From ba5e40837c6278189b8d160ea5d09df92bf0bedd Mon Sep 17 00:00:00 2001 From: Will Tebbutt Date: Tue, 26 Nov 2024 14:13:49 +0000 Subject: [PATCH] Update index.qmd (#548) * Update index.qmd * Update tutorials/docs-10-using-turing-autodiff/index.qmd * Update tutorials/docs-10-using-turing-autodiff/index.qmd Co-authored-by: Guillaume Dalle <22795598+gdalle@users.noreply.github.com> * Update tutorials/docs-10-using-turing-autodiff/index.qmd Co-authored-by: Guillaume Dalle <22795598+gdalle@users.noreply.github.com> * Update tutorials/docs-10-using-turing-autodiff/index.qmd Co-authored-by: Tor Erlend Fjelde * Update tutorials/docs-10-using-turing-autodiff/index.qmd Co-authored-by: Tor Erlend Fjelde * Add TuringBenchmarking and re-resolve manifest --------- Co-authored-by: Guillaume Dalle <22795598+gdalle@users.noreply.github.com> Co-authored-by: Tor Erlend Fjelde Co-authored-by: Penelope Yong --- Manifest.toml | 864 +++++++++++------- Project.toml | 3 +- .../docs-10-using-turing-autodiff/index.qmd | 23 +- 3 files changed, 531 insertions(+), 359 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 4eb85530f..83ba4bd2d 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,17 +1,18 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.5" +julia_version = "1.10.6" manifest_format = "2.0" -project_hash = "24c19d9af05129bd51c95e6af97ff0385a185787" +project_hash = "52677c2802b9702303d49a2f40fdefa34939b429" [[deps.ADTypes]] -git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" +git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.9.0" -weakdeps = ["ChainRulesCore", "EnzymeCore"] +version = "1.11.0" +weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] [deps.ADTypes.extensions] ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesConstructionBaseExt = "ConstructionBase" ADTypesEnzymeCoreExt = "EnzymeCore" [[deps.AbstractFFTs]] @@ -33,9 +34,9 @@ version = "0.5.21" [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] -git-tree-sha1 = "d4ab12197672f0f4a3afb850d574cfded5fd9070" +git-tree-sha1 = "aa469a7830413bd4c855963e3f648bd9d145c2c3" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "5.4.0" +version = "5.6.0" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "Accessors", "DensityInterface", "Random"] @@ -75,9 +76,9 @@ version = "0.1.38" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099" +git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.0.4" +version = "4.1.1" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -85,9 +86,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "1da0961a400c28d1e5f057e922ff75ec5d6a5747" +git-tree-sha1 = "6f6a228808fe00ad05b47d74747c800d3df18acb" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.6.2" +version = "0.6.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -101,9 +102,9 @@ version = "0.6.2" [[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"] -git-tree-sha1 = "66ac4c7b320d2434f04d48116db02e73e6dabc8b" +git-tree-sha1 = "b5f8159bffa2e6af9e080c11c4e6da8c5b05f079" uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -version = "0.8.3" +version = "0.8.4" weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] [deps.AdvancedMH.extensions] @@ -123,9 +124,9 @@ weakdeps = ["Libtask"] [[deps.AdvancedVI]] deps = ["ADTypes", "Bijectors", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "187f67ab998f25208651262fee9539d845016b26" +git-tree-sha1 = "d23ac9ecdf0ba3dfdd8ea22f42793fabc763afdc" uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" -version = "0.2.5" +version = "0.2.10" weakdeps = ["Enzyme", "Flux", "ReverseDiff", "Zygote"] [deps.AdvancedVI.extensions] @@ -141,9 +142,9 @@ uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" version = "1.1.3" [[deps.ArgCheck]] -git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" +git-tree-sha1 = "680b3b8759bd4c54052ada14e52355ab69e07876" uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" -version = "2.3.0" +version = "2.4.0" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" @@ -169,15 +170,16 @@ version = "3.5.1+1" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "3640d077b6dafd64ceb8fd5c1ec76f7ca53bcf76" +git-tree-sha1 = "d5140b60b87473df18cf4fe66382b7c3596df047" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.16.0" +version = "7.17.1" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" ArrayInterfaceReverseDiffExt = "ReverseDiff" @@ -191,6 +193,7 @@ version = "7.16.0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" @@ -199,9 +202,9 @@ version = "7.16.0" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "0dd7edaff278e346eb0ca07a7e75c9438408a3ce" +git-tree-sha1 = "492681bc44fac86804706ddb37da10880a2bd528" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.10.3" +version = "1.10.4" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -268,21 +271,36 @@ 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.Bijectors]] -deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "49491db48b1c70eefa5115e626100dbd6c0ff4c0" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "6e686c360af8375162531708acb824ae1182b1d5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.13.12" -weakdeps = ["DistributionsAD", "ForwardDiff", "LazyArrays", "ReverseDiff", "Tracker", "Zygote"] +version = "0.13.16" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" BijectorsForwardDiffExt = "ForwardDiff" BijectorsLazyArraysExt = "LazyArrays" BijectorsReverseDiffExt = "ReverseDiff" + BijectorsTapirExt = "Tapir" 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" + Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + [[deps.BitFlags]] git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" @@ -295,10 +313,10 @@ uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.6" [[deps.BoundaryValueDiffEq]] -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 = "22f36cc7199c3b0f34979c6925cf8ec05281409f" +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqShooting", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "98da8bd76b89a4ae1b8dde9fc6dcd75dcd6b5282" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "5.10.0" +version = "5.12.0" [deps.BoundaryValueDiffEq.extensions] BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" @@ -306,11 +324,35 @@ version = "5.10.0" [deps.BoundaryValueDiffEq.weakdeps] ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" +[[deps.BoundaryValueDiffEqCore]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "34c7d203f7a5002a7c27e69ae4f70f940cd22890" +uuid = "56b672f2-a5fe-4263-ab2d-da677488eb3a" +version = "1.2.0" + +[[deps.BoundaryValueDiffEqFIRK]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "6305d58ba2f53faec7bf44dfba5b591b524254b0" +uuid = "85d9eb09-370e-4000-bb32-543851f73618" +version = "1.2.0" + +[[deps.BoundaryValueDiffEqMIRK]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "ed6802d8a97a0847060d25261b7561da83a4f044" +uuid = "1a22d4ce-7765-49ea-b6f2-13c8438986a6" +version = "1.2.0" + +[[deps.BoundaryValueDiffEqShooting]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "e30c7383ae1bf5564c139a95711b910b0f4f1a3d" +uuid = "ed55bfe0-3725-4db6-871e-a1dc9f42a757" +version = "1.2.0" + [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" +git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+1" +version = "1.0.8+2" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -325,9 +367,9 @@ version = "0.2.6" [[deps.CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab" +git-tree-sha1 = "deddd8725e5e1cc49ee205a1964256043720a6c3" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.14" +version = "0.10.15" [[deps.Cairo_jll]] 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"] @@ -336,9 +378,9 @@ uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.18.2+1" [[deps.Cassette]] -git-tree-sha1 = "0970356c3bb9113309c74c27c87083cf9c73880a" +git-tree-sha1 = "f8764df8d9d2aec2812f009a1ac39e46c33354b8" uuid = "7057c7e9-c182-5462-911a-8362d720325c" -version = "0.3.13" +version = "0.3.14" [[deps.CategoricalArrays]] deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] @@ -360,9 +402,9 @@ version = "0.10.8" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "be227d253d132a6d57f9ccf5f67c0fb6488afd87" +git-tree-sha1 = "bcffdcaed50d3453673b852f3522404a94b50fad" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.71.0" +version = "1.72.