diff --git a/Manifest.toml b/Manifest.toml index c94baf232..2f8687805 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,12 +2,12 @@ julia_version = "1.11.6" manifest_format = "2.0" -project_hash = "3c5b0696513a84be8573e377b59e1ab532411868" +project_hash = "0250fe85007baf77c93e2189ee544ed354b8099e" [[deps.ADTypes]] -git-tree-sha1 = "7927b9af540ee964cc5d1b73293f1eb0b761a3a1" +git-tree-sha1 = "60665b326b75db6517939d0e1875850bc4a54368" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.16.0" +version = "1.17.0" weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] [deps.ADTypes.extensions] @@ -40,9 +40,13 @@ version = "5.7.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random", "StatsBase"] -git-tree-sha1 = "478b0b6176125cf0a5e6e9fd69fdd0923754531c" +git-tree-sha1 = "b7a856399119394a573141c553aeb5b674a500b5" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.12.0" +version = "0.13.0" +weakdeps = ["Distributions", "LinearAlgebra"] + + [deps.AbstractPPL.extensions] + AbstractPPLDistributionsExt = ["Distributions", "LinearAlgebra"] [[deps.AbstractTrees]] git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" @@ -86,9 +90,9 @@ weakdeps = ["SparseArrays", "StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Setfield", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "9f75990a04e3ee45d80b19778ba9d2bb7ad4d5ee" +git-tree-sha1 = "22496647c061d00217759e95a18d601c959df0c9" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.8.0" +version = "0.8.1" [deps.AdvancedHMC.extensions] AdvancedHMCADTypesExt = "ADTypes" @@ -223,9 +227,9 @@ version = "1.11.0" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "b5bb4dc6248fde467be2a863eb8452993e74d402" +git-tree-sha1 = "29bb0eb6f578a587a49da16564705968667f5fa8" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "1.1.1" +version = "1.1.2" [deps.Atomix.extensions] AtomixCUDAExt = "CUDA" @@ -298,9 +302,9 @@ version = "0.1.1" [[deps.Bijectors]] deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "5eb5a58ed34e012d7f8d665cb5198252e128e907" +git-tree-sha1 = "35ba30573d4f83242f1e788c87ca792c83553c9e" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.15.8" +version = "0.15.9" weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker"] [deps.Bijectors.extensions] @@ -395,10 +399,10 @@ uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.5.0" [[deps.CPUSummary]] -deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] -git-tree-sha1 = "5a97e67919535d6841172016c9530fd69494e5ec" +deps = ["CpuId", "IfElse", "PrecompileTools", "Preferences", "Static"] +git-tree-sha1 = "f3a21d7fc84ba618a779d1ed2fcca2e682865bab" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.2.6" +version = "0.2.7" [[deps.CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] @@ -443,9 +447,9 @@ version = "1.72.5" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "06ee8d1aa558d2833aa799f6f0b31b30cada405f" +git-tree-sha1 = "e4c6a16e77171a5f5e25e9646617ab1c276c5607" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.25.2" +version = "1.26.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -685,9 +689,9 @@ version = "0.1.2" [[deps.DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "FastBroadcast", "ForwardDiff", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack", "SymbolicIndexingInterface"] -git-tree-sha1 = "484cceb16c5ed95f4a2a405f3579f480ec0dff9a" +git-tree-sha1 = "d9b1e66070ce15bc2b9c3d5af6b94f693fc03ba4" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.55.0" +version = "5.58.0" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -703,9 +707,9 @@ version = "0.4.0" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "6f8f25122389ba34e491bdfe143ae16fda37cad3" +git-tree-sha1 = "6fecfae8b2d9983e939378c8eacff6562e8a2567" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.180.0" +version = "6.183.0" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -743,9 +747,9 @@ version = "6.180.0" [[deps.DiffEqCallbacks]] deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "80a782f3e65d4900dcf5f2cb71f5e19d9459c04a" +git-tree-sha1 = "397ef6fffcf418ba55264ba785b032b8a136903b" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "4.8.0" +version = "4.9.0" [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] @@ -777,9 +781,9 @@ version = "7.16.