diff --git a/Manifest.toml b/Manifest.toml index d86c9e5e0..c2e3cfde3 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,8 +1,8 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.4" +julia_version = "1.11.5" manifest_format = "2.0" -project_hash = "f8ede0ee89806fd59fc0feecd3210fa53189aa73" +project_hash = "451ef37239e6a37e494e660005a325d7a0d8517f" [[deps.ADTypes]] git-tree-sha1 = "e2478490447631aedba0823d4d7a80b2cc8cdb32" @@ -28,9 +28,9 @@ weakdeps = ["ChainRulesCore", "Test"] [[deps.AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "PDMats", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "1d15dd1f8658f4efcc4a8e779a5d688733e4a1f0" +git-tree-sha1 = "8a05cefb7c891378c89576bd4865f34d010c9ece" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.23" +version = "0.5.24" [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] @@ -40,9 +40,9 @@ version = "5.6.0" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random", "StatsBase"] -git-tree-sha1 = "b155685b5daa9d9d19dfe42684a53fa8cbbb83b8" +git-tree-sha1 = "fc3a433ade4210c5c82d8454ff060014ed94d6f0" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.10.1" +version = "0.11.0" [[deps.AbstractTrees]] git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" @@ -85,26 +85,30 @@ weakdeps = ["SparseArrays", "StaticArrays"] AdaptStaticArraysExt = "StaticArrays" [[deps.AdvancedHMC]] -deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "3027ae3794d5205a5936272b02886a6c5ebaaa60" +deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Setfield", "Statistics", "StatsBase", "StatsFuns"] +git-tree-sha1 = "a340008fc9c43f85f3b3e33c0ea66fdd33ec79a9" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.7.0" +version = "0.7.1" [deps.AdvancedHMC.extensions] + AdvancedHMCADTypesExt = "ADTypes" AdvancedHMCCUDAExt = "CUDA" + AdvancedHMCComponentArraysExt = "ComponentArrays" AdvancedHMCMCMCChainsExt = "MCMCChains" AdvancedHMCOrdinaryDiffEqExt = "OrdinaryDiffEq" [deps.AdvancedHMC.weakdeps] + ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" [[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "DocStringExtensions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"] -git-tree-sha1 = "bcf97a5390262571d64d62566673bf1e72080d11" +git-tree-sha1 = "f3a278077383e196af143ca7daf57a303d7cac2f" uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -version = "0.8.6" +version = "0.8.7" weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] [deps.AdvancedMH.extensions] @@ -176,9 +180,9 @@ version = "3.5.1+1" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "017fcb757f8e921fb44ee063a7aafe5f89b86dd1" +git-tree-sha1 = "bebb10cd3f0796dd1429ba61e43990ba391186e9" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.18.0" +version = "7.18.1" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" @@ -252,13 +256,17 @@ version = "0.4.7" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "614c6aba1d562191d9832df2af24f594aa7ebf61" +git-tree-sha1 = "e35c672b239c5105f597963c33e740eeb46cf0ab" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "1.9.3" -weakdeps = ["SparseArrays"] +version = "1.9.4" [deps.BandedMatrices.extensions] BandedMatricesSparseArraysExt = "SparseArrays" + CliqueTreesExt = "CliqueTrees" + + [deps.BandedMatrices.weakdeps] + CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.BangBang]] deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra"] @@ -291,12 +299,6 @@ git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" -[[deps.BenchmarkTools]] -deps = ["Compat", "JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "e38fbc49a620f5d0b660d7f543db1009fe0f8336" -uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.6.0" - [[deps.Bijectors]] deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics"] git-tree-sha1 = "803e3c6bfd5c2655eb040d252144b7519ce1e70e" @@ -327,10 +329,10 @@ uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.6" [[deps.BoundaryValueDiffEq]] -deps = ["ADTypes", "ArrayInterface", "BoundaryValueDiffEqAscher", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqMIRKN", "BoundaryValueDiffEqShooting", "DiffEqBase", "FastClosures", "ForwardDiff", "LinearAlgebra", "Reexport", "SciMLBase"] -git-tree-sha1 = "e3829b5aa0cb49348956c81b927b5edf64cdf6bf" +deps = ["ADTypes", "BoundaryValueDiffEqAscher", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqMIRKN", "BoundaryValueDiffEqShooting", "DiffEqBase", "FastClosures", "ForwardDiff", "LinearAlgebra", "Reexport", "SciMLBase"] +git-tree-sha1 = "ca42053e5c1f2c1ec52111a2ab3e5a0908d9276d" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "5.16.0" +version = "5.16.1" [deps.BoundaryValueDiffEq.extensions] BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" @@ -339,46 +341,46 @@ version = "5.16.0" ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" [[deps.BoundaryValueDiffEqAscher]] -deps = ["ADTypes", "AlmostBlockDiagonals", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] -git-tree-sha1 = "a3ed69c1c0249a53622bd4435384c4e76ac547d9" +deps = ["ADTypes", "AlmostBlockDiagonals", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield"] +git-tree-sha1 = "61fbc62e8277c4d540e1e1954962ec2fdfca5965" uuid = "7227322d-7511-4e07-9247-ad6ff830280e" -version = "1.5.0" +version = "1.5.1" [[deps.BoundaryValueDiffEqCore]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] -git-tree-sha1 = "832ade257129d0c222a53b66e2d7e6f5d937ae34" +deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] +git-tree-sha1 = "8278c1ff5aa1875e9167d2da8c419f5b8362a171" uuid = "56b672f2-a5fe-4263-ab2d-da677488eb3a" -version = "1.8.0" +version = "1.8.1" [[deps.BoundaryValueDiffEqFIRK]] -deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] -git-tree-sha1 = "a92feb2cbb12c6c9adc4d3c4e7427709e9477540" +deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] +git-tree-sha1 = "5030e5ef731082893f744272dc592978dd6fae7c" uuid = "85d9eb09-370e-4000-bb32-543851f73618" -version = "1.6.0" +version = "1.6.1" [[deps.BoundaryValueDiffEqMIRK]] -deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] -git-tree-sha1 = "4cd74dc128326804f780ad6e18ec4886279293de" +deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] +git-tree-sha1 = "c02fa2e95ccffe1dc7a4acb602c25740dfa8bfdf" uuid = "1a22d4ce-7765-49ea-b6f2-13c8438986a6" -version = "1.6.0" +version = "1.6.1" [[deps.BoundaryValueDiffEqMIRKN]] -deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] -git-tree-sha1 = "0db565e02c9784e254325b616a8dd6c0dfec7403" +deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] +git-tree-sha1 = "3f5635756bcffa7aa522e6dd61da39bbbe0cd3df" uuid = "9255f1d6-53bf-473e-b6bd-23f1ff009da4" -version = "1.5.0" +version = "1.5.1" [[deps.BoundaryValueDiffEqShooting]] -deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] -git-tree-sha1 = "7429a95010c57e67bd10e52dd3f276db4d2abdeb" +deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] +git-tree-sha1 = "400776e8f37030321d6e46576cf613142668cc55" uuid = "ed55bfe0-3725-4db6-871e-a1dc9f42a757" -version = "1.6.0" +version = "1.6.1" [[deps.BracketingNonlinearSolve]] deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "47d6e355097ef6df3c39080a0045ecfd00ff514e" +git-tree-sha1 = "637ebe439ba587828fd997b7810d8171eed2ea1b" uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e" -version = "1.1.1" +version = "1.2.0" weakdeps = ["ForwardDiff"] [deps.BracketingNonlinearSolve.extensions] @@ -452,11 +454,21 @@ weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] ChainRulesCoreSparseArraysExt = "SparseArrays" +[[deps.Chairmarks]] +deps = ["Printf", "Random"] +git-tree-sha1 = "9a49491e67e7a4d6f885c43d00bb101e6e5a434b" +uuid = "0ca39b1e-fe0b-4e98-acfc-b1656634c4de" +version = "1.3.1" +weakdeps = ["Statistics"] + + [deps.Chairmarks.extensions] + StatisticsChairmarksExt = ["Statistics"] + [[deps.ChangesOfVariables]] deps = ["LinearAlgebra"] -git-tree-sha1 = "799b25ca3a8a24936ae7b5c52ad194685fc3e6ef" +git-tree-sha1 = "3aa4bf1532aa2e14e0374c4fd72bed9a9d0d0f6c" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.9" +version = "0.1.10" weakdeps = ["InverseFunctions", "Test"] [deps.ChangesOfVariables.extensions] @@ -489,9 +501,9 @@ version = "3.29.