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] @@ -405,9 +447,9 @@ version = "0.7.6" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0" +git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.26.0" +version = "3.27.1" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -468,22 +510,20 @@ uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" version = "1.1.1+0" [[deps.ComponentArrays]] -deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "Functors", "LinearAlgebra", "PackageExtensionCompat", "StaticArrayInterface", "StaticArraysCore"] -git-tree-sha1 = "bc391f0c19fa242fb6f71794b949e256cfa3772c" +deps = ["Adapt", "ArrayInterface", "ChainRulesCore", "ConstructionBase", "ForwardDiff", "Functors", "LinearAlgebra", "StaticArrayInterface", "StaticArraysCore"] +git-tree-sha1 = "e9b355215c05eeaaa7bf7d2ae0d329074e3cb045" uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -version = "0.15.17" -weakdeps = ["Adapt", "ConstructionBase", "GPUArrays", "Optimisers", "RecursiveArrayTools", "ReverseDiff", "SciMLBase", "Tracker", "TruncatedStacktraces", "Zygote"] +version = "0.15.19" +weakdeps = ["GPUArrays", "KernelAbstractions", "Optimisers", "RecursiveArrayTools", "ReverseDiff", "SciMLBase", "Tracker", "Zygote"] [deps.ComponentArrays.extensions] - ComponentArraysAdaptExt = "Adapt" - ComponentArraysConstructionBaseExt = "ConstructionBase" ComponentArraysGPUArraysExt = "GPUArrays" + ComponentArraysKernelAbstractionsExt = "KernelAbstractions" ComponentArraysOptimisersExt = "Optimisers" ComponentArraysRecursiveArrayToolsExt = "RecursiveArrayTools" ComponentArraysReverseDiffExt = "ReverseDiff" ComponentArraysSciMLBaseExt = "SciMLBase" ComponentArraysTrackerExt = "Tracker" - ComponentArraysTruncatedStacktracesExt = "TruncatedStacktraces" ComponentArraysZygoteExt = "Zygote" [[deps.CompositionsBase]] @@ -589,10 +629,10 @@ uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52" version = "0.1.2" [[deps.DelayDiffEq]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack"] -git-tree-sha1 = "066f60231c1b0ae2905ffd2651e207accd91f627" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack"] +git-tree-sha1 = "cfcd0d368d6950473eab154560b22ae7a99b63be" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.48.1" +version = "5.49.0" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -607,10 +647,10 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "fa7d580038451a8df4434ef5b079ac9b2d486194" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] +git-tree-sha1 = "b7dbeaa770bad0980ddddf606de814cff2acb3bc" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.155.1" +version = "6.160.0" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -641,11 +681,10 @@ version = "6.155.1" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NonlinearSolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "19dbd44d18bbfdfcf5e56c99cea9b0ed23df350a" +deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "b1f970a2873a2cf76ce35fb0ed2b755a11b31052" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "3.9.1" -weakdeps = ["OrdinaryDiffEq", "OrdinaryDiffEqCore", "Sundials"] +version = "4.1.0" [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] @@ -671,15 +710,15 @@ 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 = "d851f2ca05f3cec9988f081b047a778a58b48aaf" +git-tree-sha1 = "d55af9d6b51c54f81ae30d1a463206d32cc4c24a" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.14.0" +version = "7.15.0" [[deps.DifferentiationInterface]] -deps = ["ADTypes", "Compat", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PackageExtensionCompat", "SparseArrays", "SparseMatrixColorings"] -git-tree-sha1 = "9b23f9a816790b8ab9914c3c86321a546e92cbe7" +deps = ["ADTypes", "LinearAlgebra"] +git-tree-sha1 = "94e3189f15c2d9011144c094a89fe3f31cc394b0" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.5.17" +version = "0.6.23" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -689,10 +728,13 @@ version = "0.5.17" DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" DifferentiationInterfaceForwardDiffExt = "ForwardDiff" + DifferentiationInterfaceMooncakeExt = "Mooncake" DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" DifferentiationInterfaceReverseDiffExt = "ReverseDiff" + DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" + DifferentiationInterfaceStaticArraysExt = "StaticArrays" DifferentiationInterfaceSymbolicsExt = "Symbolics" - DifferentiationInterfaceTapirExt = "Tapir" DifferentiationInterfaceTrackerExt = "Tracker" DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] @@ -704,18 +746,21 @@ version = "0.5.17" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.DispatchDoctor]] deps = ["MacroTools", "Preferences"] -git-tree-sha1 = "19eec8ee5cde1c10aa5e5e0f25d10a3b4c8f8f12" +git-tree-sha1 = "453df2ce2aef7de59c69a56d31dcd2ec3384dd77" uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" -version = "0.4.15" +version = "0.4.17" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.DispatchDoctor.extensions] @@ -724,9 +769,9 @@ weakdeps = ["ChainRulesCore", "EnzymeCore"] [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" +git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.11" +version = "0.10.12" weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] @@ -739,9 +784,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d7477ecdafb813ddee2ae727afa94e9dcb5f3fb0" +git-tree-sha1 = "3101c32aab536e7a27b1763c0797dba151b899ad" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.112" +version = "0.25.113" weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [deps.Distributions.extensions] @@ -781,9 +826,9 @@ version = "3.4.7" [[deps.DynamicPPL]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] -git-tree-sha1 = "a155a80a54e37e6e1f14022ac815ef000aedeed5" +git-tree-sha1 = "0ffa7629807d8bb76101516550a5efb51289a9f8" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.28.4" +version = "0.29.2" weakdeps = ["ChainRulesCore", "EnzymeCore", "ForwardDiff", "MCMCChains", "ReverseDiff", "ZygoteRules"] [deps.DynamicPPL.extensions] @@ -794,12 +839,6 @@ weakdeps = ["ChainRulesCore", "EnzymeCore", "ForwardDiff", "MCMCChains", "Revers DynamicPPLReverseDiffExt = ["ReverseDiff"] DynamicPPLZygoteRulesExt = ["ZygoteRules"] -[[deps.EllipsisNotation]] -deps = ["StaticArrayInterface"] -git-tree-sha1 = "3507300d4343e8e4ad080ad24e335274c2e297a9" -uuid = "da5c29d0-fa7d-589e-88eb-ea29b0a81949" -version = "1.8.0" - [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] git-tree-sha1 = "e611b7fdfbfb5b18d5e98776c30daede41b44542" @@ -812,10 +851,10 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.Enzyme]] -deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Preferences", "Printf", "Random"] -git-tree-sha1 = "b63695bc543a45cab4f30e039c26ca3bcc6780a1" +deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Preferences", "Printf", "Random", "SparseArrays"] +git-tree-sha1 = "d6368b8438a9812e2ae19ffed95de73dd9bfbc1b" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.12.36" +version = "0.13.16" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -832,9 +871,9 @@ version = "0.12.36" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.EnzymeCore]] -git-tree-sha1 = "8f205a601760f4798a10f138c3940f0451d95188" +git-tree-sha1 = "e333ffd38ecffcf5c6c2dafd10788404ac46fb9f" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.7.8" +version = "0.8.6" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -842,9 +881,9 @@ weakdeps = ["Adapt"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "7fb808ef6421ea58c607657eea17caa9f03c08d0" +git-tree-sha1 = "f56cc86a351767fcb3bb2890b6e1a14d0ef323ab" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.148+0" +version = "0.0.165+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -854,21 +893,25 @@ version = "0.0.20230411+0" [[deps.ExceptionUnwrapping]] deps = ["Test"] -git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" +git-tree-sha1 = "d36f682e590a83d63d1c7dbd287573764682d12a" uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.10" +version = "0.1.11" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" +git-tree-sha1 = "cc5231d52eb1771251fbd37171dbc408bcc8a1b6" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.6.2+0" +version = "2.6.4+0" [[deps.ExponentialUtilities]] deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] -git-tree-sha1 = "8e18940a5ba7f4ddb41fe2b79b6acaac50880a86" +git-tree-sha1 = "cae251c76f353e32d32d76fae2fea655eab652af" uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" -version = "1.26.1" +version = "1.27.0" +weakdeps = ["StaticArrays"] + + [deps.ExponentialUtilities.extensions] + ExponentialUtilitiesStaticArraysExt = "StaticArrays" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" @@ -945,11 +988,36 @@ git-tree-sha1 = "cbf5edddb61a43669710cbc2241bc08b36d9e660" uuid = "29a986be-02c6-4525-aec4-84b980013641" version = "2.0.4" +[[deps.FastPower]] +git-tree-sha1 = "58c3431137131577a7c379d00fea00be524338fb" +uuid = "a4df4552-cc26-4903-aec0-212e50a0e84b" +version = "1.1.1" + + [deps.FastPower.extensions] + FastPowerEnzymeExt = "Enzyme" + FastPowerForwardDiffExt = "ForwardDiff" + FastPowerMeasurementsExt = "Measurements" + FastPowerMonteCarloMeasurementsExt = "MonteCarloMeasurements" + FastPowerReverseDiffExt = "ReverseDiff" + FastPowerTrackerExt = "Tracker" + + [deps.FastPower.