diff --git a/Manifest.toml b/Manifest.toml index b74fa1de0..4eb85530f 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -5,9 +5,14 @@ manifest_format = "2.0" project_hash = "24c19d9af05129bd51c95e6af97ff0385a185787" [[deps.ADTypes]] -git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24" +git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.2.7" +version = "1.9.0" +weakdeps = ["ChainRulesCore", "EnzymeCore"] + + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesEnzymeCoreExt = "EnzymeCore" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +33,9 @@ version = "0.5.21" [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] -git-tree-sha1 = "b0489adc45a7c8cf0d8e2ddf764f89c1c3decebd" +git-tree-sha1 = "d4ab12197672f0f4a3afb850d574cfded5fd9070" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "5.2.0" +version = "5.4.0" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "Accessors", "DensityInterface", "Random"] @@ -44,31 +49,35 @@ uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" [[deps.Accessors]] -deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] -git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" +deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] +git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.37" +version = "0.1.38" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" + AccessorsDatesExt = "Dates" AccessorsIntervalSetsExt = "IntervalSets" AccessorsStaticArraysExt = "StaticArrays" AccessorsStructArraysExt = "StructArrays" + AccessorsTestExt = "Test" AccessorsUnitfulExt = "Unitful" [deps.Accessors.weakdeps] AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" Requires = "ae029012-a4dd-5104-9daa-d747884805df" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" +git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.7.2" +version = "4.0.4" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -76,9 +85,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "dfa0e3508fc3df81d28624b328f3b937c1df8bc2" +git-tree-sha1 = "1da0961a400c28d1e5f057e922ff75ec5d6a5747" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.6.1" +version = "0.6.2" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -92,9 +101,9 @@ version = "0.6.1" [[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"] -git-tree-sha1 = "fa4e8d6f9bae913aaa40224cf9407163e693d829" +git-tree-sha1 = "66ac4c7b320d2434f04d48116db02e73e6dabc8b" uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -version = "0.8.2" +version = "0.8.3" weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] [deps.AdvancedMH.extensions] @@ -114,9 +123,9 @@ weakdeps = ["Libtask"] [[deps.AdvancedVI]] deps = ["ADTypes", "Bijectors", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "3e97de1a2ccce08978cd80570d8cbb9ff3f08bd3" +git-tree-sha1 = "187f67ab998f25208651262fee9539d845016b26" uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" -version = "0.2.6" +version = "0.2.5" weakdeps = ["Enzyme", "Flux", "ReverseDiff", "Zygote"] [deps.AdvancedVI.extensions] @@ -159,16 +168,20 @@ uuid = "68821587-b530-5797-8361-c406ea357684" version = "3.5.1+1" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c5aeb516a84459e0318a02507d2261edad97eb75" +deps = ["Adapt", "LinearAlgebra"] +git-tree-sha1 = "3640d077b6dafd64ceb8fd5c1ec76f7ca53bcf76" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.7.1" +version = "7.16.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -176,7 +189,11 @@ version = "7.7.1" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" @@ -213,9 +230,9 @@ version = "0.4.7" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "0b816941273b5b162be122a6c94d706e3b3125ca" +git-tree-sha1 = "a2c85f53ddcb15b4099da59867868bd40f005579" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "0.17.38" +version = "1.7.5" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] @@ -251,36 +268,21 @@ git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" -[[deps.BenchmarkTools]] -deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "f1dff6729bc61f4d49e140da1af55dcd1ac97b2f" -uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.5.0" - [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "6e686c360af8375162531708acb824ae1182b1d5" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "49491db48b1c70eefa5115e626100dbd6c0ff4c0" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.13.16" +version = "0.13.12" +weakdeps = ["DistributionsAD", "ForwardDiff", "LazyArrays", "ReverseDiff", "Tracker", "Zygote"] [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" BijectorsForwardDiffExt = "ForwardDiff" BijectorsLazyArraysExt = "LazyArrays" BijectorsReverseDiffExt = "ReverseDiff" - BijectorsTapirExt = "Tapir" BijectorsTrackerExt = "Tracker" BijectorsZygoteExt = "Zygote" - [deps.Bijectors.weakdeps] - DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c" - ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" - LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" - [[deps.BitFlags]] git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" @@ -293,10 +295,16 @@ uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.6" [[deps.BoundaryValueDiffEq]] -deps = ["ArrayInterface", "BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NonlinearSolve", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "TruncatedStacktraces", "UnPack"] -git-tree-sha1 = "f7392ce20e6dafa8fee406142b1764de7d7cd911" +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "22f36cc7199c3b0f34979c6925cf8ec05281409f" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "4.0.1" +version = "5.10.0" + + [deps.BoundaryValueDiffEq.extensions] + BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" + + [deps.BoundaryValueDiffEq.weakdeps] + ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -323,9 +331,9 @@ version = "0.10.14" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" +git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.0+2" +version = "1.18.2+1" [[deps.Cassette]] git-tree-sha1 = "0970356c3bb9113309c74c27c87083cf9c73880a" @@ -352,15 +360,15 @@ version = "0.10.8" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "227985d885b4dbce5e18a96f9326ea1e836e5a03" +git-tree-sha1 = "be227d253d132a6d57f9ccf5f67c0fb6488afd87" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.69.0" +version = "1.71.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "71acdbf594aab5bbb2cec89b208c41b4c411e49f" +git-tree-sha1 = "3e4b134270b372f2ed4d4d0e936aabaefc1802bc" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.24.0" +version = "1.25.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -389,12 +397,6 @@ git-tree-sha1 = "9ebb045901e9bbf58767a9f34ff89831ed711aae" uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" version = "0.15.7" -[[deps.CodecBzip2]] -deps = ["Bzip2_jll", "TranscodingStreams"] -git-tree-sha1 = "e7c529cc31bb85b97631b922fa2e6baf246f5905" -uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.8.4" - [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" @@ -445,6 +447,11 @@ git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.1" +[[deps.CommonWorldInvalidations]] +git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0" +uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" +version = "1.0.0" + [[deps.Compat]] deps = ["TOML", "UUIDs"] git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" @@ -462,9 +469,9 @@ version = "1.1.1+0" [[deps.ComponentArrays]] deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "Functors", "LinearAlgebra", "PackageExtensionCompat", "StaticArrayInterface", "StaticArraysCore"] -git-tree-sha1 = "cf30651e65a87b20b12601b91169a18838eab2df" +git-tree-sha1 = "bc391f0c19fa242fb6f71794b949e256cfa3772c" uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -version = "0.15.16" +version = "0.15.17" weakdeps = ["Adapt", "ConstructionBase", "GPUArrays", "Optimisers", "RecursiveArrayTools", "ReverseDiff", "SciMLBase", "Tracker", "TruncatedStacktraces", "Zygote"] [deps.ComponentArrays.extensions] @@ -506,14 +513,14 @@ uuid = "88cd18e8-d9cc-4ea6-8889-5259c0d15c8b" version = "0.1.2" [[deps.ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "a33b7ced222c6165f624a3f2b55945fac5a598d9" +git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.7" -weakdeps = ["IntervalSets", "StaticArrays"] +version = "1.5.8" +weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"] [deps.ConstructionBase.extensions] ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseLinearAlgebraExt = "LinearAlgebra" ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.ContextVariablesX]] @@ -550,10 +557,10 @@ uuid = "124859b0-ceae-595e-8997-d05f6a7a8dfe" version = "0.7.13" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "04c738083f29f86e62c8afc341f0967d8717bdb8" +deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.6.1" +version = "1.7.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -583,9 +590,9 @@ version = "0.1.2" [[deps.DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack"] -git-tree-sha1 = "e40378efd2af7658d0a0579aa9e15b17137368f4" +git-tree-sha1 = "066f60231c1b0ae2905ffd2651e207accd91f627" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.44.0" +version = "5.48.1" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -600,39 +607,45 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "0d9982e8dee851d519145857e79a17ee33ede154" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] +git-tree-sha1 = "fa7d580038451a8df4434ef5b079ac9b2d486194" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.130.0" +version = "6.155.1" [deps.DiffEqBase.extensions] + DiffEqBaseCUDAExt = "CUDA" + DiffEqBaseChainRulesCoreExt = "ChainRulesCore" DiffEqBaseDistributionsExt = "Distributions" + DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" DiffEqBaseMPIExt = "MPI" DiffEqBaseMeasurementsExt = "Measurements" DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" DiffEqBaseReverseDiffExt = "ReverseDiff" + DiffEqBaseSparseArraysExt = "SparseArrays" DiffEqBaseTrackerExt = "Tracker" DiffEqBaseUnitfulExt = "Unitful" - DiffEqBaseZygoteExt = "Zygote" [deps.DiffEqBase.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "d0b94b3694d55e7eedeee918e7daee9e3b873399" +deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NonlinearSolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "19dbd44d18bbfdfcf5e56c99cea9b0ed23df350a" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.35.0" -weakdeps = ["OrdinaryDiffEq", "Sundials"] +version = "3.9.1" +weakdeps = ["OrdinaryDiffEq", "OrdinaryDiffEqCore", "Sundials"] [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] @@ -658,15 +671,51 @@ version = "1.15.1" [[deps.DifferentialEquations]] deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] -git-tree-sha1 = "96a19f498504e4a3b39524196b73eb60ccef30e9" +git-tree-sha1 = "d851f2ca05f3cec9988f081b047a778a58b48aaf" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.10.0" +version = "7.14.0" + +[[deps.DifferentiationInterface]] +deps = ["ADTypes", "Compat", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PackageExtensionCompat", "SparseArrays", "SparseMatrixColorings"] +git-tree-sha1 = "9b23f9a816790b8ab9914c3c86321a546e92cbe7" +uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" +version = "0.5.17" + + [deps.DifferentiationInterface.extensions] + DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" + DifferentiationInterfaceDiffractorExt = "Diffractor" + DifferentiationInterfaceEnzymeExt = "Enzyme" + DifferentiationInterfaceFastDifferentiationExt = "FastDifferentiation" + DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" + DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" + DifferentiationInterfaceForwardDiffExt = "ForwardDiff" + DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" + DifferentiationInterfaceReverseDiffExt = "ReverseDiff" + DifferentiationInterfaceSymbolicsExt = "Symbolics" + DifferentiationInterfaceTapirExt = "Tapir" + DifferentiationInterfaceTrackerExt = "Tracker" + DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] + + [deps.DifferentiationInterface.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Diffractor = "9f5e2b26-1114-432f-b630-d3fe2085c51c" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + FastDifferentiation = "eb9bf01b-bf85-4b60-bf87-ee5de06c00be" + FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" + FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.DispatchDoctor]] deps = ["MacroTools", "Preferences"] -git-tree-sha1 = "c2acd1de2c4c357928f9fb6b60b402d914621378" +git-tree-sha1 = "19eec8ee5cde1c10aa5e5e0f25d10a3b4c8f8f12" uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" -version = "0.4.14" +version = "0.4.15" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.DispatchDoctor.extensions] @@ -690,9 +739,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "e6c693a0e4394f8fda0e51a5bdf5aef26f8235e9" +git-tree-sha1 = "d7477ecdafb813ddee2ae727afa94e9dcb5f3fb0" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.111" +version = "0.25.112" weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [deps.Distributions.extensions] @@ -702,9 +751,10 @@ weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [[deps.DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "Distributions", "FillArrays", "LinearAlgebra", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsFuns", "ZygoteRules"] -git-tree-sha1 = "f4dd7727b07b4b7fff5ff4149118ee06e83dfab7" +git-tree-sha1 = "02c2e6e6a137069227439fe884d729cca5b70e56" uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c" -version = "0.6.55" +version = "0.6.57" +weakdeps = ["ForwardDiff", "LazyArrays", "ReverseDiff", "Tracker"] [deps.DistributionsAD.extensions] DistributionsADForwardDiffExt = "ForwardDiff" @@ -712,12 +762,6 @@ version = "0.6.55" DistributionsADReverseDiffExt = "ReverseDiff" DistributionsADTrackerExt = "Tracker" - [deps.DistributionsAD.weakdeps] - ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" - LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - [[deps.DocStringExtensions]] deps = ["LibGit2"] git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" @@ -737,9 +781,9 @@ version = "3.4.7" [[deps.DynamicPPL]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] -git-tree-sha1 = "79ff677df43bbad59ee704819ec6ede5a9c71b29" +git-tree-sha1 = "a155a80a54e37e6e1f14022ac815ef000aedeed5" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.28.3" +version = "0.28.4" weakdeps = ["ChainRulesCore", "EnzymeCore", "ForwardDiff", "MCMCChains", "ReverseDiff", "ZygoteRules"] [deps.DynamicPPL.extensions] @@ -769,18 +813,28 @@ version = "1.0.4" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Preferences", "Printf", "Random"] -git-tree-sha1 = "3fb48f9c18de1993c477457265b85130756746ae" +git-tree-sha1 = "b63695bc543a45cab4f30e039c26ca3bcc6780a1" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.11.20" -weakdeps = ["SpecialFunctions"] +version = "0.12.36" [deps.Enzyme.extensions] + EnzymeBFloat16sExt = "BFloat16s" + EnzymeChainRulesCoreExt = "ChainRulesCore" + EnzymeLogExpFunctionsExt = "LogExpFunctions" EnzymeSpecialFunctionsExt = "SpecialFunctions" + EnzymeStaticArraysExt = "StaticArrays" + + [deps.Enzyme.weakdeps] + BFloat16s = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.EnzymeCore]] -git-tree-sha1 = "1bc328eec34ffd80357f84a84bb30e4374e9bd60" +git-tree-sha1 = "8f205a601760f4798a10f138c3940f0451d95188" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.6.6" +version = "0.7.8" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -788,9 +842,9 @@ weakdeps = ["Adapt"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "32d418c804279c60dd38ac7868126696f3205a4f" +git-tree-sha1 = "7fb808ef6421ea58c607657eea17caa9f03c08d0" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.102+0" +version = "0.0.148+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -821,6 +875,12 @@ 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.ExternalDocstrings]] git-tree-sha1 = "1224740fc4d07c989949e1c1b508ebd49a65a5f6" uuid = "e189563c-0753-4f5e-ad5c-be4293c83fb4" @@ -828,9 +888,9 @@ version = "0.1.1" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] -git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" +git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.1" +version = "0.4.2" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] @@ -846,9 +906,9 @@ version = "1.8.