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "c7acce7a7e1078a20a285211dd73cd3941a871d6" +git-tree-sha1 = "67e11ee83a43eb71ddc950302c53bf33f0690dfe" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.12.0" +version = "0.12.1" weakdeps = ["StyledStrings"] [deps.ColorTypes.extensions] @@ -514,9 +526,9 @@ uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" version = "0.13.0" [[deps.Combinatorics]] -git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" +git-tree-sha1 = "8010b6bb3388abe68d95743dcbea77650bb2eddf" uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" -version = "1.0.2" +version = "1.0.3" [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" @@ -550,10 +562,10 @@ uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" version = "1.1.1+0" [[deps.ComponentArrays]] -deps = ["Adapt", "ArrayInterface", "ChainRulesCore", "ConstructionBase", "ForwardDiff", "Functors", "LinearAlgebra", "StaticArrayInterface", "StaticArraysCore"] -git-tree-sha1 = "eac93b2a05d33465d50e5448aefba8c06a69f738" +deps = ["Adapt", "ArrayInterface", "ChainRulesCore", "ConstructionBase", "Functors", "LinearAlgebra", "StaticArrayInterface", "StaticArraysCore"] +git-tree-sha1 = "1ad20b11ee13c672a502bd1dbb5c10a52ab92492" uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -version = "0.15.25" +version = "0.15.27" [deps.ComponentArrays.extensions] ComponentArraysGPUArraysExt = "GPUArrays" @@ -665,9 +677,9 @@ version = "1.11.0" [[deps.Dbus_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" +git-tree-sha1 = "473e9afc9cf30814eb67ffa5f2db7df82c3ad9fd" uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" -version = "1.14.10+0" +version = "1.16.2+0" [[deps.DefineSingletons]] git-tree-sha1 = "0fba8b706d0178b4dc7fd44a96a92382c9065c2c" @@ -676,9 +688,9 @@ version = "0.1.2" [[deps.DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack", "SymbolicIndexingInterface"] -git-tree-sha1 = "7123a01ba4ec2d4058bd14478afd5318c49ea6c1" +git-tree-sha1 = "8b416f6b1f9ef8df4c13dd0fe6c191752722b36f" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.52.0" +version = "5.53.1" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -693,10 +705,10 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] -git-tree-sha1 = "4263b49db273d67f13b83af609712aed69ccf38a" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"] +git-tree-sha1 = "6a0f6f17adbeb77688220cfb3e665c8f6e2a60ea" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.166.0" +version = "6.172.0" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -772,9 +784,9 @@ version = "7.16.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "cf6dcb4b21bdd893fd45be70791d6dc89ca16506" +git-tree-sha1 = "8b9f605f582f633eeb9c3ec14effaed2dca6ef5c" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.6.48" +version = "0.6.53" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -784,6 +796,7 @@ version = "0.6.48" DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" DifferentiationInterfaceForwardDiffExt = ["ForwardDiff", "DiffResults"] + DifferentiationInterfaceGPUArraysCoreExt = "GPUArraysCore" DifferentiationInterfaceGTPSAExt = "GTPSA" DifferentiationInterfaceMooncakeExt = "Mooncake" DifferentiationInterfacePolyesterForwardDiffExt = ["PolyesterForwardDiff", "ForwardDiff", "DiffResults"] @@ -806,6 +819,7 @@ version = "0.6.48" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" GTPSA = "b27dd330-f138-47c5-815b-40db9dd9b6e8" Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" @@ -847,9 +861,9 @@ version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "0b4190661e8a4e51a842070e7dd4fae440ddb7f4" +git-tree-sha1 = "6d8b535fd38293bc54b88455465a1386f8ac1c3c" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.118" +version = "0.25.119" weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [deps.Distributions.extensions] @@ -859,9 +873,9 @@ weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [[deps.DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "Distributions", "FillArrays", "LinearAlgebra", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsFuns", "ZygoteRules"] -git-tree-sha1 = "02c2e6e6a137069227439fe884d729cca5b70e56" +git-tree-sha1 = "4acbf909e892ce1f94c39a138541566c1aad5e66" uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c" -version = "0.6.57" +version = "0.6.58" weakdeps = ["ForwardDiff", "LazyArrays", "ReverseDiff", "Tracker"] [deps.DistributionsAD.extensions] @@ -871,10 +885,9 @@ weakdeps = ["ForwardDiff", "LazyArrays", "ReverseDiff", "Tracker"] DistributionsADTrackerExt = "Tracker" [[deps.DocStringExtensions]] -deps = ["LibGit2"] -git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" +git-tree-sha1 = "e7b7e6f178525d17c720ab9c081e4ef04429f860" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.3" +version = "0.9.4" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -883,15 +896,15 @@ version = "1.6.0" [[deps.DynamicHMC]] deps = ["ArgCheck", "DocStringExtensions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "LogExpFunctions", "ProgressMeter", "Random", "Statistics", "TensorCast"] -git-tree-sha1 = "ba30c83b20dce95e7353b1d7f7f3a6d151722b55" +git-tree-sha1 = "08f33c9cce36fe618efc6d37c24c157eef5f752e" uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb" -version = "3.5.0" +version = "3.5.1" [[deps.DynamicPPL]] -deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] -git-tree-sha1 = "4070ee7251d99838b474581539d83884867b4bd4" +deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Requires", "Statistics", "Test"] +git-tree-sha1 = "08ca94265f8203c605a85eb107709ede4d1c32b6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.35.5" +version = "0.36.1" [deps.DynamicPPL.extensions] DynamicPPLChainRulesCoreExt = ["ChainRulesCore"] @@ -917,15 +930,15 @@ uuid = "cad2338a-1db2-11e9-3401-43bc07c9ede2" version = "2.0.0" [[deps.EnumX]] -git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" +git-tree-sha1 = "bddad79635af6aec424f53ed8aad5d7555dc6f00" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" -version = "1.0.4" +version = "1.0.5" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "b83e375689f3c6cf769035b2a3b4332ebc692366" +git-tree-sha1 = "576002e6d84ede4fe132bff779f7841f8575e644" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.34" +version = "0.13.41" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -954,9 +967,9 @@ weakdeps = ["Adapt"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c29af735ddb2381732cdf5dd72fc32069315619d" +git-tree-sha1 = "4d023f07d5cda83b4b7d2af9b541075a81018e51" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.173+0" +version = "0.0.175+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1015,10 +1028,10 @@ uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" version = "1.8.1" [[deps.FFTW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6d6219a004b8cf1e0b4dbe27a2860b8e04eba0be" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.10+3" +version = "3.3.11+0" [[deps.FLoops]] deps = ["BangBang", "Compat", "FLoopsBase", "InitialValues", "JuliaVariables", "MLStyle", "Serialization", "Setfield", "Transducers"] @@ -1034,9 +1047,9 @@ version = "0.1.1" [[deps.FastAlmostBandedMatrices]] deps = ["ArrayInterface", "ArrayLayouts", "BandedMatrices", "ConcreteStructs", "LazyArrays", "LinearAlgebra", "MatrixFactorizations", "PrecompileTools", "Reexport"] -git-tree-sha1 = "3f03d94c71126b6cfe20d3cbcc41c5cd27e1c419" +git-tree-sha1 = "9482a2b4face8ade73792c23a54796c79ed1bcbf" uuid = "9d29842c-ecb8-4973-b1e9-a27b1157504e" -version = "0.1.4" +version = "0.1.5" [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] @@ -1056,9 +1069,9 @@ uuid = "442a2c76-b920-505d-bb47-c5924d526838" version = "1.0.2" [[deps.FastPower]] -git-tree-sha1 = "58c3431137131577a7c379d00fea00be524338fb" +git-tree-sha1 = "df32f07f373f06260cd6af5371385b5ef85dd762" uuid = "a4df4552-cc26-4903-aec0-212e50a0e84b" -version = "1.1.1" +version = "1.1.2" [deps.FastPower.extensions] FastPowerEnzymeExt = "Enzyme" @@ -1161,9 +1174,9 @@ version = "0.14.25" [[deps.Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] -git-tree-sha1 = "21fac3c77d7b5a9fc03b0ec503aa1a6392c34d2b" +git-tree-sha1 = "301b5d5d731a0654825f1f2e906990f7141a106b" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.15.0+0" +version = "2.16.0+0" [[deps.Format]] git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" @@ -1182,15 +1195,15 @@ weakdeps = ["StaticArrays"] [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "786e968a8d2fb167f2e4880baba62e0e26bd8e4e" +git-tree-sha1 = "2c5512e11c791d1baed2049c5652441b28fc6a31" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.3+1" +version = "2.13.4+0" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "846f7026a9decf3679419122b49f8a1fdb48d2d5" +git-tree-sha1 = "7a214fdac5ed5f59a22c2d9a885a16da1c74bbc7" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.16+0" +version = "1.0.17+0" [[deps.FunctionProperties]] deps = ["Cassette", "DiffRules"] @@ -1233,40 +1246,40 @@ uuid = "38e38edf-8417-5370-95a0-9cbb8c7f171a" version = "1.9.0" [[deps.GPUArrays]] -deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "62ee71528cca49be797076a76bdc654a170a523e" +deps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "ScopedValues", "Serialization", "Statistics"] +git-tree-sha1 = "eea7b3a1964b4de269bb380462a9da604be7fcdb" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "10.3.1" +version = "11.2.2" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" +git-tree-sha1 = "83cf05ab16a73219e5f6bd1bdfa9848fa24ac627" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.6" +version = "0.2.0" [[deps.GPUCompiler]] -deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "199f213e40a7982e9138bc9edc3299419d510390" +deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "Tracy", "UUIDs"] +git-tree-sha1 = "43c2e60efa2badefe7a32a50b586b4ac1b8b8249" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "1.2.0" +version = "1.4.0" [[deps.GR]] deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] -git-tree-sha1 = "0ff136326605f8e06e9bcf085a356ab312eef18a" +git-tree-sha1 = "7ffa4049937aeba2e5e1242274dc052b0362157a" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.13" +version = "0.73.14" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "9cb62849057df859575fc1dda1e91b82f8609709" +git-tree-sha1 = "98fc192b4e4b938775ecd276ce88f539bcec358e" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.13+0" +version = "0.73.14+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] -git-tree-sha1 = "af49a0851f8113fcfae2ef5027c6d49d0acec39b" +git-tree-sha1 = "f88e0ba1f6b42121a7c1dfe93a9687d8e164c91b" uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" -version = "0.5.4" +version = "0.5.5" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -1281,16 +1294,16 @@ uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" version = "2.82.4+0" [[deps.Graphite2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "01979f9b37367603e2848ea225918a3b3861b606" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a6dbda1fd736d60cc477d99f2e7a042acfa46e8" uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" -version = "1.3.14+1" +version = "1.3.15+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" +git-tree-sha1 = "3169fd3440a02f35e549728b0890904cfd4ae58a" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.12.0" +version = "1.12.1" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -1317,9 +1330,9 @@ version = "1.14.6+0" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "c67b33b085f6e2faf8bf79a61962e7339a81129c" +git-tree-sha1 = "f93655dc73d7a0b4a368e3c0bce296ae035ad76e" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.15" +version = "1.10.16" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] @@ -1410,9 +1423,9 @@ weakdeps = ["Unitful"] InterpolationsUnitfulExt = "Unitful" [[deps.IntervalSets]] -git-tree-sha1 = "dba9ddf07f77f60450fe5d2e2beb9854d9a49bd0" +git-tree-sha1 = "5fbb102dcb8b1a858111ae81d56682376130517d" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.10" +version = "0.7.11" weakdeps = ["Random", "RecipesBase", "Statistics"] [deps.IntervalSets.extensions] @@ -1451,10 +1464,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLFzf]] -deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "71b48d857e86bf7a1838c4736545699974ce79a2" +deps = ["REPL", "Random", "fzf_jll"] +git-tree-sha1 = "82f7acdc599b65e0f8ccd270ffa1467c21cb647b" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.9" +version = "0.1.11" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] @@ -1488,9 +1501,9 @@ version = "0.2.4" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] -git-tree-sha1 = "3ba034493e21efc9ba61268dc0faa0c383bb76a5" +git-tree-sha1 = "f2bdec5b4580414aee3178c8caa6e46c344c0bbc" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.14.2" +version = "9.14.3" weakdeps = ["FastBroadcast"] [[deps.KernelAbstractions]] @@ -1519,9 +1532,9 @@ version = "0.10.65" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "b29d37ce30fa401a4563b18880ab91f979a29734" +git-tree-sha1 = "b94257a1a8737099ca40bc7271a8b374033473ed" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.10" +version = "0.10.1" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1543,9 +1556,9 @@ version = "4.0.1+0" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] -git-tree-sha1 = "5fcfea6df2ff3e4da708a40c969c3812162346df" +git-tree-sha1 = "f0e861832695dbb70e710606a7d18b7f81acec92" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "9.2.0" +version = "9.3.1" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1561,9 +1574,9 @@ version = "0.0.35+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" +git-tree-sha1 = "eb62a3deb62fc6d8822c0c4bef73e4412419c5d8" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "18.1.7+0" +version = "18.1.8+0" [[deps.LRUCache]] git-tree-sha1 = "5519b95a490ff5fe629c4a7aa3b3dfc9160498b3" @@ -1593,9 +1606,9 @@ version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "cd714447457c660382fe634710fb56eb255ee42e" +git-tree-sha1 = "cd10d2cc78d34c0e2a3a36420ab607b611debfbb" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.6" +version = "0.16.7" [deps.Latexify.extensions] DataFramesExt = "DataFrames" @@ -1685,6 +1698,12 @@ deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" version = "1.11.0+1" +[[deps.LibTracyClient_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "d2bc4e1034b2d43076b50f0e34ea094c2cb0a717" +uuid = "ad6e5548-8b26-5c9f-8ef3-ef0ad883f3a5" +version = "0.9.1+6" + [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" version = "1.11.0" @@ -1695,23 +1714,11 @@ git-tree-sha1 = "27ecae93dd25ee0909666e6835051dd684cc035e" uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" version = "3.2.2+2" -[[deps.Libgcrypt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] -git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" -uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.11.0+0" - [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "ff3b4b9d35de638936a525ecd36e86a8bb919d11" +git-tree-sha1 = "d36c21b9e7c172a44a10484125024495e2625ac0" uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.7.0+0" - -[[deps.Libgpg_error_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "df37206100d39f79b3376afb6b9cee4970041c61" -uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.51.1+0" +version = "1.7.1+1" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1721,9 +1728,9 @@ version = "1.18.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "89211ea35d9df5831fca5d33552c02bd33878419" +git-tree-sha1 = "a31572773ac1b745e0343fe5e2c8ddda7a37e997" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.40.3+0" +version = "2.41.0+0" [[deps.Libtask]] deps = ["FunctionWrappers", "LRUCache", "LinearAlgebra", "Statistics"] @@ -1739,9 +1746,9 @@ version = "4.7.1+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e888ad02ce716b319e6bdb985d2ef300e7089889" +git-tree-sha1 = "321ccef73a96ba828cd51f2ab5b9f917fa73945a" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.40.3+0" +version = "2.41.0+0" [[deps.LineSearch]] deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] @@ -1766,9 +1773,9 @@ version = "1.11.0" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "c64ec326eeeb20c065afd6aa5add4fad458e460a" +git-tree-sha1 = "c5e80f547e47f00f53c290aa5d4a11034104b94d" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "3.7.0" +version = "3.11.0" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" @@ -2040,10 +2047,10 @@ uuid = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" version = "0.5.4" [[deps.MLJModelInterface]] -deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "ceaff6618408d0e412619321ae43b33b40c1a733" +deps = ["REPL", "Random", "ScientificTypesBase", "StatisticalTraits"] +git-tree-sha1 = "66626f80d5807921045d539b4f7153b1d47c5f8a" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.11.0" +version = "1.11.1" [[deps.MLLabelUtils]] deps = ["LearnBase", "MappedArrays", "StatsBase"] @@ -2081,9 +2088,9 @@ uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" version = "5.5.3+0" [[deps.MacroTools]] -git-tree-sha1 = "72aebe0b5051e5143a079a4685a46da330a40472" +git-tree-sha1 = "1e0228a030642014fe5cfe68c2c0a818f9e3f522" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.15" +version = "0.5.16" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -2228,9 +2235,9 @@ version = "0.10.3" [[deps.NLSolversBase]] deps = ["ADTypes", "DifferentiationInterface", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "1f78293864c5e48ecf97269b0e23d7be28eb1958" +git-tree-sha1 = "b14c7be6046e7d48e9063a0053f95ee0fc954176" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.9.0" +version = "7.9.1" [[deps.NLopt]] deps = ["CEnum", "NLopt_jll"] @@ -2258,9 +2265,9 @@ version = "4.5.1" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "ScopedValues", "Statistics"] -git-tree-sha1 = "e8d4268b4a438bdad98937e4bca45881363b4767" +git-tree-sha1 = "4abc63cdd8dd9dd925d8e879cda280bedc8013ca" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.29" +version = "0.9.30" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -2282,9 +2289,9 @@ version = "0.9.29" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "cc0a5deefdb12ab3a096f00a6d42133af4560d71" +git-tree-sha1 = "9b8215b1ee9e78a293f99797cd31375471b2bcae" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.1.2" +version = "1.1.3" [[deps.NameResolution]] deps = ["PrettyPrint"] @@ -2315,9 +2322,9 @@ version = "1.2.0" [[deps.NonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"] -git-tree-sha1 = "eb1007ce104fc6704ac346859bc53976c44edc38" +git-tree-sha1 = "7fd96e0e6585063a7193007349799155ba5a069f" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "4.5.0" +version = "4.8.0" [deps.NonlinearSolve.extensions] NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" @@ -2347,9 +2354,9 @@ version = "4.5.0" [[deps.NonlinearSolveBase]] deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "8a2437b5ead050301b6a6258f226e5137e511000" +git-tree-sha1 = "686fd9d0d455171e3530d3540cff94bb01222823" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "1.5.0" +version = "1.7.0" weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"] [deps.NonlinearSolveBase.extensions] @@ -2363,15 +2370,15 @@ weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "Linear [[deps.NonlinearSolveFirstOrder]] deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "aade7ab02ee4c80ec30dc8a2874fc67155c935f1" +git-tree-sha1 = "9c8cd0a986518ba317af263549b48e34ac8f776d" uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" -version = "1.3.0" +version = "1.5.0" [[deps.NonlinearSolveQuasiNewton]] deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] -git-tree-sha1 = "44a132cb32aeafcb35a6238fd91a2f3f8ff5c5b0" +git-tree-sha1 = "eafb327f5c2d9f1ac890aa2b9fbe05a1bd7e4dc8" uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" -version = "1.2.0" +version = "1.4.