diff --git a/Manifest.toml b/Manifest.toml index e41cb809e..68d15ecd9 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -5,9 +5,9 @@ manifest_format = "2.0" project_hash = "296b7e06e398e8898b40f44ed92b4d60c484484c" [[deps.ADTypes]] -git-tree-sha1 = "be7ae030256b8ef14a441726c4c37766b90b93a3" +git-tree-sha1 = "7927b9af540ee964cc5d1b73293f1eb0b761a3a1" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.15.0" +version = "1.16.0" weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] [deps.ADTypes.extensions] @@ -33,10 +33,10 @@ uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" version = "0.5.24" [[deps.AbstractMCMC]] -deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] -git-tree-sha1 = "fdf711adc3fab05756e391ff92c38645b8e6847a" +deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers", "UUIDs"] +git-tree-sha1 = "e4b6a25ba2e033c74ea11720daacafbc2ab50a7e" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "5.6.3" +version = "5.7.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random", "StatsBase"] @@ -118,9 +118,9 @@ weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] [[deps.AdvancedPS]] deps = ["AbstractMCMC", "Distributions", "Random", "Random123", "Requires", "SSMProblems", "StatsFuns"] -git-tree-sha1 = "31ba83dcaa79c29ad7205770b701950a94882b0b" +git-tree-sha1 = "5d34d826ece67ce790d4a7f3f97d837e52aba7f8" uuid = "576499cb-2369-40b2-a588-c64705576edc" -version = "0.6.2" +version = "0.7.0" weakdeps = ["Libtask"] [deps.AdvancedPS.extensions] @@ -208,10 +208,10 @@ version = "7.19.0" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ArrayLayouts]] -deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "4e25216b8fea1908a0ce0f5d87368587899f75be" +deps = ["FillArrays", "LinearAlgebra", "StaticArrays"] +git-tree-sha1 = "120e392af69350960b1d3b89d41dcc1d66543858" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.11.1" +version = "1.11.2" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -223,9 +223,9 @@ 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" @@ -344,9 +344,9 @@ version = "1.8.0" [[deps.BoundaryValueDiffEqCore]] deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] -git-tree-sha1 = "9b302ba0af3e17e8d468ae95af13415016be8ab0" +git-tree-sha1 = "b7b4d8cc80f116eab2eb6124dba58ea7aef31b85" uuid = "56b672f2-a5fe-4263-ab2d-da677488eb3a" -version = "1.11.0" +version = "1.11.1" [[deps.BoundaryValueDiffEqFIRK]] deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] @@ -395,10 +395,10 @@ 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 +443,9 @@ 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] @@ -545,9 +545,9 @@ version = "1.0.0" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "3a3dfb30697e96a440e4149c8c51bf32f818c0f3" +git-tree-sha1 = "0037835448781bb46feb39866934e243886d756a" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.17.0" +version = "4.18.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -560,9 +560,9 @@ version = "1.1.1+0" [[deps.ComponentArrays]] deps = ["Adapt", "ArrayInterface", "ChainRulesCore", "ConstructionBase", "Functors", "LinearAlgebra", "StaticArrayInterface", "StaticArraysCore"] -git-tree-sha1 = "03aaee628bc8bb682570d70b16d8102b8220ff5a" +git-tree-sha1 = "d8b02e2226568644b6758b2d113fe5b08884eec0" uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -version = "0.15.28" +version = "0.15.29" [deps.ComponentArrays.extensions] ComponentArraysGPUArraysExt = "GPUArrays" @@ -684,10 +684,10 @@ uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52" 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 = "8b416f6b1f9ef8df4c13dd0fe6c191752722b36f" +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 = "d9b1e66070ce15bc2b9c3d5af6b94f693fc03ba4" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.53.1" +version = "5.58.0" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -703,9 +703,9 @@ 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 = "e9b34e0eb3443492f396c97e7fed08630752a4f2" +git-tree-sha1 = "6fecfae8b2d9983e939378c8eacff6562e8a2567" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.177.2" +version = "6.183.0" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -743,9 +743,9 @@ version = "6.177.2" [[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 +777,9 @@ version = "7.16.