d7db3aa" +git-tree-sha1 = "ab4363bad2f3eaec96076a71adb37d2a516f2e99" uuid = "b717d2d3-19c6-5ced-b36a-114a71eec478" -version = "0.2.0" +version = "0.1.0" [[deps.RelocatableFolders]] deps = ["SHA", "Scratch"] @@ -2365,9 +2441,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"] -git-tree-sha1 = "754acd3031a9f2eaf6632ba4850b1c01fe4460c1" +git-tree-sha1 = "1ab580704784260ee5f45bffac810b152922747b" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.1.2" +version = "2.1.5" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -2383,20 +2459,14 @@ version = "2.1.2" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "6aacc5eefe8415f47b3e34214c1d79d2674a0ba2" +git-tree-sha1 = "04c968137612c4a5629fa531334bb81ad5680f00" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.12" +version = "0.5.13" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" -[[deps.SIMD]] -deps = ["PrecompileTools"] -git-tree-sha1 = "d8911cc125da009051fb35322415641d02d9e37f" -uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.4.6" - [[deps.SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" uuid = "94e857df-77ce-4151-89e5-788b33177be4" @@ -2409,26 +2479,35 @@ uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" version = "0.6.42" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "916b8a94c0d61fa5f7c5295649d3746afb866aff" +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "397367599b9526a49cc06a4db70835807498b561" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.98.1" -weakdeps = ["Zygote"] +version = "2.36.1" [deps.SciMLBase.extensions] - ZygoteExt = "Zygote" + SciMLBaseChainRulesCoreExt = "ChainRulesCore" + SciMLBaseMakieExt = "Makie" + SciMLBasePartialFunctionsExt = "PartialFunctions" + SciMLBasePyCallExt = "PyCall" + SciMLBasePythonCallExt = "PythonCall" + SciMLBaseRCallExt = "RCall" + SciMLBaseZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" + PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" + PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" + PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" + RCall = "6f49c342-dc21-5d91-9882-a32aef131414" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLExpectations]] deps = ["DiffEqBase", "DiffEqNoiseProcess", "Distributions", "Integrals", "KernelDensity", "LinearAlgebra", "Parameters", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "Statistics", "Zygote"] -git-tree-sha1 = "ed39fbfbb8a69e87ee05f564d4e8e34e8d762131" +git-tree-sha1 = "6332835c431ed3da99dcc391e84e11a65fe31c50" uuid = "afe9f18d-7609-4d0e-b7b7-af0cb72b8ea8" -version = "2.1.0" - -[[deps.SciMLNLSolve]] -deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "765b788339abd7d983618c09cfc0192e2b6b15fd" -uuid = "e9a6253c-8580-4d32-9898-8661bb511710" -version = "0.1.9" +version = "2.2.0" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools", "Setfield", "SparseArrays", "StaticArraysCore"] @@ -2436,6 +2515,11 @@ git-tree-sha1 = "10499f619ef6e890f3f4a38914481cc868689cd5" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" version = "0.3.8" +[[deps.SciMLStructures]] +git-tree-sha1 = "5833c10ce83d690c124beedfe5f621b50b02ba4d" +uuid = "53ae85a6-f571-4167-b2af-e1d143709226" +version = "1.1.0" + [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" uuid = "30f210dd-8aff-4c5f-94ba-8e64358c1161" @@ -2449,9 +2533,9 @@ version = "1.2.1" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "0e7508ff27ba32f26cd459474ca2ede1bc10991f" +git-tree-sha1 = "363c4e82b66be7b9f7c7c7da7478fdae07de44b9" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.4.1" +version = "1.4.2" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -2478,14 +2562,26 @@ uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" version = "1.1.0" [[deps.SimpleNonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PackageExtensionCompat", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "15ff97fa4881133caa324dacafe28b5ac47ad8a2" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "c020028bb22a2f23cbd88cb92cf47cbb8c98513f" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "0.1.23" -weakdeps = ["NNlib"] +version = "1.8.0" [deps.SimpleNonlinearSolve.extensions] - SimpleNonlinearSolveNNlibExt = "NNlib" + SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" + SimpleNonlinearSolvePolyesterForwardDiffExt = "PolyesterForwardDiff" + SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" + SimpleNonlinearSolveStaticArraysExt = "StaticArrays" + SimpleNonlinearSolveTrackerExt = "Tracker" + SimpleNonlinearSolveZygoteExt = "Zygote" + + [deps.SimpleNonlinearSolve.