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + 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" + [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322" +git-tree-sha1 = "2dd20384bf8c6d411b5c7370865b1e9b26cb2ea3" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.3" +version = "1.16.6" +weakdeps = ["HTTP"] + + [deps.FileIO.extensions] + HTTPExt = "HTTP" [[deps.FilePathsBase]] deps = ["Compat", "Dates"] @@ -979,9 +1047,9 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] -git-tree-sha1 = "b10bdafd1647f57ace3885143936749d61638c3b" +git-tree-sha1 = "84e3a47db33be7248daa6274b287507dd6ff84e8" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.26.0" +version = "2.26.2" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" @@ -1002,10 +1070,10 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.5" [[deps.Flux]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] -git-tree-sha1 = "f3b4e96288e8bee94cd1e230c1a9387d3e03f788" +deps = ["Adapt", "ChainRulesCore", "Compat", "Functors", "LinearAlgebra", "MLDataDevices", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] +git-tree-sha1 = "df520a0727f843576801a0294f5be1a94be28e23" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.14.21" +version = "0.14.25" [deps.Flux.extensions] FluxAMDGPUExt = "AMDGPU" @@ -1014,14 +1082,12 @@ version = "0.14.21" FluxEnzymeExt = "Enzyme" FluxMPIExt = "MPI" FluxMPINCCLExt = ["CUDA", "MPI", "NCCL"] - FluxMetalExt = "Metal" [deps.Flux.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" - Metal = "dde4c033-4e86-420c-a63e-0dd931031962" NCCL = "3fe64909-d7a1-4096-9b7d-7a0f12cf0f6b" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" @@ -1050,9 +1116,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.36" +version = "0.10.38" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -1060,9 +1126,9 @@ weakdeps = ["StaticArrays"] [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc" +git-tree-sha1 = "fa8e19f44de37e225aa0f1695bc223b05ed51fb4" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.2+0" +version = "2.13.3+0" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1123,21 +1189,21 @@ version = "0.1.6" [[deps.GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "b8c120986fce117469760119f44592ff148da93e" +git-tree-sha1 = "72408a76694e87e735f515a499ba1e069d232d39" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.27.5" +version = "1.0.1" [[deps.GR]] deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] -git-tree-sha1 = "629693584cef594c3f6f99e76e7a7ad17e60e8d5" +git-tree-sha1 = "ee28ddcd5517d54e417182fec3886e7412d3926f" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.7" +version = "0.73.8" [[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 = "a8863b69c2a0859f2c2c87ebdc4c6712e88bdf0d" +git-tree-sha1 = "f31929b9e67066bee48eec8b03c0df47d31a74b3" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.7+0" +version = "0.73.8+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -1153,15 +1219,15 @@ 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 = "674ff0db93fffcd11a3573986e550d66cd4fd71f" +git-tree-sha1 = "b36c7e110080ae48fdef61b0c31e6b17ada23b33" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.5+0" +version = "2.82.2+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" +git-tree-sha1 = "01979f9b37367603e2848ea225918a3b3861b606" uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" -version = "1.3.14+0" +version = "1.3.14+1" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] @@ -1193,10 +1259,10 @@ uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" version = "1.14.2+1" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "ae350b8225575cc3ea385d4131c81594f86dfe4f" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.8" +version = "1.10.12" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] @@ -1222,15 +1288,15 @@ weakdeps = ["AbstractTrees"] [[deps.Hwloc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "dd3b49277ec2bb2c6b94eb1604d4d0616016f7a6" +git-tree-sha1 = "50aedf345a709ab75872f80a2779568dc0bb461b" uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.11.2+0" +version = "2.11.2+1" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" +git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.24" +version = "0.3.25" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools"] @@ -1335,15 +1401,15 @@ version = "1.0.0" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "39d64b09147620f5ffbf6b2d3255be3c901bec63" +git-tree-sha1 = "71b48d857e86bf7a1838c4736545699974ce79a2" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.8" +version = "0.1.9" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40" +git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.6.0" +version = "1.6.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1365,9 +1431,9 @@ version = "0.2.4" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] -git-tree-sha1 = "6e0fb267f2c869df59b6bf9f8cb0f2794f2d85e9" +git-tree-sha1 = "c3a2cb6f968404ed3b1d5382bbdd7b7d83966598" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.13.7" +version = "9.14.0" weakdeps = ["FastBroadcast"] [[deps.KLU]] @@ -1378,9 +1444,9 @@ version = "0.6.0" [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "04e52f596d0871fa3890170fa79cb15e481e4cd8" +git-tree-sha1 = "e73a077abc7fe798fe940deabe30ef6c66bdde52" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.28" +version = "0.9.29" weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"] [deps.KernelAbstractions.extensions] @@ -1402,9 +1468,9 @@ version = "0.10.64" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "267dad6b4b7b5d529c76d40ff48d33f7e94cb834" +git-tree-sha1 = "4f20a2df85a9e5d55c9e84634bbf808ed038cabd" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.6" +version = "0.9.8" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1419,16 +1485,16 @@ uuid = "5be7bae1-8223-5378-bac3-9e7378a2f6e6" version = "0.4.1" [[deps.LERC_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "36bdbc52f13a7d1dcb0f3cd694e01677a515655b" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "3.0.0+1" +version = "4.0.0+0" [[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] -git-tree-sha1 = "b351d72436ddecd27381a07c242ba27282a6c8a7" +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] +git-tree-sha1 = "d422dfd9707bec6617335dc2ea3c5172a87d5908" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "9.0.0" +version = "9.1.3" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1438,9 +1504,9 @@ version = "9.0.0" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "f42bec1e12f42ec251541f6d0482d520a4638b17" +git-tree-sha1 = "05a8bd5a42309a9ec82f700876903abce1017dd3" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.33+0" +version = "0.0.34+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1470,9 +1536,9 @@ uuid = "81d17ec3-03a1-5e46-b53e-bddc35a13473" version = "3.0.1+0" [[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" +version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] @@ -1497,15 +1563,23 @@ uuid = "10f19ff3-798f-405d-979b-55457f8fc047" version = "0.1.17" [[deps.LazyArrays]] -deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays"] -git-tree-sha1 = "35079a6a869eecace778bcda8641f9a54ca3a828" +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] +git-tree-sha1 = "376bc148ae72e68a08f0d5d8a69e287025a37687" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "1.10.0" -weakdeps = ["StaticArrays"] +version = "2.2.2" [deps.LazyArrays.extensions] + LazyArraysBandedMatricesExt = "BandedMatrices" + LazyArraysBlockArraysExt = "BlockArrays" + LazyArraysBlockBandedMatricesExt = "BlockBandedMatrices" LazyArraysStaticArraysExt = "StaticArrays" + [deps.LazyArrays.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" @@ -1569,9 +1643,9 @@ version = "3.2.2+1" [[deps.Libgcrypt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] -git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" +git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.11+0" +version = "1.11.0+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -1581,39 +1655,49 @@ version = "1.6.0+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" +git-tree-sha1 = "c6ce1e19f3aec9b59186bdf06cdf3c4fc5f5f3e6" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.49.0+0" +version = "1.50.