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "c092fd1dd0d94e609cd0d29e13897b2825c804bb" +git-tree-sha1 = "54d7b8c74408048aea9c055ac8573b2b5c5ec11f" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.7.2" +version = "0.7.4" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -929,9 +929,9 @@ 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 = "6d85ffa95b11e51f82dd72efea1f88b88d7ec444" +git-tree-sha1 = "1a9c9e3401f5d024612a70d24a19517b2dbc1824" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.59" +version = "0.13.67" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -960,9 +960,9 @@ weakdeps = ["Adapt"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "7ea609b06402406450cd8c73bc6adbbb1f7fffc0" +git-tree-sha1 = "a357a553f8dfd461756ff8ed66fd541bdf2d1588" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.185+0" +version = "0.0.188+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1004,15 +1004,15 @@ version = "0.10.14" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] -git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" +git-tree-sha1 = "83dc665d0312b41367b7263e8a4d172eac1897f4" uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.2" +version = "0.4.4" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e" +git-tree-sha1 = "3a948313e7a41eb1db7a1e733e6335f17b4ab3c4" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.4+1" +version = "7.1.1+0" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] @@ -1147,9 +1147,9 @@ version = "0.8.5" [[deps.Flux]] deps = ["Adapt", "ChainRulesCore", "Compat", "EnzymeCore", "Functors", "LinearAlgebra", "MLCore", "MLDataDevices", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] -git-tree-sha1 = "2c35003ec8dafabdc48549102208b1b15552cb33" +git-tree-sha1 = "d0751ca4c9762d9033534057274235dfef86aaf9" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.16.4" +version = "0.16.5" [deps.Flux.extensions] FluxAMDGPUExt = "AMDGPU" @@ -1392,9 +1392,9 @@ version = "1.4.4" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] -git-tree-sha1 = "0f14a5456bdc6b9731a5682f439a672750a09e48" +git-tree-sha1 = "ec1debd61c300961f98064cfb21287613ad7f303" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2025.0.4+0" +version = "2025.2.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -1460,9 +1460,9 @@ version = "0.1.11" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "a007feb38b422fbdab534406aeca1b86823cb4d6" +git-tree-sha1 = "0533e564aae234aff59ab625543145446d8b6ec2" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.7.0" +version = "1.7.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1490,16 +1490,19 @@ 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"] -git-tree-sha1 = "38a03910123867c11af988e8718d12c98bf6a234" +git-tree-sha1 = "83c617e9e9b02306a7acab79e05ec10253db7c87" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.37" +version = "0.9.38" weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"] [deps.KernelAbstractions.extensions] @@ -1567,15 +1570,6 @@ git-tree-sha1 = "eb62a3deb62fc6d8822c0c4bef73e4412419c5d8" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" version = "18.1.8+0" -[[deps.LRUCache]] -git-tree-sha1 = "5519b95a490ff5fe629c4a7aa3b3dfc9160498b3" -uuid = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637" -version = "1.6.2" -weakdeps = ["Serialization"] - - [deps.LRUCache.extensions] - SerializationExt = ["Serialization"] - [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "1c602b1127f4751facb671441ca72715cc95938a" @@ -1595,9 +1589,9 @@ 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" @@ -1619,9 +1613,9 @@ version = "0.1.17" [[deps.LazyArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "866ce84b15e54d758c11946aacd4e5df0e60b7a3" +git-tree-sha1 = "76627adb8c542c6b73f68d4bfd0aa71c9893a079" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "2.6.1" +version = "2.6.2" [deps.LazyArrays.extensions] LazyArraysBandedMatricesExt = "BandedMatrices" @@ -1654,9 +1648,9 @@ version = "0.3.0" [[deps.LeftChildRightSiblingTrees]] deps = ["AbstractTrees"] -git-tree-sha1 = "fb6803dafae4a5d62ea5cab204b1e657d9737e7f" +git-tree-sha1 = "95ba48564903b43b2462318aa243ee79d81135ff" uuid = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e" -version = "0.2.0" +version = "0.2.1" [[deps.LevyArea]] deps = ["LinearAlgebra", "Random", "SpecialFunctions"] @@ -1724,10 +1718,10 @@ uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" version = "2.41.0+0" [[deps.Libtask]] -deps = ["FunctionWrappers", "LRUCache", "LinearAlgebra", "Statistics"] -git-tree-sha1 = "902ece54b0cb5c5413a8a15db0ad2aa2ec4172d2" +deps = ["MistyClosures", "Test"] +git-tree-sha1 = "6a9b56c32b39c6e45f8265cfd3ce971c3a8f7b75" uuid = "6f1fad26-d15e-5dc8-ae53-837a1d7b8c9f" -version = "0.8.8" +version = "0.9.4" [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] @@ -1764,15 +1758,18 @@ 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 = "062c11f1d84ffc80d00fddaa515f7e37e8e9f9d5" +git-tree-sha1 = "1c597eceb5ead73dae17ffa4dcc1160e3e4da1f3" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "3.18.2" +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" @@ -1788,10 +1785,12 @@ version = "3.18.2" 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" @@ -1800,11 +1799,13 @@ version = "3.18.2" 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"] @@ -1903,9 +1904,9 @@ 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"] @@ -1931,9 +1932,9 @@ version = "1.2.6" [[deps.LuxLib]] deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "Compat", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "a3c5d3485c6cdf0c13d81678b9c82a6f4e5e4eca" +git-tree-sha1 = "bf64921ca8182e3ee34a56b05b9f1ed568141a13" uuid = "82251201-b29d-42c6-8e01-566dec8acb11" -version = "1.10.0" +version = "1.10.1" [deps.LuxLib.extensions] LuxLibAppleAccelerateExt = "AppleAccelerate" @@ -1975,15 +1976,15 @@ version = "6.0.7" [[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"] -git-tree-sha1 = "5de60bc6cb3899cd318d80d627560fae2e2d99ae" +git-tree-sha1 = "282cadc186e7b2ae0eeadbd7a4dffed4196ae2aa" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2025.0.1+1" +version = "2025.2.0+0" [[deps.MLCore]] deps = ["DataAPI", "SimpleTraits", "Tables"] @@ -1993,9 +1994,9 @@ version = "1.0.0" [[deps.MLDataDevices]] deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"] -git-tree-sha1 = "209390b236bb04b289c708054fe1df06a4b314b5" +git-tree-sha1 = "0ad0d8f83ddf28a7eba28ed94d0d68015ce645b7" uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" -version = "1.11.0" +version = "1.11.1" [deps.MLDataDevices.extensions] MLDataDevicesAMDGPUExt = "AMDGPU" @@ -2050,10 +2051,10 @@ uuid = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" version = "0.5.4" [[deps.MLJModelInterface]] -deps = ["REPL", "Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "66626f80d5807921045d539b4f7153b1d47c5f8a" +deps = ["InteractiveUtils", "REPL", "Random", "ScientificTypesBase", "StatisticalTraits"] +git-tree-sha1 = "ccaa3f7938890ee8042cc970ba275115428bd592" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.11.1" +version = "1.12.0" [[deps.MLLabelUtils]] deps = ["LearnBase", "MappedArrays", "StatsBase"] @@ -2177,9 +2178,9 @@ 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" @@ -2193,9 +2194,9 @@ version = "0.8.1" [[deps.Mooncake]] deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DispatchDoctor", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Test"] -git-tree-sha1 = "005e57fd321b90e9ae47c7cbb5dbdfff78651623" +git-tree-sha1 = "88bb6e5054ba4a341c8fb7047af859720669628d" uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" -version = "0.4.138" +version = "0.4.142" [deps.Mooncake.extensions] MooncakeAllocCheckExt = "AllocCheck" @@ -2248,9 +2249,9 @@ version = "7.10.0" [[deps.NLopt]] deps = ["CEnum", "NLopt_jll"] -git-tree-sha1 = "de3a001641c8b9fb52b96082327f5f99ae302fcc" +git-tree-sha1 = "624785b15005a0e0f4e462b27ee745dbe5941863" uuid = "76087f3c-5699-56af-9a33-bf431cd00edd" -version = "1.2.0" +version = "1.2.1" [deps.NLopt.extensions] NLoptMathOptInterfaceExt = ["MathOptInterface"] @@ -2272,9 +2273,9 @@ version = "4.5.1" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "ScopedValues", "Statistics"] -git-tree-sha1 = "4abc63cdd8dd9dd925d8e879cda280bedc8013ca" +git-tree-sha1 = "eb6eb10b675236cee09a81da369f94f16d77dc2f" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.30" +version = "0.9.31" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -2329,9 +2330,9 @@ 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 = "aeb6fb02e63b4d4f90337ed90ce54ceb4c0efe77" +git-tree-sha1 = "d2ec18c1e4eccbb70b64be2435fc3b06fbcdc0a1" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "4.9.0" +version = "4.10.0" [deps.NonlinearSolve.extensions] NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" @@ -2361,9 +2362,9 @@ version = "4.9.0" [[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 = "404d71dd057759f4d590191a643113485c4a482a" +git-tree-sha1 = "1d42a315ba627ca0027d49d0efb44e3d88db24aa" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "1.12.0" +version = "1.14.0" weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"] [deps.NonlinearSolveBase.extensions] @@ -2377,15 +2378,15 @@ 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 = "9c8cd0a986518ba317af263549b48e34ac8f776d" +git-tree-sha1 = "3f1198ae5cbf21e84b8251a9e62fa1f888f3e4cb" uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" -version = "1.5.0" +version = "1.7.0" [[deps.NonlinearSolveQuasiNewton]] deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] -git-tree-sha1 = "e3888bdbab6e0bfadbc3164ef4595e40e7b7e954" +git-tree-sha1 = "40dfaf1bf74f1f700f81d0002d4dd90999598eb2" uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" -version = "1.6.0" +version = "1.8.