diff --git a/Manifest.toml b/Manifest.toml index 92b7fafc8..d86c9e5e0 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.3" +julia_version = "1.11.4" manifest_format = "2.0" -project_hash = "547d92b7c2cee83d66812c3662de0a43b46d819f" +project_hash = "f8ede0ee89806fd59fc0feecd3210fa53189aa73" [[deps.ADTypes]] -git-tree-sha1 = "e1ce448a0d7f88168ffe2eeac4549c32d45a42d1" +git-tree-sha1 = "e2478490447631aedba0823d4d7a80b2cc8cdb32" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.12.1" +version = "1.14.0" weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] [deps.ADTypes.extensions] @@ -28,9 +28,9 @@ weakdeps = ["ChainRulesCore", "Test"] [[deps.AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "PDMats", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "010e6b5e06a9a6b1be6b146a7f29d5848490cc64" +git-tree-sha1 = "1d15dd1f8658f4efcc4a8e779a5d688733e4a1f0" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.21" +version = "0.5.23" [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] @@ -51,9 +51,9 @@ version = "0.4.5" [[deps.Accessors]] deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "MacroTools"] -git-tree-sha1 = "0ba8f4c1f06707985ffb4804fdad1bf97b233897" +git-tree-sha1 = "3b86719127f50670efe356bc11073d84b4ed7a5d" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.41" +version = "0.1.42" [deps.Accessors.extensions] AxisKeysExt = "AxisKeys" @@ -68,7 +68,6 @@ version = "0.1.41" AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" - Requires = "ae029012-a4dd-5104-9daa-d747884805df" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" @@ -76,19 +75,20 @@ version = "0.1.41" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" +git-tree-sha1 = "f7817e2e585aa6d924fd714df1e2a84be7896c60" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.1.1" -weakdeps = ["StaticArrays"] +version = "4.3.0" +weakdeps = ["SparseArrays", "StaticArrays"] [deps.Adapt.extensions] + AdaptSparseArraysExt = "SparseArrays" AdaptStaticArraysExt = "StaticArrays" [[deps.AdvancedHMC]] -deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "6f6a228808fe00ad05b47d74747c800d3df18acb" +deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] +git-tree-sha1 = "3027ae3794d5205a5936272b02886a6c5ebaaa60" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.6.4" +version = "0.7.0" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -102,9 +102,9 @@ version = "0.6.4" [[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "DocStringExtensions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"] -git-tree-sha1 = "6e3d18037861bf220ed77f1a2c5f24a21a68d4b7" +git-tree-sha1 = "bcf97a5390262571d64d62566673bf1e72080d11" uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -version = "0.8.5" +version = "0.8.6" weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] [deps.AdvancedMH.extensions] @@ -148,9 +148,9 @@ uuid = "a95523ee-d6da-40b5-98cc-27bc505739d5" version = "0.1.10" [[deps.ArgCheck]] -git-tree-sha1 = "680b3b8759bd4c54052ada14e52355ab69e07876" +git-tree-sha1 = "f9e9a66c9b7be1ad7372bbd9b062d9230c30c5ce" uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" -version = "2.4.0" +version = "2.5.0" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" @@ -208,9 +208,9 @@ version = "7.18.0" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "2bf6e01f453284cb61c312836b4680331ddfc44b" +git-tree-sha1 = "4e25216b8fea1908a0ce0f5d87368587899f75be" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.11.0" +version = "1.11.1" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -222,9 +222,9 @@ version = "1.11.0" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "93da6c8228993b0052e358ad592ee7c1eccaa639" +git-tree-sha1 = "b5bb4dc6248fde467be2a863eb8452993e74d402" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "1.1.0" +version = "1.1.1" [deps.Atomix.extensions] AtomixCUDAExt = "CUDA" @@ -252,19 +252,19 @@ version = "0.4.7" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "fc8d8197de6c69ad6fd01c255b6b386ca8199331" +git-tree-sha1 = "614c6aba1d562191d9832df2af24f594aa7ebf61" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "1.9.0" +version = "1.9.3" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] BandedMatricesSparseArraysExt = "SparseArrays" [[deps.BangBang]] -deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires"] -git-tree-sha1 = "e2144b631226d9eeab2d746ca8880b7ccff504ae" +deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra"] +git-tree-sha1 = "26f41e1df02c330c4fa1e98d4aa2168fdafc9b1f" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.4.3" +version = "0.4.4" [deps.BangBang.extensions] BangBangChainRulesCoreExt = "ChainRulesCore" @@ -299,10 +299,10 @@ version = "1.6.0" [[deps.Bijectors]] deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "af42d5383609f5cd167a2f9b1b2371c2d6604d02" +git-tree-sha1 = "803e3c6bfd5c2655eb040d252144b7519ce1e70e" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.15.4" -weakdeps = ["DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker", "Zygote"] +version = "0.15.6" +weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker", "Zygote"] [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -310,6 +310,7 @@ weakdeps = ["DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Moonc BijectorsForwardDiffExt = "ForwardDiff" BijectorsLazyArraysExt = "LazyArrays" BijectorsMooncakeExt = "Mooncake" + BijectorsReverseDiffChainRulesExt = ["ChainRules", "ReverseDiff"] BijectorsReverseDiffExt = "ReverseDiff" BijectorsTrackerExt = "Tracker" BijectorsZygoteExt = "Zygote" @@ -327,9 +328,9 @@ version = "0.1.6" [[deps.BoundaryValueDiffEq]] deps = ["ADTypes", "ArrayInterface", "BoundaryValueDiffEqAscher", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqMIRKN", "BoundaryValueDiffEqShooting", "DiffEqBase", "FastClosures", "ForwardDiff", "LinearAlgebra", "Reexport", "SciMLBase"] -git-tree-sha1 = "c6f965b14b4073171b5404e005d0abda3888f8b6" +git-tree-sha1 = "e3829b5aa0cb49348956c81b927b5edf64cdf6bf" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "5.14.0" +version = "5.16.0" [deps.BoundaryValueDiffEq.extensions] BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" @@ -338,56 +339,56 @@ version = "5.14.0" ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" [[deps.BoundaryValueDiffEqAscher]] -deps = ["ADTypes", "Adapt", "AlmostBlockDiagonals", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "ab8999d481e102421361f8ca514aa75fcc4feb3f" +deps = ["ADTypes", "AlmostBlockDiagonals", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] +git-tree-sha1 = "a3ed69c1c0249a53622bd4435384c4e76ac547d9" uuid = "7227322d-7511-4e07-9247-ad6ff830280e" -version = "1.3.0" +version = "1.5.0" [[deps.BoundaryValueDiffEqCore]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "54eef71b725661a87089b11c629b1a410fd65c90" +deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] +git-tree-sha1 = "832ade257129d0c222a53b66e2d7e6f5d937ae34" uuid = "56b672f2-a5fe-4263-ab2d-da677488eb3a" -version = "1.6.0" +version = "1.8.0" [[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 = "314c6e0ea597f6d733f78c0d553fdfacc7abb6c1" +deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] +git-tree-sha1 = "a92feb2cbb12c6c9adc4d3c4e7427709e9477540" uuid = "85d9eb09-370e-4000-bb32-543851f73618" -version = "1.4.0" +version = "1.6.0" [[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 = "4be1e7bbe1681a713427ab8384774c7edaf20f73" +deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] +git-tree-sha1 = "4cd74dc128326804f780ad6e18ec4886279293de" uuid = "1a22d4ce-7765-49ea-b6f2-13c8438986a6" -version = "1.4.0" +version = "1.6.0" [[deps.BoundaryValueDiffEqMIRKN]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "62bdd5cb9b8dbcb5a6a728d12efa5d20b538370a" +deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] +git-tree-sha1 = "0db565e02c9784e254325b616a8dd6c0dfec7403" uuid = "9255f1d6-53bf-473e-b6bd-23f1ff009da4" -version = "1.3.0" +version = "1.5.0" [[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 = "4d4ced45c733f6691bdcda11ae62ec0de02ddf06" +deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] +git-tree-sha1 = "7429a95010c57e67bd10e52dd3f276db4d2abdeb" uuid = "ed55bfe0-3725-4db6-871e-a1dc9f42a757" -version = "1.4.0" +version = "1.6.0" [[deps.BracketingNonlinearSolve]] deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "95cb19c37ea427617e9795655667712f03058d98" +git-tree-sha1 = "47d6e355097ef6df3c39080a0045ecfd00ff514e" uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e" -version = "1.1.0" +version = "1.1.1" weakdeps = ["ForwardDiff"] [deps.BracketingNonlinearSolve.extensions] BracketingNonlinearSolveForwardDiffExt = "ForwardDiff" [[deps.Bzip2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1b96ea4a01afe0ea4090c5c8039690672dd13f2e" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+4" +version = "1.0.9+0" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -408,9 +409,9 @@ 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"] -git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" +git-tree-sha1 = "2ac646d71d0d24b44f3f8c84da8c9f4d70fb67df" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.2+1" +version = "1.18.4+0" [[deps.Cassette]] git-tree-sha1 = "f8764df8d9d2aec2812f009a1ac39e46c33354b8" @@ -437,9 +438,9 @@ version = "0.10.8" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "4312d7869590fab4a4f789e97bd82f0a04eaaa05" +git-tree-sha1 = "a975ae558af61a2a48720a6271661bf2621e0f4e" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.72.2" +version = "1.72.3" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] @@ -476,15 +477,15 @@ version = "0.15.8" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" +git-tree-sha1 = "962834c22b66e32aa10f7611c08c8ca4e20749a9" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.6" +version = "0.7.8" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "26ec26c98ae1453c692efded2b17e15125a5bea1" +git-tree-sha1 = "403f2d8e209681fcbd9468a8514efff3ea08452e" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.28.0" +version = "3.29.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -550,9 +551,9 @@ version = "1.1.1+0" [[deps.ComponentArrays]] deps = ["Adapt", "ArrayInterface", "ChainRulesCore", "ConstructionBase", "ForwardDiff", "Functors", "LinearAlgebra", "StaticArrayInterface", "StaticArraysCore"] -git-tree-sha1 = "b926f8f322026c3a1d9539253ab111735eb540f8" +git-tree-sha1 = "eac93b2a05d33465d50e5448aefba8c06a69f738" uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -version = "0.15.22" +version = "0.15.25" [deps.ComponentArrays.extensions] ComponentArraysGPUArraysExt = "GPUArrays" @@ -592,9 +593,9 @@ version = "0.2.3" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "f36e5e8fdffcb5646ea5da81495a5a7566005127" +git-tree-sha1 = "d9d26935a0bcffc87d2613ce14c527c99fc543fd" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.3" +version = "2.5.0" [[deps.ConsoleProgressMonitor]] deps = ["Logging", "ProgressMeter"] @@ -648,9 +649,9 @@ version = "1.7.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" +git-tree-sha1 = "4e1fe97fdaed23e9dc21d4d664bea76b65fc50a0" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.20" +version = "0.18.22" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -692,16 +693,18 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -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 = "b1e23a7fe7371934d9d538114a7e7166c1d09e05" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] +git-tree-sha1 = "4263b49db273d67f13b83af609712aed69ccf38a" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.161.0" +version = "6.166.0" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" DiffEqBaseChainRulesCoreExt = "ChainRulesCore" DiffEqBaseDistributionsExt = "Distributions" DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] + DiffEqBaseForwardDiffExt = ["ForwardDiff"] + DiffEqBaseGTPSAExt = "GTPSA" DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" DiffEqBaseMPIExt = "MPI" DiffEqBaseMeasurementsExt = "Measurements" @@ -716,6 +719,8 @@ version = "6.161.0" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + GTPSA = "b27dd330-f138-47c5-815b-40db9dd9b6e8" GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" @@ -761,15 +766,15 @@ version = "0.1.2" [[deps.DifferentialEquations]] deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] -git-tree-sha1 = "d55af9d6b51c54f81ae30d1a463206d32cc4c24a" +git-tree-sha1 = "afdc7dfee475828b4f0286d63ffe66b97d7a3fa7" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.15.0" +version = "7.16.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "b44d8cedd863c1c7a9f3ec82555539ec9935d07f" +git-tree-sha1 = "cf6dcb4b21bdd893fd45be70791d6dc89ca16506" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.6.33" +version = "0.6.48" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -781,9 +786,10 @@ version = "0.6.33" DifferentiationInterfaceForwardDiffExt = ["ForwardDiff", "DiffResults"] DifferentiationInterfaceGTPSAExt = "GTPSA" DifferentiationInterfaceMooncakeExt = "Mooncake" - DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" + DifferentiationInterfacePolyesterForwardDiffExt = ["PolyesterForwardDiff", "ForwardDiff", "DiffResults"] DifferentiationInterfaceReverseDiffExt = ["ReverseDiff", "DiffResults"] DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseConnectivityTracerExt = "SparseConnectivityTracer" DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" DifferentiationInterfaceStaticArraysExt = "StaticArrays" DifferentiationInterfaceSymbolicsExt = "Symbolics" @@ -805,6 +811,7 @@ version = "0.6.33" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" @@ -840,9 +847,9 @@ version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "03aa5d44647eaec98e1920635cdfed5d5560a8b9" +git-tree-sha1 = "0b4190661e8a4e51a842070e7dd4fae440ddb7f4" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.117" +version = "0.25.118" weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [deps.Distributions.extensions] @@ -881,10 +888,10 @@ uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb" version = "3.5.0" [[deps.DynamicPPL]] -deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "InteractiveUtils", "KernelAbstractions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] -git-tree-sha1 = "18fcc77ba683967339473b731143fa269ea671f5" +deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] +git-tree-sha1 = "4070ee7251d99838b474581539d83884867b4bd4" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.34.2" +version = "0.35.5" [deps.DynamicPPL.extensions] DynamicPPLChainRulesCoreExt = ["ChainRulesCore"] @@ -893,16 +900,15 @@ version = "0.34.2" DynamicPPLJETExt = ["JET"] DynamicPPLMCMCChainsExt = ["MCMCChains"] DynamicPPLMooncakeExt = ["Mooncake"] - DynamicPPLZygoteRulesExt = ["ZygoteRules"] [deps.DynamicPPL.