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" +git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.10+0" +version = "3.3.10+1" [[deps.FLoops]] deps = ["BangBang", "Compat", "FLoopsBase", "InitialValues", "JuliaVariables", "MLStyle", "Serialization", "Setfield", "Transducers"] @@ -862,11 +922,17 @@ git-tree-sha1 = "656f7a6859be8673bf1f35da5670246b923964f7" uuid = "b9860ae5-e623-471e-878b-f6a53c775ea6" version = "0.1.1" +[[deps.FastAlmostBandedMatrices]] +deps = ["ArrayInterface", "ArrayLayouts", "BandedMatrices", "ConcreteStructs", "LazyArrays", "LinearAlgebra", "MatrixFactorizations", "PrecompileTools", "Reexport"] +git-tree-sha1 = "3f03d94c71126b6cfe20d3cbcc41c5cd27e1c419" +uuid = "9d29842c-ecb8-4973-b1e9-a27b1157504e" +version = "0.1.4" + [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "a6e756a880fc419c8b41592010aebe6a5ce09136" +git-tree-sha1 = "ab1b34570bcdf272899062e1a56285a53ecaae08" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.2.8" +version = "0.3.5" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -912,19 +978,21 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] -git-tree-sha1 = "2de436b72c3422940cbe1367611d137008af7ec3" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] +git-tree-sha1 = "b10bdafd1647f57ace3885143936749d61638c3b" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.23.1" +version = "2.26.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffSparseArraysExt = "SparseArrays" FiniteDiffStaticArraysExt = "StaticArrays" [deps.FiniteDiff.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] @@ -934,21 +1002,27 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.5" [[deps.Flux]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] -git-tree-sha1 = "edacf029ed6276301e455e34d7ceeba8cc34078a" +deps = ["Adapt", "ChainRulesCore", "Compat", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] +git-tree-sha1 = "f3b4e96288e8bee94cd1e230c1a9387d3e03f788" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.14.16" +version = "0.14.21" [deps.Flux.extensions] FluxAMDGPUExt = "AMDGPU" FluxCUDAExt = "CUDA" FluxCUDAcuDNNExt = ["CUDA", "cuDNN"] + FluxEnzymeExt = "Enzyme" + FluxMPIExt = "MPI" + FluxMPINCCLExt = ["CUDA", "MPI", "NCCL"] FluxMetalExt = "Metal" [deps.Flux.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + NCCL = "3fe64909-d7a1-4096-9b7d-7a0f12cf0f6b" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.Folds]] @@ -1037,21 +1111,21 @@ version = "1.9.0" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "85d7fb51afb3def5dcb85ad31c3707795c8bccc1" +git-tree-sha1 = "62ee71528cca49be797076a76bdc654a170a523e" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "9.1.0" +version = "10.3.1" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" +git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.5" +version = "0.1.6" [[deps.GPUCompiler]] -deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "a846f297ce9d09ccba02ead0cae70690e072a119" +deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "TimerOutputs", "UUIDs"] +git-tree-sha1 = "b8c120986fce117469760119f44592ff148da93e" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.25.0" +version = "0.27.5" [[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"] @@ -1079,9 +1153,9 @@ version = "0.21.0+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" +git-tree-sha1 = "674ff0db93fffcd11a3573986e550d66cd4fd71f" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.2+0" +version = "2.80.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1091,9 +1165,9 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9" +git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.11.2" +version = "1.12.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -1136,11 +1210,21 @@ git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" version = "0.1.17" +[[deps.Hwloc]] +deps = ["CEnum", "Hwloc_jll", "Printf"] +git-tree-sha1 = "6a3d80f31ff87bc94ab22a7b8ec2f263f9a6a583" +uuid = "0e44f5e4-bd66-52a0-8798-143a42290a1d" +version = "3.3.0" +weakdeps = ["AbstractTrees"] + + [deps.Hwloc.extensions] + HwlocTrees = "AbstractTrees" + [[deps.Hwloc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "5e19e1e4fa3e71b774ce746274364aef0234634e" +git-tree-sha1 = "dd3b49277ec2bb2c6b94eb1604d4d0616016f7a6" uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.11.1+0" +version = "2.11.2+0" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] @@ -1220,9 +1304,9 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsStatisticsExt = "Statistics" [[deps.InverseFunctions]] -git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1" +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.16" +version = "0.1.17" weakdeps = ["Dates", "Test"] [deps.InverseFunctions.extensions] @@ -1235,9 +1319,9 @@ uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" version = "1.3.0" [[deps.IrrationalConstants]] -git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.1" +version = "0.2.2" [[deps.IterTools]] git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023" @@ -1269,9 +1353,9 @@ version = "0.21.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" +git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.3+0" +version = "3.0.4+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1280,30 +1364,29 @@ uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" [[deps.JumpProcesses]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "UnPack"] -git-tree-sha1 = "c451feb97251965a9fe40bacd62551a72cc5902c" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] +git-tree-sha1 = "6e0fb267f2c869df59b6bf9f8cb0f2794f2d85e9" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.10.1" +version = "9.13.7" weakdeps = ["FastBroadcast"] - [deps.JumpProcesses.extensions] - JumpProcessFastBroadcastExt = "FastBroadcast" - [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] -git-tree-sha1 = "884c2968c2e8e7e6bf5956af88cb46aa745c854b" +git-tree-sha1 = "07649c499349dad9f08dde4243a4c597064663e9" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" -version = "0.4.1" +version = "0.6.0" [[deps.KernelAbstractions]] -deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "ed7167240f40e62d97c1f5f7735dea6de3cc5c49" +deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "04e52f596d0871fa3890170fa79cb15e481e4cd8" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.18" -weakdeps = ["EnzymeCore"] +version = "0.9.28" +weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"] [deps.KernelAbstractions.extensions] EnzymeExt = "EnzymeCore" + LinearAlgebraExt = "LinearAlgebra" + SparseArraysExt = "SparseArrays" [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] @@ -1329,6 +1412,12 @@ git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" version = "3.100.2+0" +[[deps.LBFGSB]] +deps = ["L_BFGS_B_jll"] +git-tree-sha1 = "e2e6f53ee20605d0ea2be473480b7480bd5091b5" +uuid = "5be7bae1-8223-5378-bac3-9e7378a2f6e6" +version = "0.4.1" + [[deps.LERC_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" @@ -1337,9 +1426,9 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] -git-tree-sha1 = "839c82932db86740ae729779e610f07a1640be9a" +git-tree-sha1 = "b351d72436ddecd27381a07c242ba27282a6c8a7" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.6.3" +version = "9.0.0" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1349,15 +1438,15 @@ version = "6.6.3" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "88b916503aac4fb7f701bb625cd84ca5dd1677bc" +git-tree-sha1 = "f42bec1e12f42ec251541f6d0482d520a4638b17" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.29+0" +version = "0.0.33+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e16271d212accd09d52ee0ae98956b8a05c4b626" +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "17.0.6+0" +version = "18.1.7+0" [[deps.LRUCache]] git-tree-sha1 = "b3cc6698599b10e652832c2f23db3cab99d51b59" @@ -1370,9 +1459,15 @@ weakdeps = ["Serialization"] [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" +git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.2+0" +version = "2.10.2+1" + +[[deps.L_BFGS_B_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "77feda930ed3f04b2b0fbb5bea89e69d3677c6b0" +uuid = "81d17ec3-03a1-5e46-b53e-bddc35a13473" +version = "3.0.1+0" [[deps.LaTeXStrings]] git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" @@ -1401,6 +1496,16 @@ git-tree-sha1 = "a9eaadb366f5493a5654e843864c13d8b107548c" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" version = "0.1.17" +[[deps.LazyArrays]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays"] +git-tree-sha1 = "35079a6a869eecace778bcda8641f9a54ca3a828" +uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" +version = "1.10.0" +weakdeps = ["StaticArrays"] + + [deps.LazyArrays.extensions] + LazyArraysStaticArraysExt = "StaticArrays" + [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" @@ -1521,44 +1626,53 @@ deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] -deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "EnzymeCore", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] -git-tree-sha1 = "9f27ba34f5821a0495efb09ea3a465c31326495a" +deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "6c5e4555ac2bc449a28604e184f759d18fc08420" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.10.0" +version = "2.34.0" [deps.LinearSolve.extensions] + LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" - LinearSolveEnzymeExt = "Enzyme" + LinearSolveCUDSSExt = "CUDSS" + LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] + LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" LinearSolveKrylovKitExt = "KrylovKit" LinearSolveMetalExt = "Metal" LinearSolvePardisoExt = "Pardiso" + LinearSolveRecursiveArrayToolsExt = "RecursiveArrayTools" [deps.LinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" + RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" [[deps.LogDensityProblems]] deps = ["ArgCheck", "DocStringExtensions", "Random"] -git-tree-sha1 = "f9a11237204bc137617194d79d813069838fcf61" +git-tree-sha1 = "4e0128c1590d23a50dcdb106c7e2dbca99df85c0" uuid = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" -version = "2.1.1" +version = "2.1.2" [[deps.LogDensityProblemsAD]] -deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "98cad2db1c46f2fff70a5e305fb42c97a251422a" +deps = ["DocStringExtensions", "LogDensityProblems"] +git-tree-sha1 = "457e6b347a87bfcd25a9eaf44a7bd5415559582f" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.9.0" +version = "1.10.1" [deps.LogDensityProblemsAD.extensions] LogDensityProblemsADADTypesExt = "ADTypes" @@ -1612,76 +1726,86 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] SpecialFunctionsExt = "SpecialFunctions" +[[deps.LossFunctions]] +deps = ["Markdown", "Requires", "Statistics"] +git-tree-sha1 = "8073538845227d3acf8a0c149bf0e150e60d0ced" +uuid = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7" +version = "0.11.2" +weakdeps = ["CategoricalArrays"] + + [deps.LossFunctions.extensions] + LossFunctionsCategoricalArraysExt = "CategoricalArrays" + [[deps.Lux]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "ChainRulesCore", "ConcreteStructs", "ConstructionBase", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxDeviceUtils", "LuxLib", "MacroTools", "Markdown", "Optimisers", "PrecompileTools", "Random", "Reexport", "Setfield", "SparseArrays", "Statistics", "TruncatedStacktraces", "WeightInitializers"] -git-tree-sha1 = "979b0437f42453b65175c6390314b2fd76eefbd4" +deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LossFunctions", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "VectorizationBase", "WeightInitializers"] +git-tree-sha1 = "8001e387f5d07fef98160d62fc89aafacbc3266f" uuid = "b2108857-7c20-44ae-9111-449ecde12c47" -version = "0.5.16" +version = "1.0.5" [deps.Lux.extensions] - LuxChainRulesExt = "ChainRules" LuxComponentArraysExt = "ComponentArrays" - LuxComponentArraysReverseDiffExt = ["ComponentArrays", "ReverseDiff"] - LuxFluxTransformExt = "Flux" - LuxLuxAMDGPUExt = "LuxAMDGPU" - LuxReverseDiffExt = "ReverseDiff" + LuxEnzymeExt = "Enzyme" + LuxFluxExt = "Flux" + LuxMLUtilsExt = "MLUtils" + LuxMPIExt = "MPI" + LuxMPINCCLExt = ["CUDA", "MPI", "NCCL"] + LuxReverseDiffExt = ["FunctionWrappers", "ReverseDiff"] + LuxSimpleChainsExt = "SimpleChains" LuxTrackerExt = "Tracker" LuxZygoteExt = "Zygote" [deps.Lux.weakdeps] - ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" - FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" - LuxAMDGPU = "83120cb1-ca15-4f04-bf3b-6967d2e6b60b" + FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" + MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54" + MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" + NCCL = "3fe64909-d7a1-4096-9b7d-7a0f12cf0f6b" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SimpleChains = "de6bee2f-e2f4-4ec7-b6ed-219cc6f6e9e5" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.LuxCore]] -deps = ["Compat", "DispatchDoctor", "Functors", "Random", "Setfield"] -git-tree-sha1 = "c3aeb50a8b894f9975e6b89c0ee67ccc6f256bb3" +deps = ["Compat", "DispatchDoctor", "Random"] +git-tree-sha1 = "1c1e81a6d0613d13ea9f7dff7291ea407624d74a" uuid = "bb33d45b-7691-41d6-9220-0943567d0623" -version = "0.1.19" - -[[deps.LuxDeviceUtils]] -deps = ["Adapt", "ChainRulesCore", "Functors", "LuxCore", "Preferences", "Random", "SparseArrays"] -git-tree-sha1 = "cffc2222bf9dc01730f6fc904266f8056abb8e83" -uuid = "34f89e08-e1d5-43b4-8944-0b49ac560553" -version = "0.1.11" +version = "1.0.1" +weakdeps = ["ArrayInterface", "ChainRulesCore", "EnzymeCore", "Functors", "MLDataDevices", "ReverseDiff", "Setfield", "Tracker"] - [deps.LuxDeviceUtils.extensions] - LuxDeviceUtilsFillArraysExt = "FillArrays" - LuxDeviceUtilsLuxAMDGPUExt = "LuxAMDGPU" - LuxDeviceUtilsLuxCUDAExt = "LuxCUDA" - LuxDeviceUtilsMetalExt = "Metal" - LuxDeviceUtilsZygoteExt = "Zygote" - - [deps.LuxDeviceUtils.weakdeps] - FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" - LuxAMDGPU = "83120cb1-ca15-4f04-bf3b-6967d2e6b60b" - LuxCUDA = "d0bbae9a-e099-4d5b-a835-1c6931763bda" - Metal = "dde4c033-4e86-420c-a63e-0dd931031962" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + [deps.LuxCore.extensions] + LuxCoreArrayInterfaceReverseDiffExt = ["ArrayInterface", "ReverseDiff"] + LuxCoreArrayInterfaceTrackerExt = ["ArrayInterface", "Tracker"] + LuxCoreChainRulesCoreExt = "ChainRulesCore" + LuxCoreEnzymeCoreExt = "EnzymeCore" + LuxCoreFunctorsExt = "Functors" + LuxCoreMLDataDevicesExt = "MLDataDevices" + LuxCoreSetfieldExt = "Setfield" [[deps.LuxLib]] -deps = ["ChainRulesCore", "FastClosures", "KernelAbstractions", "LuxCore", "Markdown", "NNlib", "PrecompileTools", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "b1f81a8aa8313c1f1b4cbfb18733db17c023427e" +deps = ["ArrayInterface", "ChainRulesCore", "Compat", "CpuId", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Hwloc", "KernelAbstractions", "LinearAlgebra", "LoopVectorization", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Octavian", "Polyester", "Random", "Reexport", "SLEEFPirates", "Static", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "d9a3531a7772c09a763cc4da2d9d0394d3417cdc" uuid = "82251201-b29d-42c6-8e01-566dec8acb11" -version = "0.3.14" +version = "1.2.4" [deps.LuxLib.extensions] - LuxLibForwardDiffExt = "ForwardDiff" + LuxLibAppleAccelerateExt = "AppleAccelerate" + LuxLibBLISBLASExt = "BLISBLAS" + LuxLibCUDAExt = "CUDA" + LuxLibMKLExt = "MKL" LuxLibReverseDiffExt = "ReverseDiff" LuxLibTrackerAMDGPUExt = ["AMDGPU", "Tracker"] LuxLibTrackerExt = "Tracker" - LuxLibTrackercuDNNExt = ["CUDA", "Tracker", "cuDNN"] LuxLibcuDNNExt = ["CUDA", "cuDNN"] [deps.LuxLib.