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveQuasiNewton.extensions] @@ -2379,9 +2386,9 @@ weakdeps = ["ForwardDiff"] [[deps.NonlinearSolveSpectralMethods]] deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "f28b1ab17b5f15eb2b174eaf8813cf17f0b3e6c0" +git-tree-sha1 = "3398222199e4b9ca0b5840907fb509f28f1a2fdc" uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" -version = "1.1.0" +version = "1.2.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveSpectralMethods.extensions] @@ -2399,9 +2406,9 @@ uuid = "510215fc-4207-5dde-b226-833fc4488ee2" version = "0.5.5" [[deps.OffsetArrays]] -git-tree-sha1 = "a414039192a155fb38c4599a60110f0018c6ec82" +git-tree-sha1 = "117432e406b5c023f665fa73dc26e79ec3630151" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.16.0" +version = "1.17.0" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -2415,9 +2422,9 @@ version = "1.3.5+1" [[deps.OneHotArrays]] deps = ["Adapt", "ChainRulesCore", "Compat", "GPUArraysCore", "LinearAlgebra", "NNlib"] -git-tree-sha1 = "c8c7f6bfabe581dc40b580313a75f1ecce087e27" +git-tree-sha1 = "3685584454b04cd52169c787ba4d196da8a04d10" uuid = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" -version = "0.2.6" +version = "0.2.9" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] @@ -2427,13 +2434,13 @@ version = "0.3.27+1" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+4" +version = "0.8.5+0" [[deps.OpenMPI_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"] -git-tree-sha1 = "da913f03f17b449951e0461da960229d4a3d1a8c" +git-tree-sha1 = "047b66eb62f3cae59ed260ebb9075a32a04350f1" uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" -version = "5.0.7+1" +version = "5.0.7+2" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] @@ -2443,9 +2450,9 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a9697f1d06cc3eb3fb3ad49cc67f2cfabaac31ea" +git-tree-sha1 = "9216a80ff3682833ac4b733caa8c00390620ba5d" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.16+0" +version = "3.5.0+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -2454,10 +2461,10 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.6+0" [[deps.Optim]] -deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "c1f51f704f689f87f28b33836fd460ecf9b34583" +deps = ["Compat", "EnumX", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] +git-tree-sha1 = "31b3b1b8e83ef9f1d50d74f1dd5f19a37a304a1f" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.11.0" +version = "1.12.0" [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" @@ -2473,9 +2480,9 @@ version = "0.3.4" [[deps.Optimization]] deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "e72af10f1c6ffe2f295455c4c35534d713be62bb" +git-tree-sha1 = "c8eaa77c745cff7e58affa7e325bc4b5168cf964" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "4.1.2" +version = "4.2.0" [[deps.OptimizationBase]] deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] @@ -2513,9 +2520,9 @@ version = "0.3.2" [[deps.OptimizationOptimJL]] deps = ["Optim", "Optimization", "PrecompileTools", "Reexport", "SparseArrays"] -git-tree-sha1 = "980ec7190741db164a2923dc42d6f1e7ce2cc434" +git-tree-sha1 = "6f228118b81ce4e849091ee0d00805f2ecb18f54" uuid = "36348300-93cb-4f02-beb5-3c3902f8871e" -version = "0.4.1" +version = "0.4.3" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2529,10 +2536,10 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.8.0" [[deps.OrdinaryDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "798f5e1a1f8b5a1bbba1e6134b77a77ccc509678" +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", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "dfae5ed215f5949f52de22b92e2e42ea3e3e652d" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.92.0" +version = "6.96.0" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2542,15 +2549,15 @@ version = "1.2.0" [[deps.OrdinaryDiffEqBDF]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "970ac761ae1c4249fc70d75760c328269a518585" +git-tree-sha1 = "a72bf554d5fd1f33a8d2aead3562eddd28ba4c76" uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" -version = "1.3.0" +version = "1.5.0" [[deps.OrdinaryDiffEqCore]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "f47451c0ca3a2b0f11e966ed7731f2bd17d9b0e3" +git-tree-sha1 = "af7374f4af1b9a67ce29524e7fd328fa3da33189" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.19.0" +version = "1.23.0" weakdeps = ["EnzymeCore"] [deps.OrdinaryDiffEqCore.extensions] @@ -2558,15 +2565,15 @@ weakdeps = ["EnzymeCore"] [[deps.OrdinaryDiffEqDefault]] deps = ["ADTypes", "DiffEqBase", "EnumX", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "PrecompileTools", "Preferences", "Reexport"] -git-tree-sha1 = "835c06684b6ff1b8904ceae4d18cc8fe45b9a7cc" +git-tree-sha1 = "8eeed32442874d1bdcc2192a874a73f1a9a07e31" uuid = "50262376-6c5a-4cf5-baba-aaf4f84d72d7" -version = "1.3.0" +version = "1.4.0" [[deps.OrdinaryDiffEqDifferentiation]] -deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays"] -git-tree-sha1 = "9a535370247496c1375ba6d08b0493c0d856d25b" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"] +git-tree-sha1 = "6595287379a518d7eb8f02edc49a96a02396e887" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.4.0" +version = "1.7.0" [[deps.OrdinaryDiffEqExplicitRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"] @@ -2588,9 +2595,9 @@ version = "1.5.0" [[deps.OrdinaryDiffEqFIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastGaussQuadrature", "FastPower", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators"] -git-tree-sha1 = "7dfc32df06db3d9d10128053c0e53deb213fb28d" +git-tree-sha1 = "7d2c82c13a634f7400a3f398d33f1354ab38a090" uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125" -version = "1.8.0" +version = "1.10.0" [[deps.OrdinaryDiffEqFeagin]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2636,9 +2643,9 @@ version = "1.3.0" [[deps.OrdinaryDiffEqNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "PreallocationTools", "RecursiveArrayTools", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "StaticArrays"] -git-tree-sha1 = "1b89e3e84752a3cbd2c94db565e6ea7acb5279b2" +git-tree-sha1 = "d75cf29dea3a72bac7a5b21523ac969b71f43e96" uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8" -version = "1.5.0" +version = "1.6.1" [[deps.OrdinaryDiffEqNordsieck]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2671,10 +2678,10 @@ uuid = "af6ede74-add8-4cfd-b1df-9a4dbb109d7a" version = "1.1.0" [[deps.OrdinaryDiffEqRosenbrock]] -deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "a0d1e65771e087a84c398f20ea5f189043869997" +deps = ["ADTypes", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"] +git-tree-sha1 = "baa4a9b4380b2fb65f1e2b4ec01d3bd019a6dcea" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.7.0" +version = "1.9.0" [[deps.OrdinaryDiffEqSDIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] @@ -2684,9 +2691,9 @@ version = "1.3.0" [[deps.OrdinaryDiffEqSSPRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "StaticArrays"] -git-tree-sha1 = "b97b9691437063ae7d9b1ef130e8b0d81415116f" +git-tree-sha1 = "651756c030df7a1d49ad484288937f8c398e8a08" uuid = "669c94d9-1f4b-4b64-b377-1aa079aa2388" -version = "1.2.1" +version = "1.3.0" [[deps.OrdinaryDiffEqStabilizedIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "StaticArrays"] @@ -2714,9 +2721,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqVerner]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "81d7841e73e385b9925d5c8e4427f2adcdda55db" +git-tree-sha1 = "08f2d3be30874b6e2e937a06b501fb9811f7d8bd" uuid = "79d7bb75-1356-48c1-b8c0-6832512096c2" -version = "1.1.1" +version = "1.2.