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b" + KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" - ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444" [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -917,9 +923,9 @@ version = "1.0.4" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "f39747b06eb299ca32c237d8423f092a8391e60f" +git-tree-sha1 = "b83e375689f3c6cf769035b2a3b4332ebc692366" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.28" +version = "0.13.34" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -948,9 +954,9 @@ weakdeps = ["Adapt"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "b81b0143399acd84a2ed2a1fa0b4ab55e25ee625" +git-tree-sha1 = "c29af735ddb2381732cdf5dd72fc32069315619d" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.172+0" +version = "0.0.173+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -966,9 +972,9 @@ version = "0.1.11" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e51db81749b0777b2147fbe7b783ee79045b8e99" +git-tree-sha1 = "d55dffd9ae73ff72f1c0482454dcf2ec6c6c4a63" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.6.4+3" +version = "2.6.5+0" [[deps.ExponentialUtilities]] deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] @@ -985,11 +991,10 @@ git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" -[[deps.Expronicon]] -deps = ["MLStyle", "Pkg", "TOML"] -git-tree-sha1 = "fc3951d4d398b5515f91d7fe5d45fc31dccb3c9b" -uuid = "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636" -version = "0.8.5" +[[deps.ExproniconLite]] +git-tree-sha1 = "c13f0b150373771b0fdc1713c97860f8df12e6c2" +uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" +version = "0.10.14" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -1050,12 +1055,6 @@ git-tree-sha1 = "fd923962364b645f3719855c88f7074413a6ad92" uuid = "442a2c76-b920-505d-bb47-c5924d526838" version = "1.0.2" -[[deps.FastLapackInterface]] -deps = ["LinearAlgebra"] -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" @@ -1079,9 +1078,9 @@ version = "1.1.1" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "2dd20384bf8c6d411b5c7370865b1e9b26cb2ea3" +git-tree-sha1 = "b66970a70db13f45b7e57fbda1736e1cf72174ea" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.6" +version = "1.17.0" weakdeps = ["HTTP"] [deps.FileIO.extensions] @@ -1089,9 +1088,9 @@ weakdeps = ["HTTP"] [[deps.FilePathsBase]] deps = ["Compat", "Dates"] -git-tree-sha1 = "7878ff7172a8e6beedd1dea14bd27c3c6340d361" +git-tree-sha1 = "3bab2c5aa25e7840a4b065805c0cdfc01f3068d2" uuid = "48062228-2e41-5def-b9a4-89aafe57970f" -version = "0.9.22" +version = "0.9.24" weakdeps = ["Mmap", "Test"] [deps.FilePathsBase.extensions] @@ -1116,9 +1115,9 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] -git-tree-sha1 = "84e3a47db33be7248daa6274b287507dd6ff84e8" +git-tree-sha1 = "f089ab1f834470c525562030c8cfde4025d5e915" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.26.2" +version = "2.27.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" @@ -1247,21 +1246,21 @@ version = "0.1.6" [[deps.GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "8e30cd0b1934f03dd925416970061c1014c6686f" +git-tree-sha1 = "199f213e40a7982e9138bc9edc3299419d510390" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "1.1.0" +version = "1.2.0" [[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 = "9bf00ba4c45867c86251a7fd4cb646dcbeb41bf0" +git-tree-sha1 = "0ff136326605f8e06e9bcf085a356ab312eef18a" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.12" +version = "0.73.13" [[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 = "36d5430819123553bf31dfdceb3653ca7d9e62d7" +git-tree-sha1 = "9cb62849057df859575fc1dda1e91b82f8609709" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.12+0" +version = "0.73.13+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -1311,10 +1310,10 @@ version = "0.17.2" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" [[deps.HDF5_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] -git-tree-sha1 = "38c8874692d48d5440d5752d6c74b0c6b0b60739" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] +git-tree-sha1 = "e94f84da9af7ce9c6be049e9067e511e17ff89ec" uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" -version = "1.14.2+1" +version = "1.14.6+0" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] @@ -1328,11 +1327,10 @@ git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" version = "8.5.0+0" -[[deps.HostCPUFeatures]] -deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293" -uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.17" +[[deps.HashArrayMappedTries]] +git-tree-sha1 = "2eaa69a7cab70a52b9687c8bf950a5a93ec895ae" +uuid = "076d061b-32b6-4027-95e0-9a2c6f6d7e74" +version = "0.2.0" [[deps.Hwloc]] deps = ["CEnum", "Hwloc_jll", "Printf"] @@ -1346,15 +1344,15 @@ weakdeps = ["AbstractTrees"] [[deps.Hwloc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "50aedf345a709ab75872f80a2779568dc0bb461b" +git-tree-sha1 = "f93a9ce66cd89c9ba7a4695a47fd93b4c6bc59fa" uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.11.2+3" +version = "2.12.0+0" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "2bd56245074fab4015b9174f24ceba8293209053" +git-tree-sha1 = "68c173f4f449de5b438ee67ed0c9c748dc31a2ec" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.27" +version = "0.3.28" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools"] @@ -1378,9 +1376,9 @@ uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" version = "0.3.1" [[deps.InlineStrings]] -git-tree-sha1 = "45521d31238e87ee9f9732561bfee12d4eebd52d" +git-tree-sha1 = "6a9fde685a7ac1eb3495f8e812c5a7c3711c2d5e" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.4.2" +version = "1.4.3" [deps.InlineStrings.extensions] ArrowTypesExt = "ArrowTypes" @@ -1390,12 +1388,6 @@ version = "1.4.2" ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd" Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -[[deps.InplaceOps]] -deps = ["LinearAlgebra", "Test"] -git-tree-sha1 = "50b41d59e7164ab6fda65e71049fee9d890731ff" -uuid = "505f98c9-085e-5b2c-8e89-488be7bf1f34" -version = "0.3.0" - [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] git-tree-sha1 = "0f14a5456bdc6b9731a5682f439a672750a09e48" @@ -1444,9 +1436,9 @@ uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" version = "1.3.1" [[deps.IrrationalConstants]] -git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" +git-tree-sha1 = "e2222959fbc6c19554dc15174c81bf7bf3aa691c" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.2.2" +version = "0.2.4" [[deps.IterTools]] git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023" @@ -1476,6 +1468,12 @@ git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.4" +[[deps.Jieko]] +deps = ["ExproniconLite"] +git-tree-sha1 = "2f05ed29618da60c06a87e9c033982d4f71d0b6c" +uuid = "ae98c720-c025-4a4a-838c-29b094483192" +version = "0.2.1" + [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "eac1206917768cb54957c65a615460d87b455fc1" @@ -1490,22 +1488,16 @@ 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 = "ed3b5f80be8fc7d1b0185edb862f2273e02cbec2" +git-tree-sha1 = "3ba034493e21efc9ba61268dc0faa0c383bb76a5" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.14.1" +version = "9.14.2" weakdeps = ["FastBroadcast"] -[[deps.KLU]] -deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] -git-tree-sha1 = "07649c499349dad9f08dde4243a4c597064663e9" -uuid = "ef3ab10e-7fda-4108-b977-705223b18434" -version = "0.6.0" - [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] -git-tree-sha1 = "b9a838cd3028785ac23822cded5126b3da394d1a" +git-tree-sha1 = "80d268b2f4e396edc5ea004d1e0f569231c71e9e" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.31" +version = "0.9.34" weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"] [deps.KernelAbstractions.extensions] @@ -1521,15 +1513,15 @@ version = "0.6.9" [[deps.KernelFunctions]] deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Random", "Requires", "SpecialFunctions", "Statistics", "StatsBase", "TensorCore", "Test", "ZygoteRules"] -git-tree-sha1 = "4a38fbd48503f2839b1d6033e0f7ffaec90dda33" +git-tree-sha1 = "0b8ef8b51580b0d87d0b7a5233bb8ea6d948feb4" uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.64" +version = "0.10.65" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "d1c697c53d3041a371c1da21305d0dc9259dbc8a" +git-tree-sha1 = "b29d37ce30fa401a4563b18880ab91f979a29734" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.9" +version = "0.9.10" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1574,9 +1566,9 @@ uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" version = "18.1.7+0" [[deps.LRUCache]] -git-tree-sha1 = "b3cc6698599b10e652832c2f23db3cab99d51b59" +git-tree-sha1 = "5519b95a490ff5fe629c4a7aa3b3dfc9160498b3" uuid = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637" -version = "1.6.1" +version = "1.6.2" weakdeps = ["Serialization"] [deps.LRUCache.extensions] @@ -1601,9 +1593,9 @@ version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" +git-tree-sha1 = "cd714447457c660382fe634710fb56eb255ee42e" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.5" +version = "0.16.6" [deps.Latexify.extensions] DataFramesExt = "DataFrames" @@ -1623,9 +1615,9 @@ version = "0.1.17" [[deps.LazyArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "795ae125c98c58ceb1de562633703e0b120a1b17" +git-tree-sha1 = "866ce84b15e54d758c11946aacd4e5df0e60b7a3" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "2.4.0" +version = "2.6.1" [deps.LazyArrays.extensions] LazyArraysBandedMatricesExt = "BandedMatrices" @@ -1773,10 +1765,10 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" version = "1.11.0" [[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 = "9d5872d134bd33dd3e120767004f760770958863" +deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "c64ec326eeeb20c065afd6aa5add4fad458e460a" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.38.0" +version = "3.7.0" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" @@ -1785,13 +1777,16 @@ version = "2.38.0" LinearSolveCUDSSExt = "CUDSS" LinearSolveEnzymeExt = "EnzymeCore" LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" + LinearSolveFastLapackInterfaceExt = "FastLapackInterface" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" LinearSolveKrylovKitExt = "KrylovKit" LinearSolveMetalExt = "Metal" - LinearSolvePardisoExt = "Pardiso" - LinearSolveRecursiveArrayToolsExt = "RecursiveArrayTools" + LinearSolvePardisoExt = ["Pardiso", "SparseArrays"] + LinearSolveRecursiveFactorizationExt = "RecursiveFactorization" + LinearSolveSparseArraysExt = "SparseArrays" + LinearSolveSparspakExt = ["SparseArrays", "Sparspak"] [deps.LinearSolve.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" @@ -1800,13 +1795,16 @@ version = "2.38.0" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" + FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" - RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" + RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + Sparspak = "e56a9233-b9d6-4f03-8d0f-1825330902ac" [[deps.LogDensityProblems]] deps = ["ArgCheck", "DocStringExtensions", "Random"] @@ -1864,17 +1862,6 @@ git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" 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"] -git-tree-sha1 = "8084c25a250e00ae427a379a5b607e7aed96a2dd" -uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.171" -weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] - - [deps.LoopVectorization.extensions] - ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] - SpecialFunctionsExt = "SpecialFunctions" - [[deps.Lux]] 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" @@ -1990,6 +1977,12 @@ git-tree-sha1 = "5de60bc6cb3899cd318d80d627560fae2e2d99ae" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" version = "2025.0.1+1" +[[deps.MLCore]] +deps = ["DataAPI", "SimpleTraits", "Tables"] +git-tree-sha1 = "73907695f35bc7ffd9f11f6c4f2ee8c1302084be" +uuid = "c2834f40-e789-41da-a90e-33b280584a8c" +version = "1.0.0" + [[deps.MLDataDevices]] deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"] git-tree-sha1 = "85b47bc5a8bf0c886286638585df3bec7c9f8269" @@ -2064,16 +2057,16 @@ uuid = "d8e11817-5142-5d16-987a-aa16d5891078" version = "0.4.17" [[deps.MLUtils]] -deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] -git-tree-sha1 = "7940c0af802586b97009f254aa6065000a16fa1d" +deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "MLCore", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] +git-tree-sha1 = "a772d8d1987433538a5c226f79393324b55f7846" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" -version = "0.4.5" +version = "0.4.8" [[deps.MPICH_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "7715e65c47ba3941c502bffb7f266a41a7f54423" +git-tree-sha1 = "3aa3210044138a1749dbd350a9ba8680869eb503" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.2.3+0" +version = "4.3.0+1" [[deps.MPIPreferences]] deps = ["Libdl", "Preferences"] @@ -2083,9 +2076,9 @@ version = "0.1.11" [[deps.MPItrampoline_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142" +git-tree-sha1 = "ff91ca13c7c472cef700f301c8d752bc2aaff1a8" uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" -version = "5.5.1+2" +version = "5.5.3+0" [[deps.MacroTools]] git-tree-sha1 = "72aebe0b5051e5143a079a4685a46da330a40472" @@ -2190,9 +2183,9 @@ version = "0.8.1" [[deps.Mooncake]] deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DiffTests", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Setfield", "Test"] -git-tree-sha1 = "057bcb5b614aef0452aafca4d444bba7da2f4b3f" +git-tree-sha1 = "68c31b62f4957a76aaf379092d13475a62f7658b" uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" -version = "0.4.78" +version = "0.4.104" [deps.Mooncake.extensions] MooncakeAllocCheckExt = "AllocCheck" @@ -2212,6 +2205,12 @@ version = "0.4.78" SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa" SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" +[[deps.Moshi]] +deps = ["ExproniconLite", "Jieko"] +git-tree-sha1 = "453de0fc2be3d11b9b93ca4d0fddd91196dcf1ed" +uuid = "2e0e35c7-a2e4-4343-998d-7ef72827ed2d" +version = "0.3.5" + [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" version = "2023.12.12" @@ -2228,16 +2227,16 @@ uuid = "6f286f6a-111f-5878-ab1e-185364afe411" version = "0.10.3" [[deps.NLSolversBase]] -deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" +deps = ["ADTypes", "DifferentiationInterface", "Distributed", "FiniteDiff", "ForwardDiff"] +git-tree-sha1 = "1f78293864c5e48ecf97269b0e23d7be28eb1958" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.3" +version = "7.9.0" [[deps.NLopt]] deps = ["CEnum", "NLopt_jll"] -git-tree-sha1 = "dd79cb2a2d779209e42d76795edfde1c778eb5e0" +git-tree-sha1 = "ddb22a00a2dd27c98e0a94879544eb92d192184a" uuid = "76087f3c-5699-56af-9a33-bf431cd00edd" -version = "1.1.2" +version = "1.1.3" [deps.NLopt.extensions] NLoptMathOptInterfaceExt = ["MathOptInterface"] @@ -2247,9 +2246,9 @@ version = "1.1.2" [[deps.NLopt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "dd645a206cc1e8bc4ff0dcfe3da08e39b60dd662" +git-tree-sha1 = "b0154a615d5b2b6cf7a2501123b793577d0b9950" uuid = "079eb43e-fd8e-5478-9966-2cf3e3edb778" -version = "2.9.0+0" +version = "2.10.0+0" [[deps.NLsolve]] deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] @@ -2258,10 +2257,10 @@ uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" version = "4.5.1" [[deps.NNlib]] -deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "bdc9d30f151590aca0af22690f5ab7dc18a551cb" +deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "ScopedValues", "Statistics"] +git-tree-sha1 = "e8d4268b4a438bdad98937e4bca45881363b4767" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.27" +version = "0.9.29" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -2270,6 +2269,7 @@ version = "0.9.27" NNlibEnzymeCoreExt = "EnzymeCore" NNlibFFTWExt = "FFTW" NNlibForwardDiffExt = "ForwardDiff" + NNlibSpecialFunctionsExt = "SpecialFunctions" [deps.NNlib.