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveQuasiNewton.extensions] @@ -2393,9 +2394,9 @@ 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] @@ -2403,9 +2404,9 @@ 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" @@ -2457,9 +2458,9 @@ 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"] @@ -2497,15 +2498,15 @@ version = "0.4.6" [[deps.Optimization]] deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "c385fdca85f0d6f2f6ade194b4236eaad621e77d" +git-tree-sha1 = "41902230755effe29a8599ea4b61dc3ffc2c952d" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "4.4.0" +version = "4.5.0" [[deps.OptimizationBase]] deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] -git-tree-sha1 = "d42ca664e1fd78cdbe4186d4773d4fa51e1a0e78" +git-tree-sha1 = "474b2fa6de9288d34b8ad42c9c500088132621a7" uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb" -version = "2.8.0" +version = "2.10.0" [deps.OptimizationBase.extensions] OptimizationEnzymeExt = "Enzyme" @@ -2554,27 +2555,27 @@ version = "1.8.1" [[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", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "1c2b2df870944e0dc01454fd87479847c55fa26c" +git-tree-sha1 = "55c21fdb4626037cdbcb04fec3afa192345a24de" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.98.0" +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 = "9124a686af119063bb4d3a8f87044a8f312fcad9" +deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "8fdcc6e46e55eb7c6332e4040df82c3f69fe5b9c" uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" -version = "1.6.0" +version = "1.10.0" [[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 = "1bd20b621e8dee5f2d170ae31631bf573ab77eec" +git-tree-sha1 = "e579c9a4f9102e82da3d97c349a74d6bc11cf8dc" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.26.2" +version = "1.30.0" weakdeps = ["EnzymeCore", "Mooncake"] [deps.OrdinaryDiffEqCore.extensions] @@ -2582,166 +2583,166 @@ weakdeps = ["EnzymeCore", "Mooncake"] OrdinaryDiffEqCoreMooncakeExt = "Mooncake" [[deps.OrdinaryDiffEqDefault]] -deps = ["ADTypes", "DiffEqBase", "EnumX", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "PrecompileTools", "Preferences", "Reexport"] -git-tree-sha1 = "7e2f4ec76ebac709401064fd2cf73ad993d1e694" +deps = ["ADTypes", "DiffEqBase", "EnumX", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "PrecompileTools", "Preferences", "Reexport", "SciMLBase"] +git-tree-sha1 = "7d5ddeee97e1bdcc848f1397cbc3d03bd57f33e7" uuid = "50262376-6c5a-4cf5-baba-aaf4f84d72d7" -version = "1.5.0" +version = "1.8.0" [[deps.OrdinaryDiffEqDifferentiation]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"] -git-tree-sha1 = "efecf0c4cc44e16251b0e718f08b0876b2a82b80" +git-tree-sha1 = "c7c01ae1a6eb15ac73f3d3da2161df9af2117085" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.10.0" +version = "1.13.0" [[deps.OrdinaryDiffEqExplicitRK]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"] -git-tree-sha1 = "4dbce3f9e6974567082ce5176e21aab0224a69e9" +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] +git-tree-sha1 = "4c0633f587395d7aaec0679dc649eb03fcc74e73" uuid = "9286f039-9fbf-40e8-bf65-aa933bdc4db0" -version = "1.1.0" +version = "1.4.0" [[deps.OrdinaryDiffEqExponentialRK]] -deps = ["ADTypes", "DiffEqBase", "ExponentialUtilities", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqVerner", "RecursiveArrayTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "8d2ab84d7fabdfde995e5f567361f238069497f5" +deps = ["ADTypes", "DiffEqBase", "ExponentialUtilities", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "RecursiveArrayTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "3b81416ff11e55ea0ae7b449efc818256d9d450b" uuid = "e0540318-69ee-4070-8777-9e2de6de23de" -version = "1.4.0" +version = "1.8.0" [[deps.OrdinaryDiffEqExtrapolation]] -deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "80a636aac325c546b04e3bf20f0c80eaa0173dd4" +deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", 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"FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "e8dd5ab225287947016dc144a5ded1fb83885638" uuid = "fa646aed-7ef9-47eb-84c4-9443fc8cbfa8" -version = "1.3.0" +version = "1.7.0" [[deps.OrdinaryDiffEqTsit5]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "96552f7d4619fabab4038a29ed37dd55e9eb513a" +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "778c7d379265f17f40dbe9aaa6f6a2a08bc7fa3e" uuid = "b1df2697-797e-41e3-8120-5422d3b24e4a" -version = "1.1.0" +version = "1.5.0" [[deps.OrdinaryDiffEqVerner]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "08f2d3be30874b6e2e937a06b501fb9811f7d8bd" +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 = "1.2.0" +version = "1.6.