From 88661bff6693527b748905e20e7854c5bfed428a Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Mon, 18 Aug 2025 23:37:17 +0100 Subject: [PATCH] Update all deps except DelayDiffEq --- Manifest.toml | 379 ++++++++++++++++++++++++++------------------------ Project.toml | 2 + 2 files changed, 201 insertions(+), 180 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index c94baf232..ccb972de6 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,12 +2,12 @@ julia_version = "1.11.6" manifest_format = "2.0" -project_hash = "3c5b0696513a84be8573e377b59e1ab532411868" +project_hash = "2db94c909342da49eb3ff313436b75e25977ace6" [[deps.ADTypes]] -git-tree-sha1 = "7927b9af540ee964cc5d1b73293f1eb0b761a3a1" +git-tree-sha1 = "60665b326b75db6517939d0e1875850bc4a54368" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.16.0" +version = "1.17.0" weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] [deps.ADTypes.extensions] @@ -86,9 +86,9 @@ weakdeps = ["SparseArrays", "StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Setfield", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "9f75990a04e3ee45d80b19778ba9d2bb7ad4d5ee" +git-tree-sha1 = "22496647c061d00217759e95a18d601c959df0c9" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.8.0" +version = "0.8.1" [deps.AdvancedHMC.extensions] AdvancedHMCADTypesExt = "ADTypes" @@ -223,9 +223,9 @@ version = "1.11.0" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "b5bb4dc6248fde467be2a863eb8452993e74d402" +git-tree-sha1 = "29bb0eb6f578a587a49da16564705968667f5fa8" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "1.1.1" +version = "1.1.2" [deps.Atomix.extensions] AtomixCUDAExt = "CUDA" @@ -298,9 +298,9 @@ version = "0.1.1" [[deps.Bijectors]] deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "5eb5a58ed34e012d7f8d665cb5198252e128e907" +git-tree-sha1 = "35ba30573d4f83242f1e788c87ca792c83553c9e" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.15.8" +version = "0.15.9" weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker"] [deps.Bijectors.extensions] @@ -395,10 +395,10 @@ uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.5.0" [[deps.CPUSummary]] -deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] -git-tree-sha1 = "5a97e67919535d6841172016c9530fd69494e5ec" +deps = ["CpuId", "IfElse", "PrecompileTools", "Preferences", "Static"] +git-tree-sha1 = "f3a21d7fc84ba618a779d1ed2fcca2e682865bab" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.2.6" +version = "0.2.7" [[deps.CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] @@ -443,9 +443,9 @@ version = "1.72.5" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "06ee8d1aa558d2833aa799f6f0b31b30cada405f" +git-tree-sha1 = "e4c6a16e77171a5f5e25e9646617ab1c276c5607" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.25.2" +version = "1.26.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -685,9 +685,9 @@ version = "0.1.2" [[deps.DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "FastBroadcast", "ForwardDiff", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack", "SymbolicIndexingInterface"] -git-tree-sha1 = "484cceb16c5ed95f4a2a405f3579f480ec0dff9a" +git-tree-sha1 = "c50981fb5b6441a1213debb1423385a462e88032" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.55.0" +version = "5.56.0" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -703,9 +703,9 @@ version = "0.4.0" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "6f8f25122389ba34e491bdfe143ae16fda37cad3" +git-tree-sha1 = "1b1e070e57681d1176d99a5ec455717e24686612" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.180.0" +version = "6.183.2" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -743,9 +743,9 @@ version = "6.180.0" [[deps.DiffEqCallbacks]] deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "80a782f3e65d4900dcf5f2cb71f5e19d9459c04a" +git-tree-sha1 = "397ef6fffcf418ba55264ba785b032b8a136903b" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "4.8.0" +version = "4.9.0" [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] @@ -777,9 +777,9 @@ version = "7.16.