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "f620da805b82bec64ab4d5f881c7592c82dbc08a" +git-tree-sha1 = "54d7b8c74408048aea9c055ac8573b2b5c5ec11f" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.7.3" +version = "0.7.4" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -894,10 +898,10 @@ uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb" version = "3.5.1" [[deps.DynamicPPL]] -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 = "07218fc45d4f1abc9de4498e8cf966b6672c84f0" +deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Printf", "Random", "Requires", "Statistics", "Test"] +git-tree-sha1 = "e36add2952240379bd53b83e76cfd3a8c56748d6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.36.15" +version = "0.37.0" [deps.DynamicPPL.extensions] DynamicPPLChainRulesCoreExt = ["ChainRulesCore"] @@ -929,9 +933,9 @@ version = "1.0.5" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "e36968f0a43d9a3b627ac94d5346b458ce14066d" +git-tree-sha1 = "1a9c9e3401f5d024612a70d24a19517b2dbc1824" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.65" +version = "0.13.67" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -1123,9 +1127,9 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] -git-tree-sha1 = "f089ab1f834470c525562030c8cfde4025d5e915" +git-tree-sha1 = "d84e026183bb3fc764110ae98792c2e004f8c240" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.27.0" +version = "2.28.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" @@ -1466,10 +1470,13 @@ version = "0.2.4" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] -git-tree-sha1 = "f8da88993c914357031daf0023f18748ff473924" +git-tree-sha1 = "f5b57507a36f05509e72120aa84d5c3747dbd70e" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.16.1" -weakdeps = ["FastBroadcast"] +version = "9.17.0" +weakdeps = ["Adapt", "FastBroadcast", "KernelAbstractions"] + + [deps.JumpProcesses.extensions] + JumpProcessesKernelAbstractionsExt = ["Adapt", "KernelAbstractions"] [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] @@ -1562,9 +1569,9 @@ version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "4f34eaabe49ecb3fb0d58d6015e32fd31a733199" +git-tree-sha1 = "52e1296ebbde0db845b356abbbe67fb82a0a116c" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.8" +version = "0.16.9" [deps.Latexify.extensions] DataFramesExt = "DataFrames" @@ -1731,15 +1738,18 @@ version = "1.11.0" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "d768ff40cc3fe42581708696b24ee65dccc9c6ba" +git-tree-sha1 = "1c597eceb5ead73dae17ffa4dcc1160e3e4da1f3" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "3.24.0" +version = "3.28.0" [deps.LinearSolve.extensions] + LinearSolveAMDGPUExt = "AMDGPU" + LinearSolveBLISExt = ["blis_jll", "LAPACK_jll"] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" LinearSolveCUDSSExt = "CUDSS" + LinearSolveCUSOLVERRFExt = ["CUSOLVERRF", "SparseArrays"] LinearSolveEnzymeExt = "EnzymeCore" LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveFastLapackInterfaceExt = "FastLapackInterface" @@ -1755,10 +1765,12 @@ version = "3.24.0" LinearSolveSparspakExt = ["SparseArrays", "Sparspak"] [deps.LinearSolve.