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -2807,9 +2808,9 @@ 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 = "55818b50883d7141bd98cdf5fc2f4ced96ee075f" +git-tree-sha1 = "9a9216c0cf706cb2cc58fd194878180e3e51e8c0" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.16" +version = "1.40.18" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -2827,9 +2828,9 @@ version = "1.40.16" [[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"] @@ -2856,13 +2857,14 @@ uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" [[deps.PreallocationTools]] -deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "7a5e02659e293b25a4bfaeeb6cd268acd0742eba" +deps = ["Adapt", "ArrayInterface", "PrecompileTools"] +git-tree-sha1 = "a0d5f963cfee70bee26dfa137a732e759e24436a" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.28" -weakdeps = ["ReverseDiff", "SparseConnectivityTracer"] +version = "0.4.31" +weakdeps = ["ForwardDiff", "ReverseDiff", "SparseConnectivityTracer"] [deps.PreallocationTools.extensions] + PreallocationToolsForwardDiffExt = "ForwardDiff" PreallocationToolsReverseDiffExt = "ReverseDiff" PreallocationToolsSparseConnectivityTracerExt = "SparseConnectivityTracer" @@ -2874,9 +2876,9 @@ 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" @@ -3013,10 +3015,10 @@ 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 = "efc718978d97745c58e69c5115a35c51a080e45e" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "7c7ac305885b1e0292585d087ecd60331a705965" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.34.1" +version = "3.37.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -3027,6 +3029,7 @@ version = "3.34.1" RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] RecursiveArrayToolsStructArraysExt = "StructArrays" + RecursiveArrayToolsTablesExt = ["Tables"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" @@ -3039,6 +3042,7 @@ version = "3.34.1" 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" @@ -3120,15 +3124,15 @@ 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 = "e6a28a9a2dd9bc3ed46391fa0e6c35839bde4028" +git-tree-sha1 = "c056c723b68700fec386dfde8c577089df720c8e" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.103.0" +version = "2.108.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3153,15 +3157,15 @@ version = "2.103.0" [[deps.SciMLJacobianOperators]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] -git-tree-sha1 = "7da1216346ad79499d08d7e2a3dbf297dc80c829" +git-tree-sha1 = "3414071e3458f3065de7fa5aed55283b236b4907" uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" -version = "0.1.6" +version = "0.1.8" [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "3249fe77f322fe539e935ecb388c8290cd38a3fc" +git-tree-sha1 = "aea915a39b547c48a18ee041120db1ae8df5a691" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "1.3.1" +version = "1.5.0" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -3170,9 +3174,9 @@ 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 = "f4af350e4b1e7200a2143a4fb16362133f2ef288" +git-tree-sha1 = "e1b5f9b3be1452591c40a88de9efb265ebe76030" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.87.0" +version = "7.89.0" weakdeps = ["Mooncake"] [deps.SciMLSensitivity.extensions] @@ -3191,9 +3195,9 @@ version = "3.0.0" [[deps.ScopedValues]] deps = ["HashArrayMappedTries", "Logging"] -git-tree-sha1 = "1147f140b4c8ddab224c94efa9569fc23d63ab44" +git-tree-sha1 = "7f44eef6b1d284465fafc66baf4d9bdcc239a15b" uuid = "7e506255-f358-4e82-b7e4-beb19740aa63" -version = "1.3.0" +version = "1.4.0" [[deps.Scratch]] deps = ["Dates"] @@ -3245,9 +3249,9 @@ 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 = "7aaa5fe4617271b64fce0466d187f2a72edbd81a" +git-tree-sha1 = "09d986e27a606f172c5b6cffbd8b8b2f10bf1c75" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "2.5.0" +version = "2.7.0" weakdeps = ["ChainRulesCore", "DiffEqBase", "ReverseDiff", "Tracker"] [deps.SimpleNonlinearSolve.extensions] @@ -3258,9 +3262,9 @@ 