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" + AppleAccelerate = "13e28ba4-7ad8-5781-acae-3021b1ed3924" + BLISBLAS = "6f275bd8-fec0-4d39-945b-7e95a765fa1e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" @@ -1704,6 +1828,46 @@ git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" version = "2024.2.0+0" +[[deps.MLDataDevices]] +deps = ["Adapt", "Functors", "Preferences", "Random"] +git-tree-sha1 = "e16288e37e76d68c3f1c418e0a2bec88d98d55fc" +uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" +version = "1.2.0" + + [deps.MLDataDevices.extensions] + MLDataDevicesAMDGPUExt = "AMDGPU" + MLDataDevicesCUDAExt = "CUDA" + MLDataDevicesChainRulesCoreExt = "ChainRulesCore" + MLDataDevicesFillArraysExt = "FillArrays" + MLDataDevicesGPUArraysExt = "GPUArrays" + MLDataDevicesMLUtilsExt = "MLUtils" + MLDataDevicesMetalExt = ["GPUArrays", "Metal"] + MLDataDevicesReactantExt = "Reactant" + MLDataDevicesRecursiveArrayToolsExt = "RecursiveArrayTools" + MLDataDevicesReverseDiffExt = "ReverseDiff" + MLDataDevicesSparseArraysExt = "SparseArrays" + MLDataDevicesTrackerExt = "Tracker" + MLDataDevicesZygoteExt = "Zygote" + MLDataDevicescuDNNExt = ["CUDA", "cuDNN"] + MLDataDevicesoneAPIExt = ["GPUArrays", "oneAPI"] + + [deps.MLDataDevices.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" + GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" + MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" + RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" + oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" + [[deps.MLDataPattern]] deps = ["LearnBase", "MLLabelUtils", "Random", "SparseArrays", "StatsBase"] git-tree-sha1 = "e99514e96e8b8129bb333c69e063a56ab6402b5b" @@ -1741,9 +1905,9 @@ version = "0.4.4" [[deps.MPICH_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "19d4bd098928a3263693991500d05d74dbdc2004" +git-tree-sha1 = "7715e65c47ba3941c502bffb7f266a41a7f54423" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.2.2+0" +version = "4.2.3+0" [[deps.MPIPreferences]] deps = ["Libdl", "Preferences"] @@ -1753,9 +1917,9 @@ version = "0.1.11" [[deps.MPItrampoline_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "8c35d5420193841b2f367e658540e8d9e0601ed0" +git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142" uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" -version = "5.4.0+0" +version = "5.5.1+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1777,17 +1941,21 @@ version = "0.4.2" deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -[[deps.MathOptInterface]] -deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] -git-tree-sha1 = "5b246fca5420ae176d65ed43a2d0ee5897775216" -uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "1.31.2" +[[deps.MatrixFactorizations]] +deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] +git-tree-sha1 = "6731e0574fa5ee21c02733e397beb133df90de35" +uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" +version = "2.2.0" -[[deps.MathProgBase]] -deps = ["LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "9abbe463a1e9fc507f12a69e7f29346c2cdc472c" -uuid = "fdba3010-5040-5b88-9595-932c9decdf73" -version = "0.7.8" +[[deps.MaybeInplace]] +deps = ["ArrayInterface", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "54e2fdc38130c05b42be423e90da3bade29b74bd" +uuid = "bb5d69b7-63fc-4a16-80bd-7e42200c7bdb" +version = "0.1.4" +weakdeps = ["SparseArrays"] + + [deps.MaybeInplace.extensions] + MaybeInplaceSparseArraysExt = "SparseArrays" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -1812,10 +1980,10 @@ uuid = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" version = "0.2.1" [[deps.MicroCanonicalHMC]] -deps = ["AbstractMCMC", "Adapt", "Distributions", "ForwardDiff", "HDF5", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "MCMCDiagnosticTools", "Markdown", "ProgressMeter", "Random", "Statistics"] -git-tree-sha1 = "99fd367f8b8fc9d479420d33e8f16f3dab3162f4" +deps = ["AbstractMCMC", "Adapt", "Distributions", "DynamicPPL", "ForwardDiff", "HDF5", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "MCMCDiagnosticTools", "Markdown", "ProgressMeter", "Random", "Statistics", "Turing"] +git-tree-sha1 = "7f509e51bb8c63128c84119718d92e85ddb2f0c9" uuid = "234d2aa0-2291-45f7-9047-6fa6f316b0a8" -version = "0.1.6" +version = "0.1.7" [[deps.MicroCollections]] deps = ["Accessors", "BangBang", "InitialValues"] @@ -1859,12 +2027,6 @@ git-tree-sha1 = "816620e3aac93e5b5359e4fdaf23ca4525b00ddf" uuid = "6f286f6a-111f-5878-ab1e-185364afe411" version = "0.10.3" -[[deps.MutableArithmetics]] -deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "d0a6b1096b584a2b88efb70a92f8cb8c881eb38a" -uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.6" - [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" @@ -1872,10 +2034,16 @@ uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" version = "7.8.3" [[deps.NLopt]] -deps = ["MathOptInterface", "MathProgBase", "NLopt_jll"] -git-tree-sha1 = "5a7e32c569200a8a03c3d55d286254b0321cd262" +deps = ["CEnum", "NLopt_jll"] +git-tree-sha1 = "81a321298aed95631447a1f3afc2ea83682d44a4" uuid = "76087f3c-5699-56af-9a33-bf431cd00edd" -version = "0.6.5" +version = "1.1.1" + + [deps.NLopt.extensions] + NLoptMathOptInterfaceExt = ["MathOptInterface"] + + [deps.NLopt.weakdeps] + MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" [[deps.NLopt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1890,10 +2058,10 @@ uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" version = "4.5.1" [[deps.NNlib]] -deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "ae52c156a63bb647f80c26319b104e99e5977e51" +deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "Statistics"] +git-tree-sha1 = "da09a1e112fd75f9af2a5229323f01b56ec96a4c" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.22" +version = "0.9.24" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1901,12 +2069,14 @@ version = "0.9.22" NNlibCUDAExt = "CUDA" NNlibEnzymeCoreExt = "EnzymeCore" NNlibFFTWExt = "FFTW" + NNlibForwardDiffExt = "ForwardDiff" [deps.NNlib.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.NaNMath]] @@ -1934,19 +2104,45 @@ version = "1.0.0" [[deps.NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "91a67b4d73842da90b526011fa85c5c4c9343fe0" +git-tree-sha1 = "3cebfc94a0754cc329ebc3bab1e6c89621e791ad" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.18" +version = "0.4.20" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "e10debcea868cd6e51249e8eeaf191c25f68a640" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "bcd8812e751326ff1d4b2dd50764b93df51f143b" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "1.10.1" +version = "3.14.0" + + [deps.NonlinearSolve.extensions] + NonlinearSolveBandedMatricesExt = "BandedMatrices" + NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" + NonlinearSolveFixedPointAccelerationExt = "FixedPointAcceleration" + NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" + NonlinearSolveMINPACKExt = "MINPACK" + NonlinearSolveNLSolversExt = "NLSolvers" + NonlinearSolveNLsolveExt = "NLsolve" + NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" + NonlinearSolveSpeedMappingExt = "SpeedMapping" + NonlinearSolveSymbolicsExt = "Symbolics" + NonlinearSolveZygoteExt = "Zygote" + + [deps.NonlinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce" + FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176" + LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" + MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9" + NLSolvers = "337daf1e-9722-11e9-073e-8b9effe078ba" + NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" + SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4" + SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.ObjectFile]] deps = ["Reexport", "StructIO"] @@ -1959,6 +2155,20 @@ git-tree-sha1 = "7438a59546cf62428fc9d1bc94729146d37a7225" uuid = "510215fc-4207-5dde-b226-833fc4488ee2" version = "0.5.5" +[[deps.Octavian]] +deps = ["CPUSummary", "IfElse", "LoopVectorization", "ManualMemory", "PolyesterWeave", "PrecompileTools", "Static", "StaticArrayInterface", "ThreadingUtilities", "VectorizationBase"] +git-tree-sha1 = "92410e147bdcaf9e2f982a7cc9b1341fc5dd1a77" +uuid = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4" +version = "0.3.28" + + [deps.Octavian.extensions] + ForwardDiffExt = "ForwardDiff" + HyperDualNumbersExt = "HyperDualNumbers" + + [deps.Octavian.weakdeps] + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + HyperDualNumbers = "50ceba7f-c3ee-5a84-a6e8-3ad40456ec97" + [[deps.OffsetArrays]] git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" @@ -2004,9 +2214,9 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a028ee3cb5641cccc4c24e90c36b0a4f7707bdf5" +git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.14+0" +version = "3.0.15+1" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -2019,11 +2229,13 @@ deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89" uuid = "429524aa-4258-5aef-a3af-852621145aeb" version = "1.9.4" -weakdeps = ["MathOptInterface"] [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" + [deps.Optim.weakdeps] + MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" + [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] git-tree-sha1 = "6572fe0c5b74431aaeb0b18a4aa5ef03c84678be" @@ -2031,12 +2243,18 @@ uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" version = "0.3.3" [[deps.Optimization]] -deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LinearAlgebra", "Logging", "LoggingExtras", "Pkg", "Printf", "ProgressLogging", "Reexport", "Requires", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "1aa7ffea6e171167e9cae620d749e16d5874414a" +deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Pkg", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] +git-tree-sha1 = "81abd38353faaf0297a964fa6115a54c6a066cab" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "3.19.3" +version = "3.26.3" + +[[deps.OptimizationBase]] +deps = ["ADTypes", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "Reexport", "Requires", "SciMLBase", "SparseArrays"] +git-tree-sha1 = "dcb1f85b0da580e2363c0197b0366406031a69cd" +uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb" +version = "1.2.0" - [deps.Optimization.extensions] + [deps.OptimizationBase.extensions] OptimizationEnzymeExt = "Enzyme" OptimizationFiniteDiffExt = "FiniteDiff" OptimizationForwardDiffExt = "ForwardDiff" @@ -2046,7 +2264,7 @@ version = "3.19.3" OptimizationTrackerExt = "Tracker" OptimizationZygoteExt = "Zygote" - [deps.Optimization.weakdeps] + [deps.OptimizationBase.weakdeps] Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" @@ -2059,15 +2277,15 @@ version = "3.19.3" [[deps.OptimizationNLopt]] deps = ["NLopt", "Optimization", "Reexport"] -git-tree-sha1 = "dc1b76eae7c47ae77560803587911d4d219af531" +git-tree-sha1 = "83b7f5218c6ff83f65fff32923630fe8be9f5131" uuid = "4e6fcdb7-1186-4e1f-a706-475e75c168bb" -version = "0.1.8" +version = "0.2.2" [[deps.OptimizationOptimJL]] deps = ["Optim", "Optimization", "Reexport", "SparseArrays"] -git-tree-sha1 = "bea24fb320d58cb639e3cbc63f8eedde6c667bd3" +git-tree-sha1 = "43870d726f883a47d158beebb1fc3c9fab1da9d6" uuid = "36348300-93cb-4f02-beb5-3c3902f8871e" -version = "0.1.14" +version = "0.3.2" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2081,10 +2299,194 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.3" [[deps.OrdinaryDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "f0f43037c0ba045e96f32d65858eb825a211b817" +deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "cd892f12371c287dc50d6ad3af075b088b6f2d48" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.58.2" +version = "6.89.0" + 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"79d7bb75-1356-48c1-b8c0-6832512096c2" +version = "1.1.1" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -2099,9 +2501,9 @@ version = "0.11.31" [[deps.PSIS]] deps = ["LinearAlgebra", "LogExpFunctions", "Printf", "RecipesBase", "Statistics"] -git-tree-sha1 = "72a16ef4d76e0cb071d704ff50dc086b6715d2f9" +git-tree-sha1 = "08598dfcf5dd14db4425641abfc301b817b921f0" uuid = "ce719bf2-d5d0-4fb9-925d-10a81b42ad04" -version = "0.7.2" +version = "0.9.6" [[deps.PackageExtensionCompat]] git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" @@ -2127,17 +2529,16 @@ git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" version = "2.8.1" -[[deps.PartialFunctions]] -deps = ["MacroTools"] -git-tree-sha1 = "47b49a4dbc23b76682205c646252c0f9e1eb75af" -uuid = "570af359-4316-4cb7-8c74-252c00c2016b" -version = "1.2.0" - [[deps.Pathfinder]] -deps = ["Accessors", "Distributions", "Folds", "ForwardDiff", "IrrationalConstants", "LinearAlgebra", "LogDensityProblems", "Optim", "Optimization", "OptimizationOptimJL", "PDMats", "PSIS", "ProgressLogging", "Random", "Requires", "SciMLBase", "Statistics", "StatsBase", "Transducers", "UnPack"] -git-tree-sha1 = "9276ab48cb3a900e0bca214912c756d52625dadb" +deps = ["ADTypes", "Distributions", "Folds", "IrrationalConstants", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "Optim", "Optimization", "OptimizationOptimJL", "PDMats", "PSIS", "ProgressLogging", "Random", "Requires", "SciMLBase", "Statistics", "StatsBase", "Transducers", "UnPack"] +git-tree-sha1 = "51c7b11dfd7249bfb22165902fa1b699f03e26f6" uuid = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454" -version = "0.7.0" +version = "0.9.2" +weakdeps = ["Accessors", "DynamicHMC", "DynamicPPL", "MCMCChains", "Turing"] + + [deps.Pathfinder.extensions] + PathfinderDynamicHMCExt = "DynamicHMC" + PathfinderTuringExt = ["Accessors", "DynamicPPL", "MCMCChains", "Turing"] [[deps.Pipe]] git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" @@ -2246,18 +2647,14 @@ version = "0.2.0" [[deps.PrettyTables]] deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "66b20dd35966a748321d3b2537c4584cf40387c7" +git-tree-sha1 = "1101cd475833706e4d0e7b122218257178f48f34" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.3.2" +version = "2.4.0" [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -[[deps.Profile]] -deps = ["Printf"] -uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" - [[deps.ProgressLogging]] deps = ["Logging", "SHA", "UUIDs"] git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539" @@ -2301,9 +2698,13 @@ version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "e237232771fdafbae3db5c31275303e056afaa9f" +git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.10.1" +version = "2.11.1" +weakdeps = ["Enzyme"] + + [deps.QuadGK.extensions] + QuadGKEnzymeExt = "Enzyme" [[deps.RData]] deps = ["CategoricalArrays", "CodecZlib", "DataFrames", "Dates", "FileIO", "Requires", "TimeZones", "Unicode"] @@ -2371,20 +2772,28 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "d7087c013e8a496ff396bae843b1e16d9a30ede8" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "b034171b93aebc81b3e1890a036d13a9c4a9e3e0" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.10" +version = "3.27.0" [deps.RecursiveArrayTools.extensions] + RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" + RecursiveArrayToolsForwardDiffExt = "ForwardDiff" RecursiveArrayToolsMeasurementsExt = "Measurements" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" + RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] + RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" [deps.RecursiveArrayTools.weakdeps] + FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -2431,29 +2840,31 @@ version = "1.15.3" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e60724fd3beea548353984dc61c943ecddb0e29a" +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.3+0" +version = "0.5.1+0" [[deps.Roots]] -deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"] -git-tree-sha1 = "12e0a0e549c8545db615a2ec48664d56e1aad44d" +deps = ["Accessors", "CommonSolve", "Printf"] +git-tree-sha1 = "3a7c7e5c3f015415637f5debdf8a674aa2c979c4" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.1.7" +version = "2.2.1" [deps.Roots.extensions] + RootsChainRulesCoreExt = "ChainRulesCore" RootsForwardDiffExt = "ForwardDiff" RootsIntervalRootFindingExt = "IntervalRootFinding" RootsSymPyExt = "SymPy" RootsSymPyPythonCallExt = "SymPyPythonCall" [deps.Roots.