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2520,9 +2616,9 @@ version = "1.10.0" [[deps.SparseDiffTools]] deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "a616ac46c38da60ac05cecf52064d44732edd05e" +git-tree-sha1 = "cce98ad7c896e52bb0eded174f02fc2a29c38477" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.17.0" +version = "2.18.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -2557,9 +2653,9 @@ version = "0.1.6" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" +git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.1" +version = "2.4.0" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -2623,9 +2719,9 @@ version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" +git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.21" +version = "0.34.3" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] @@ -2639,22 +2735,22 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] StatsFunsInverseFunctionsExt = "InverseFunctions" [[deps.SteadyStateDiffEq]] -deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "2ca69f4be3294e4cd987d83d6019037d420d9fc1" +deps = ["ConcreteStructs", "DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "Reexport", "SciMLBase"] +git-tree-sha1 = "3875ef009bc726f12c8af2ea9a8bb115ff545d6d" uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" -version = "1.16.1" +version = "2.1.0" [[deps.StochasticDiffEq]] -deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "b341540a647b39728b6d64eaeda82178e848f76e" +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "97e5d0b7e5ec2e68eec6626af97c59e9f6b6c3d0" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.62.0" +version = "6.65.1" [[deps.StrideArraysCore]] -deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "d6415f66f3d89c615929af907fdc6a3e17af0d8c" +deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] +git-tree-sha1 = "25349bf8f63aa36acbff5e3550a86e9f5b0ef682" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.5.2" +version = "0.5.6" [[deps.StringEncodings]] deps = ["Libiconv_jll"] @@ -2704,9 +2800,9 @@ version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "71dc65a2d7decdde5500299c9b04309e0138d1b4" +git-tree-sha1 = "e15f5a73f0d14b9079b807a9d1dac13e4302e997" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.20.1" +version = "4.24.0" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] @@ -2721,27 +2817,39 @@ uuid = "1b6eb727-ad4b-44eb-9669-b9596a6e760f" version = "0.2.1" [[deps.SymbolicIndexingInterface]] -deps = ["DocStringExtensions"] -git-tree-sha1 = "f8ab052bfcbdb9b48fad2c80c873aa0d0344dfe5" +deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] +git-tree-sha1 = "b479c7a16803f08779ac5b7f9844a42621baeeda" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.2.2" +version = "0.3.21" + +[[deps.SymbolicLimits]] +deps = ["SymbolicUtils"] +git-tree-sha1 = "89aa6b25a75418c8fffc42073b2e7dce69847394" +uuid = "19f23fe9-fdab-4a78-91af-e7b7767979c3" +version = "0.2.0" [[deps.SymbolicUtils]] -deps = ["AbstractTrees", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LabelledArrays", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "TimerOutputs", "Unityper"] -git-tree-sha1 = "2f3fa844bcd33e40d8c29de5ee8dded7a0a70422" +deps = ["AbstractTrees", "Bijections", "ChainRulesCore", "Combinatorics", "ConstructionBase", "DataStructures", "DocStringExtensions", "DynamicPolynomials", "IfElse", "LabelledArrays", "LinearAlgebra", "MultivariatePolynomials", "NaNMath", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "TermInterface", "TimerOutputs", "Unityper"] +git-tree-sha1 = "20339c0dd70abdb73494955df4fcd9e9ccaff861" uuid = "d1185830-fcd6-423d-90d6-eec64667417b" -version = "1.4.0" +version = "1.6.0" [[deps.Symbolics]] -deps = ["ArrayInterface", "Bijections", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "Groebner", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "RecipesBase", "RecursiveArrayTools", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicUtils"] -git-tree-sha1 = "28f55dcd865e4a97f262fc476306cee14e8d4651" +deps = ["ArrayInterface", "Bijections", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "ForwardDiff", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils"] +git-tree-sha1 = "4104548fff14d7370b278ee767651d6ec61eb195" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "5.11.0" +version = "5.28.0" [deps.Symbolics.extensions] + SymbolicsGroebnerExt = "Groebner" + SymbolicsLuxCoreExt = "LuxCore" + SymbolicsPreallocationToolsExt = "PreallocationTools" SymbolicsSymPyExt = "SymPy" [deps.Symbolics.weakdeps] + Groebner = "0b43b601-686d-58a3-8a1c-6623616c7cd4" + LuxCore = "bb33d45b-7691-41d6-9220-0943567d0623" + PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" [[deps.TOML]] @@ -2751,9 +2859,9 @@ version = "1.0.3" [[deps.TZJData]] deps = ["Artifacts"] -git-tree-sha1 = "b69f8338df046774bd975b13be9d297eca5efacb" +git-tree-sha1 = "1607ad46cf8d642aa779a1d45af1c8620dbf6915" uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" -version = "1.1.0+2023d" +version = "1.2.0+2024a" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -2792,9 +2900,14 @@ version = "0.1.1" [[deps.Term]] deps = ["AbstractTrees", "CodeTracking", "Dates", "Highlights", "InteractiveUtils", "Logging", "Markdown", "MyterialColors", "OrderedCollections", "Parameters", "PrecompileTools", "ProgressLogging", "REPL", "Tables", "UUIDs", "Unicode", "UnicodeFun"] -git-tree-sha1 = "ffac67f6fbcbb32027d924b93ba91b7633af9220" +git-tree-sha1 = "387e63d0b12d43982a3aacaef81cbbfb465715ae" uuid = "22787eb5-b846-44ae-b979-8e399b8463ab" -version = "2.0.5" +version = "2.0.6" + +[[deps.TermInterface]] +git-tree-sha1 = "6f0cee95e74d1f6891ba6b35b8b219fd3d11b567" +uuid = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c" +version = "0.4.1" [[deps.TerminalLoggers]] deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"] @@ -2825,10 +2938,10 @@ uuid = "ac1d9e8a-700a-412c-b207-f0111f4b6c0d" version = "0.1.12" [[deps.TimeZones]] -deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] -git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03" +deps = ["Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "96793c9316d6c9f9be4641f2e5b1319a205e6f27" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.13.0" +version = "1.15.0" weakdeps = ["RecipesBase"] [deps.TimeZones.extensions] @@ -2841,24 +2954,24 @@ uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" version = "0.5.23" [[deps.Tokenize]] -git-tree-sha1 = "5b5a892ba7704c0977013bd0f9c30f5d962181e0" +git-tree-sha1 = "468b4685af4abe0e9fd4d7bf495a6554a6276e75" uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624" -version = "0.5.28" +version = "0.5.29" [[deps.Tracker]] -deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "5c942be30a85ac75d14e9e527b55504031e1bbd3" +deps = ["Adapt", "ChainRulesCore", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] +git-tree-sha1 = "5158100ed55411867674576788e710a815a0af02" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.31" +version = "0.2.34" weakdeps = ["PDMats"] [deps.Tracker.extensions] TrackerPDMatsExt = "PDMats" [[deps.TranscodingStreams]] -git-tree-sha1 = "54194d92959d8ebaa8e26227dbe3cdefcdcd594f" +git-tree-sha1 = "5d54d076465da49d6746c647022f3b3674e64156" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.10.3" +version = "0.10.8" weakdeps = ["Random", "Test"] [deps.TranscodingStreams.extensions] @@ -2891,9 +3004,9 @@ version = "2.0.3" [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "fadebab77bf3ae041f77346dd1c290173da5a443" +git-tree-sha1 = "66c68a20907800c0b7c04ff8a6164115e8747de2" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.20" +version = "0.2.0" [[deps.Tricks]] git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" @@ -2907,10 +3020,18 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "26cdfce1cc0301fe832eaa419a5d0edd6a554004" +deps = ["ADTypes", "AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "4170ff68a0aa2b26b3944ba7bd8789a46d34e6bc" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.24.4" +version = "0.30.9" + + [deps.Turing.extensions] + TuringDynamicHMCExt = "DynamicHMC" + TuringOptimExt = "Optim" + + [deps.Turing.weakdeps] + DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb" + Optim = "429524aa-4258-5aef-a3af-852621145aeb" [[deps.URIs]] git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" @@ -2937,9 +3058,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "3c793be6df9dd77a0cf49d80984ef9ff996948fa" +git-tree-sha1 = "352edac1ad17e018186881b051960bfca78a075a" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.19.0" +version = "1.19.1" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -2976,9 +3097,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "7209df901e6ed7489fe9b7aa3e46fb788e15db85" +git-tree-sha1 = "6129a4faf6242e7c3581116fbe3270f3ab17c90d" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.65" +version = "0.21.67" [[deps.VertexSafeGraphs]] deps = ["Graphs"] @@ -3029,9 +3150,9 @@ version = "1.6.1" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "07e470dabc5a6a4254ffebc29a1b3fc01464e105" +git-tree-sha1 = "532e22cf7be8462035d092ff21fada7527e2c488" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.12.5+0" +version = "2.12.6+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -3041,21 +3162,21 @@ version = "1.1.34+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "37195dcb94a5970397ad425b95a9a26d0befce3a" +git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.6.0+0" +version = "5.4.6+0" [[deps.Xorg_libICE_jll]] -deps = ["Libdl", "Pkg"] -git-tree-sha1 = "e5becd4411063bdcac16be8b66fc2f9f6f1e8fe5" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c" uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" -version = "1.0.10+1" +version = "1.1.1+0" [[deps.Xorg_libSM_jll]] -deps = ["Libdl", "Pkg", "Xorg_libICE_jll"] -git-tree-sha1 = "4a9d9e4c180e1e8119b5ffc224a7b59d3a7f7e18" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"] +git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce" uuid = "c834827a-8449-5923-a945-d239c165b7dd" -version = "1.2.3+0" +version = "1.2.4+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] @@ -3082,10 +3203,10 @@ uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" version = "1.1.4+0" [[deps.Xorg_libXext_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.4+4" +version = "1.3.6+0" [[deps.Xorg_libXfixes_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] @@ -3112,10 +3233,10 @@ uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" version = "1.5.2+4" [[deps.Xorg_libXrender_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.10+4" +version = "0.9.11+0" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -3202,15 +3323,15 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" +git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.5+0" +version = "1.5.6+0" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "4ddb4470e47b0094c93055a3bcae799165cc68f1" +git-tree-sha1 = "19c586905e78a26f7e4e97f81716057bd6b1bc54" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.69" +version = "0.6.70" weakdeps = ["Colors", "Distances", "Tracker"] [deps.Zygote.extensions] @@ -3284,9 +3405,9 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "873b4f805771d3e4bafe63af759a26ea8ca84d14" +git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.42+0" +version = "1.6.43+1" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] @@ -3305,6 +3426,12 @@ deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" version = "1.52.0+1" +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" + [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" diff --git a/Project.toml b/Project.toml index c063030..62221a5 100644 --- a/Project.toml +++ b/Project.toml @@ -42,7 +42,9 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" [compat] -julia = "1.10.1" +ModelingToolkit = "9.13.0" +julia = "1.10" +EasyModelAnalysis = "1" [extras] Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" diff --git a/src/SimulationService.jl b/src/SimulationService.jl index 71cff8f..ac628c9 100644 --- a/src/SimulationService.jl +++ b/src/SimulationService.jl @@ -19,7 +19,7 @@ import JSON3 import JSONSchema import LinearAlgebra: norm import MathML -import ModelingToolkit: @parameters, substitute, Differential, Num, @variables, ODESystem, ODEProblem, ODESolution, structural_simplify, states, observed, parameters +import ModelingToolkit: @parameters, substitute, Differential, Num, @variables, ODESystem, ODEProblem, ODESolution, structural_simplify, unknowns, observed, parameters import OpenAPI import Oxygen import Pkg diff --git a/src/model_parsers/RegNets.jl b/src/model_parsers/RegNets.jl index e8b00ba..63e7ac7 100644 --- a/src/model_parsers/RegNets.jl +++ b/src/model_parsers/RegNets.jl @@ -92,5 +92,5 @@ function ASKEM_ACSet_to_MTK(sg::ASKEMRegNetUntyped) eqs = [D(vertex_funcs[i]) ~ v_rate_vars[i]*vertex_funcs[i] + sum((sg[e,:sign] ? 1 : -1) * e_rate_vars[e] * vertex_funcs[i] * vertex_funcs[sg[e,:src]] for e in incident(sg,i,:tgt); init = 0.0) for i in 1:nv(sg)] - sys = ODESystem(eqs, t, vertex_funcs, all_params; name = :system, defaults) + sys = structural_simplify(ODESystem(eqs, t, vertex_funcs, all_params; name = :system, defaults)) end diff --git a/src/operations.jl b/src/operations.jl index dc57aae..354857c 100644 --- a/src/operations.jl +++ b/src/operations.jl @@ -163,7 +163,7 @@ end # data function amr_get(df::DataFrame, sys::ODESystem, ::Val{:data}) @info "parse dataset into calibrate format" - statelist = states(sys) + statelist = unknowns(sys) statenames = string.(statelist) statenames = [replace(nm, "(t)" => "") for nm in statenames] @@ -188,7 +188,7 @@ function (o::IntermediateResults)(integrator) (; iter, f, t, u, p) = integrator if o.last_callback + o.every == iter o.last_callback = iter - state_dict = Dict(states(f.sys) .=> u) + state_dict = Dict(unknowns(f.sys) .=> u) param_dict = Dict(parameters(f.sys) .=> p) publish_to_rabbitmq(; iter=iter, state=state_dict, params = param_dict, id=o.id, retcode=SciMLBase.check_error(integrator)) @@ -197,12 +197,12 @@ function (o::IntermediateResults)(integrator) end # Intermediate results functor for calibrate -function (o::IntermediateResults)(p,lossval, ode_sol, ts) +function (o::IntermediateResults)(state,loss_val, ode_sol, ts) if o.last_callback + o.every == o.iter o.last_callback = o.iter - param_dict = Dict(parameters(ode_sol.prob.f.sys) .=> ode_sol.prob.p) - state_dict = Dict([state => ode_sol(first(ts))[state] for state in states(ode_sol.prob.f.sys)]) - publish_to_rabbitmq(; iter = o.iter, loss = lossval, sol_data = state_dict, timesteps = first(ts), params = param_dict, id=o.id) + param_dict = Dict(parameters(ode_sol.prob.f.sys) .=> state.u) + state_dict = Dict([state => ode_sol(first(ts))[state] for state in unknowns(ode_sol.prob.f.sys)]) + publish_to_rabbitmq(; iter = o.iter, loss = loss_val, sol_data = state_dict, timesteps = first(ts), params = param_dict, id=o.id) end o.iter = o.iter + 1 return false @@ -210,7 +210,7 @@ end #----------------------------------------------------------------------# dataframe_with_observables function dataframe_with_observables(sol::ODESolution) sys = sol.prob.f.sys - names = [states(sys); getproperty.(observed(sys), :lhs)] + names = [unknowns(sys); getproperty.(observed(sys), :lhs)] cols = ["timestamp" => sol.t; [string(n) => sol[n] for n in names]] DataFrame(cols) end @@ -280,7 +280,7 @@ end function solve(o::Calibrate; callback) prob = ODEProblem(o.sys, [], o.timespan) - statenames = [states(o.sys);getproperty.(observed(o.sys), :lhs)] + statenames = [unknowns(o.sys);getproperty.(observed(o.sys), :lhs)] # bayesian datafit if o.calibrate_method == "bayesian" diff --git a/test/runtests.jl b/test/runtests.jl index f0e5757..1eb5a2e 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -105,7 +105,7 @@ end @testset "Petrinet AMR parsing" begin amr = JSON3.read(HTTP.get("https://raw.githubusercontent.com/DARPA-ASKEM/simulation-integration/main/data/models/sidarthe.json").body) sys = SimulationService.amr_get(amr.configuration, ODESystem) - @test string.