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+0" +version = "1.17.0+1" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" +git-tree-sha1 = "84eef7acd508ee5b3e956a2ae51b05024181dee0" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.40.1+0" +version = "2.40.2+0" [[deps.Libtask]] deps = ["FunctionWrappers", "LRUCache", "LinearAlgebra", "Statistics"] -git-tree-sha1 = "ed1f362b3fd13f00b65e61d98669c652c17663ab" +git-tree-sha1 = "902ece54b0cb5c5413a8a15db0ad2aa2ec4172d2" uuid = "6f1fad26-d15e-5dc8-ae53-837a1d7b8c9f" -version = "0.8.7" +version = "0.8.8" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "2da088d113af58221c52828a80378e16be7d037a" +git-tree-sha1 = "b404131d06f7886402758c9ce2214b636eb4d54a" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.5.1+1" +version = "4.7.0+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" +git-tree-sha1 = "edbf5309f9ddf1cab25afc344b1e8150b7c832f9" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.40.1+0" +version = "2.40.2+0" + +[[deps.LineSearch]] +deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] +git-tree-sha1 = "97d502765cc5cf3a722120f50da03c2474efce04" +uuid = "87fe0de2-c867-4266-b59a-2f0a94fc965b" +version = "0.1.4" +weakdeps = ["LineSearches"] + + [deps.LineSearch.extensions] + LineSearchLineSearchesExt = "LineSearches" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] @@ -1627,17 +1711,17 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] 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 = "6c5e4555ac2bc449a28604e184f759d18fc08420" +git-tree-sha1 = "6b79df6e803fb62b79a364b86c790e7e21bd38ce" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.34.0" +version = "2.37.0" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" LinearSolveCUDSSExt = "CUDSS" - LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] - LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] + LinearSolveEnzymeExt = "EnzymeCore" + LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" @@ -1651,7 +1735,6 @@ version = "2.34.0" 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" @@ -1670,12 +1753,13 @@ version = "2.1.2" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems"] -git-tree-sha1 = "457e6b347a87bfcd25a9eaf44a7bd5415559582f" +git-tree-sha1 = "a10e798ac8c44fe1594ad7d6e02898e16e4eafa3" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.10.1" +version = "1.13.0" [deps.LogDensityProblemsAD.extensions] LogDensityProblemsADADTypesExt = "ADTypes" + LogDensityProblemsADDifferentiationInterfaceExt = ["ADTypes", "DifferentiationInterface"] LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -1687,6 +1771,7 @@ version = "1.10.1" [deps.LogDensityProblemsAD.weakdeps] ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" + DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" @@ -1711,9 +1796,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" +git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.3" +version = "1.1.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] @@ -1726,29 +1811,21 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] SpecialFunctionsExt = "SpecialFunctions" -[[deps.LossFunctions]] -deps = ["Markdown", "Requires", "Statistics"] -git-tree-sha1 = "8073538845227d3acf8a0c149bf0e150e60d0ced" -uuid = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7" -version = "0.11.2" -weakdeps = ["CategoricalArrays"] - - [deps.LossFunctions.extensions] - LossFunctionsCategoricalArraysExt = "CategoricalArrays" - [[deps.Lux]] -deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LossFunctions", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "VectorizationBase", "WeightInitializers"] -git-tree-sha1 = "8001e387f5d07fef98160d62fc89aafacbc3266f" +deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "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 = "39cc335d2601d4b0d74b209f718e7e3641771448" uuid = "b2108857-7c20-44ae-9111-449ecde12c47" -version = "1.0.5" +version = "1.2.3" [deps.Lux.extensions] LuxComponentArraysExt = "ComponentArrays" LuxEnzymeExt = "Enzyme" LuxFluxExt = "Flux" + LuxLossFunctionsExt = "LossFunctions" LuxMLUtilsExt = "MLUtils" LuxMPIExt = "MPI" LuxMPINCCLExt = ["CUDA", "MPI", "NCCL"] + LuxReactantExt = ["Enzyme", "Reactant"] LuxReverseDiffExt = ["FunctionWrappers", "ReverseDiff"] LuxSimpleChainsExt = "SimpleChains" LuxTrackerExt = "Tracker" @@ -1760,9 +1837,11 @@ version = "1.0.5" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" + LossFunctions = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7" MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" NCCL = "3fe64909-d7a1-4096-9b7d-7a0f12cf0f6b" + Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SimpleChains = "de6bee2f-e2f4-4ec7-b6ed-219cc6f6e9e5" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" @@ -1770,10 +1849,9 @@ version = "1.0.5" [[deps.LuxCore]] deps = ["Compat", "DispatchDoctor", "Random"] -git-tree-sha1 = "1c1e81a6d0613d13ea9f7dff7291ea407624d74a" +git-tree-sha1 = "9f71aea19be890e429ee21adfeda1e63d01ec610" uuid = "bb33d45b-7691-41d6-9220-0943567d0623" -version = "1.0.1" -weakdeps = ["ArrayInterface", "ChainRulesCore", "EnzymeCore", "Functors", "MLDataDevices", "ReverseDiff", "Setfield", "Tracker"] +version = "1.1.0" [deps.LuxCore.extensions] LuxCoreArrayInterfaceReverseDiffExt = ["ArrayInterface", "ReverseDiff"] @@ -1782,20 +1860,36 @@ weakdeps = ["ArrayInterface", "ChainRulesCore", "EnzymeCore", "Functors", "MLDat LuxCoreEnzymeCoreExt = "EnzymeCore" LuxCoreFunctorsExt = "Functors" LuxCoreMLDataDevicesExt = "MLDataDevices" + LuxCoreReactantExt = "Reactant" LuxCoreSetfieldExt = "Setfield" + [deps.LuxCore.weakdeps] + ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196" + MLDataDevices = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" + Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + [[deps.LuxLib]] -deps = ["ArrayInterface", "ChainRulesCore", "Compat", "CpuId", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Hwloc", "KernelAbstractions", "LinearAlgebra", "LoopVectorization", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Octavian", "Polyester", "Random", "Reexport", "SLEEFPirates", "Static", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "d9a3531a7772c09a763cc4da2d9d0394d3417cdc" +deps = ["ArrayInterface", "ChainRulesCore", "Compat", "CpuId", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Hwloc", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "a9e0f1477ac91623079f7a230f4de46170dc8817" uuid = "82251201-b29d-42c6-8e01-566dec8acb11" -version = "1.2.4" +version = "1.3.7" [deps.LuxLib.extensions] LuxLibAppleAccelerateExt = "AppleAccelerate" LuxLibBLISBLASExt = "BLISBLAS" LuxLibCUDAExt = "CUDA" + LuxLibEnzymeExt = "Enzyme" + LuxLibLoopVectorizationExt = "LoopVectorization" LuxLibMKLExt = "MKL" + LuxLibOctavianExt = ["Octavian", "LoopVectorization"] LuxLibReverseDiffExt = "ReverseDiff" + LuxLibSLEEFPiratesExt = "SLEEFPirates" LuxLibTrackerAMDGPUExt = ["AMDGPU", "Tracker"] LuxLibTrackerExt = "Tracker" LuxLibcuDNNExt = ["CUDA", "cuDNN"] @@ -1805,8 +1899,12 @@ version = "1.2.4" AppleAccelerate = "13e28ba4-7ad8-5781-acae-3021b1ed3924" BLISBLAS = "6f275bd8-fec0-4d39-945b-7e95a765fa1e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890" MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2" + Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" @@ -1818,9 +1916,9 @@ version = "6.0.6" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "8ba8b1840d3ab5b38e7c71c23c3193bb5cbc02b5" +git-tree-sha1 = "4e1d6c34e22ee75892f9b371494ec98e8a6bf46a" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.3.10" +version = "0.3.12" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] @@ -1829,19 +1927,21 @@ uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" version = "2024.2.0+0" [[deps.MLDataDevices]] -deps = ["Adapt", "Functors", "Preferences", "Random"] -git-tree-sha1 = "e16288e37e76d68c3f1c418e0a2bec88d98d55fc" +deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"] +git-tree-sha1 = "85b47bc5a8bf0c886286638585df3bec7c9f8269" uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" -version = "1.2.0" +version = "1.5.3" [deps.MLDataDevices.extensions] MLDataDevicesAMDGPUExt = "AMDGPU" MLDataDevicesCUDAExt = "CUDA" MLDataDevicesChainRulesCoreExt = "ChainRulesCore" + MLDataDevicesChainRulesExt = "ChainRules" MLDataDevicesFillArraysExt = "FillArrays" MLDataDevicesGPUArraysExt = "GPUArrays" MLDataDevicesMLUtilsExt = "MLUtils" MLDataDevicesMetalExt = ["GPUArrays", "Metal"] + MLDataDevicesOneHotArraysExt = "OneHotArrays" MLDataDevicesReactantExt = "Reactant" MLDataDevicesRecursiveArrayToolsExt = "RecursiveArrayTools" MLDataDevicesReverseDiffExt = "ReverseDiff" @@ -1854,11 +1954,13 @@ version = "1.2.0" [deps.MLDataDevices.