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + CUSOLVERRF = "a8cc9031-bad2-4722-94f5-40deabb4245c" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641" @@ -1767,11 +1779,13 @@ version = "3.24.0" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" + LAPACK_jll = "51474c39-65e3-53ba-86ba-03b1b862ec14" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Sparspak = "e56a9233-b9d6-4f03-8d0f-1825330902ac" + blis_jll = "6136c539-28a5-5bf0-87cc-b183200dce32" [[deps.LogDensityProblems]] deps = ["ArgCheck", "DocStringExtensions", "Random"] @@ -1870,9 +1884,9 @@ version = "1.16.0" [[deps.LuxCore]] deps = ["Compat", "DispatchDoctor", "Random"] -git-tree-sha1 = "48d45736aae190b1b41c1db5242fad955f0eff1d" +git-tree-sha1 = "a72b6b530f39a87d1327b90f5def4bce48eb1a52" uuid = "bb33d45b-7691-41d6-9220-0943567d0623" -version = "1.2.6" +version = "1.3.0" [deps.LuxCore.extensions] LuxCoreArrayInterfaceReverseDiffExt = ["ArrayInterface", "ReverseDiff"] @@ -1942,9 +1956,9 @@ version = "7.1.0" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "a586f05dd16a50c490ed95415b2a829b8cf5d57f" +git-tree-sha1 = "526c98cd41028da22c01cb8a203246799ad853a8" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.3.14" +version = "0.3.15" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] @@ -2114,9 +2128,9 @@ uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" version = "1.2.0" [[deps.MistyClosures]] -git-tree-sha1 = "1142aefd845c608f3c70e4c202c4aae725cab67b" +git-tree-sha1 = "d1a692e293c2a0dc8fda79c04cad60582f3d4de3" uuid = "dbe65cb8-6be2-42dd-bbc5-4196aaced4f4" -version = "2.0.0" +version = "2.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -2298,9 +2312,9 @@ version = "4.10.0" [[deps.NonlinearSolveBase]] deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "ee395563ae6ffaecbdf86d430440fddc779253a4" +git-tree-sha1 = "1d42a315ba627ca0027d49d0efb44e3d88db24aa" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "1.13.0" +version = "1.14.0" weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"] [deps.NonlinearSolveBase.extensions] @@ -2314,15 +2328,15 @@ weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "Linear [[deps.NonlinearSolveFirstOrder]] deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "65101a20b135616a13625ae6f84b052ef5780363" +git-tree-sha1 = "3f1198ae5cbf21e84b8251a9e62fa1f888f3e4cb" uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" -version = "1.6.0" +version = "1.7.0" [[deps.NonlinearSolveQuasiNewton]] deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] -git-tree-sha1 = "3e04c917d4e3cd48b2a5091b6f76c720bb3f7362" +git-tree-sha1 = "40dfaf1bf74f1f700f81d0002d4dd90999598eb2" uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" -version = "1.7.0" +version = "1.8.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveQuasiNewton.extensions] @@ -2330,9 +2344,9 @@ weakdeps = ["ForwardDiff"] [[deps.NonlinearSolveSpectralMethods]] deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "3398222199e4b9ca0b5840907fb509f28f1a2fdc" +git-tree-sha1 = "84de5a469e119eb2c22ae07c543dc4e7f7001ee7" uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" -version = "1.2.0" +version = "1.3.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveSpectralMethods.extensions] @@ -2340,9 +2354,9 @@ weakdeps = ["ForwardDiff"] [[deps.ObjectFile]] deps = ["Reexport", "StructIO"] -git-tree-sha1 = "09b1fe6ff16e6587fa240c165347474322e77cf1" +git-tree-sha1 = "22faba70c22d2f03e60fbc61da99c4ebfc3eb9ba" uuid = "d8793406-e978-5875-9003-1fc021f44a92" -version = "0.4.4" +version = "0.5.0" [[deps.Observables]] git-tree-sha1 = "7438a59546cf62428fc9d1bc94729146d37a7225" @@ -2388,9 +2402,9 @@ version = "1.5.0" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "87510f7292a2b21aeff97912b0898f9553cc5c2c" +git-tree-sha1 = "2ae7d4ddec2e13ad3bddf5c0796f7547cf682391" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.5.1+0" +version = "3.5.2+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -2490,22 +2504,22 @@ uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" version = "6.101.0" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] -deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "82f78099ecf4e0fa53545811318520d87e7fe0b8" +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] +git-tree-sha1 = "09aae1486c767caa6bce9de892455cbdf5a6fbc8" uuid = "89bda076-bce5-4f1c-845f-551c83cdda9a" -version = "1.2.0" +version = "1.5.0" [[deps.OrdinaryDiffEqBDF]] -deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "b0bbc6541ea4a27974bd67e0a10b26211cb95e58" +deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "ce8db53fd1e4e41c020fd53961e7314f75e4c21c" uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" -version = "1.7.0" +version = "1.10.1" [[deps.OrdinaryDiffEqCore]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", 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"OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "778c7d379265f17f40dbe9aaa6f6a2a08bc7fa3e" uuid = "b1df2697-797e-41e3-8120-5422d3b24e4a" -version = "1.2.0" +version = "1.5.0" [[deps.OrdinaryDiffEqVerner]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "91f0a004785791c8c538d34a67c19cf3f7776e85" +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "185578fa7c38119d4318326f9375f1cba0f0ce53" uuid = "79d7bb75-1356-48c1-b8c0-6832512096c2" -version = "1.3.0" +version = "1.6.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -2738,9 +2752,9 @@ version = "1.4.3" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "3db9167c618b290a05d4345ca70de6d95304a32a" +git-tree-sha1 = "9a9216c0cf706cb2cc58fd194878180e3e51e8c0" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.17" +version = "1.40.18" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -2758,9 +2772,9 @@ version = "1.40.17" [[deps.PoissonRandom]] deps = ["LogExpFunctions", "Random"] -git-tree-sha1 = "bb178012780b34046c6d1600a315d8dbee89d83d" +git-tree-sha1 = "c1ea45aa9f209fe97192afa233907bc4e551c8aa" uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" -version = "0.4.5" +version = "0.4.6" [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] @@ -2787,13 +2801,14 @@ uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" [[deps.PreallocationTools]] -deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "2cc315bb7f6e4d59081bad744cdb911d6374fc7f" +deps = ["Adapt", "ArrayInterface", "PrecompileTools"] +git-tree-sha1 = "a0d5f963cfee70bee26dfa137a732e759e24436a" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.29" -weakdeps = ["ReverseDiff", "SparseConnectivityTracer"] +version = "0.4.31" +weakdeps = ["ForwardDiff", "ReverseDiff", "SparseConnectivityTracer"] [deps.PreallocationTools.extensions] + PreallocationToolsForwardDiffExt = "ForwardDiff" PreallocationToolsReverseDiffExt = "ReverseDiff" PreallocationToolsSparseConnectivityTracerExt = "SparseConnectivityTracer" @@ -2805,9 +2820,9 @@ version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" +git-tree-sha1 = "0f27480397253da18fe2c12a4ba4eb9eb208bf3d" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.3" +version = "1.5.0" [[deps.PrettyPrint]] git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" @@ -2944,10 +2959,10 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "f8726bd5a8b7f5f5d3f6c0ce4793454a599b5243" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "7c7ac305885b1e0292585d087ecd60331a705965" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.36.0" +version = "3.37.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -2958,6 +2973,7 @@ version = "3.36.0" RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] RecursiveArrayToolsStructArraysExt = "StructArrays" + RecursiveArrayToolsTablesExt = ["Tables"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" @@ -2970,6 +2986,7 @@ version = "3.36.0" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -3051,15 +3068,15 @@ version = "0.1.0" [[deps.SSMProblems]] deps = ["AbstractMCMC", "Distributions", "Random"] -git-tree-sha1 = "4fedd69d5a5392cfed4edc647972de5b5b25a90a" +git-tree-sha1 = "b00814e67e8aacda2073865a3832e6cc378ea504" uuid = "26aad666-b158-4e64-9d35-0e672562fa48" -version = "0.5.0" +version = "0.5.1" [[deps.SciMLBase]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] -git-tree-sha1 = "1c7fd50df465f0684f04f3a63736eac01999c659" +git-tree-sha1 = "95ce48fe76b9530799429244392853b5405469c1" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.107.0" +version = "2.109.