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" @@ -3273,9 +3277,9 @@ 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"] @@ -3284,24 +3288,17 @@ version = "1.11.0" [[deps.SparseConnectivityTracer]] deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "182990067a09adf950274f97f38f68c76f81d2d0" +git-tree-sha1 = "7bd2b8981cc57adcf5cf1add282aba2713a7058f" uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" -version = "0.6.21" +version = "1.0.0" +weakdeps = ["LogExpFunctions", "NNlib", "NaNMath", "SpecialFunctions"] [deps.SparseConnectivityTracer.extensions] - SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions" SparseConnectivityTracerNNlibExt = "NNlib" SparseConnectivityTracerNaNMathExt = "NaNMath" SparseConnectivityTracerSpecialFunctionsExt = "SpecialFunctions" - [deps.SparseConnectivityTracer.weakdeps] - DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" - LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" - NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" - NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" - SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" - [[deps.SparseInverseSubset]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] git-tree-sha1 = "52962839426b75b3021296f7df242e40ecfc0852" @@ -3365,9 +3362,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "0feb6b9031bd5c51f9072393eb5ab3efd31bf9e4" +git-tree-sha1 = "cbea8a6bd7bed51b1619658dec70035e07b8502f" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.13" +version = "1.9.14" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -3420,9 +3417,9 @@ 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"] @@ -3438,9 +3435,9 @@ 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", "StaticArrays", "UnPack"] -git-tree-sha1 = "2992af2739fdcf5862b12dcf53a5f6e3e4acd358" +git-tree-sha1 = "c3a55a2a1e180e249a0550d30a58c700487aa7ef" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.80.0" +version = "6.81.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] @@ -3520,9 +3517,9 @@ version = "5.2.3+0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "PrettyTables", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "658f6d01bfe68d6bf47915bf5d868228138c7d71" +git-tree-sha1 = "59ca6eddaaa9849e7de9fd1153b6faf0b1db7b80" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.41" +version = "0.3.42" [[deps.TOML]] deps = ["Dates"] @@ -3589,9 +3586,9 @@ version = "0.5.5" [[deps.TimeZones]] deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] -git-tree-sha1 = "2c705e96825b66c4a3f25031a683c06518256dd3" +git-tree-sha1 = "1f9a3f379a2ce2a213a0f606895567a08a1a2d08" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.21.3" +version = "1.22.0" weakdeps = ["RecipesBase"] [deps.TimeZones.extensions] @@ -3677,9 +3674,9 @@ 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 = "ed8145c83b824e67a94b5bbe5be231991deda154" +git-tree-sha1 = "58ad6cfe65311dc4ddc0e13e6747f3fad26f1034" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.39.4" +version = "0.39.10" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] @@ -3713,9 +3710,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "d2282232f8a4d71f79e85dc4dd45e5b12a6297fb" +git-tree-sha1 = "6258d453843c466d84c17a58732dda5deeb8d3af" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.23.1" +version = "1.24.0" weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "Printf"] [deps.Unitful.extensions] @@ -3764,9 +3761,9 @@ version = "1.4.2" [[deps.WeightInitializers]] deps = ["ArgCheck", "ConcreteStructs", "GPUArraysCore", "LinearAlgebra", "Random", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "57db7a10930d4ccc9e4ee3d9122748f845e645cf" +git-tree-sha1 = "dd2e8eb0120c12eed3446cedee395ca7ac42a5db" uuid = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d" -version = "1.1.3" +version = "1.1.4" [deps.WeightInitializers.extensions] WeightInitializersAMDGPUExt = ["AMDGPU", "GPUArrays"] @@ -4002,15 +3999,15 @@ version = "1.1.3+0" [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "522c1df09d05a71785765d19c9524661234738e9" +git-tree-sha1 = "4bba74fa59ab0755167ad24f98800fe5d727175b" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.11.0+0" +version = "3.12.1+0" [[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" +git-tree-sha1 = "125eedcb0a4a0bba65b657251ce1d27c8714e9d6" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.2+0" +version = "0.17.4+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] @@ -4076,16 +4073,16 @@ uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" version = "17.4.0+2" [[deps.x264_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "14cc7083fc6dff3cc44f2bc435ee96d06ed79aa7" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2021.5.5+0" +version = "10164.0.1+0" [[deps.x265_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e7b67590c14d487e734dcb925924c5dc43ec85f3" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.5.0+0" +version = "4.1.0+0" [[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] diff --git a/_quarto.yml b/_quarto.yml index 288cf5259..7c0ee07e1 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -57,6 +57,7 @@ website: collapse-level: 1 contents: - usage/automatic-differentiation/index.qmd + - usage/stochastic-gradient-samplers/index.qmd - usage/submodels/index.qmd - usage/custom-distribution/index.qmd - usage/probability-interface/index.qmd diff --git a/usage/stochastic-gradient-samplers/index.qmd b/usage/stochastic-gradient-samplers/index.qmd new file mode 100644 index 000000000..2b018c8ea --- /dev/null +++ b/usage/stochastic-gradient-samplers/index.qmd @@ -0,0 +1,235 @@ +--- +title: Stochastic Gradient Samplers +engine: julia +--- + +```{julia} +#| echo: false +#| output: false +using Pkg; +Pkg.instantiate(); +``` + +Turing.jl provides stochastic gradient-based MCMC samplers: **Stochastic Gradient Langevin Dynamics (SGLD)** and **Stochastic Gradient Hamiltonian Monte Carlo (SGHMC)**. + +## Current Capabilities + +The current implementation in Turing.jl is primarily useful for: +- **Research purposes**: Studying stochastic gradient MCMC methods +- **Streaming data**: When data arrives continuously +- **Experimental applications**: Testing stochastic sampling approaches + +**Important**: The current implementation computes full gradients with added stochastic noise rather than true mini-batch stochastic gradients. This means these samplers don't currently provide the computational benefits typically associated with stochastic gradient methods for large datasets. They require very careful hyperparameter tuning and often perform slower than standard samplers like HMC or NUTS for most practical applications. + +## Setup + +```{julia} +using Turing +using Distributions +using StatsPlots +using Random +using LinearAlgebra + +Random.seed!(123) + +# Disable progress bars for cleaner output +Turing.setprogress!(false) +``` + +## SGLD (Stochastic Gradient Langevin Dynamics) + +SGLD adds properly scaled noise to gradient descent steps to enable MCMC sampling. The key insight is that the right amount of noise transforms optimization into sampling from the posterior distribution. + +Let's start with a simple Gaussian model: + +```{julia} +# Generate synthetic data +true_μ = 2.0 +true_σ = 1.5 +N = 100 +data = rand(Normal(true_μ, true_σ), N) + +# Define a simple Gaussian model +@model function gaussian_model(x) + μ ~ Normal(0, 10) + σ ~ truncated(Normal(0, 5); lower=0) + + for i in 1:length(x) + x[i] ~ Normal(μ, σ) + end +end + +model = gaussian_model(data) +``` + +SGLD requires very small step sizes to ensure stability. We use a `PolynomialStepsize` that decreases over time. Note: Currently, `PolynomialStepsize` is the primary stepsize schedule available in Turing for SGLD: + +```{julia} +# SGLD with polynomial stepsize schedule +# stepsize(t) = a / (b + t)^γ +sgld_stepsize = Turing.PolynomialStepsize(0.0001, 10000, 0.55) +chain_sgld = sample(model, SGLD(stepsize=sgld_stepsize), 5000) + +summarystats(chain_sgld) +``` + + +```{julia} +plot(chain_sgld) +``` + +## SGHMC (Stochastic Gradient Hamiltonian Monte Carlo) + +SGHMC extends HMC to the stochastic gradient setting by incorporating friction to counteract the noise from stochastic gradients: + +```{julia} +# SGHMC with very small learning rate +chain_sghmc = sample(model, SGHMC(learning_rate=0.00001, momentum_decay=0.1), 5000) + +summarystats(chain_sghmc) +``` + +```{julia} +plot(chain_sghmc) +``` + +## Comparison with Standard HMC + +For comparison, let's sample the same model using standard HMC: + +```{julia} +chain_hmc = sample(model, HMC(0.01, 10), 1000) + +println("True values: μ = ", true_μ, ", σ = ", true_σ) +summarystats(chain_hmc) +``` + +Compare the trace plots to see how the different samplers explore the posterior: + +```{julia} +p1 = plot(chain_sgld[:μ], label="SGLD", title="μ parameter traces") +hline!([true_μ], label="True value", linestyle=:dash, color=:red) + +p2 = plot(chain_sghmc[:μ], label="SGHMC") +hline!([true_μ], label="True value", linestyle=:dash, color=:red) + +p3 = plot(chain_hmc[:μ], label="HMC") +hline!