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "f620da805b82bec64ab4d5f881c7592c82dbc08a" +git-tree-sha1 = "38989b1532a3c6e2341d52b77c5475c42c3318a8" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.7.3" +version = "0.7.6" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -929,9 +929,9 @@ version = "1.0.5" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "e36968f0a43d9a3b627ac94d5346b458ce14066d" +git-tree-sha1 = "7297613272c67cb7f11969679960419c5e463974" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.65" +version = "0.13.68" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -1123,9 +1123,9 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] -git-tree-sha1 = "f089ab1f834470c525562030c8cfde4025d5e915" +git-tree-sha1 = "31fd32af86234b6b71add76229d53129aa1b87a9" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.27.0" +version = "2.28.1" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" @@ -1290,9 +1290,9 @@ version = "1.3.15+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "c5abfa0ae0aaee162a3fbb053c13ecda39be545b" +git-tree-sha1 = "7a98c6502f4632dbe9fb1973a4244eaa3324e84d" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.13.0" +version = "1.13.1" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -1454,9 +1454,9 @@ version = "0.2.1" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "eac1206917768cb54957c65a615460d87b455fc1" +git-tree-sha1 = "e95866623950267c1e4878846f848d94810de475" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.1.1+0" +version = "3.1.2+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1466,10 +1466,13 @@ version = "0.2.4" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] -git-tree-sha1 = "f8da88993c914357031daf0023f18748ff473924" +git-tree-sha1 = "f5b57507a36f05509e72120aa84d5c3747dbd70e" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.16.1" -weakdeps = ["FastBroadcast"] +version = "9.17.0" +weakdeps = ["Adapt", "FastBroadcast", "KernelAbstractions"] + + [deps.JumpProcesses.extensions] + JumpProcessesKernelAbstractionsExt = ["Adapt", "KernelAbstractions"] [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] @@ -1562,9 +1565,9 @@ version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "4f34eaabe49ecb3fb0d58d6015e32fd31a733199" +git-tree-sha1 = "52e1296ebbde0db845b356abbbe67fb82a0a116c" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.8" +version = "0.16.9" [deps.Latexify.extensions] DataFramesExt = "DataFrames" @@ -1731,15 +1734,19 @@ version = "1.11.0" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "d768ff40cc3fe42581708696b24ee65dccc9c6ba" +git-tree-sha1 = "7d0e40cefc7f5f4920dc91e4d5f361ace40e1124" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "3.24.0" +version = "3.32.0" [deps.LinearSolve.extensions] + LinearSolveAMDGPUExt = "AMDGPU" + LinearSolveBLISExt = ["blis_jll", "LAPACK_jll"] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" LinearSolveCUDSSExt = "CUDSS" + LinearSolveCUSOLVERRFExt = ["CUSOLVERRF", "SparseArrays"] + LinearSolveCliqueTreesExt = ["CliqueTrees", "SparseArrays"] LinearSolveEnzymeExt = "EnzymeCore" LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveFastLapackInterfaceExt = "FastLapackInterface" @@ -1755,10 +1762,13 @@ version = "3.24.0" LinearSolveSparspakExt = ["SparseArrays", "Sparspak"] [deps.LinearSolve.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + CUSOLVERRF = "a8cc9031-bad2-4722-94f5-40deabb4245c" + CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641" @@ -1767,11 +1777,13 @@ version = "3.24.0" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" + LAPACK_jll = "51474c39-65e3-53ba-86ba-03b1b862ec14" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Sparspak = "e56a9233-b9d6-4f03-8d0f-1825330902ac" + blis_jll = "6136c539-28a5-5bf0-87cc-b183200dce32" [[deps.LogDensityProblems]] deps = ["ArgCheck", "DocStringExtensions", "Random"] @@ -1831,9 +1843,9 @@ version = "1.1.0" [[deps.Lux]] deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DiffResults", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "WeightInitializers"] -git-tree-sha1 = "c05e5c3dca1810e728429771763b485057322ad2" +git-tree-sha1 = "c01b012bbf84e6d5aab7b75782a73f453d34be87" uuid = "b2108857-7c20-44ae-9111-449ecde12c47" -version = "1.16.0" +version = "1.17.0" [deps.Lux.extensions] LuxComponentArraysExt = "ComponentArrays" @@ -1870,9 +1882,9 @@ version = "1.16.0" [[deps.LuxCore]] deps = ["Compat", "DispatchDoctor", "Random"] -git-tree-sha1 = "48d45736aae190b1b41c1db5242fad955f0eff1d" +git-tree-sha1 = "a72b6b530f39a87d1327b90f5def4bce48eb1a52" uuid = "bb33d45b-7691-41d6-9220-0943567d0623" -version = "1.2.6" +version = "1.3.0" [deps.LuxCore.extensions] LuxCoreArrayInterfaceReverseDiffExt = ["ArrayInterface", "ReverseDiff"] @@ -1898,9 +1910,9 @@ version = "1.2.6" [[deps.LuxLib]] deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "Compat", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "bf64921ca8182e3ee34a56b05b9f1ed568141a13" +git-tree-sha1 = "5d1d796c8b2878b5cad2849970c52897ff8c0271" uuid = "82251201-b29d-42c6-8e01-566dec8acb11" -version = "1.10.1" +version = "1.10.2" [deps.LuxLib.extensions] LuxLibAppleAccelerateExt = "AppleAccelerate" @@ -1909,7 +1921,6 @@ version = "1.10.1" LuxLibEnzymeExt = "Enzyme" LuxLibLoopVectorizationExt = "LoopVectorization" LuxLibMKLExt = "MKL" - LuxLibMooncakeExt = "Mooncake" LuxLibOctavianExt = ["Octavian", "LoopVectorization"] LuxLibReactantExt = "Reactant" LuxLibReverseDiffExt = "ReverseDiff" @@ -1926,7 +1937,6 @@ version = "1.10.1" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890" MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2" - Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4" Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" @@ -1936,15 +1946,15 @@ version = "1.10.1" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "DataAPI", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] -git-tree-sha1 = "a1b9bf62acb012e4a717562f83f859257c5b6fec" +git-tree-sha1 = "f3993c723865f670102011ef22811e2bbb0ef1a8" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "7.1.0" +version = "7.2.0" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "a586f05dd16a50c490ed95415b2a829b8cf5d57f" +git-tree-sha1 = "526c98cd41028da22c01cb8a203246799ad853a8" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.3.14" +version = "0.3.15" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] @@ -2114,9 +2124,9 @@ uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" version = "1.2.0" [[deps.MistyClosures]] -git-tree-sha1 = "1142aefd845c608f3c70e4c202c4aae725cab67b" +git-tree-sha1 = "d1a692e293c2a0dc8fda79c04cad60582f3d4de3" uuid = "dbe65cb8-6be2-42dd-bbc5-4196aaced4f4" -version = "2.0.0" +version = "2.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -2130,9 +2140,9 @@ version = "0.8.1" [[deps.Mooncake]] deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DispatchDoctor", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Test"] -git-tree-sha1 = "88bb6e5054ba4a341c8fb7047af859720669628d" +git-tree-sha1 = "955bad945bc815c4b48fb4d17ce39cf3ba6abcf3" uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" -version = "0.4.142" +version = "0.4.150" [deps.Mooncake.extensions] MooncakeAllocCheckExt = "AllocCheck" @@ -2140,7 +2150,7 @@ version = "0.4.142" MooncakeDynamicExpressionsExt = "DynamicExpressions" MooncakeFluxExt = "Flux" MooncakeJETExt = "JET" - MooncakeLuxLibExt = "LuxLib" + MooncakeLuxLibExt = ["LuxLib", "MLDataDevices", "Static"] MooncakeLuxLibSLEEFPiratesExtension = ["LuxLib", "SLEEFPirates"] MooncakeNNlibExt = "NNlib" MooncakeSpecialFunctionsExt = "SpecialFunctions" @@ -2152,9 +2162,11 @@ version = "0.4.142" Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b" LuxLib = "82251201-b29d-42c6-8e01-566dec8acb11" + MLDataDevices = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa" SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" [[deps.Moshi]] deps = ["ExproniconLite", "Jieko"] @@ -2298,9 +2310,9 @@ version = "4.10.0" [[deps.NonlinearSolveBase]] deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "ee395563ae6ffaecbdf86d430440fddc779253a4" +git-tree-sha1 = "1d42a315ba627ca0027d49d0efb44e3d88db24aa" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "1.13.0" +version = "1.14.0" weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"] [deps.NonlinearSolveBase.extensions] @@ -2314,15 +2326,15 @@ weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "Linear [[deps.NonlinearSolveFirstOrder]] deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "65101a20b135616a13625ae6f84b052ef5780363" +git-tree-sha1 = "3f1198ae5cbf21e84b8251a9e62fa1f888f3e4cb" uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" -version = "1.6.0" +version = "1.7.0" [[deps.NonlinearSolveQuasiNewton]] deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] -git-tree-sha1 = "3e04c917d4e3cd48b2a5091b6f76c720bb3f7362" +git-tree-sha1 = "40dfaf1bf74f1f700f81d0002d4dd90999598eb2" uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" -version = "1.7.0" +version = "1.8.