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + OneHotArrays = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" @@ -1943,9 +2045,13 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MatrixFactorizations]] deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] -git-tree-sha1 = "6731e0574fa5ee21c02733e397beb133df90de35" +git-tree-sha1 = "16a726dba99685d9e94c8d0a8f655383121fc608" uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" -version = "2.2.0" +version = "3.0.1" +weakdeps = ["BandedMatrices"] + + [deps.MatrixFactorizations.extensions] + MatrixFactorizationsBandedMatricesExt = "BandedMatrices" [[deps.MaybeInplace]] deps = ["ArrayInterface", "LinearAlgebra", "MacroTools"] @@ -1975,15 +2081,15 @@ version = "0.3.2" [[deps.Memoization]] deps = ["MacroTools"] -git-tree-sha1 = "073f080e733bc6697411901224ed4fd15fefaffa" +git-tree-sha1 = "7dbf904fa6c4447bd1f1d316886bfbe29feacf45" uuid = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" -version = "0.2.1" +version = "0.2.2" [[deps.MicroCanonicalHMC]] -deps = ["AbstractMCMC", "Adapt", "Distributions", "DynamicPPL", "ForwardDiff", "HDF5", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "MCMCDiagnosticTools", "Markdown", "ProgressMeter", "Random", "Statistics", "Turing"] -git-tree-sha1 = "7f509e51bb8c63128c84119718d92e85ddb2f0c9" +deps = ["AbstractMCMC", "Adapt", "Distributions", "ForwardDiff", "HDF5", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "MCMCDiagnosticTools", "Markdown", "ProgressMeter", "Random", "Statistics"] +git-tree-sha1 = "99fd367f8b8fc9d479420d33e8f16f3dab3162f4" uuid = "234d2aa0-2291-45f7-9047-6fa6f316b0a8" -version = "0.1.7" +version = "0.1.6" [[deps.MicroCollections]] deps = ["Accessors", "BangBang", "InitialValues"] @@ -1993,9 +2099,9 @@ version = "0.2.0" [[deps.MicrosoftMPI_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f12a29c4400ba812841c6ace3f4efbb6dbb3ba01" +git-tree-sha1 = "bc95bf4149bf535c09602e3acdf950d9b4376227" uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" -version = "10.1.4+2" +version = "10.1.4+3" [[deps.Missings]] deps = ["DataAPI"] @@ -2059,9 +2165,9 @@ version = "4.5.1" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "da09a1e112fd75f9af2a5229323f01b56ec96a4c" +git-tree-sha1 = "1177f161cda2083543b9967d7ca2a3e24e721e13" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.24" +version = "0.9.26" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -2104,19 +2210,19 @@ version = "1.0.0" [[deps.NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "3cebfc94a0754cc329ebc3bab1e6c89621e791ad" +git-tree-sha1 = "8a3271d8309285f4db73b4f662b1b290c715e85e" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.20" +version = "0.4.21" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -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 = "bcd8812e751326ff1d4b2dd50764b93df51f143b" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "4d8944f32db2b07a2bdf8477e878bcb9c9ea2308" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.14.0" +version = "3.15.1" [deps.NonlinearSolve.extensions] NonlinearSolveBandedMatricesExt = "BandedMatrices" @@ -2128,8 +2234,6 @@ version = "3.14.0" NonlinearSolveNLsolveExt = "NLsolve" NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" NonlinearSolveSpeedMappingExt = "SpeedMapping" - NonlinearSolveSymbolicsExt = "Symbolics" - NonlinearSolveZygoteExt = "Zygote" [deps.NonlinearSolve.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" @@ -2141,8 +2245,28 @@ version = "3.14.0" 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.NonlinearSolveBase]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "FunctionProperties", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "46772fc296d9f16c3ab78a8ef00008ab075de677" +uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" +version = "1.3.3" +weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"] + + [deps.NonlinearSolveBase.extensions] + NonlinearSolveBaseBandedMatricesExt = "BandedMatrices" + NonlinearSolveBaseDiffEqBaseExt = "DiffEqBase" + NonlinearSolveBaseForwardDiffExt = "ForwardDiff" + NonlinearSolveBaseLineSearchExt = "LineSearch" + NonlinearSolveBaseLinearSolveExt = "LinearSolve" + NonlinearSolveBaseSparseArraysExt = "SparseArrays" + NonlinearSolveBaseSparseMatrixColoringsExt = "SparseMatrixColorings" + +[[deps.NonlinearSolveFirstOrder]] +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "05a42691900f8f14e930478d5638a5f0fc973601" +uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" +version = "1.1.0" [[deps.ObjectFile]] deps = ["Reexport", "StructIO"] @@ -2155,20 +2279,6 @@ git-tree-sha1 = "7438a59546cf62428fc9d1bc94729146d37a7225" uuid = "510215fc-4207-5dde-b226-833fc4488ee2" version = "0.5.5" -[[deps.Octavian]] -deps = ["CPUSummary", "IfElse", "LoopVectorization", "ManualMemory", "PolyesterWeave", "PrecompileTools", "Static", "StaticArrayInterface", "ThreadingUtilities", "VectorizationBase"] -git-tree-sha1 = "92410e147bdcaf9e2f982a7cc9b1341fc5dd1a77" -uuid = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4" -version = "0.3.28" - - [deps.Octavian.extensions] - ForwardDiffExt = "ForwardDiff" - HyperDualNumbersExt = "HyperDualNumbers" - - [deps.Octavian.weakdeps] - ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" - HyperDualNumbers = "50ceba7f-c3ee-5a84-a6e8-3ad40456ec97" - [[deps.OffsetArrays]] git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" @@ -2186,9 +2296,9 @@ version = "1.3.5+1" [[deps.OneHotArrays]] deps = ["Adapt", "ChainRulesCore", "Compat", "GPUArraysCore", "LinearAlgebra", "NNlib"] -git-tree-sha1 = "963a3f28a2e65bb87a68033ea4a616002406037d" +git-tree-sha1 = "c8c7f6bfabe581dc40b580313a75f1ecce087e27" uuid = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" -version = "0.2.5" +version = "0.2.6" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] @@ -2202,9 +2312,9 @@ version = "0.8.1+2" [[deps.OpenMPI_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"] -git-tree-sha1 = "bfce6d523861a6c562721b262c0d1aaeead2647f" +git-tree-sha1 = "2dace87e14256edb1dd0724ab7ba831c779b96bd" uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" -version = "5.0.5+0" +version = "5.0.6+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] @@ -2226,9 +2336,9 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89" +git-tree-sha1 = "ab7edad78cdef22099f43c54ef77ac63c2c9cc64" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.9.4" +version = "1.10.0" [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" @@ -2238,54 +2348,55 @@ version = "1.9.4" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "6572fe0c5b74431aaeb0b18a4aa5ef03c84678be" +git-tree-sha1 = "c9ff5c686240c31eb8570b662dd1f66f4b183116" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.3.3" +version = "0.3.4" [[deps.Optimization]] -deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Pkg", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "81abd38353faaf0297a964fa6115a54c6a066cab" +deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] +git-tree-sha1 = "4b59eef21418fbdf28afbe2d7e945d8efbe5057d" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "3.26.3" +version = "4.0.5" [[deps.OptimizationBase]] -deps = ["ADTypes", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "Reexport", "Requires", "SciMLBase", "SparseArrays"] -git-tree-sha1 = "dcb1f85b0da580e2363c0197b0366406031a69cd" +deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] +git-tree-sha1 = "9e8569bc1c511c425fdc63f7ee41f2da057f8662" uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb" -version = "1.2.0" +version = "2.4.0" [deps.OptimizationBase.extensions] OptimizationEnzymeExt = "Enzyme" OptimizationFiniteDiffExt = "FiniteDiff" OptimizationForwardDiffExt = "ForwardDiff" + OptimizationMLDataDevicesExt = "MLDataDevices" + OptimizationMLUtilsExt = "MLUtils" OptimizationMTKExt = "ModelingToolkit" OptimizationReverseDiffExt = "ReverseDiff" - OptimizationSparseDiffExt = ["SparseDiffTools", "Symbolics", "ReverseDiff"] - OptimizationTrackerExt = "Tracker" + OptimizationSymbolicAnalysisExt = "SymbolicAnalysis" OptimizationZygoteExt = "Zygote" [deps.OptimizationBase.weakdeps] Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + MLDataDevices = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" + MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54" ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804" - Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + SymbolicAnalysis = "4297ee4d-0239-47d8-ba5d-195ecdf594fe" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.OptimizationNLopt]] -deps = ["NLopt", "Optimization", "Reexport"] -git-tree-sha1 = "83b7f5218c6ff83f65fff32923630fe8be9f5131" +deps = ["NLopt", "Optimization", "Random", "Reexport"] +git-tree-sha1 = "da55bae039168c0ef977bd5926cd5208c6cd13cf" uuid = "4e6fcdb7-1186-4e1f-a706-475e75c168bb" -version = "0.2.2" +version = "0.3.2" [[deps.OptimizationOptimJL]] -deps = ["Optim", "Optimization", "Reexport", "SparseArrays"] -git-tree-sha1 = "43870d726f883a47d158beebb1fc3c9fab1da9d6" +deps = ["Optim", "Optimization", "PrecompileTools", "Reexport", "SparseArrays"] +git-tree-sha1 = "980ec7190741db164a2923dc42d6f1e7ce2cc434" uuid = "36348300-93cb-4f02-beb5-3c3902f8871e" -version = "0.3.2" +version = "0.4.1" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2300,9 +2411,9 @@ version = "1.6.3" [[deps.OrdinaryDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "cd892f12371c287dc50d6ad3af075b088b6f2d48" +git-tree-sha1 = "36ce9bfc14a4b3dcf1490e80b5f1f4d35bfddf39" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.89.0" +version = "6.90.1" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2317,10 +2428,10 @@ uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" version = "1.1.2" [[deps.OrdinaryDiffEqCore]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "TruncatedStacktraces"] -git-tree-sha1 = "5595eb94d0dd3cde2f5cf456394a1e0a61237e95" +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 = "a458dc1117f289f830ad772a5a02fb36201d1df4" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.6.0" +version = "1.12.1" weakdeps = ["EnzymeCore"] [deps.OrdinaryDiffEqCore.extensions] @@ -2334,9 +2445,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqDifferentiation]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays"] -git-tree-sha1 = "e63ec633b1efa99e3caa2e26a01faaa88ba6cef9" +git-tree-sha1 = "8977f283a7d89c5d5c06c933467ed4af0a99f2f7" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.1.0" +version = "1.2.0" [[deps.OrdinaryDiffEqExplicitRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"] @@ -2351,16 +2462,16 @@ uuid = "e0540318-69ee-4070-8777-9e2de6de23de" version = "1.1.0" [[deps.OrdinaryDiffEqExtrapolation]] -deps = ["DiffEqBase", "FastBroadcast", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "fea595528a160ed5cade9eee217a9691b1d97714" +deps = ["DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] +git-tree-sha1 = "048bcccc8f59c20d5b4ad268eef4d7d21c005a94" uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4" -version = "1.1.0" +version = "1.2.1" [[deps.OrdinaryDiffEqFIRK]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLOperators"] -git-tree-sha1 = "795221c662698851328cb7787965ab4a180d9468" +deps = ["DiffEqBase", "FastBroadcast", "FastPower", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLOperators"] +git-tree-sha1 = "7a6e3996dc0850aee6cdc10c8afa377242fce702" uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125" -version = "1.1.1" +version = "1.5.0" [[deps.OrdinaryDiffEqFeagin]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2406,9 +2517,9 @@ version = "1.2.1" [[deps.OrdinaryDiffEqNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "PreallocationTools", "RecursiveArrayTools", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "StaticArrays"] -git-tree-sha1 = "a2a4119f3e35f7982f78e17beea7b12485d179e9" +git-tree-sha1 = "5e1b316555fa95892edc13f6a429ac784d0be4dd" uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8" -version = "1.2.1" +version = "1.2.4" [[deps.OrdinaryDiffEqNordsieck]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2442,9 +2553,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqRosenbrock]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "96b47cdd12cb4ce8f70d701b49f855271a462bd4" +git-tree-sha1 = "760a51a626d0065455847e4a3f788b07e86e5090" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.2.0" +version = "1.3.1" [[deps.OrdinaryDiffEqSDIRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] @@ -2531,9 +2642,9 @@ version = "2.8.1" [[deps.Pathfinder]] deps = ["ADTypes", "Distributions", "Folds", "IrrationalConstants", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "Optim", "Optimization", "OptimizationOptimJL", "PDMats", "PSIS", "ProgressLogging", "Random", "Requires", "SciMLBase", "Statistics", "StatsBase", "Transducers", "UnPack"] -git-tree-sha1 = "51c7b11dfd7249bfb22165902fa1b699f03e26f6" +git-tree-sha1 = "4207ff39e325bd90056ef58ce2584666129fbca9" uuid = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454" -version = "0.9.2" +version = "0.9.5" weakdeps = ["Accessors", "DynamicHMC", "DynamicPPL", "MCMCChains", "Turing"] [deps.Pathfinder.extensions] @@ -2558,21 +2669,21 @@ version = "1.10.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "6e55c6841ce3411ccb3457ee52fc48cb698d6fb0" +git-tree-sha1 = "41031ef3a1be6f5bbbf3e8073f210556daeae5ca" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.2.0" +version = "3.3.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] +git-tree-sha1 = "3ca9a356cd2e113c420f2c13bea19f8d3fb1cb18" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.1" +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 = "45470145863035bb124ca51b320ed35d071cc6c2" +git-tree-sha1 = "dae01f8c2e069a683d3a6e17bbae5070ab94786f" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.8" +version = "1.40.9" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -2655,6 +2766,10 @@ version = "2.4.0" 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" @@ -2773,9 +2888,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "b034171b93aebc81b3e1890a036d13a9c4a9e3e0" +git-tree-sha1 = "32f824db4e5bab64e25a12b22483a30a6b813d08" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.27.0" +version = "3.27.4" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -2784,6 +2899,7 @@ version = "3.27.0" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] + RecursiveArrayToolsStructArraysExt = "StructArrays" RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" @@ -2794,6 +2910,7 @@ version = "3.27.0" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -2852,9 +2969,9 @@ version = "0.5.1+0" [[deps.Roots]] deps = ["Accessors", "CommonSolve", "Printf"] -git-tree-sha1 = "3a7c7e5c3f015415637f5debdf8a674aa2c979c4" +git-tree-sha1 = "8e3694d669323cdfb560e344dc872b984de23b71" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.2.1" +version = "2.2.2" [deps.Roots.extensions] RootsChainRulesCoreExt = "ChainRulesCore" @@ -2898,10 +3015,10 @@ uuid = "26aad666-b158-4e64-9d35-0e672562fa48" version = "0.1.1" [[deps.SciMLBase]] -deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "50ed64cd5ad79b0bef71fdb6a11d10c3448bfef0" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "6f156f48d3603e8023e59917547b141218f2656d" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.56.1" +version = "2.64.