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -2725,9 +2732,9 @@ version = "10.42.0+1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "966b85253e959ea89c53a9abebbf2e964fbf593b" +git-tree-sha1 = "0e1340b5d98971513bddaa6bbed470670cebbbfe" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.32" +version = "0.11.34" [[deps.PackageExtensionCompat]] git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" @@ -2749,14 +2756,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" +git-tree-sha1 = "7d2f8f21da5db6a806faf7b9b292296da42b2810" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.8.1" - -[[deps.Pipe]] -git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" -uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" -version = "1.3.0" +version = "2.8.3" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] @@ -2787,9 +2789,9 @@ version = "1.4.3" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "24be21541580495368c35a6ccef1454e7b5015be" +git-tree-sha1 = "809ba625a00c605f8d00cd2a9ae19ce34fc24d68" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.11" +version = "1.40.13" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -2837,9 +2839,9 @@ version = "0.2.4" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "8765738bc5a6f1554cb61c5ddfae5bf279e8b110" +git-tree-sha1 = "6d98eace73d82e47f5b16c393de198836d9f790a" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.25" +version = "0.4.27" weakdeps = ["ReverseDiff", "SparseConnectivityTracer"] [deps.PreallocationTools.extensions] @@ -2874,10 +2876,6 @@ deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" version = "1.11.0" -[[deps.Profile]] -uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" -version = "1.11.0" - [[deps.ProgressLogging]] deps = ["Logging", "SHA", "UUIDs"] git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539" @@ -2886,9 +2884,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "8f6bc219586aef8baf0ff9a5fe16ee9c70cb65e4" +git-tree-sha1 = "13c5103482a8ed1536a54c08d0e742ae3dca2d42" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.10.2" +version = "1.10.4" [[deps.PtrArrays]] git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d" @@ -2998,9 +2996,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "35ac79a85c8086892258581d8b6df9cd8db5c91a" +git-tree-sha1 = "2e154f7d7e38db1af0a14ec751aba33360c3bef9" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.31.1" +version = "3.33.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -3049,9 +3047,9 @@ version = "1.1.1" [[deps.ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "cc6cd622481ea366bb9067859446a8b01d92b468" +git-tree-sha1 = "3ab8eee3620451b09f0272c271875b4bc02146d9" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.15.3" +version = "1.16.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -3067,9 +3065,9 @@ version = "0.5.1+0" [[deps.Roots]] deps = ["Accessors", "CommonSolve", "Printf"] -git-tree-sha1 = "442b4353ee8c26756672afb2db81894fc28811f3" +git-tree-sha1 = "3ac13765751ffc81e3531223782d9512f6023f71" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.2.6" +version = "2.2.7" [deps.Roots.extensions] RootsChainRulesCoreExt = "ChainRulesCore" @@ -3087,9 +3085,9 @@ version = "2.2.6" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "04c968137612c4a5629fa531334bb81ad5680f00" +git-tree-sha1 = "7cb9d10026d630ce2dd2a1fc6006a3d5041b34c0" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.13" +version = "0.5.14" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -3108,9 +3106,9 @@ version = "0.1.1" [[deps.SciMLBase]] deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] -git-tree-sha1 = "fe9bbf68543d5f72ae2218f3d8c8faeab761dd52" +git-tree-sha1 = "2fd047893cb0089b180fcbb7e8434ba15dcc2841" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.77.2" +version = "2.87.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3135,15 +3133,15 @@ version = "2.77.2" [[deps.SciMLJacobianOperators]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] -git-tree-sha1 = "f66048bb969e67bd7d1bdd03cd0b81219642bbd0" +git-tree-sha1 = "1e2033bdf0792aa2a2f21de8e9378197f13386ec" uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" -version = "0.1.1" +version = "0.1.4" [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "6149620767866d4b0f0f7028639b6e661b6a1e44" +git-tree-sha1 = "1c4b7f6c3e14e6de0af66e66b86d525cae10ecb4" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.12" +version = "0.3.13" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -3151,10 +3149,10 @@ weakdeps = ["SparseArrays", "StaticArraysCore"] SciMLOperatorsStaticArraysCoreExt = "StaticArraysCore" [[deps.SciMLSensitivity]] -deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "Enzyme", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"] -git-tree-sha1 = "40094b8d6afe1bcfee252ce2ab3c4a09d08c60c4" +deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "Enzyme", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEqCore", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"] +git-tree-sha1 = "019c278424ec840ddf21c8effed1ee61e0009bd4" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.75.0" +version = "7.78.0" weakdeps = ["Mooncake"] [deps.SciMLSensitivity.extensions] @@ -3227,9 +3225,9 @@ version = "1.2.0" [[deps.SimpleNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "f42f8b8b728812e485ad099ee5e959d9b49cdb3d" +git-tree-sha1 = "068c16a16834c1483c299b0e27e901599439570d" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "2.2.0" +version = "2.4.0" weakdeps = ["ChainRulesCore", "DiffEqBase", "ReverseDiff", "Tracker"] [deps.SimpleNonlinearSolve.extensions] @@ -3266,9 +3264,9 @@ version = "1.11.0" [[deps.SparseConnectivityTracer]] deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "9603842a7a68464a066b5754e89fc7f810db8ae7" +git-tree-sha1 = "fadb2d7010dd92912e5eb31a493613ad4b8c9583" uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" -version = "0.6.15" +version = "0.6.18" [deps.SparseConnectivityTracer.extensions] SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" @@ -3311,20 +3309,24 @@ uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" version = "0.1.2" [[deps.SparseMatrixColorings]] -deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "e0ae9189392572abe85bc9fd4ce35e772b1e1e10" +deps = ["ADTypes", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "76e9564f0de0d1d7a46095e758ae13ceba680cfb" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.4.14" -weakdeps = ["Colors"] +version = "0.4.19" [deps.SparseMatrixColorings.extensions] + SparseMatrixColoringsCliqueTreesExt = "CliqueTrees" SparseMatrixColoringsColorsExt = "Colors" + [deps.SparseMatrixColorings.weakdeps] + CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8" + Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "64cca0c26b4f31ba18f13f6c12af7c85f478cfde" +git-tree-sha1 = "41852b8679f78c8d8961eeadc8f62cef861a52e3" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.5.0" +version = "2.5.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -3338,9 +3340,9 @@ version = "0.1.15" [[deps.StableRNGs]] deps = ["Random"] -git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5" +git-tree-sha1 = "95af145932c2ed859b63329952ce8d633719f091" uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" -version = "1.0.2" +version = "1.0.3" [[deps.Static]] deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] @@ -3405,9 +3407,9 @@ version = "0.33.21" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" +git-tree-sha1 = "8e45cecc66f3b42633b8ce14d431e8e57a3e242e" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.2" +version = "1.5.0" weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] @@ -3434,9 +3436,9 @@ version = "2.5.0" [[deps.StochasticDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "9c524fdc91dee5fb73795f1ec06cee022bf6e13d" +git-tree-sha1 = "f354a21a3272fd8ac1509da58e61dffba6925dbe" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.74.1" +version = "6.78.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] @@ -3446,21 +3448,23 @@ version = "0.5.7" [[deps.Strided]] deps = ["LinearAlgebra", "StridedViews", "TupleTools"] -git-tree-sha1 = "f9ce8284e6eec72a21de3603493eb5355fcf7f39" +git-tree-sha1 = "4a1128f5237b5d0170d934a2eb4fa7a273639c9f" uuid = "5e0ebb24-38b0-5f93-81fe-25c709ecae67" -version = "2.2.0" +version = "2.3.0" [[deps.StridedViews]] deps = ["LinearAlgebra", "PackageExtensionCompat"] -git-tree-sha1 = "b60baf1998bcdccc57e1cc2c6703df1f619a3754" +git-tree-sha1 = "425158c52aa58d42593be6861befadf8b2541e9b" uuid = "4db3bf67-4bd7-4b4e-b153-31dc3fb37143" -version = "0.3.2" +version = "0.4.1" [deps.StridedViews.extensions] StridedViewsCUDAExt = "CUDA" + StridedViewsPtrArraysExt = "PtrArrays" [deps.StridedViews.weakdeps] CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + PtrArrays = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" [[deps.StringManipulation]] deps = ["PrecompileTools"] @@ -3470,14 +3474,15 @@ version = "0.4.1" [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] -git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be" +git-tree-sha1 = "8ad2e38cbb812e29348719cc63580ec1dfeb9de4" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.18" -weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] +version = "0.7.1" +weakdeps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "SparseArrays", "StaticArrays"] [deps.StructArrays.extensions] StructArraysAdaptExt = "Adapt" - StructArraysGPUArraysCoreExt = "GPUArraysCore" + StructArraysGPUArraysCoreExt = ["GPUArraysCore", "KernelAbstractions"] + StructArraysLinearAlgebraExt = "LinearAlgebra" StructArraysSparseArraysExt = "SparseArrays" StructArraysStaticArraysExt = "StaticArrays" @@ -3501,9 +3506,9 @@ version = "7.7.0+0" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "c135b599cec3558be36eaf86ab1ce7e259ef9534" +git-tree-sha1 = "7c7a7ee705724b3c80d5451ac49779db36c6f758" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.27.0" +version = "4.28.0" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] @@ -3512,10 +3517,10 @@ uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164" version = "5.2.3+0" [[deps.SymbolicIndexingInterface]] -deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "d6c04e26aa1c8f7d144e1a8c47f1c73d3013e289" +deps = ["Accessors", "ArrayInterface", "PrettyTables", "RuntimeGeneratedFunctions", "StaticArraysCore"] +git-tree-sha1 = "b6a641e38efa01355aa721246dd246e10c7dcd4d" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.38" +version = "0.3.40" [[deps.TOML]] deps = ["Dates"] @@ -3524,9 +3529,9 @@ version = "1.0.3" [[deps.TZJData]] deps = ["Artifacts"] -git-tree-sha1 = "7def47e953a91cdcebd08fbe76d69d2715499a7d" +git-tree-sha1 = "72df96b3a595b7aab1e101eb07d2a435963a97e2" uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" -version = "1.4.0+2025a" +version = "1.5.0+2025b" [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] @@ -3553,9 +3558,9 @@ version = "1.10.0" [[deps.TensorCast]] deps = ["ChainRulesCore", "Compat", "LazyStack", "LinearAlgebra", "MacroTools", "Random", "StaticArrays", "TransmuteDims"] -git-tree-sha1 = "82a477d3afe53673393dd387806e34cd682a5ac4" +git-tree-sha1 = "67606dd3e705cc852c032975a6454e7130fed92c" uuid = "02d47bb6-7ce6-556a-be16-bb1710789e2b" -version = "0.4.8" +version = "0.4.9" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -3576,9 +3581,9 @@ version = "1.11.0" [[deps.ThreadingUtilities]] deps = ["ManualMemory"] -git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" +git-tree-sha1 = "18ad3613e129312fe67789a71720c3747e598a61" uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" -version = "0.5.2" +version = "0.5.3" [[deps.TimeZones]] deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] @@ -3604,14 +3609,26 @@ version = "0.5.28" [[deps.Tracker]] deps = ["Adapt", "ChainRulesCore", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "c266e49953dadd0923caa17b3ea464ab6b97b3f2" +git-tree-sha1 = "83697ba2237663355de8fb0a800144cda44848a0" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.37" +version = "0.2.38" weakdeps = ["PDMats"] [deps.Tracker.extensions] TrackerPDMatsExt = "PDMats" +[[deps.Tracy]] +deps = ["ExprTools", "LibTracyClient_jll", "Libdl"] +git-tree-sha1 = "16439d004690d4086da35528f0c6b4d7006d6dae" +uuid = "e689c965-62c8-4b79-b2c5-8359227902fd" +version = "0.1.4" + + [deps.Tracy.extensions] + TracyProfilerExt = "TracyProfiler_jll" + + [deps.Tracy.weakdeps] + TracyProfiler_jll = "0c351ed6-8a68-550e-8b79-de6f926da83c" + [[deps.TranscodingStreams]] git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" @@ -3641,9 +3658,9 @@ version = "0.4.84" [[deps.TransmuteDims]] deps = ["Adapt", "ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Requires", "Strided"] -git-tree-sha1 = "5b6f1f2ba5e91983eabc47cb362f92d9a96b579f" +git-tree-sha1 = "488b1a1effa8c0b97cd3335a7c1cbd23a3f2f6d3" uuid = "24ddb15e-299a-5cc3-8414-dbddc482d9ca" -version = "0.1.16" +version = "0.1.17" [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] @@ -3658,31 +3675,19 @@ version = "1.6.0" [[deps.Turing]] deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "f21402d4be463b3f5c4017e11fa00280fefc5c2f" +git-tree-sha1 = "69d34ae3bacf554dc51b48624e07649e5ca16e4a" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.37.0" +version = "0.38.0" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" TuringOptimExt = "Optim" -[[deps.TuringBenchmarking]] -deps = ["ADTypes", "AbstractMCMC", "BenchmarkTools", "DynamicPPL", "ForwardDiff", "LinearAlgebra", "LogDensityProblems", "PrettyTables", "Requires", "ReverseDiff", "Zygote"] -git-tree-sha1 = "a03f2d71dfc88bf370d67c8ae84dfa109b2702bb" -uuid = "0db1332d-5c25-4deb-809f-459bc696f94f" -version = "0.5.9" - - [deps.TuringBenchmarking.extensions] - TuringBenchmarkingBridgeStanExt = "BridgeStan" - - [deps.TuringBenchmarking.weakdeps] - BridgeStan = "c88b6f0a-829e-4b0b-94b7-f06ab5908f5a" - [[deps.URIs]] -git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" +git-tree-sha1 = "cbbebadbcc76c5ca1cc4b4f3b0614b3e603b5000" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.5.1" +version = "1.5.2" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -3812,107 +3817,95 @@ git-tree-sha1 = "b8b243e47228b4a3877f1dd6aee0c5d56db7fcf4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" version = "2.13.6+1" -[[deps.XSLT_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "7d1671acbe47ac88e981868a078bd6b4e27c5191" -uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.42+0" - [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "56c6604ec8b2d82cc4cfe01aa03b00426aac7e1f" +git-tree-sha1 = "fee71455b0aaa3440dfdd54a9a36ccef829be7d4" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.6.4+1" +version = "5.8.1+0" [[deps.Xorg_libICE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c" +git-tree-sha1 = "a3ea76ee3f4facd7a64684f9af25310825ee3668" uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" -version = "1.1.1+0" +version = "1.1.2+0" [[deps.Xorg_libSM_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"] -git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce" +git-tree-sha1 = "9c7ad99c629a44f81e7799eb05ec2746abb5d588" uuid = "c834827a-8449-5923-a945-d239c165b7dd" -version = "1.2.4+0" +version = "1.2.6+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "9dafcee1d24c4f024e7edc92603cedba72118283" +git-tree-sha1 = "b5899b25d17bf1889d25906fb9deed5da0c15b3b" uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.8.6+3" +version = "1.8.12+0" [[deps.Xorg_libXau_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e9216fdcd8514b7072b43653874fd688e4c6c003" +git-tree-sha1 = "aa1261ebbac3ccc8d16558ae6799524c450ed16b" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.12+0" +version = "1.0.13+0" [[deps.Xorg_libXcursor_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] -git-tree-sha1 = "807c226eaf3651e7b2c468f687ac788291f9a89b" +git-tree-sha1 = "6c74ca84bbabc18c4547014765d194ff0b4dc9da" uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" -version = "1.2.3+0" +version = "1.2.4+0" [[deps.Xorg_libXdmcp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "89799ae67c17caa5b3b5a19b8469eeee474377db" +git-tree-sha1 = "52858d64353db33a56e13c341d7bf44cd0d7b309" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.5+0" +version = "1.1.6+0" [[deps.Xorg_libXext_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "d7155fea91a4123ef59f42c4afb5ab3b4ca95058" +git-tree-sha1 = 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"XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "1a74296303b6524a0472a8cb12d3d87a78eb3612" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXau_jll", "Xorg_libXdmcp_jll"] +git-tree-sha1 = "bfcaf7ec088eaba362093393fe11aa141fa15422" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.17.0+3" +version = "1.17.1+0" [[deps.Xorg_libxkbfile_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "dbc53e4cf7701c6c7047c51e17d6e64df55dca94" +git-tree-sha1 = "e3150c7400c41e207012b41659591f083f3ef795" uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" -version = "1.1.2+1" +version = "1.1.3+0" [[deps.Xorg_xcb_util_cursor_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"] @@ -3952,21 +3945,21 @@ version = "0.4.1+1" [[deps.Xorg_xkbcomp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] -git-tree-sha1 = "ab2221d309eda71020cdda67a973aa582aa85d69" +git-tree-sha1 = "801a858fc9fb90c11ffddee1801bb06a738bda9b" uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" -version = "1.4.6+1" +version = "1.4.7+0" [[deps.Xorg_xkeyboard_config_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] -git-tree-sha1 = "691634e5453ad362044e2ad653e79f3ee3bb98c3" +git-tree-sha1 = "00af7ebdc563c9217ecc67776d1bbf037dbcebf4" uuid = "33bec58e-1273-512f-9401-5d533626f822" -version = "2.39.0+0" +version = "2.44.0+0" [[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6dba04dbfb72ae3ebe5418ba33d087ba8aa8cb00" +git-tree-sha1 = "a63799ff68005991f9d9491b6e95bd3478d783cb" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.5.1+0" +version = "1.6.0+0" [[deps.Zlib_jll]] deps = ["Libdl"] @@ -3981,9 +3974,9 @@ version = "1.5.7+1" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "0b3c944f5d2d8b466c5d20a84c229c17c528f49e" +git-tree-sha1 = "8462a20f0fd85b4ef4a1b7310d33e7475d2bb14f" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.75" +version = "0.6.77" weakdeps = ["Colors", "Distances", "Tracker"] [deps.Zygote.extensions] @@ -4005,9 +3998,9 @@ version = "3.2.9+0" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6e50f145003024df4f5cb96c7fce79466741d601" +git-tree-sha1 = "b6a34e0e0960190ac2a4363a1bd003504772d631" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.56.3+0" +version = "0.61.1+0" [[deps.gperf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -4064,9 +4057,9 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "068dfe202b0a05b8332f1e8e6b4080684b9c7700" +git-tree-sha1 = "002748401f7b520273e2b506f61cab95d4701ccf" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.47+0" +version = "1.6.48+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] @@ -4109,7 +4102,7 @@ uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" version = "3.5.0+0" [[deps.xkbcommon_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "63406453ed9b33a0df95d570816d5366c92b7809" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +git-tree-sha1 = "c950ae0a3577aec97bfccf3381f66666bc416729" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+2" +version = "1.8.1+0" diff --git a/Project.toml b/Project.toml index daed8daf6..98434868e 