(states(sys)) == ["Susceptible(t)", "Diagnosed(t)", "Infected(t)", "Ailing(t)", "Recognized(t)", "Healed(t)", "Threatened(t)", "Extinct(t)"] + @test string.(unknowns(sys)) == ["Susceptible(t)", "Diagnosed(t)", "Infected(t)", "Ailing(t)", "Recognized(t)", "Healed(t)", "Threatened(t)", "Extinct(t)"] @test string.(parameters(sys)) == ["beta", "gamma", "delta", "alpha", "epsilon", "zeta", "lambda", "eta", "rho", "theta", "kappa", "mu", "nu", "xi", "tau", "sigma"] @test map(x->string(x.lhs), observed(sys)) == ["Cases(t)", "Hospitalizations(t)", "Deaths(t)"] @@ -117,14 +117,14 @@ end df = CSV.read(HTTP.get("https://raw.githubusercontent.com/DARPA-ASKEM/simulation-integration/main/data/datasets/SIDARTHE_dataset.csv").body,DataFrame) data = SimulationService.amr_get(df, sys, Val(:data)) @test data isa Vector{Pair{SymbolicUtils.BasicSymbolic{Real}, Tuple{Vector{Int64}, Vector{Float64}}}} - @test string.(first.(data)) == string.(states(sys)) + @test string.(first.(data)) == string.(unknowns(sys)) @test all(all.(map(first.(last.(data))) do x; x .== 0:89; end)) end @testset "Stock and Flow AMR parsing" begin amr = JSON3.read(HTTP.get("https://raw.githubusercontent.com/DARPA-ASKEM/simulation-integration/main/data/models/SIR_stockflow.json").body) sys = SimulationService.amr_get(amr, ODESystem) - @test string.(states(sys)) == ["S(t)", "I(t)", "R(t)"] + @test string.(unknowns(sys)) == ["S(t)", "I(t)", "R(t)"] @test string.(parameters(sys)) == ["p_cbeta","p_N", "p_tr"] priors = SimulationService.amr_get(amr, sys, Val(:priors)) @@ -138,7 +138,7 @@ end @testset "RegNet AMR parsing" begin amr = JSON3.read(HTTP.get("https://raw.githubusercontent.com/DARPA-ASKEM/simulation-integration/main/data/models/LV_sheep_foxes_regnet.json").body) sys = SimulationService.amr_get(amr, ODESystem) - @test string.(states(sys)) == ["S(t)", "F(t)"] + @test string.(unknowns(sys)) == ["S(t)", "F(t)"] @test string.(parameters(sys)) == ["beta","delta", "alpha","gamma"] priors = SimulationService.amr_get(amr, sys, Val(:priors)) @@ -247,19 +247,19 @@ end dfsim, dfparam = solve(o, callback = SimulationService.get_callback(op,SimulationService.Calibrate)) - statenames = [states(o.sys); getproperty.(observed(o.sys), :lhs)] + statenames = [unknowns(o.sys); getproperty.(observed(o.sys), :lhs)] @test names(dfsim) == vcat("timestamp",reduce(vcat,[string.("ensemble",i,"_", statenames) for i in 1:size(dfsim,2)÷length(statenames)])) @test names(dfparam) == string.(parameters(sys)) - #calibrate_method = "local" - #o = SimulationService.Calibrate(sys, (0.0, 89.0), priors, data, num_chains, num_iterations, calibrate_method, ode_method) - #dfsim, dfparam = SimulationService.solve(o; callback = nothing) + calibrate_method = "local" + o = SimulationService.Calibrate(sys, (0.0, 89.0), priors, data, num_chains, num_iterations, calibrate_method, ode_method) + dfsim, dfparam = SimulationService.solve(o; callback = SimulationService.get_callback(op,SimulationService.Calibrate)) calibrate_method = "global" o = SimulationService.Calibrate(sys, (0.0, 89.0), priors, data, num_chains, num_iterations, calibrate_method, ode_method) dfsim, dfparam = SimulationService.solve(o; callback = SimulationService.get_callback(op,SimulationService.Calibrate)) - statenames = [states(o.sys);getproperty.(observed(o.sys), :lhs)] + statenames = [unknowns(o.sys);getproperty.(observed(o.sys), :lhs)] @test names(dfsim) == vcat("timestamp",string.(statenames)) @test names(dfparam) == string.(parameters(sys)) end @@ -415,7 +415,7 @@ end op.id = "1" dfsim, dfparam = SimulationService.solve(o, callback = SimulationService.get_callback(op,SimulationService.Calibrate)) - statenames = [states(o.sys);getproperty.(observed(o.sys), :lhs)] + statenames = [unknowns(o.sys);getproperty.(observed(o.sys), :lhs)] @test names(dfsim) == vcat("timestamp",string.(statenames)) end end