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" @@ -2487,20 +2898,29 @@ uuid = "26aad666-b158-4e64-9d35-0e672562fa48" version = "0.1.1" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "916b8a94c0d61fa5f7c5295649d3746afb866aff" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "50ed64cd5ad79b0bef71fdb6a11d10c3448bfef0" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.98.1" -weakdeps = ["Zygote"] +version = "2.56.1" [deps.SciMLBase.extensions] - ZygoteExt = "Zygote" - -[[deps.SciMLNLSolve]] -deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "765b788339abd7d983618c09cfc0192e2b6b15fd" -uuid = "e9a6253c-8580-4d32-9898-8661bb511710" -version = "0.1.9" + SciMLBaseChainRulesCoreExt = "ChainRulesCore" + SciMLBaseMakieExt = "Makie" + SciMLBasePartialFunctionsExt = "PartialFunctions" + SciMLBasePyCallExt = "PyCall" + SciMLBasePythonCallExt = "PythonCall" + SciMLBaseRCallExt = "RCall" + SciMLBaseZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" + PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" + PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" + PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" + RCall = "6f49c342-dc21-5d91-9882-a32aef131414" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] @@ -2514,10 +2934,16 @@ weakdeps = ["SparseArrays", "StaticArraysCore"] SciMLOperatorsStaticArraysCoreExt = "StaticArraysCore" [[deps.SciMLSensitivity]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEq", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLOperators", "SparseDiffTools", "StaticArrays", "StaticArraysCore", "Statistics", "StochasticDiffEq", "Tracker", "TruncatedStacktraces", "Zygote"] -git-tree-sha1 = "3b0fde1944502bd736bcdc3d0df577dddb54d189" +deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLOperators", "SciMLStructures", "SparseDiffTools", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "TruncatedStacktraces", "Zygote"] +git-tree-sha1 = "b669eb03c0d5a92ab6a337549afcaad2c9b381e0" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.51.0" +version = "7.68.0" + +[[deps.SciMLStructures]] +deps = ["ArrayInterface"] +git-tree-sha1 = "25514a6f200219cd1073e4ff23a6324e4a7efe64" +uuid = "53ae85a6-f571-4167-b2af-e1d143709226" +version = "1.5.0" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -2566,19 +2992,22 @@ uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.SimpleNonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PackageExtensionCompat", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "15ff97fa4881133caa324dacafe28b5ac47ad8a2" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "97a7e10717bd27e600ba55da9d90a5628c1a403b" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "0.1.23" -weakdeps = ["NNlib"] +version = "1.12.2" +weakdeps = ["ChainRulesCore", "ReverseDiff", "Tracker", "Zygote"] [deps.SimpleNonlinearSolve.extensions] - SimpleNonlinearSolveNNlibExt = "NNlib" + SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" + SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" + SimpleNonlinearSolveTrackerExt = "Tracker" + SimpleNonlinearSolveZygoteExt = "Zygote" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2607,9 +3036,9 @@ version = "1.10.0" [[deps.SparseDiffTools]] deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "cce98ad7c896e52bb0eded174f02fc2a29c38477" +git-tree-sha1 = "c9e5d7ee75cf6a1ca3a22c9a6a4ef451792cf62b" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.18.0" +version = "2.20.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -2631,6 +3060,12 @@ git-tree-sha1 = "52962839426b75b3021296f7df242e40ecfc0852" uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" version = "0.1.2" +[[deps.SparseMatrixColorings]] +deps = ["ADTypes", "Compat", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "ad17e2069015839e58a1f9275608b405fae1f28e" +uuid = "0a514795-09f3-496d-8182-132a7b665d35" +version = "0.4.6" + [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" @@ -2654,10 +3089,10 @@ uuid = "171d559e-b47b-412a-8079-5efa626c420e" version = "0.1.15" [[deps.Static]] -deps = ["IfElse"] -git-tree-sha1 = "d2fdac9ff3906e27f7a618d47b676941baa6c80c" +deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] +git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.8.10" +version = "1.1.1" [[deps.StaticArrayInterface]] deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] @@ -2711,9 +3146,9 @@ version = "0.33.21" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" +git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.1" +version = "1.3.2" weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] @@ -2733,16 +3168,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.7" [[deps.SteadyStateDiffEq]] -deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "2ca69f4be3294e4cd987d83d6019037d420d9fc1" +deps = ["ConcreteStructs", "DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "Reexport", "SciMLBase"] +git-tree-sha1 = "920acf6ae36c86f23969fea1d317e040dbfccf53" uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" -version = "1.16.1" +version = "2.4.1" [[deps.StochasticDiffEq]] -deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "b341540a647b39728b6d64eaeda82178e848f76e" +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "b49030a24847e8c3e85eed3359825297ffb70dfa" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.62.0" +version = "6.69.1" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] @@ -2770,9 +3205,9 @@ version = "0.3.1" [[deps.StringManipulation]] deps = ["PrecompileTools"] -git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" +git-tree-sha1 = "a6b1675a536c5ad1a60e5a5153e1fee12eb146e3" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.4" +version = "0.4.0" [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] @@ -2803,9 +3238,9 @@ version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "71dc65a2d7decdde5500299c9b04309e0138d1b4" +git-tree-sha1 = "82304990120934137261aa085e0d05a412fe0825" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.20.1" +version = "4.25.0" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] @@ -2814,10 +3249,10 @@ uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164" version = "5.2.2+0" [[deps.SymbolicIndexingInterface]] -deps = ["DocStringExtensions"] -git-tree-sha1 = "f8ab052bfcbdb9b48fad2c80c873aa0d0344dfe5" +deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] +git-tree-sha1 = "0225f7c62f5f78db35aae6abb2e5cabe38ce578f" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.2.2" +version = "0.3.31" [[deps.TOML]] deps = ["Dates"] @@ -2826,9 +3261,9 @@ version = "1.0.3" [[deps.TZJData]] deps = ["Artifacts"] -git-tree-sha1 = "1607ad46cf8d642aa779a1d45af1c8620dbf6915" +git-tree-sha1 = "36b40607bf2bf856828690e097e1c799623b0602" uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" -version = "1.2.0+2024a" +version = "1.3.0+2024b" [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] @@ -2889,9 +3324,9 @@ version = "0.5.2" [[deps.TimeZones]] deps = ["Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] -git-tree-sha1 = "b92aebdd3555f3a7e3267cf17702033c2814ef48" +git-tree-sha1 = "8323074bc977aa85cf5ad71099a83ac75b0ac107" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.18.0" +version = "1.18.1" weakdeps = ["RecipesBase"] [deps.TimeZones.extensions] @@ -2899,9 +3334,9 @@ weakdeps = ["RecipesBase"] [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "5a13ae8a41237cff5ecf34f73eb1b8f42fff6531" +git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.24" +version = "0.5.25" [[deps.Tracker]] deps = ["Adapt", "ChainRulesCore", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -2914,17 +3349,18 @@ weakdeps = ["PDMats"] TrackerPDMatsExt = "PDMats" [[deps.TranscodingStreams]] -git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2" +git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.11.2" +version = "0.11.3" [[deps.Transducers]] -deps = ["Accessors", "Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] -git-tree-sha1 = "5215a069867476fc8e3469602006b9670e68da23" +deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] +git-tree-sha1 = "2485554c5b6b039316634f9c676e1bdd84a13e31" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.82" +version = "0.4.83" [deps.Transducers.extensions] + TransducersAdaptExt = "Adapt" TransducersBlockArraysExt = "BlockArrays" TransducersDataFramesExt = "DataFrames" TransducersLazyArraysExt = "LazyArrays" @@ -2932,6 +3368,7 @@ version = "0.4.82" TransducersReferenceablesExt = "Referenceables" [deps.Transducers.weakdeps] + Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" @@ -2968,9 +3405,9 @@ version = "1.5.0" [[deps.Turing]] deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "e4ccbd30d20705f0a4e208dd414e0fb812ab8287" +git-tree-sha1 = "f69f33f7862a66674c279fe9b86b457a96767e35" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.34.0" +version = "0.34.1" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] @@ -3024,9 +3461,9 @@ version = "0.2.1" [[deps.UnsafeAtomicsLLVM]] deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "bf2c553f25e954a9b38c9c0593a59bb13113f9e5" +git-tree-sha1 = "2d17fabcd17e67d7625ce9c531fb9f40b7c42ce4" uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.1.5" +version = "0.2.1" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -3070,16 +3507,26 @@ uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" version = "1.4.2" [[deps.WeightInitializers]] -deps = ["ChainRulesCore", "LinearAlgebra", "PartialFunctions", "PrecompileTools", "Random", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "f0e6760ef9d22f043710289ddf29e4a4048c4822" +deps = ["ArgCheck", "ConcreteStructs", "GPUArraysCore", "LinearAlgebra", "Random", "SpecialFunctions", "Statistics"] +git-tree-sha1 = "ed1cfb44422eaa9804c8a596a8227a6e2baaeef7" uuid = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d" -version = "0.1.7" +version = "1.0.3" [deps.WeightInitializers.extensions] - WeightInitializersCUDAExt = "CUDA" + WeightInitializersAMDGPUExt = ["AMDGPU", "GPUArrays"] + WeightInitializersCUDAExt = ["CUDA", "GPUArrays"] + WeightInitializersChainRulesCoreExt = "ChainRulesCore" + WeightInitializersGPUArraysExt = "GPUArrays" + WeightInitializersMetalExt = ["Metal", "GPUArrays"] + WeightInitializersoneAPIExt = ["oneAPI", "GPUArrays"] [deps.WeightInitializers.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" [[deps.Widgets]] deps = ["Colors", "Dates", "Observables", "OrderedCollections"] @@ -3267,15 +3714,15 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" +git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.6+0" +version = "1.5.6+1" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "19c586905e78a26f7e4e97f81716057bd6b1bc54" +git-tree-sha1 = "f2f85ad73ca67b5d3c94239b0fde005e0fe2d900" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.70" +version = "0.6.71" weakdeps = ["Colors", "Distances", "Tracker"] [deps.Zygote.extensions] @@ -3356,9 +3803,9 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.43+1" +version = "1.6.44+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] diff --git a/README.md b/README.md index 742bfd692..139153703 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,8 @@ This repository is part of [Turing.jl's](https://turinglang.org/) website (i.e. - The `master` branch contains the quarto source - The `gh-pages` branch contains the `html` version of these documents compiled from the `master` branch. +## Local development + To get started with the docs website locally, you'll need to have [Quarto](https://quarto.org/docs/download/) installed. Make sure you have at least version 1.5 of Quarto installed, as this is required to correctly run [the native Julia engine](https://quarto.org/docs/computations/julia.html#using-the-julia-engine). @@ -50,6 +52,16 @@ Once you have the prerequisite installed, you can follow these steps: quarto render path/to/index.qmd ``` +## Troubleshooting build issues + +As described in the [Quarto docs](https://quarto.org/docs/computations/julia.html#using-the-julia-engine), Quarto's Julia engine uses a worker process behind the scenes. +Sometimes this can result in issues with old package code not being unloaded (e.g. when package versions are upgraded). +If you find that Quarto's execution is failing with errors that aren't reproducible via a normal REPL, try adding the `--execute-daemon-restart` flag to the `quarto render` command: + +```bash +quarto render /path/to/index.qmd --execute-daemon-restart +``` + ## License This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details. diff --git a/tutorials/03-bayesian-neural-network/index.qmd b/tutorials/03-bayesian-neural-network/index.qmd index fa5863a1b..fcfa7502f 100755 --- a/tutorials/03-bayesian-neural-network/index.qmd +++ b/tutorials/03-bayesian-neural-network/index.qmd @@ -142,8 +142,6 @@ graph G { The `nn_initial` is an instance that acts as a function and can take data as inputs and output predictions. We will define distributions on the neural network parameters. - ```{julia} # Construct a neural network using Lux @@ -152,7 +150,7 @@ nn_initial = Chain(Dense(2 => 3, tanh), Dense(3 => 2, tanh), Dense(2 => 1, σ)) # Initialize the model weights and state ps, st = Lux.setup(rng, nn_initial) -Lux.parameterlength(nn_initial) # number of paraemters in NN +Lux.parameterlength(nn_initial) # number of parameters in NN ``` The probabilistic model specification below creates a `parameters` variable, which has IID normal variables. The `parameters` vector represents all parameters of our neural net (weights and biases). @@ -163,7 +161,8 @@ alpha = 0.09 sigma = sqrt(1.0 / alpha) ``` -Construct named tuple from a sampled parameter vector. We could also use ComponentArrays here and simply broadcast to avoid doing this. But let's do it this way to avoid dependencies. +We also define a function to construct a named tuple from a vector of sampled parameters. +(We could use [`ComponentArrays`](https://github.com/jonniedie/ComponentArrays.jl) here and broadcast to avoid doing this, but this way avoids introducing an extra dependency.) ```{julia} function vector_to_parameters(ps_new::AbstractVector, ps::NamedTuple) @@ -178,10 +177,10 @@ function vector_to_parameters(ps_new::AbstractVector, ps::NamedTuple) end ``` -To interface with external libraries it is often desirable to use the [`StatefulLuxLayer`](https://lux.csail.mit.edu/stable/api/Lux/contrib#StatefulLuxLayer) to automatically handle the neural network states. +To interface with external libraries it is often desirable to use the [`StatefulLuxLayer`](https://lux.csail.mit.edu/stable/api/Lux/utilities#Lux.StatefulLuxLayer) to automatically handle the neural network states. ```{julia} -const nn = StatefulLuxLayer(nn_initial, st) +const nn = StatefulLuxLayer{true}(nn_initial, nothing, st) # Specify the probabilistic model. @model function bayes_nn(xs, ts; sigma = sigma, ps = ps, nn = nn)