100644 --- a/Project.toml +++ b/Project.toml @@ -48,9 +48,8 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c" StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -TuringBenchmarking = "0db1332d-5c25-4deb-809f-459bc696f94f" UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] -Turing = "0.37" +Turing = "0.38" diff --git a/_quarto.yml b/_quarto.yml index cf43d47c1..81cd0613d 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -32,7 +32,7 @@ website: text: Team right: # Current version - - text: "v0.37" + - text: "v0.38" menu: - text: Changelog href: https://turinglang.org/docs/changelog.html @@ -60,7 +60,7 @@ website: - usage/custom-distribution/index.qmd - usage/probability-interface/index.qmd - usage/modifying-logprob/index.qmd - - usage/generated-quantities/index.qmd + - usage/tracking-extra-quantities/index.qmd - usage/mode-estimation/index.qmd - usage/performance-tips/index.qmd - usage/sampler-visualisation/index.qmd @@ -190,7 +190,7 @@ using-turing-external-samplers: tutorials/docs-16-using-turing-external-samplers using-turing-mode-estimation: tutorials/docs-17-mode-estimation usage-probability-interface: tutorials/usage-probability-interface usage-custom-distribution: tutorials/usage-custom-distribution -usage-generated-quantities: tutorials/usage-generated-quantities +usage-tracking-extra-quantities: tutorials/tracking-extra-quantities usage-modifying-logprob: tutorials/usage-modifying-logprob contributing-guide: developers/contributing diff --git a/tutorials/bayesian-time-series-analysis/index.qmd b/tutorials/bayesian-time-series-analysis/index.qmd index 3f722dcaf..33dcb9962 100755 --- a/tutorials/bayesian-time-series-analysis/index.qmd +++ b/tutorials/bayesian-time-series-analysis/index.qmd @@ -175,7 +175,7 @@ end function get_decomposition(model, x, cyclic_features, chain, op) chain_params = Turing.MCMCChains.get_sections(chain, :parameters) - return generated_quantities(model(x, cyclic_features, op), chain_params) + return returned(model(x, cyclic_features, op), chain_params) end function plot_fit(x, y, decomp, ymax) diff --git a/tutorials/gaussian-mixture-models/index.qmd b/tutorials/gaussian-mixture-models/index.qmd index 145d55c62..b93bb6f3e 100755 --- a/tutorials/gaussian-mixture-models/index.qmd +++ b/tutorials/gaussian-mixture-models/index.qmd @@ -403,7 +403,7 @@ chains = sample(model, sampler, MCMCThreads(), nsamples, nchains, discard_initia Given a sample from the marginalized posterior, these assignments can be recovered with: ```{julia} -assignments = mean(generated_quantities(gmm_recover(x), chains)); +assignments = mean(returned(gmm_recover(x), chains)); ``` ```{julia} diff --git a/tutorials/gaussian-processes-introduction/index.qmd b/tutorials/gaussian-processes-introduction/index.qmd index 5f7378157..649f80484 100755 --- a/tutorials/gaussian-processes-introduction/index.qmd +++ b/tutorials/gaussian-processes-introduction/index.qmd @@ -146,7 +146,7 @@ posterior probability of success at any distance we choose: ```{julia} d_pred = 1:0.2:21 -samples = map(generated_quantities(m_post, chn)[1:10:end]) do x +samples = map(returned(m_post, chn)[1:10:end]) do x return logistic.(rand(posterior(x.fx, x.f_latent)(d_pred, 1e-4))) end p = plot() diff --git a/tutorials/hidden-markov-models/index.qmd b/tutorials/hidden-markov-models/index.qmd index 2e318a8c8..51aa68d5c 100755 --- a/tutorials/hidden-markov-models/index.qmd +++ b/tutorials/hidden-markov-models/index.qmd @@ -123,11 +123,11 @@ The priors on our transition matrix are noninformative, using `T[i] ~ Dirichlet( end; ``` -We will use a combination of two samplers ([HMC](https://turinglang.org/dev/docs/library/#Turing.Inference.HMC) and [Particle Gibbs](https://turinglang.org/dev/docs/library/#Turing.Inference.PG)) by passing them to the [Gibbs](https://turinglang.org/dev/docs/library/#Turing.Inference.Gibbs) sampler. The Gibbs sampler allows for compositional inference, where we can utilize different samplers on different parameters. +We will use a combination of two samplers (HMC and Particle Gibbs) by passing them to the Gibbs sampler. The Gibbs sampler allows for compositional inference, where we can utilize different samplers on different parameters. (For API details of these samplers, please see [Turing.jl's API documentation](https://turinglang.org/Turing.jl/stable/api/Inference/).) In this case, we use HMC for `m` and `T`, representing the emission and transition matrices respectively. We use the Particle Gibbs sampler for `s`, the state sequence. You may wonder why it is that we are not assigning `s` to the HMC sampler, and why it is that we need compositional Gibbs sampling at all. -The parameter `s` is not a continuous variable. It is a vector of **integers**, and thus Hamiltonian methods like HMC and [NUTS](https://turinglang.org/dev/docs/library/#Turing.Inference.NUTS) won't work correctly. Gibbs allows us to apply the right tools to the best effect. If you are a particularly advanced user interested in higher performance, you may benefit from setting up your Gibbs sampler to use [different automatic differentiation]({{}}#compositional-sampling-with-differing-ad-modes) backends for each parameter space. +The parameter `s` is not a continuous variable. It is a vector of **integers**, and thus Hamiltonian methods like HMC and NUTS won't work correctly. Gibbs allows us to apply the right tools to the best effect. If you are a particularly advanced user interested in higher performance, you may benefit from setting up your Gibbs sampler to use [different automatic differentiation]({{}}#compositional-sampling-with-differing-ad-modes) backends for each parameter space. Time to run our sampler. diff --git a/usage/automatic-differentiation/index.qmd b/usage/automatic-differentiation/index.qmd index e95d28083..9143712a6 100755 --- a/usage/automatic-differentiation/index.qmd +++ b/usage/automatic-differentiation/index.qmd @@ -14,8 +14,8 @@ Pkg.instantiate(); ## Switching AD Modes -Turing currently supports four automatic differentiation (AD) backends for sampling: [ForwardDiff](https://github.com/JuliaDiff/ForwardDiff.jl) for forward-mode AD; and [Mooncake](https://github.com/compintell/Mooncake.jl), [ReverseDiff](https://github.com/JuliaDiff/ReverseDiff.jl), and [Zygote](https://github.com/FluxML/Zygote.jl) for reverse-mode AD. -`ForwardDiff` is automatically imported by Turing. To utilize `Mooncake`, `Zygote`, or `ReverseDiff` for AD, users must explicitly import them with `import Mooncake`, `import Zygote` or `import ReverseDiff`, alongside `using Turing`. +Turing currently supports four automatic differentiation (AD) backends for sampling: [ForwardDiff](https://github.com/JuliaDiff/ForwardDiff.jl) for forward-mode AD; and [Mooncake](https://github.com/compintell/Mooncake.jl) and [ReverseDiff](https://github.com/JuliaDiff/ReverseDiff.jl) for reverse-mode AD. +`ForwardDiff` is automatically imported by Turing. To utilize `Mooncake` or `ReverseDiff` for AD, users must explicitly import them with `import Mooncake` or `import ReverseDiff`, alongside the usual `using Turing`. As of Turing version v0.30, the global configuration flag for the AD backend has been removed in favour of [`AdTypes.jl`](https://github.com/SciML/ADTypes.jl), allowing users to specify the AD backend for individual samplers independently. Users can pass the `adtype` keyword argument to the sampler constructor to select the desired AD backend, with the default being `AutoForwardDiff(; chunksize=0)`. @@ -24,8 +24,6 @@ For `ForwardDiff`, pass `adtype=AutoForwardDiff(; chunksize)` to the sampler con For `ReverseDiff`, pass `adtype=AutoReverseDiff()` to the sampler constructor. An additional keyword argument called `compile` can be provided to `AutoReverseDiff`. It specifies whether to pre-record the tape only once and reuse it later (`compile` is set to `false` by default, which means no pre-recording). This can substantially improve performance, but risks silently incorrect results if not used with care. - - Pre-recorded tapes should only be used if you are absolutely certain that the sequence of operations performed in your code does not change between different executions of your model. Thus, e.g., in the model definition and all implicitly and explicitly called functions in the model, all loops should be of fixed size, and `if`-statements should consistently execute the same branches. @@ -33,9 +31,9 @@ For instance, `if`-statements with conditions that can be determined at compile However, `if`-statements that depend on the model parameters can take different branches during sampling; hence, the compiled tape might be incorrect. Thus you must not use compiled tapes when your model makes decisions based on the model parameters, and you should be careful if you compute functions of parameters that those functions do not have branching which might cause them to execute different code for different values of the parameter. -For `Zygote`, pass `adtype=AutoZygote()` to the sampler constructor. +The previously used interface functions including `ADBackend`, `setadbackend`, `setsafe`, `setchunksize`, and `setrdcache` have