([true_μ], label="True value", linestyle=:dash, color=:red) + +plot(p1, p2, p3, layout=(3,1), size=(800,600)) +``` + +The comparison shows that: +- **SGLD** exhibits slower convergence and higher variance due to the injected noise, requiring longer chains to achieve stable estimates +- **SGHMC** shows slightly better mixing than SGLD due to the momentum term, but still requires careful tuning +- **HMC** converges quickly and efficiently explores the posterior, demonstrating why it's preferred for small to medium-sized problems + +## Bayesian Linear Regression Example + +Here's a more complex example using Bayesian linear regression: + +```{julia} +# Generate regression data +n_features = 3 +n_samples = 100 +X = randn(n_samples, n_features) +true_β = [0.5, -1.2, 2.1] +true_σ_noise = 0.3 +y = X * true_β + true_σ_noise * randn(n_samples) + +@model function linear_regression(X, y) + n_features = size(X, 2) + + # Priors + β ~ MvNormal(zeros(n_features), 3 * I) + σ ~ truncated(Normal(0, 1); lower=0) + + # Likelihood + y ~ MvNormal(X * β, σ^2 * I) +end + +lr_model = linear_regression(X, y) +``` + +Sample using the stochastic gradient methods: + +```{julia} +# Very conservative parameters for stability +sgld_lr_stepsize = Turing.PolynomialStepsize(0.00005, 10000, 0.55) +chain_lr_sgld = sample(lr_model, SGLD(stepsize=sgld_lr_stepsize), 5000) + +chain_lr_sghmc = sample(lr_model, SGHMC(learning_rate=0.00005, momentum_decay=0.1), 5000) + +chain_lr_hmc = sample(lr_model, HMC(0.01, 10), 1000) +``` + +Compare the results to evaluate the performance of stochastic gradient samplers on a more complex model: + +```{julia} +println("True β values: ", true_β) +println("True σ value: ", true_σ_noise) +println() + +println("SGLD estimates:") +summarystats(chain_lr_sgld) +``` + +The linear regression example demonstrates that stochastic gradient samplers can recover the true parameters, but: +- They require significantly longer chains (5000 vs 1000 for HMC) +- The estimates may have higher variance +- Convergence diagnostics should be carefully examined before trusting the results + +## Automatic Differentiation Backends + +Both samplers support different AD backends. For more information about automatic differentiation in Turing, see the [Automatic Differentiation](../automatic-differentiation/) documentation. + +```{julia} +using ADTypes + +# ForwardDiff (default) - good for few parameters +sgld_forward = SGLD(stepsize=sgld_stepsize, adtype=AutoForwardDiff()) + +# ReverseDiff - better for many parameters +sgld_reverse = SGLD(stepsize=sgld_stepsize, adtype=AutoReverseDiff()) + +# Zygote - good for complex models +sgld_zygote = SGLD(stepsize=sgld_stepsize, adtype=AutoZygote()) +``` + +## Best Practices and Recommendations + +### When to Consider Stochastic Gradient Samplers + +- **Streaming data**: When data arrives continuously and you need online inference +- **Research**: For studying stochastic gradient MCMC methods +- **Educational purposes**: For understanding stochastic gradient MCMC algorithms + +### Critical Hyperparameters + +**For SGLD:** +- Use `PolynomialStepsize` with very small initial values (≤ 0.0001) +- Larger `b` values in `PolynomialStepsize(a, b, γ)` provide more stability +- The stepsize decreases as `a / (b + t)^γ` + +**For SGHMC:** +- Use extremely small learning rates (≤ 0.00001) +- Momentum decay (friction) typically between 0.1-0.5 +- Higher momentum decay improves stability but slows convergence + +### Current Limitations + +1. **No mini-batching**: Full gradients are computed despite "stochastic" name +2. **Hyperparameter sensitivity**: Requires extensive tuning +3. **Computational overhead**: Often slower than HMC/NUTS for small-medium datasets +4. **Convergence**: Typically requires longer chains + +### General Recommendations + +- **Start conservatively**: Use very small step sizes initially +- **Monitor convergence**: Check trace plots and diagnostics carefully +- **Compare with HMC/NUTS**: Validate results when possible +- **Consider alternatives**: For most applications, HMC or NUTS will be more efficient + +## Summary + +Stochastic gradient samplers in Turing.jl provide an interface to gradient-based MCMC methods with added stochasticity. While designed for large-scale problems, the current implementation uses full gradients, making them primarily useful for research or specialized applications. For most practical Bayesian inference tasks, standard samplers like HMC or NUTS will be more efficient and easier to tune. \ No newline at end of file