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3090,9 +3107,9 @@ version = "0.1.8" [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "7d3a1519dc4d433a6b20035eaff20bde8be77c66" +git-tree-sha1 = "aea915a39b547c48a18ee041120db1ae8df5a691" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "1.4.0" +version = "1.5.0" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -3101,9 +3118,9 @@ weakdeps = ["SparseArrays", "StaticArraysCore"] [[deps.SciMLSensitivity]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "Enzyme", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEqCore", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLJacobianOperators", "SciMLStructures", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"] -git-tree-sha1 = "a5d3e3ccedbce9c0c07b4ffa60787b58bdc6d360" +git-tree-sha1 = "e1b5f9b3be1452591c40a88de9efb265ebe76030" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.88.0" +version = "7.89.0" weakdeps = ["Mooncake"] [deps.SciMLSensitivity.extensions] @@ -3189,9 +3206,9 @@ weakdeps = ["ChainRulesCore", "DiffEqBase", "ReverseDiff", "Tracker"] [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] -git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" +git-tree-sha1 = "be8eeac05ec97d379347584fa9fe2f5f76795bcb" uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" -version = "0.9.4" +version = "0.9.5" [[deps.SimpleUnPack]] git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" @@ -3204,9 +3221,9 @@ version = "1.11.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" +git-tree-sha1 = "64d974c2e6fdf07f8155b5b2ca2ffa9069b608d9" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.2.1" +version = "1.2.2" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] @@ -3344,9 +3361,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] [[deps.StatsModels]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "9022bcaa2fc1d484f1326eaa4db8db543ca8c66d" +git-tree-sha1 = "728d276a5adc2f1cbb800eec4b63d0a8221024b4" uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" -version = "0.7.4" +version = "0.7.5" [[deps.StatsPlots]] deps = ["AbstractFFTs", "Clustering", "DataStructures", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] @@ -3443,10 +3460,14 @@ uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164" version = "5.2.3+0" [[deps.SymbolicIndexingInterface]] -deps = ["Accessors", "ArrayInterface", "PrettyTables", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "59ca6eddaaa9849e7de9fd1153b6faf0b1db7b80" +deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] +git-tree-sha1 = "93104ca226670c0cb92ba8bc6998852ad55a2d4c" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.42" +version = "0.3.43" +weakdeps = ["PrettyTables"] + + [deps.SymbolicIndexingInterface.extensions] + SymbolicIndexingInterfacePrettyTablesExt = "PrettyTables" [[deps.TOML]] deps = ["Dates"] @@ -3601,9 +3622,9 @@ version = "1.6.0" [[deps.Turing]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "3fd5118fd33c708bec35d892f86a5455e9402d66" +git-tree-sha1 = "ed944065575fd4a6d9d2b802bbd914b53f08bce8" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.39.9" +version = "0.40.1" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] diff --git a/Project.toml b/Project.toml index af37a3fd6..852391861 100644 --- a/Project.toml +++ b/Project.toml @@ -55,4 +55,4 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" [compat] -Turing = "0.39" +Turing = "0.40" diff --git a/_quarto.yml b/_quarto.yml index 9bab2644c..4ecace484 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -41,7 +41,7 @@ website: href: https://turinglang.org/team/ right: # Current version - - text: "v0.39" + - text: "v0.40" menu: - text: Changelog href: https://turinglang.org/docs/changelog.html diff --git a/usage/automatic-differentiation/index.qmd b/usage/automatic-differentiation/index.qmd index 768845942..5ae168473 100755 --- a/usage/automatic-differentiation/index.qmd +++ b/usage/automatic-differentiation/index.qmd @@ -91,7 +91,7 @@ model = gdemo(1.5, 2) for adtype in [AutoForwardDiff(), AutoReverseDiff()] result = run_ad(model, adtype; benchmark=true) - @show result.time_vs_primal + @show result.grad_time / result.primal_time end ```