been removed. -And the previously used interface functions including `ADBackend`, `setadbackend`, `setsafe`, `setchunksize`, and `setrdcache` are deprecated and removed. +For `Mooncake`, pass `adtype=AutoMooncake(; config=nothing)` to the sampler constructor. ## Compositional Sampling with Differing AD Modes @@ -70,9 +68,22 @@ Generally, reverse-mode AD, for instance `ReverseDiff`, is faster when sampling If the differentiation method is not specified in this way, Turing will default to using whatever the global AD backend is. Currently, this defaults to `ForwardDiff`. -The most reliable way to ensure you are using the fastest AD that works for your problem is to benchmark them using [`TuringBenchmarking`](https://github.com/TuringLang/TuringBenchmarking.jl): +The most reliable way to ensure you are using the fastest AD that works for your problem is to benchmark them using the functionality in DynamicPPL (see [the API documentation](https://turinglang.org/DynamicPPL.jl/stable/api/#AD-testing-and-benchmarking-utilities)): ```{julia} -using TuringBenchmarking -benchmark_model(gdemo(1.5, 2), adbackends=[AutoForwardDiff(), AutoReverseDiff()]) +using DynamicPPL.TestUtils.AD: run_ad, ADResult +using ForwardDiff, ReverseDiff + +model = gdemo(1.5, 2) + +for adtype in [AutoForwardDiff(), AutoReverseDiff()] + result = run_ad(model, adtype; benchmark=true) + @show result.time_vs_primal +end ``` + +In this specific instance, ForwardDiff is clearly faster (due to the small size of the model). + +We also have a table of benchmarks for various models and AD backends in [the ADTests website](https://turinglang.org/ADTests/). +These models aim to capture a variety of different Turing.jl features. +If you have suggestions for things to include, please do let us know by [creating an issue on GitHub](https://github.com/TuringLang/ADTests/issues/new)! diff --git a/usage/generated-quantities/index.qmd b/usage/generated-quantities/index.qmd deleted file mode 100755 index c702e215e..000000000 --- a/usage/generated-quantities/index.qmd +++ /dev/null @@ -1,68 +0,0 @@ ---- -title: Generated Quantities -engine: julia -aliases: - - ../../tutorials/usage-generated-quantities/index.html ---- - -```{julia} -#| echo: false -#| output: false -using Pkg; -Pkg.instantiate(); -``` - -Often, the most natural parameterization for a model is not the most computationally feasible. -Consider the following (efficiently reparametrized) implementation of Neal's funnel [(Neal, 2003)](https://arxiv.org/abs/physics/0009028): - -```{julia} -using Turing - -@model function Neal() - # Raw draws - y_raw ~ Normal(0, 1) - x_raw ~ arraydist([Normal(0, 1) for i in 1:9]) - - # Transform: - y = 3 * y_raw - x = exp.(y ./ 2) .* x_raw - - # Return: - return [x; y] -end -``` - -In this case, the random variables exposed in the chain (`x_raw`, `y_raw`) are not in a helpful form — what we're after are the deterministically transformed variables `x` and `y`. - -More generally, there are often quantities in our models that we might be interested in viewing, but which are not explicitly present in our chain. - -We can generate draws from these variables — in this case, `x` and `y` — by adding them as a return statement to the model, and then calling `generated_quantities(model, chain)`. Calling this function outputs an array of values specified in the return statement of the model. - -For example, in the above reparametrization, we sample from our model: - -```{julia} -chain = sample(Neal(), NUTS(), 1000; progress=false) -``` - -Notice that only `x_raw` and `y_raw` are stored in the chain; `x` and `y` are not because they do not appear on the left-hand side of a tilde-statement. - -To get `x` and `y`, we can then call: - -```{julia} -generated_quantities(Neal(), chain) -``` - -Each element of this corresponds to an array with the values of `x1, x2, ..., x9, y` for each posterior sample. - -In this case, it might be useful to reorganize our output into a matrix for plotting: - -```{julia} -reparam_chain = reduce(hcat, generated_quantities(Neal(), chain))' -``` - -from which we can recover a vector of our samples: - -```{julia} -x1_samples = reparam_chain[:, 1] -y_samples = reparam_chain[:, 10] -``` diff --git a/usage/tracking-extra-quantities/index.qmd b/usage/tracking-extra-quantities/index.qmd new file mode 100755 index 000000000..40017716d --- /dev/null +++ b/usage/tracking-extra-quantities/index.qmd @@ -0,0 +1,152 @@ +--- +title: Tracking Extra Quantities +engine: julia +aliases: + - ../../tutorials/usage-generated-quantities/index.html + - ../generated-quantities/index.html +--- + +```{julia} +#| echo: false +#| output: false +using Pkg; +Pkg.instantiate(); +``` + +Often, there are quantities in models that we might be interested in viewing the values of, but which are not random variables in the model that are explicitly drawn from a distribution. + +As a motivating example, the most natural parameterization for a model might not be the most computationally feasible. +Consider the following (efficiently reparametrized) implementation of Neal's funnel [(Neal, 2003)](https://arxiv.org/abs/physics/0009028): + +```{julia} +using Turing +setprogress!(false) + +@model function Neal() + # Raw draws + y_raw ~ Normal(0, 1) + x_raw ~ arraydist([Normal(0, 1) for i in 1:9]) + + # Transform: + y = 3 * y_raw + x = exp.(y ./ 2) .* x_raw + return nothing +end +``` + +In this case, the random variables exposed in the chain (`x_raw`, `y_raw`) are not in a helpful form — what we're after are the deterministically transformed variables `x` and `y`. + +There are two ways to track these extra quantities in Turing.jl. + +## Using `:=` (during inference) + +The first way is to use the `:=` operator, which behaves exactly like `=` except that the values of the variables on its left-hand side are automatically added to the chain returned by the sampler. +For example: + +```{julia} +@model function Neal_coloneq() + # Raw draws + y_raw ~ Normal(0, 1) + x_raw ~ arraydist([Normal(0, 1) for i in 1:9]) + + # Transform: + y := 3 * y_raw + x := exp.(y ./ 2) .* x_raw +end + +sample(Neal_coloneq(), NUTS(), 1000) +``` + +## Using `returned` (post-inference) + +Alternatively, one can specify the extra quantities as part of the model function's return statement: + +```{julia} +@model function Neal_return() + # Raw draws + y_raw ~ Normal(0, 1) + x_raw ~ arraydist([Normal(0, 1) for i in 1:9]) + + # Transform and return as a NamedTuple + y = 3 * y_raw + x = exp.(y ./ 2) .* x_raw + return (x=x, y=y) +end + +chain = sample(Neal_return(), NUTS(), 1000) +``` + +The sampled chain does not contain `x` and `y`, but we can extract the values using the `returned` function. +Calling this function outputs an array: + +```{julia} +nts = returned(Neal_return(), chain) +``` + +where each element of which is a NamedTuple, as specified in the return statement of the model. + +```{julia} +nts[1] +``` + +## Which to use? + +There are some pros and cons of using `returned`, as opposed to `:=`. + +Firstly, `returned` is more flexible, as it allows you to track any type of object; `:=` only works with variables that can be inserted into an `MCMCChains.Chains` object. +(Notice that `x` is a vector, and in the first case where we used `:=`, reconstructing the vector value of `x` can also be rather annoying as the chain stores each individual element of `x` separately.) + +A drawback is that naively using `returned` can lead to unnecessary computation during inference. +This is because during the sampling process, the return values are also calculated (since they are part of the model function), but then thrown away. +So, if the extra quantities are expensive to compute, this can be a problem. + +To avoid this, you will essentially have to create two different models, one for inference and one for post-inference. +The simplest way of doing this is to add a parameter to the model argument: + +```{julia} +@model function Neal_coloneq_optional(track::Bool) + # Raw draws + y_raw ~ Normal(0, 1) + x_raw ~ arraydist([Normal(0, 1) for i in 1:9]) + + if track + y = 3 * y_raw + x = exp.(y ./ 2) .* x_raw + return (x=x, y=y) + else + return nothing + end +end + +chain = sample(Neal_coloneq_optional(false), NUTS(), 1000) +``` + +The above ensures that `x` and `y` are not calculated during inference, but allows us to still use `returned` to extract them: + +```{julia} +returned(Neal_coloneq_optional(true), chain) +``` + +Another equivalent option is to use a submodel: + +```{julia} +@model function Neal() + y_raw ~ Normal(0, 1) + x_raw ~ arraydist([Normal(0, 1) for i in 1:9]) + return (x_raw=x_raw, y_raw=y_raw) +end + +chain = sample(Neal(), NUTS(), 1000) + +@model function Neal_with_extras() + neal ~ to_submodel(Neal(), false) + y = 3 * neal.y_raw + x = exp.(y ./ 2) .* neal.x_raw + return (x=x, y=y) +end + +returned(Neal_with_extras(), chain) +``` + +Note that for the `returned` call to work, the `Neal_with_extras()` model must have the same variable names as stored in `chain`. +This means the submodel `Neal()` must not be prefixed, i.e. `to_submodel()` must be passed a second parameter `false`.