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -2922,11 +3039,17 @@ version = "2.56.1" RCall = "6f49c342-dc21-5d91-9882-a32aef131414" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +[[deps.SciMLJacobianOperators]] +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] +git-tree-sha1 = "f66048bb969e67bd7d1bdd03cd0b81219642bbd0" +uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" +version = "0.1.1" + [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "e39c5f217f9aca640c8e27ab21acf557a3967db5" +git-tree-sha1 = "6149620767866d4b0f0f7028639b6e661b6a1e44" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.10" +version = "0.3.12" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -2934,16 +3057,16 @@ weakdeps = ["SparseArrays", "StaticArraysCore"] SciMLOperatorsStaticArraysCoreExt = "StaticArraysCore" [[deps.SciMLSensitivity]] -deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLOperators", "SciMLStructures", "SparseDiffTools", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "TruncatedStacktraces", "Zygote"] -git-tree-sha1 = "b669eb03c0d5a92ab6a337549afcaad2c9b381e0" +deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "Enzyme", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"] +git-tree-sha1 = "40a44437d426816aaa73e78da77e9bb931baf980" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.68.0" +version = "7.71.2" [[deps.SciMLStructures]] deps = ["ArrayInterface"] -git-tree-sha1 = "25514a6f200219cd1073e4ff23a6324e4a7efe64" +git-tree-sha1 = "0444a37a25fab98adbd90baa806ee492a3af133a" uuid = "53ae85a6-f571-4167-b2af-e1d143709226" -version = "1.5.0" +version = "1.6.1" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -2958,9 +3081,9 @@ version = "1.2.1" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a" +git-tree-sha1 = "d0553ce4031a081cc42387a9b9c8441b7d99f32d" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.4.5" +version = "1.4.7" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -2998,9 +3121,9 @@ version = "1.2.0" [[deps.SimpleNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "97a7e10717bd27e600ba55da9d90a5628c1a403b" +git-tree-sha1 = "44021f3efc023be3871195d8ad98b865001a2fa1" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.12.2" +version = "1.12.3" weakdeps = ["ChainRulesCore", "ReverseDiff", "Tracker", "Zygote"] [deps.SimpleNonlinearSolve.extensions] @@ -3034,11 +3157,31 @@ deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" version = "1.10.0" +[[deps.SparseConnectivityTracer]] +deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "010b3c44301805d1ede9159f449a351d61172aa6" +uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" +version = "0.6.9" + + [deps.SparseConnectivityTracer.extensions] + SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" + SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions" + SparseConnectivityTracerNNlibExt = "NNlib" + SparseConnectivityTracerNaNMathExt = "NaNMath" + SparseConnectivityTracerSpecialFunctionsExt = "SpecialFunctions" + + [deps.SparseConnectivityTracer.weakdeps] + DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + [[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 = "c9e5d7ee75cf6a1ca3a22c9a6a4ef451792cf62b" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "b906758c107b049b6b71599b9f928d9b14e5554a" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.20.0" +version = "2.23.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -3061,10 +3204,14 @@ uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" version = "0.1.2" [[deps.SparseMatrixColorings]] -deps = ["ADTypes", "Compat", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "ad17e2069015839e58a1f9275608b405fae1f28e" +deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "76b44c879661552d64f382acf66faa29ab56b3d9" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.4.6" +version = "0.4.10" +weakdeps = ["Colors"] + + [deps.SparseMatrixColorings.extensions] + SparseMatrixColoringsColorsExt = "Colors" [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] @@ -3088,6 +3235,12 @@ git-tree-sha1 = "e08a62abc517eb79667d0a29dc08a3b589516bb5" uuid = "171d559e-b47b-412a-8079-5efa626c420e" version = "0.1.15" +[[deps.StableRNGs]] +deps = ["Random"] +git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5" +uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" +version = "1.0.2" + [[deps.Static]] deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" @@ -3107,9 +3260,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50" +git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.7" +version = "1.9.8" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -3174,10 +3327,10 @@ uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" version = "2.4.1" [[deps.StochasticDiffEq]] -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 = "b49030a24847e8c3e85eed3359825297ffb70dfa" +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "2310e4cca114797f09a4ff0a58a81278e690a584" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.69.1" +version = "6.71.1" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] @@ -3187,15 +3340,15 @@ version = "0.5.7" [[deps.Strided]] deps = ["LinearAlgebra", "StridedViews", "TupleTools"] -git-tree-sha1 = "d85461cb47420b6dcecf51de8142fc60484dd0b3" +git-tree-sha1 = "f9ce8284e6eec72a21de3603493eb5355fcf7f39" uuid = "5e0ebb24-38b0-5f93-81fe-25c709ecae67" -version = "2.1.1" +version = "2.2.0" [[deps.StridedViews]] deps = ["LinearAlgebra", "PackageExtensionCompat"] -git-tree-sha1 = "2917996ce0fa6b8a3a85240a5e9ff930e2aeaa43" +git-tree-sha1 = "b60baf1998bcdccc57e1cc2c6703df1f619a3754" uuid = "4db3bf67-4bd7-4b4e-b153-31dc3fb37143" -version = "0.3.1" +version = "0.3.2" [deps.StridedViews.extensions] StridedViewsCUDAExt = "CUDA" @@ -3238,9 +3391,9 @@ version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "82304990120934137261aa085e0d05a412fe0825" +git-tree-sha1 = "56661ac133ea6df96fea8d6bb4eb18875b002206" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.25.0" +version = "4.26.1" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] @@ -3250,9 +3403,9 @@ version = "5.2.2+0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "0225f7c62f5f78db35aae6abb2e5cabe38ce578f" +git-tree-sha1 = "6c6761e08bf5a270905cdd065be633abfa1b155b" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.31" +version = "0.3.35" [[deps.TOML]] deps = ["Dates"] @@ -3324,9 +3477,9 @@ version = "0.5.2" [[deps.TimeZones]] deps = ["Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] -git-tree-sha1 = "8323074bc977aa85cf5ad71099a83ac75b0ac107" +git-tree-sha1 = "33c771f2157712ff4c85931186a4984efbe58934" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.18.1" +version = "1.19.0" weakdeps = ["RecipesBase"] [deps.TimeZones.extensions] @@ -3340,9 +3493,9 @@ version = "0.5.25" [[deps.Tracker]] deps = ["Adapt", "ChainRulesCore", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "da45269e1da051c2a13624194fcdc74d6483fad5" +git-tree-sha1 = "c266e49953dadd0923caa17b3ea464ab6b97b3f2" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.35" +version = "0.2.37" weakdeps = ["PDMats"] [deps.Tracker.extensions] @@ -3355,9 +3508,9 @@ version = "0.11.3" [[deps.Transducers]] deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] -git-tree-sha1 = "2485554c5b6b039316634f9c676e1bdd84a13e31" +git-tree-sha1 = "7deeab4ff96b85c5f72c824cae53a1398da3d1cb" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.83" +version = "0.4.84" [deps.Transducers.extensions] TransducersAdaptExt = "Adapt" @@ -3387,11 +3540,6 @@ git-tree-sha1 = "be986ad9dac14888ba338c2554dcfec6939e1393" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" version = "0.2.1" -[[deps.Tricks]] -git-tree-sha1 = "7822b97e99a1672bfb1b49b668a6d46d58d8cbcb" -uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.9" - [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] git-tree-sha1 = "ea3e54c2bdde39062abf5a9758a23735558705e1" @@ -3399,21 +3547,33 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.TupleTools]] -git-tree-sha1 = "41d61b1c545b06279871ef1a4b5fcb2cac2191cd" +git-tree-sha1 = "41e43b9dc950775eac654b9f845c839cd2f1821e" uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6" -version = "1.5.0" +version = "1.6.0" [[deps.Turing]] -deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "f69f33f7862a66674c279fe9b86b457a96767e35" +deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "3453ab63621f1a06df04d995da2eb6fcd422617c" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.34.1" +version = "0.35.1" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" TuringOptimExt = "Optim" +[[deps.TuringBenchmarking]] +deps = ["ADTypes", "AbstractMCMC", "BenchmarkTools", "DynamicPPL", "ForwardDiff", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "PrettyTables", "Requires", "ReverseDiff", "Zygote"] +git-tree-sha1 = "b512c8ab665cb6396f19533b6960cc3e0fc4d556" +uuid = "0db1332d-5c25-4deb-809f-459bc696f94f" +version = "0.5.5" + + [deps.TuringBenchmarking.extensions] + TuringBenchmarkingBridgeStanExt = "BridgeStan" + + [deps.TuringBenchmarking.weakdeps] + BridgeStan = "c88b6f0a-829e-4b0b-94b7-f06ab5908f5a" + [[deps.URIs]] git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" @@ -3472,9 +3632,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "e7f5b81c65eb858bed630fe006837b935518aca5" +git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.70" +version = "0.21.71" [[deps.VertexSafeGraphs]] deps = ["Graphs"] @@ -3508,9 +3668,9 @@ version = "1.4.2" [[deps.WeightInitializers]] deps = ["ArgCheck", "ConcreteStructs", "GPUArraysCore", "LinearAlgebra", "Random", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "ed1cfb44422eaa9804c8a596a8227a6e2baaeef7" +git-tree-sha1 = "0b935265795ccccf12bc89e693b6380934451780" uuid = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d" -version = "1.0.3" +version = "1.0.4" [deps.WeightInitializers.extensions] WeightInitializersAMDGPUExt = ["AMDGPU", "GPUArrays"] @@ -3530,9 +3690,9 @@ version = "1.0.3" [[deps.Widgets]] deps = ["Colors", "Dates", "Observables", "OrderedCollections"] -git-tree-sha1 = "fcdae142c1cfc7d89de2d11e08721d0f2f86c98a" +git-tree-sha1 = "e9aeb174f95385de31e70bd15fa066a505ea82b9" uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62" -version = "0.6.6" +version = "0.6.7" [[deps.WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] @@ -3547,21 +3707,21 @@ version = "1.6.1" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127" +git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.13.3+0" +version = "2.13.5+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "a54ee957f4c86b526460a720dbc882fa5edcbefc" +git-tree-sha1 = "7d1671acbe47ac88e981868a078bd6b4e27c5191" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.41+0" +version = "1.1.42+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" +git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.4.6+0" +version = "5.6.3+0" [[deps.Xorg_libICE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -3583,9 +3743,9 @@ version = "1.8.6+0" [[deps.Xorg_libXau_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8" +git-tree-sha1 = "2b0e27d52ec9d8d483e2ca0b72b3cb1a8df5c27a" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.11+0" +version = "1.0.11+1" [[deps.Xorg_libXcursor_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] @@ -3595,9 +3755,9 @@ version = "1.2.0+4" [[deps.Xorg_libXdmcp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7" +git-tree-sha1 = "02054ee01980c90297412e4c809c8694d7323af3" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.4+0" +version = "1.1.4+1" [[deps.Xorg_libXext_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] @@ -3637,9 +3797,9 @@ version = "0.9.11+0" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" +git-tree-sha1 = "fee57a273563e273f0f53275101cd41a8153517a" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.1+0" +version = "0.1.1+1" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] @@ -3703,9 +3863,9 @@ version = "2.39.0+0" [[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" +git-tree-sha1 = "b9ead2d2bdb27330545eb14234a2e300da61232e" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.5.0+0" +version = "1.5.0+1" [[deps.Zlib_jll]] deps = ["Libdl"] @@ -3720,9 +3880,9 @@ version = "1.5.6+1" [[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 = "f2f85ad73ca67b5d3c94239b0fde005e0fe2d900" +git-tree-sha1 = "c7dc3148a64d1cd3768c29b3db5972d1c302661b" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.71" +version = "0.6.73" weakdeps = ["Colors", "Distances", "Tracker"] [deps.Zygote.extensions] @@ -3744,9 +3904,9 @@ version = "3.2.9+0" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "936081b536ae4aa65415d869287d43ef3cb576b2" +git-tree-sha1 = "6e50f145003024df4f5cb96c7fce79466741d601" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.53.0+0" +version = "0.56.3+0" [[deps.gperf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/Project.toml b/Project.toml index 44e8bc64d..b14761bea 100644 --- a/Project.toml +++ b/Project.toml @@ -50,8 +50,9 @@ StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c" StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" +TuringBenchmarking = "0db1332d-5c25-4deb-809f-459bc696f94f" UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] -Turing = "0.34" +Turing = "0.35" diff --git a/tutorials/docs-10-using-turing-autodiff/index.qmd b/tutorials/docs-10-using-turing-autodiff/index.qmd index 9a0aaa8d1..d5753447e 100755 --- a/tutorials/docs-10-using-turing-autodiff/index.qmd +++ b/tutorials/docs-10-using-turing-autodiff/index.qmd @@ -19,12 +19,16 @@ While `Tracker` is still available, its use is discouraged due to a lack of acti As of Turing version v0.30, the global configuration flag for the AD backend has been removed in favour of [`AdTypes.jl`](https://github.com/SciML/ADTypes.jl), allowing users to specify the AD backend for individual samplers independently. Users can pass the `adtype` keyword argument to the sampler constructor to select the desired AD backend, with the default being `AutoForwardDiff(; chunksize=0)`. -For `ForwardDiff`, pass `adtype=AutoForwardDiff(; chunksize)` to the sampler constructor. A `chunksize` of 0 permits the chunk size to be automatically determined. For more information regarding the selection of `chunksize`, please refer to [related section of `ForwardDiff`'s documentation](https://juliadiff.org/ForwardDiff.jl/dev/user/advanced/#Configuring-Chunk-Size). -For `ReverseDiff`, pass `adtype=AutoReverseDiff()` to the sampler constructor. An additional argument can be provided to `AutoReverseDiff` to specify whether to to compile the tape only once and cache it for later use (`false` by default, which means no caching tape). Be aware that the use of caching in certain types of models can lead to incorrect results and/or errors. +For `ForwardDiff`, pass `adtype=AutoForwardDiff(; chunksize)` to the sampler constructor. A `chunksize` of `nothing` permits the chunk size to be automatically determined. For more information regarding the selection of `chunksize`, please refer to [related section of `ForwardDiff`'s documentation](https://juliadiff.org/ForwardDiff.jl/dev/user/advanced/#Configuring-Chunk-Size). -Compiled tapes should only be used if you are absolutely certain that the computation doesn't change between different executions of your model. -Thus, e.g., in the model definition and all im- and explicitly called functions in the model all loops should be of fixed size, and `if`-statements should consistently execute the same branches. -For instance, `if`-statements with conditions that can be determined at compile time or conditions that depend only on the data will always execute the same branches during sampling (if the data is constant throughout sampling and, e.g., no mini-batching is used). +For `ReverseDiff`, pass `adtype=AutoReverseDiff()` to the sampler constructor. An additional keyword argument called `compile` can be provided to `AutoReverseDiff`. It specifies whether to pre-record the tape only once and reuse it later (`compile` is set to `false` by default, which means no pre-recording). This can substantially improve performance, but risks silently incorrect results if not used with care. + + + +Pre-recorded tapes should only be used if you are absolutely certain that the sequence of operations performed in your code does not change between different executions of your model. + +Thus, e.g., in the model definition and all implicitly and explicitly called functions in the model, all loops should be of fixed size, and `if`-statements should consistently execute the same branches. +For instance, `if`-statements with conditions that can be determined at compile time or conditions that depend only on fixed properties of the model, e.g. fixed data. However, `if`-statements that depend on the model parameters can take different branches during sampling; hence, the compiled tape might be incorrect. Thus you must not use compiled tapes when your model makes decisions based on the model parameters, and you should be careful if you compute functions of parameters that those functions do not have branching which might cause them to execute different code for different values of the parameter. @@ -62,4 +66,11 @@ c = sample( Generally, reverse-mode AD, for instance `ReverseDiff`, is faster when sampling from variables of high dimensionality (greater than 20), while forward-mode AD, for instance `ForwardDiff`, is more efficient for lower-dimension variables. This functionality allows those who are performance sensitive to fine tune their automatic differentiation for their specific models. -If the differentiation method is not specified in this way, Turing will default to using whatever the global AD backend is. Currently, this defaults to `ForwardDiff`. \ No newline at end of file +If the differentiation method is not specified in this way, Turing will default to using whatever the global AD backend is. +Currently, this defaults to `ForwardDiff`. + +The most reliable way to ensure you are using the fastest AD that works for your problem is to benchmark them using `TuringBenchmarking`: +```{julia} +using TuringBenchmarking +benchmark_model(gdemo(1.5, 2), adbackends=[AutoForwardDiff(), AutoReverseDiff()]) +```