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveQuasiNewton.extensions] @@ -2330,9 +2342,9 @@ weakdeps = ["ForwardDiff"] [[deps.NonlinearSolveSpectralMethods]] deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "3398222199e4b9ca0b5840907fb509f28f1a2fdc" +git-tree-sha1 = "84de5a469e119eb2c22ae07c543dc4e7f7001ee7" uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" -version = "1.2.0" +version = "1.3.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveSpectralMethods.extensions] @@ -2340,9 +2352,9 @@ weakdeps = ["ForwardDiff"] [[deps.ObjectFile]] deps = ["Reexport", "StructIO"] -git-tree-sha1 = "09b1fe6ff16e6587fa240c165347474322e77cf1" +git-tree-sha1 = "22faba70c22d2f03e60fbc61da99c4ebfc3eb9ba" uuid = "d8793406-e978-5875-9003-1fc021f44a92" -version = "0.4.4" +version = "0.5.0" [[deps.Observables]] git-tree-sha1 = "7438a59546cf62428fc9d1bc94729146d37a7225" @@ -2388,9 +2400,9 @@ version = "1.5.0" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "87510f7292a2b21aeff97912b0898f9553cc5c2c" +git-tree-sha1 = "2ae7d4ddec2e13ad3bddf5c0796f7547cf682391" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.5.1+0" +version = "3.5.2+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -2490,22 +2502,22 @@ uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" version = "6.101.0" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] -deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "82f78099ecf4e0fa53545811318520d87e7fe0b8" +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] +git-tree-sha1 = "09aae1486c767caa6bce9de892455cbdf5a6fbc8" uuid = "89bda076-bce5-4f1c-845f-551c83cdda9a" -version = "1.2.0" +version = "1.5.0" [[deps.OrdinaryDiffEqBDF]] -deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "b0bbc6541ea4a27974bd67e0a10b26211cb95e58" +deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "ce8db53fd1e4e41c020fd53961e7314f75e4c21c" uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" -version = "1.7.0" +version = "1.10.1" [[deps.OrdinaryDiffEqCore]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "1bd20b621e8dee5f2d170ae31631bf573ab77eec" +git-tree-sha1 = "e579c9a4f9102e82da3d97c349a74d6bc11cf8dc" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.26.2" +version = "1.30.0" weakdeps = ["EnzymeCore", "Mooncake"] [deps.OrdinaryDiffEqCore.extensions] @@ -2513,166 +2525,166 @@ weakdeps = ["EnzymeCore", "Mooncake"] OrdinaryDiffEqCoreMooncakeExt = "Mooncake" [[deps.OrdinaryDiffEqDefault]] -deps = ["ADTypes", "DiffEqBase", "EnumX", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "PrecompileTools", "Preferences", "Reexport"] -git-tree-sha1 = "7e2f4ec76ebac709401064fd2cf73ad993d1e694" +deps = ["ADTypes", "DiffEqBase", "EnumX", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "PrecompileTools", "Preferences", "Reexport", "SciMLBase"] +git-tree-sha1 = "7d5ddeee97e1bdcc848f1397cbc3d03bd57f33e7" uuid = "50262376-6c5a-4cf5-baba-aaf4f84d72d7" -version = "1.5.0" +version = "1.8.0" [[deps.OrdinaryDiffEqDifferentiation]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"] -git-tree-sha1 = "382a4bf7795eee0298221c37099db770be524bab" +git-tree-sha1 = "4c270747152db513dd80bfd5f2f9df48befff28a" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.10.1" +version = "1.14.0" [[deps.OrdinaryDiffEqExplicitRK]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"] -git-tree-sha1 = "4dbce3f9e6974567082ce5176e21aab0224a69e9" +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] +git-tree-sha1 = "4c0633f587395d7aaec0679dc649eb03fcc74e73" uuid = "9286f039-9fbf-40e8-bf65-aa933bdc4db0" -version = "1.1.0" +version = "1.4.0" [[deps.OrdinaryDiffEqExponentialRK]] deps = ["ADTypes", "DiffEqBase", "ExponentialUtilities", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "RecursiveArrayTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "585f73f10a1b444654d739853a9328d1bb7fce6b" +git-tree-sha1 = "3b81416ff11e55ea0ae7b449efc818256d9d450b" uuid = "e0540318-69ee-4070-8777-9e2de6de23de" -version = "1.5.0" +version = "1.8.0" [[deps.OrdinaryDiffEqExtrapolation]] -deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "80a636aac325c546b04e3bf20f0c80eaa0173dd4" +deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "ee2cba2533e9faf71b09a319a910d4886931e7a6" uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4" -version = "1.5.0" +version = "1.8.0" [[deps.OrdinaryDiffEqFIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastGaussQuadrature", "FastPower", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators"] -git-tree-sha1 = "d7cbd84ba96a91e765fc20d2c3b3b1702c15eeed" +git-tree-sha1 = "b968d66de3de5ffcf18544bc202ca792bad20710" uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125" -version = "1.13.0" +version = "1.16.0" [[deps.OrdinaryDiffEqFeagin]] -deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "a7cc74d3433db98e59dc3d58bc28174c6c290adf" +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] +git-tree-sha1 = "815b54211201ec42b8829e0275ab3c9632d16cbe" uuid = "101fe9f7-ebb6-4678-b671-3a81e7194747" -version = "1.1.0" +version = "1.4.0" [[deps.OrdinaryDiffEqFunctionMap]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] -git-tree-sha1 = "a4cb67794464352b69331c903cfa91a40e9a79ac" +git-tree-sha1 = "fe750e4b8c1b1b9e1c1319ff2e052e83ad57b3ac" uuid = "d3585ca7-f5d3-4ba6-8057-292ed1abd90f" -version = "1.2.0" +version = "1.5.0" [[deps.OrdinaryDiffEqHighOrderRK]] -deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", 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[[deps.OrdinaryDiffEqNordsieck]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "ef44754f10e0dfb9bb55ded382afed44cd94ab57" +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] +git-tree-sha1 = "c90aa7fa0d725472c4098096adf6a08266c2f682" uuid = "c9986a66-5c92-4813-8696-a7ec84c806c8" -version = "1.1.0" +version = "1.4.0" [[deps.OrdinaryDiffEqPDIRK]] -deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "Reexport", "StaticArrays"] -git-tree-sha1 = "ab9897e4bc8e3cf8e15f1cf61dbdd15d6a2341d7" +deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", 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"RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] +git-tree-sha1 = "63fb643a956b27cd0e33a3c6d910c3c118082e0f" uuid = "04162be5-8125-4266-98ed-640baecc6514" -version = "1.1.0" +version = "1.4.0" [[deps.OrdinaryDiffEqRKN]] -deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "6548bff67665b13a60abfb33e95fcf7ae08d186d" +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "a31c41f9dbea7c7179c6e544c25c7e144d63868c" uuid = "af6ede74-add8-4cfd-b1df-9a4dbb109d7a" -version = "1.2.0" +version = "1.5.0" [[deps.OrdinaryDiffEqRosenbrock]] -deps = ["ADTypes", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "a2f83c9b6e977c8dc5f37e0b448ad64f17c3a9c1" +deps = ["ADTypes", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] +git-tree-sha1 = "a06c1263d71ea42a1881b4d49c8a087035d4a3ff" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.12.0" +version = "1.16.1" [[deps.OrdinaryDiffEqSDIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] -git-tree-sha1 = "62327171ae40737b7874d4bdf70e0a213d60086a" +git-tree-sha1 = "20caa72c004414435fb5769fadb711e96ed5bcd4" uuid = "2d112036-d095-4a1e-ab9a-08536f3ecdbf" -version = "1.4.0" +version = "1.7.0" [[deps.OrdinaryDiffEqSSPRK]] -deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "StaticArrays"] -git-tree-sha1 = "651756c030df7a1d49ad484288937f8c398e8a08" +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "StaticArrays"] +git-tree-sha1 = "af955c61407631d281dd4c2e8331cdfea1af49be" uuid = "669c94d9-1f4b-4b64-b377-1aa079aa2388" -version = "1.3.0" +version = "1.6.0" [[deps.OrdinaryDiffEqStabilizedIRK]] -deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "StaticArrays"] -git-tree-sha1 = "111c23b68ad644b47e38242af920d5805c7bedb1" +deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqStabilizedRK", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays"] +git-tree-sha1 = "75abe7462f4b0b2a2463bb512c8a5458bbd39185" uuid = "e3e12d00-db14-5390-b879-ac3dd2ef6296" -version = "1.3.0" +version = "1.6.0" [[deps.OrdinaryDiffEqStabilizedRK]] -deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "StaticArrays"] -git-tree-sha1 = "8b54bcaf8634548bd13c0bd9a0522f15e5438b67" +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays"] +git-tree-sha1 = "7e94d3d1b3528b4bcf9e0248198ee0a2fd65a697" uuid = "358294b1-0aab-51c3-aafe-ad5ab194a2ad" -version = "1.2.0" +version = "1.4.0" [[deps.OrdinaryDiffEqSymplecticRK]] -deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "0d3e0527149d7ece68850c51de67e99bc4477b1b" +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "e8dd5ab225287947016dc144a5ded1fb83885638" uuid = "fa646aed-7ef9-47eb-84c4-9443fc8cbfa8" -version = "1.4.0" +version = "1.7.0" [[deps.OrdinaryDiffEqTsit5]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "d0b069075f4a5e54b29e412419e5a733a83e6240" +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "778c7d379265f17f40dbe9aaa6f6a2a08bc7fa3e" uuid = "b1df2697-797e-41e3-8120-5422d3b24e4a" -version = "1.2.0" +version = "1.5.0" [[deps.OrdinaryDiffEqVerner]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "91f0a004785791c8c538d34a67c19cf3f7776e85" +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "185578fa7c38119d4318326f9375f1cba0f0ce53" uuid = "79d7bb75-1356-48c1-b8c0-6832512096c2" -version = "1.3.0" +version = "1.6.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -2738,9 +2750,9 @@ version = "1.4.3" [[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", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "3db9167c618b290a05d4345ca70de6d95304a32a" +git-tree-sha1 = "9a9216c0cf706cb2cc58fd194878180e3e51e8c0" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.17" +version = "1.40.18" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -2758,9 +2770,9 @@ version = "1.40.17" [[deps.PoissonRandom]] deps = ["LogExpFunctions", "Random"] -git-tree-sha1 = "bb178012780b34046c6d1600a315d8dbee89d83d" +git-tree-sha1 = "c1ea45aa9f209fe97192afa233907bc4e551c8aa" uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" -version = "0.4.5" +version = "0.4.6" [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] @@ -2787,13 +2799,14 @@ uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" [[deps.PreallocationTools]] -deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "2cc315bb7f6e4d59081bad744cdb911d6374fc7f" +deps = ["Adapt", "ArrayInterface", "PrecompileTools"] +git-tree-sha1 = "520070df581845686c8c488b6dadce6b2c316856" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.29" -weakdeps = ["ReverseDiff", "SparseConnectivityTracer"] +version = "0.4.32" +weakdeps = ["ForwardDiff", "ReverseDiff", "SparseConnectivityTracer"] [deps.PreallocationTools.extensions] + PreallocationToolsForwardDiffExt = "ForwardDiff" PreallocationToolsReverseDiffExt = "ReverseDiff" PreallocationToolsSparseConnectivityTracerExt = "SparseConnectivityTracer" @@ -2805,9 +2818,9 @@ version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" +git-tree-sha1 = "0f27480397253da18fe2c12a4ba4eb9eb208bf3d" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.3" +version = "1.5.0" [[deps.PrettyPrint]] git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" @@ -2944,10 +2957,10 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "f8726bd5a8b7f5f5d3f6c0ce4793454a599b5243" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "96bef5b9ac123fff1b379acf0303cf914aaabdfd" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.36.0" +version = "3.37.1" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -2958,6 +2971,7 @@ version = "3.36.0" RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] RecursiveArrayToolsStructArraysExt = "StructArrays" + RecursiveArrayToolsTablesExt = ["Tables"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" @@ -2970,6 +2984,7 @@ version = "3.36.0" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -3051,15 +3066,15 @@ version = "0.1.0" [[deps.SSMProblems]] deps = ["AbstractMCMC", "Distributions", "Random"] -git-tree-sha1 = "4fedd69d5a5392cfed4edc647972de5b5b25a90a" +git-tree-sha1 = "b00814e67e8aacda2073865a3832e6cc378ea504" uuid = "26aad666-b158-4e64-9d35-0e672562fa48" -version = "0.5.0" +version = "0.5.1" [[deps.SciMLBase]] -deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] -git-tree-sha1 = "1c7fd50df465f0684f04f3a63736eac01999c659" +deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PreallocationTools", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "4398bda451c3c7aaca91a8077bcba227fe236d72" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.107.0" +version = "2.111.1" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3090,9 +3105,9 @@ version = "0.1.8" [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "7d3a1519dc4d433a6b20035eaff20bde8be77c66" +git-tree-sha1 = "aea915a39b547c48a18ee041120db1ae8df5a691" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "1.4.0" +version = "1.5.0" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -3101,9 +3116,9 @@ weakdeps = ["SparseArrays", "StaticArraysCore"] [[deps.SciMLSensitivity]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "Enzyme", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEqCore", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLJacobianOperators", "SciMLStructures", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"] -git-tree-sha1 = "a5d3e3ccedbce9c0c07b4ffa60787b58bdc6d360" +git-tree-sha1 = "e1b5f9b3be1452591c40a88de9efb265ebe76030" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.88.0" +version = "7.89.0" weakdeps = ["Mooncake"] [deps.SciMLSensitivity.extensions] @@ -3189,9 +3204,9 @@ weakdeps = ["ChainRulesCore", "DiffEqBase", "ReverseDiff", "Tracker"] [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] -git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" +git-tree-sha1 = "be8eeac05ec97d379347584fa9fe2f5f76795bcb" uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" -version = "0.9.4" +version = "0.9.5" [[deps.SimpleUnPack]] git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" @@ -3204,9 +3219,9 @@ version = "1.11.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" +git-tree-sha1 = "64d974c2e6fdf07f8155b5b2ca2ffa9069b608d9" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.2.1" +version = "1.2.2" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] @@ -3344,9 +3359,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] [[deps.StatsModels]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "9022bcaa2fc1d484f1326eaa4db8db543ca8c66d" +git-tree-sha1 = "728d276a5adc2f1cbb800eec4b63d0a8221024b4" uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" -version = "0.7.4" +version = "0.7.5" [[deps.StatsPlots]] deps = ["AbstractFFTs", "Clustering", "DataStructures", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] @@ -3443,10 +3458,14 @@ uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164" version = "5.2.3+0" [[deps.SymbolicIndexingInterface]] -deps = ["Accessors", "ArrayInterface", "PrettyTables", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "59ca6eddaaa9849e7de9fd1153b6faf0b1db7b80" +deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] +git-tree-sha1 = "93104ca226670c0cb92ba8bc6998852ad55a2d4c" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.42" +version = "0.3.43" +weakdeps = ["PrettyTables"] + + [deps.SymbolicIndexingInterface.extensions] + SymbolicIndexingInterfacePrettyTablesExt = "PrettyTables" [[deps.TOML]] deps = ["Dates"] @@ -3601,9 +3620,9 @@ version = "1.6.0" [[deps.Turing]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "3fd5118fd33c708bec35d892f86a5455e9402d66" +git-tree-sha1 = "58ad6cfe65311dc4ddc0e13e6747f3fad26f1034" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.39.9" +version = "0.39.10" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] diff --git a/Project.toml b/Project.toml index af37a3fd6..68ca649e1 100644 --- a/Project.toml +++ b/Project.toml @@ -11,6 +11,7 @@ CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" +DelayDiffEq = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" @@ -56,3 +57,4 @@ UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" [compat] Turing = "0.39" +DelayDiffEq = "~5.56"