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" @@ -2277,13 +2277,14 @@ version = "0.9.27" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "fe891aea7ccd23897520db7f16931212454e277e" +git-tree-sha1 = "cc0a5deefdb12ab3a096f00a6d42133af4560d71" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.1.1" +version = "1.1.2" [[deps.NameResolution]] deps = ["PrettyPrint"] @@ -2314,9 +2315,9 @@ version = "1.2.0" [[deps.NonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"] -git-tree-sha1 = "d0caebdb5a31e1a11ca9f7f189cdbf341ac89f0e" +git-tree-sha1 = "eb1007ce104fc6704ac346859bc53976c44edc38" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "4.3.0" +version = "4.5.0" [deps.NonlinearSolve.extensions] NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" @@ -2346,9 +2347,9 @@ version = "4.3.0" [[deps.NonlinearSolveBase]] deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "5bca24ce7b0c034dcbdc6ad6d658b02e0eed566e" +git-tree-sha1 = "8a2437b5ead050301b6a6258f226e5137e511000" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "1.4.0" +version = "1.5.0" weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"] [deps.NonlinearSolveBase.extensions] @@ -2362,15 +2363,15 @@ weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "Linear [[deps.NonlinearSolveFirstOrder]] deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "a1ea35ab0bcc99753e26d574ba1e339f19d100fa" +git-tree-sha1 = "aade7ab02ee4c80ec30dc8a2874fc67155c935f1" uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" -version = "1.2.0" +version = "1.3.0" [[deps.NonlinearSolveQuasiNewton]] deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] -git-tree-sha1 = "8f14b848afcfc0a2941cd3cca1bef04c987465bb" +git-tree-sha1 = "44a132cb32aeafcb35a6238fd91a2f3f8ff5c5b0" uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" -version = "1.1.0" +version = "1.2.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveQuasiNewton.extensions] @@ -2388,9 +2389,9 @@ weakdeps = ["ForwardDiff"] [[deps.ObjectFile]] deps = ["Reexport", "StructIO"] -git-tree-sha1 = "dfcc26739b1ffa3ab51fb16f01ba7eb144f7bc50" +git-tree-sha1 = "09b1fe6ff16e6587fa240c165347474322e77cf1" uuid = "d8793406-e978-5875-9003-1fc021f44a92" -version = "0.4.3" +version = "0.4.4" [[deps.Observables]] git-tree-sha1 = "7438a59546cf62428fc9d1bc94729146d37a7225" @@ -2398,9 +2399,9 @@ uuid = "510215fc-4207-5dde-b226-833fc4488ee2" version = "0.5.5" [[deps.OffsetArrays]] -git-tree-sha1 = "5e1897147d1ff8d98883cda2be2187dcf57d8f0c" +git-tree-sha1 = "a414039192a155fb38c4599a60110f0018c6ec82" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.15.0" +version = "1.16.0" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -2426,13 +2427,13 @@ version = "0.3.27+1" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+2" +version = "0.8.1+4" [[deps.OpenMPI_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"] -git-tree-sha1 = "2dace87e14256edb1dd0724ab7ba831c779b96bd" +git-tree-sha1 = "da913f03f17b449951e0461da960229d4a3d1a8c" uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" -version = "5.0.6+0" +version = "5.0.7+1" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] @@ -2442,9 +2443,9 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" +git-tree-sha1 = "a9697f1d06cc3eb3fb3ad49cc67f2cfabaac31ea" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.15+3" +version = "3.0.16+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -2472,15 +2473,15 @@ version = "0.3.4" [[deps.Optimization]] deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "e246ed7381acdc9d39042ba4c263b19f29232de9" +git-tree-sha1 = "e72af10f1c6ffe2f295455c4c35534d713be62bb" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "4.1.0" +version = "4.1.2" [[deps.OptimizationBase]] deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] -git-tree-sha1 = "9e8569bc1c511c425fdc63f7ee41f2da057f8662" +git-tree-sha1 = "070d2c33da5f0b33d57b61f7f601c4ea6185af15" uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb" -version = "2.4.0" +version = "2.5.0" [deps.OptimizationBase.extensions] OptimizationEnzymeExt = "Enzyme" @@ -2523,33 +2524,33 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.3+0" [[deps.OrderedCollections]] -git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad" +git-tree-sha1 = "cc4054e898b852042d7b503313f7ad03de99c3dd" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.7.0" +version = "1.8.0" [[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 = "36ce9bfc14a4b3dcf1490e80b5f1f4d35bfddf39" +git-tree-sha1 = "798f5e1a1f8b5a1bbba1e6134b77a77ccc509678" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.90.1" +version = "6.92.0" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] -deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "8e3c5978d0531a961f70d2f2730d1d16ed3bbd12" +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] +git-tree-sha1 = "82f78099ecf4e0fa53545811318520d87e7fe0b8" uuid = "89bda076-bce5-4f1c-845f-551c83cdda9a" -version = "1.1.0" +version = "1.2.0" [[deps.OrdinaryDiffEqBDF]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "86ccea2bd0fdfa5570172a9717061f6417e21dea" +git-tree-sha1 = "970ac761ae1c4249fc70d75760c328269a518585" uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" -version = "1.2.0" +version = "1.3.0" [[deps.OrdinaryDiffEqCore]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "6a58da59c5f7640fd09636231bd73dfb4744ce53" +git-tree-sha1 = "f47451c0ca3a2b0f11e966ed7731f2bd17d9b0e3" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.15.1" +version = "1.19.0" weakdeps = ["EnzymeCore"] [deps.OrdinaryDiffEqCore.extensions] @@ -2557,15 +2558,15 @@ weakdeps = ["EnzymeCore"] [[deps.OrdinaryDiffEqDefault]] deps = ["ADTypes", "DiffEqBase", "EnumX", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "PrecompileTools", "Preferences", "Reexport"] -git-tree-sha1 = "2ee6ef0bbed24976e4acfccf609801f8a5bf8223" +git-tree-sha1 = "835c06684b6ff1b8904ceae4d18cc8fe45b9a7cc" uuid = "50262376-6c5a-4cf5-baba-aaf4f84d72d7" -version = "1.2.0" +version = "1.3.0" [[deps.OrdinaryDiffEqDifferentiation]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays"] -git-tree-sha1 = "e4adff09a6d47b74c16e7e08f10fa32000e2e5ed" +git-tree-sha1 = "9a535370247496c1375ba6d08b0493c0d856d25b" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.3.0" +version = "1.4.0" [[deps.OrdinaryDiffEqExplicitRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"] @@ -2575,21 +2576,21 @@ version = "1.1.0" [[deps.OrdinaryDiffEqExponentialRK]] deps = ["ADTypes", "DiffEqBase", "ExponentialUtilities", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqVerner", "RecursiveArrayTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "8659d5fdfe0798bbb5bcd8dc8d08092744b6dfa4" +git-tree-sha1 = "8d2ab84d7fabdfde995e5f567361f238069497f5" uuid = "e0540318-69ee-4070-8777-9e2de6de23de" -version = "1.2.0" +version = "1.4.0" [[deps.OrdinaryDiffEqExtrapolation]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "b8d852b23246b1427178520442e8e7d89aa1c64c" +git-tree-sha1 = "80a636aac325c546b04e3bf20f0c80eaa0173dd4" uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4" -version = "1.3.0" +version = "1.5.0" [[deps.OrdinaryDiffEqFIRK]] -deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastGaussQuadrature", "FastPower", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators"] -git-tree-sha1 = "39a52e278e21018585fc02c04a54f0ab98d03369" +deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastGaussQuadrature", "FastPower", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators"] +git-tree-sha1 = "7dfc32df06db3d9d10128053c0e53deb213fb28d" uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125" -version = "1.6.0" +version = "1.8.0" [[deps.OrdinaryDiffEqFeagin]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2611,9 +2612,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqIMEXMultistep]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Reexport"] -git-tree-sha1 = "b35b6db127ad50bc502f72dbd5a84a1e1d1bbf01" +git-tree-sha1 = "095bab73a3ff185e9ef971fc42ecc93c7824e589" uuid = "9f002381-b378-40b7-97a6-27a27c83f129" -version = "1.2.0" +version = "1.3.0" [[deps.OrdinaryDiffEqLinear]] deps = ["DiffEqBase", "ExponentialUtilities", "LinearAlgebra", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators"] @@ -2629,15 +2630,15 @@ version = "1.2.0" [[deps.OrdinaryDiffEqLowStorageRK]] deps = ["Adapt", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "StaticArrays"] -git-tree-sha1 = "590561f3af623d5485d070b4d7044f8854535f5a" +git-tree-sha1 = "52ec7081e65291fa5c19749312df0818db2fa1bc" uuid = "b0944070-b475-4768-8dec-fb6eb410534d" -version = "1.2.1" +version = "1.3.0" [[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 = "3a3eb0b7ef3f996c468d6f8013eac9525bcfd788" +git-tree-sha1 = "1b89e3e84752a3cbd2c94db565e6ea7acb5279b2" uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8" -version = "1.3.0" +version = "1.5.0" [[deps.OrdinaryDiffEqNordsieck]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2647,9 +2648,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqPDIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "Reexport", "StaticArrays"] -git-tree-sha1 = "70e348c116ce62df4e4b4f90f3c8bb4a8164df31" +git-tree-sha1 = "f74b27b8b811a83d77a9cad6293e793ab0804cdc" uuid = "5dd0a6cf-3d4b-4314-aa06-06d4e299bc89" -version = "1.2.0" +version = "1.3.0" [[deps.OrdinaryDiffEqPRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "Reexport"] @@ -2671,27 +2672,27 @@ 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 = "749518f27e886164ee07e6df49b631beaca8c9ac" +git-tree-sha1 = "a0d1e65771e087a84c398f20ea5f189043869997" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.4.0" +version = "1.7.0" [[deps.OrdinaryDiffEqSDIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] -git-tree-sha1 = "45eed1444fbfa510e1806d4153f83bd862d2d035" +git-tree-sha1 = "b3a7e3a2f355d837c823b435630f035aef446b45" uuid = "2d112036-d095-4a1e-ab9a-08536f3ecdbf" -version = "1.2.0" +version = "1.3.0" [[deps.OrdinaryDiffEqSSPRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "StaticArrays"] -git-tree-sha1 = "7dbe4ac56f930df5e9abd003cedb54e25cbbea86" +git-tree-sha1 = "b97b9691437063ae7d9b1ef130e8b0d81415116f" uuid = "669c94d9-1f4b-4b64-b377-1aa079aa2388" -version = "1.2.0" +version = "1.2.1" [[deps.OrdinaryDiffEqStabilizedIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "StaticArrays"] -git-tree-sha1 = "f2533f086540db6eb3a5eddbecf963cbc4ab6015" +git-tree-sha1 = "111c23b68ad644b47e38242af920d5805c7bedb1" uuid = "e3e12d00-db14-5390-b879-ac3dd2ef6296" -version = "1.2.0" +version = "1.3.0" [[deps.OrdinaryDiffEqStabilizedRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "StaticArrays"] @@ -2701,9 +2702,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqSymplecticRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "4e8b8c8b81df3df17e2eb4603115db3b30a88235" +git-tree-sha1 = "a13d59a2d6cfb6a3332a7782638ca6e1cb6ca688" uuid = "fa646aed-7ef9-47eb-84c4-9443fc8cbfa8" -version = "1.1.0" +version = "1.3.0" [[deps.OrdinaryDiffEqTsit5]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] @@ -2736,9 +2737,9 @@ weakdeps = ["Requires", "TOML"] [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "ed6834e95bd326c52d5675b4181386dfbe885afb" +git-tree-sha1 = "3b31172c032a1def20c98dae3f2cdc9d10e3b561" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.55.5+0" +version = "1.56.1+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -2759,9 +2760,9 @@ version = "1.3.0" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] -git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" +git-tree-sha1 = "db76b1ecd5e9715f3d043cec13b2ec93ce015d53" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.43.4+0" +version = "0.44.2+0" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"] @@ -2786,9 +2787,9 @@ version = "1.4.3" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "dae01f8c2e069a683d3a6e17bbae5070ab94786f" +git-tree-sha1 = "24be21541580495368c35a6ccef1454e7b5015be" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.9" +version = "1.40.11" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -2836,13 +2837,14 @@ version = "0.2.4" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "6c62ce45f268f3f958821a1e5192cf91c75ae89c" +git-tree-sha1 = "8765738bc5a6f1554cb61c5ddfae5bf279e8b110" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.24" -weakdeps = ["ReverseDiff"] +version = "0.4.25" +weakdeps = ["ReverseDiff", "SparseConnectivityTracer"] [deps.PreallocationTools.extensions] PreallocationToolsReverseDiffExt = "ReverseDiff" + PreallocationToolsSparseConnectivityTracerExt = "SparseConnectivityTracer" [[deps.PrecompileTools]] deps = ["Preferences"] @@ -2919,9 +2921,9 @@ version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" +git-tree-sha1 = "9da16da70037ba9d701192e27befedefb91ec284" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.11.1" +version = "2.11.2" weakdeps = ["Enzyme"] [deps.QuadGK.extensions] @@ -2996,9 +2998,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "ea6ad53c168c7c1c2e8f870aefda269692a8a91f" +git-tree-sha1 = "35ac79a85c8086892258581d8b6df9cd8db5c91a" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.28.0" +version = "3.31.1" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -3022,12 +3024,6 @@ version = "3.28.0" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" -[[deps.RecursiveFactorization]] -deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "PrecompileTools", "StrideArraysCore", "TriangularSolve"] -git-tree-sha1 = "6db1a75507051bc18bfa131fbc7c3f169cc4b2f6" -uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.2.23" - [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" @@ -3041,9 +3037,9 @@ version = "1.0.1" [[deps.Requires]] deps = ["UUIDs"] -git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" +git-tree-sha1 = "62389eeff14780bfe55195b7204c0d8738436d64" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.3.0" +version = "1.3.1" [[deps.ResettableStacks]] deps = ["StaticArrays"] @@ -3071,9 +3067,9 @@ version = "0.5.1+0" [[deps.Roots]] deps = ["Accessors", "CommonSolve", "Printf"] -git-tree-sha1 = "f233e0a3de30a6eed170b8e1be0440f732fdf456" +git-tree-sha1 = "442b4353ee8c26756672afb2db81894fc28811f3" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.2.4" +version = "2.2.6" [deps.Roots.extensions] RootsChainRulesCoreExt = "ChainRulesCore" @@ -3104,12 +3100,6 @@ git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" uuid = "94e857df-77ce-4151-89e5-788b33177be4" version = "0.1.0" -[[deps.SLEEFPirates]] -deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "456f610ca2fbd1c14f5fcf31c6bfadc55e7d66e0" -uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.43" - [[deps.SSMProblems]] deps = ["AbstractMCMC"] git-tree-sha1 = "f640e4e8343c9d5f470e2f6ca6ce79f708ab6376" @@ -3117,23 +3107,25 @@ 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"] -git-tree-sha1 = "fcb73c66a5071d4d026aa84f9950a4d1f0dadf33" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "fe9bbf68543d5f72ae2218f3d8c8faeab761dd52" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.72.1" +version = "2.77.2" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" + SciMLBaseMLStyleExt = "MLStyle" SciMLBaseMakieExt = "Makie" SciMLBasePartialFunctionsExt = "PartialFunctions" SciMLBasePyCallExt = "PyCall" SciMLBasePythonCallExt = "PythonCall" SciMLBaseRCallExt = "RCall" - SciMLBaseZygoteExt = "Zygote" + SciMLBaseZygoteExt = ["Zygote", "ChainRulesCore"] [deps.SciMLBase.weakdeps] ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078" Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" @@ -3160,9 +3152,9 @@ weakdeps = ["SparseArrays", "StaticArraysCore"] [[deps.SciMLSensitivity]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "Enzyme", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"] -git-tree-sha1 = "9eff93778a5c61244027bfe9c4f016153bbbf156" +git-tree-sha1 = "40094b8d6afe1bcfee252ce2ab3c4a09d08c60c4" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.72.0" +version = "7.75.0" weakdeps = ["Mooncake"] [deps.SciMLSensitivity.extensions] @@ -3170,15 +3162,21 @@ weakdeps = ["Mooncake"] [[deps.SciMLStructures]] deps = ["ArrayInterface"] -git-tree-sha1 = "0444a37a25fab98adbd90baa806ee492a3af133a" +git-tree-sha1 = "566c4ed301ccb2a44cbd5a27da5f885e0ed1d5df" uuid = "53ae85a6-f571-4167-b2af-e1d143709226" -version = "1.6.1" +version = "1.7.0" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" uuid = "30f210dd-8aff-4c5f-94ba-8e64358c1161" version = "3.0.0" +[[deps.ScopedValues]] +deps = ["HashArrayMappedTries", "Logging"] +git-tree-sha1 = "1147f140b4c8ddab224c94efa9569fc23d63ab44" +uuid = "7e506255-f358-4e82-b7e4-beb19740aa63" +version = "1.3.0" + [[deps.Scratch]] deps = ["Dates"] git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" @@ -3197,9 +3195,9 @@ version = "1.11.0" [[deps.Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] -git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" +git-tree-sha1 = "c5391c6ace3bc430ca630251d02ea9687169ca68" uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" -version = "1.1.1" +version = "1.1.2" [[deps.SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] @@ -3229,9 +3227,9 @@ version = "1.2.0" [[deps.SimpleNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "a3868a6add9f5989d1f4bd21de0333ef89fb9d9f" +git-tree-sha1 = "f42f8b8b728812e485ad099ee5e959d9b49cdb3d" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "2.1.0" +version = "2.2.0" weakdeps = ["ChainRulesCore", "DiffEqBase", "ReverseDiff", "Tracker"] [deps.SimpleNonlinearSolve.extensions] @@ -3268,9 +3266,9 @@ version = "1.11.0" [[deps.SparseConnectivityTracer]] deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "f6d636dcf886cf498b3bc484f48c37741d8aac6e" +git-tree-sha1 = "9603842a7a68464a066b5754e89fc7f810db8ae7" uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" -version = "0.6.10" +version = "0.6.15" [deps.SparseConnectivityTracer.extensions] SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" @@ -3314,20 +3312,14 @@ version = "0.1.2" [[deps.SparseMatrixColorings]] deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "45b5ef11e75839e174d5728fd1e73597e7593634" +git-tree-sha1 = "e0ae9189392572abe85bc9fd4ce35e772b1e1e10" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.4.12" +version = "0.4.14" weakdeps = ["Colors"] [deps.SparseMatrixColorings.extensions] SparseMatrixColoringsColorsExt = "Colors" -[[deps.Sparspak]] -deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] -git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" -uuid = "e56a9233-b9d6-4f03-8d0f-1825330902ac" -version = "0.3.9" - [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] git-tree-sha1 = "64cca0c26b4f31ba18f13f6c12af7c85f478cfde" @@ -3352,9 +3344,9 @@ version = "1.0.2" [[deps.Static]] deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] -git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" +git-tree-sha1 = "f737d444cb0ad07e61b3c1bef8eb91203c321eff" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "1.1.1" +version = "1.2.0" [[deps.StaticArrayInterface]] deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] @@ -3369,9 +3361,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "02c8bd479d26dbeff8a7eb1d77edfc10dacabc01" +git-tree-sha1 = "0feb6b9031bd5c51f9072393eb5ab3efd31bf9e4" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.11" +version = "1.9.13" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -3435,16 +3427,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.7" [[deps.SteadyStateDiffEq]] -deps = ["ConcreteStructs", "DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "Reexport", "SciMLBase"] -git-tree-sha1 = "920acf6ae36c86f23969fea1d317e040dbfccf53" +deps = ["ConcreteStructs", "DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NonlinearSolveBase", "Reexport", "SciMLBase"] +git-tree-sha1 = "66a028f9a2bb44d0f6de0814a2b9840af548143a" uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" -version = "2.4.1" +version = "2.5.0" [[deps.StochasticDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "1f1161aca132f7f776acfb3785abf449aa99a1e9" +git-tree-sha1 = "9c524fdc91dee5fb73795f1ec06cee022bf6e13d" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.73.0" +version = "6.74.1" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] @@ -3472,9 +3464,9 @@ version = "0.3.2" [[deps.StringManipulation]] deps = ["PrecompileTools"] -git-tree-sha1 = "a6b1675a536c5ad1a60e5a5153e1fee12eb146e3" +git-tree-sha1 = "725421ae8e530ec29bcbdddbe91ff8053421d023" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.4.0" +version = "0.4.1" [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] @@ -3509,9 +3501,9 @@ version = "7.7.0+0" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "56661ac133ea6df96fea8d6bb4eb18875b002206" +git-tree-sha1 = "c135b599cec3558be36eaf86ab1ce7e259ef9534" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.26.1" +version = "4.27.0" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] @@ -3521,9 +3513,9 @@ version = "5.2.3+0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "fd2d4f0499f6bb4a0d9f5030f5c7d61eed385e03" +git-tree-sha1 = "d6c04e26aa1c8f7d144e1a8c47f1c73d3013e289" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.37" +version = "0.3.38" [[deps.TOML]] deps = ["Dates"] @@ -3532,9 +3524,9 @@ version = "1.0.3" [[deps.TZJData]] deps = ["Artifacts"] -git-tree-sha1 = "006a327222dda856e2304959e566ff0104ac8594" +git-tree-sha1 = "7def47e953a91cdcebd08fbe76d69d2715499a7d" uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" -version = "1.3.1+2024b" +version = "1.4.0+2025a" [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] @@ -3590,9 +3582,9 @@ version = "0.5.2" [[deps.TimeZones]] deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] -git-tree-sha1 = "fcbcffdc11524d08523e92ae52214b29d90b50bb" +git-tree-sha1 = "2c705e96825b66c4a3f25031a683c06518256dd3" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.20.0" +version = "1.21.3" weakdeps = ["RecipesBase"] [deps.TimeZones.extensions] @@ -3600,9 +3592,15 @@ weakdeps = ["RecipesBase"] [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "d7298ebdfa1654583468a487e8e83fae9d72dac3" +git-tree-sha1 = "f57facfd1be61c42321765d3551b3df50f7e09f6" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.26" +version = "0.5.28" + + [deps.TimerOutputs.extensions] + FlameGraphsExt = "FlameGraphs" + + [deps.TimerOutputs.weakdeps] + FlameGraphs = "08572546-2f56-4bcf-ba4e-bab62c3a3f89" [[deps.Tracker]] deps = ["Adapt", "ChainRulesCore", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -3647,12 +3645,6 @@ git-tree-sha1 = "5b6f1f2ba5e91983eabc47cb362f92d9a96b579f" uuid = "24ddb15e-299a-5cc3-8414-dbddc482d9ca" version = "0.1.16" -[[deps.TriangularSolve]] -deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "be986ad9dac14888ba338c2554dcfec6939e1393" -uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.2.1" - [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] git-tree-sha1 = "ea3e54c2bdde39062abf5a9758a23735558705e1" @@ -3665,10 +3657,10 @@ uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6" 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", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "5218eb833eaaffa0021de7a550564ff6bd53b96c" +deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "f21402d4be463b3f5c4017e11fa00280fefc5c2f" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.36.2" +version = "0.37.0" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] @@ -3676,10 +3668,10 @@ weakdeps = ["DynamicHMC", "Optim"] TuringOptimExt = "Optim" [[deps.TuringBenchmarking]] -deps = ["ADTypes", "AbstractMCMC", "BenchmarkTools", "DynamicPPL", "ForwardDiff", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "PrettyTables", "Requires", "ReverseDiff", "Zygote"] -git-tree-sha1 = "bac1a0af7e13099ff24a7315f1b4728b503abca2" +deps = ["ADTypes", "AbstractMCMC", "BenchmarkTools", "DynamicPPL", "ForwardDiff", "LinearAlgebra", "LogDensityProblems", "PrettyTables", "Requires", "ReverseDiff", "Zygote"] +git-tree-sha1 = "a03f2d71dfc88bf370d67c8ae84dfa109b2702bb" uuid = "0db1332d-5c25-4deb-809f-459bc696f94f" -version = "0.5.8" +version = "0.5.9" [deps.TuringBenchmarking.extensions] TuringBenchmarkingBridgeStanExt = "BridgeStan" @@ -3743,12 +3735,6 @@ git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" version = "0.2.0" -[[deps.VectorizationBase]] -deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" -uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.71" - [[deps.VertexSafeGraphs]] deps = ["Graphs"] git-tree-sha1 = "8351f8d73d7e880bfc042a8b6922684ebeafb35c" @@ -3822,9 +3808,9 @@ version = "1.6.1" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6" +git-tree-sha1 = "b8b243e47228b4a3877f1dd6aee0c5d56db7fcf4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.13.5+0" +version = "2.13.6+1" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] @@ -3989,9 +3975,9 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "622cf78670d067c738667aaa96c553430b65e269" +git-tree-sha1 = "446b23e73536f84e8037f5dce465e92275f6a308" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.7+0" +version = "1.5.7+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"] @@ -4078,9 +4064,9 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7b5bbf1efbafb5eca466700949625e07533aff2" +git-tree-sha1 = "068dfe202b0a05b8332f1e8e6b4080684b9c7700" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.45+1" +version = "1.6.47+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] @@ -4101,9 +4087,9 @@ version = "1.59.0+0" [[deps.oneTBB_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +git-tree-sha1 = "d5a767a3bb77135a99e433afe0eb14cd7f6914c3" uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" -version = "2021.12.0+0" +version = "2022.0.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] diff --git a/Project.toml b/Project.toml index 13df0a8fc..daed8daf6 100644 --- a/Project.toml +++ b/Project.toml @@ -53,4 +53,4 @@ UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] -Turing = "0.36.2" +Turing = "0.37" diff --git a/_quarto.yml b/_quarto.yml index 654f0100a..cf43d47c1 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -32,7 +32,7 @@ website: text: Team right: # Current version - - text: "v0.36" + - text: "v0.37" menu: - text: Changelog href: https://turinglang.org/docs/changelog.html diff --git a/core-functionality/index.qmd b/core-functionality/index.qmd index 69a819d9d..5bd8ec061 100755 --- a/core-functionality/index.qmd +++ b/core-functionality/index.qmd @@ -475,7 +475,10 @@ Example usage: k = length(unique(g)) a ~ filldist(Exponential(), k) # = Product(fill(Exponential(), k)) mu = a[g] - return x .~ Normal.(mu) + for i in eachindex(x) + x[i] ~ Normal(mu[i]) + end + return mu end ``` @@ -491,7 +494,10 @@ Example usage: k = length(unique(g)) a ~ arraydist([Exponential(i) for i in 1:k]) mu = a[g] - return x .~ Normal.(mu) + for i in eachindex(x) + x[i] ~ Normal(mu[i]) + end + return mu end ``` diff --git a/developers/compiler/model-manual/index.qmd b/developers/compiler/model-manual/index.qmd index 24cb77365..cdf3fa829 100755 --- a/developers/compiler/model-manual/index.qmd +++ b/developers/compiler/model-manual/index.qmd @@ -16,7 +16,9 @@ using Turing m ~ Normal(0, sqrt(s²)) # Observe each value of x. - @. x ~ Normal(m, sqrt(s²)) + x .~ Normal(m, sqrt(s²)) + + return nothing end model = gdemo([1.5, 2.0]) @@ -28,6 +30,8 @@ However, models can be constructed by hand without the use of a macro. Taking the `gdemo` model above as an example, the macro-based definition can be implemented also (a bit less generally) with the macro-free version ```{julia} +using DynamicPPL + # Create the model function. function gdemo2(model, varinfo, context, x) # Assume s² has an InverseGamma distribution. @@ -41,9 +45,15 @@ function gdemo2(model, varinfo, context, x) ) # Observe each value of x[i] according to a Normal distribution. - return DynamicPPL.dot_tilde_observe!!( - context, Normal(m, sqrt(s²)), x, Turing.@varname(x), varinfo - ) + for i in eachindex(x) + _retval, varinfo = DynamicPPL.tilde_observe!!( + context, Normal(m, sqrt(s²)), x[i], Turing.@varname(x[i]), varinfo + ) + end + + # The final return statement should comprise both the original return + # value and the updated varinfo. + return nothing, varinfo end gdemo2(x) = Turing.Model(gdemo2, (; x)) diff --git a/tutorials/gaussian-mixture-models/index.qmd b/tutorials/gaussian-mixture-models/index.qmd index a2f1b689d..145d55c62 100755 --- a/tutorials/gaussian-mixture-models/index.qmd +++ b/tutorials/gaussian-mixture-models/index.qmd @@ -167,10 +167,12 @@ One solution here is to enforce an ordering on our $\mu$ vector, requiring $\mu_ `Bijectors.jl` [provides](https://turinglang.org/Bijectors.jl/dev/transforms/#Bijectors.OrderedBijector) an easy transformation (`ordered()`) for this purpose: ```{julia} +using Bijectors: ordered + @model function gaussian_mixture_model_ordered(x) # Draw the parameters for each of the K=2 clusters from a standard normal distribution. K = 2 - μ ~ Bijectors.ordered(MvNormal(Zeros(K), I)) + μ ~ ordered(MvNormal(Zeros(K), I)) # Draw the weights for the K clusters from a Dirichlet distribution with parameters αₖ = 1. w ~ Dirichlet(K, 1.0) # Alternatively, one could use a fixed set of weights. @@ -285,7 +287,7 @@ using LogExpFunctions @model function gmm_marginalized(x) K = 2 D, N = size(x) - μ ~ Bijectors.ordered(MvNormal(Zeros(K), I)) + μ ~ ordered(MvNormal(Zeros(K), I)) w ~ Dirichlet(K, 1.0) dists = [MvNormal(Fill(μₖ, D), I) for μₖ in μ] for i in 1:N @@ -325,7 +327,7 @@ The `logpdf` implementation for a `MixtureModel` distribution is exactly the mar @model function gmm_marginalized(x) K = 2 D, _ = size(x) - μ ~ Bijectors.ordered(MvNormal(Zeros(K), I)) + μ ~ ordered(MvNormal(Zeros(K), I)) w ~ Dirichlet(K, 1.0) x ~ MixtureModel([MvNormal(Fill(μₖ, D), I) for μₖ in μ], w) end @@ -381,7 +383,7 @@ end @model function gmm_recover(x) K = 2 D, N = size(x) - μ ~ Bijectors.ordered(MvNormal(Zeros(K), I)) + μ ~ ordered(MvNormal(Zeros(K), I)) w ~ Dirichlet(K, 1.0) dists = [MvNormal(Fill(μₖ, D), I) for μₖ in μ] x ~ MixtureModel(dists, w) diff --git a/tutorials/hidden-markov-models/index.qmd b/tutorials/hidden-markov-models/index.qmd index dd7d1237b..2e318a8c8 100755 --- a/tutorials/hidden-markov-models/index.qmd +++ b/tutorials/hidden-markov-models/index.qmd @@ -96,7 +96,7 @@ The priors on our transition matrix are noninformative, using `T[i] ~ Dirichlet( N = length(y) # State sequence. - s = tzeros(Int, N) + s = zeros(Int, N) # Emission matrix. m = Vector(undef, K) diff --git a/tutorials/infinite-mixture-models/index.qmd b/tutorials/infinite-mixture-models/index.qmd index 3969ac576..8b14aac49 100755 --- a/tutorials/infinite-mixture-models/index.qmd +++ b/tutorials/infinite-mixture-models/index.qmd @@ -188,10 +188,10 @@ In Turing we can implement an infinite Gaussian mixture model using the Chinese H = Normal(μ0, σ0) # Latent assignment. - z = tzeros(Int, length(x)) + z = zeros(Int, length(x)) # Locations of the infinitely many clusters. - μ = tzeros(Float64, 0) + μ = zeros(Float64, 0) for i in 1:length(x) diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd index ebbe7b467..f25808534 100755 --- a/tutorials/variational-inference/index.qmd +++ b/tutorials/variational-inference/index.qmd @@ -36,6 +36,7 @@ We first import the packages to be used: using Random using Turing using Turing: Variational +using Bijectors: bijector using StatsPlots, Measures Random.seed!(42); diff --git a/usage/probability-interface/index.qmd b/usage/probability-interface/index.qmd index 6d1b8d210..7ec1b0bab 100644 --- a/usage/probability-interface/index.qmd +++ b/usage/probability-interface/index.qmd @@ -18,7 +18,7 @@ Let's use a simple model of normally-distributed data as an example. ```{julia} using Turing -using LinearAlgebra: I +using DynamicPPL using Random @model function gdemo(n) @@ -98,11 +98,9 @@ logjoint(model, sample) ``` For models with many variables `rand(model)` can be prohibitively slow since it returns a `NamedTuple` of samples from the prior distribution of the unconditioned variables. -We recommend working with samples of type `DataStructures.OrderedDict` in this case: +We recommend working with samples of type `DataStructures.OrderedDict` in this case (which Turing re-exports, so can be used directly): ```{julia} -using DataStructures: OrderedDict - Random.seed!(124) sample_dict = rand(OrderedDict, model) ```