diff --git a/Manifest.toml b/Manifest.toml index e41cb809e..c94baf232 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,12 +2,12 @@ julia_version = "1.11.6" manifest_format = "2.0" -project_hash = "296b7e06e398e8898b40f44ed92b4d60c484484c" +project_hash = "3c5b0696513a84be8573e377b59e1ab532411868" [[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] @@ -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"] @@ -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 = "484cceb16c5ed95f4a2a405f3579f480ec0dff9a" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.53.1" +version = "5.55.0" [[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 = "6f8f25122389ba34e491bdfe143ae16fda37cad3" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.177.2" +version = "6.180.0" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -777,9 +777,9 @@ version = "7.16.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "c092fd1dd0d94e609cd0d29e13897b2825c804bb" +git-tree-sha1 = "f620da805b82bec64ab4d5f881c7592c82dbc08a" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.7.2" +version = "0.7.3" [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 = "e36968f0a43d9a3b627ac94d5346b458ce14066d" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.59" +version = "0.13.65" [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" @@ -1180,9 +1180,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853" +git-tree-sha1 = "910febccb28d493032495b7009dce7d7f7aee554" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.38" +version = "1.0.1" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -1299,24 +1299,6 @@ git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" -[[deps.HDF5]] -deps = ["Compat", "HDF5_jll", "Libdl", "MPIPreferences", "Mmap", "Preferences", "Printf", "Random", "Requires", "UUIDs"] -git-tree-sha1 = "e856eef26cf5bf2b0f95f8f4fc37553c72c8641c" -uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" -version = "0.17.2" - - [deps.HDF5.extensions] - MPIExt = "MPI" - - [deps.HDF5.weakdeps] - MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" - -[[deps.HDF5_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] -git-tree-sha1 = "e94f84da9af7ce9c6be049e9067e511e17ff89ec" -uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" -version = "1.14.6+0" - [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] git-tree-sha1 = "ed5e9c58612c4e081aecdb6e1a479e18462e041e" @@ -1344,12 +1326,6 @@ weakdeps = ["Distributions"] [deps.HiddenMarkovModels.extensions] HiddenMarkovModelsDistributionsExt = "Distributions" -[[deps.Hwloc_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "92f65c4d78ce8cdbb6b68daf88889950b0a99d11" -uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.12.1+0" - [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] git-tree-sha1 = "68c173f4f449de5b438ee67ed0c9c748dc31a2ec" @@ -1392,9 +1368,9 @@ 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 +1436,9 @@ 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"] @@ -1497,9 +1473,9 @@ weakdeps = ["FastBroadcast"] [[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 +1543,6 @@ 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" @@ -1619,9 +1586,9 @@ 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 +1621,9 @@ 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 +1691,10 @@ 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"] @@ -1764,9 +1731,9 @@ 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 = "062c11f1d84ffc80d00fddaa515f7e37e8e9f9d5" +git-tree-sha1 = "d768ff40cc3fe42581708696b24ee65dccc9c6ba" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "3.18.2" +version = "3.24.0" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" @@ -1931,9 +1898,9 @@ 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" @@ -1968,10 +1935,10 @@ version = "1.10.0" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.MCMCChains]] -deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] -git-tree-sha1 = "cd7aee22384792c726e19f2a22dc060b886edded" +deps = ["AbstractMCMC", "AxisArrays", "DataAPI", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] +git-tree-sha1 = "a1b9bf62acb012e4a717562f83f859257c5b6fec" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "6.0.7" +version = "7.1.0" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] @@ -1981,9 +1948,9 @@ version = "0.3.14" [[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 +1960,9 @@ 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 +2017,10 @@ 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"] @@ -2072,24 +2039,6 @@ git-tree-sha1 = "a772d8d1987433538a5c226f79393324b55f7846" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" version = "0.4.8" -[[deps.MPICH_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "d72d0ecc3f76998aac04e446547259b9ae4c265f" -uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.3.1+0" - -[[deps.MPIPreferences]] -deps = ["Libdl", "Preferences"] -git-tree-sha1 = "c105fe467859e7f6e9a852cb15cb4301126fac07" -uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" -version = "0.1.11" - -[[deps.MPItrampoline_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "e214f2a20bdd64c04cd3e4ff62d3c9be7e969a59" -uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" -version = "5.5.4+0" - [[deps.MacroTools]] git-tree-sha1 = "1e0228a030642014fe5cfe68c2c0a818f9e3f522" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" @@ -2152,24 +2101,12 @@ git-tree-sha1 = "7dbf904fa6c4447bd1f1d316886bfbe29feacf45" uuid = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" version = "0.2.2" -[[deps.MicroCanonicalHMC]] -deps = ["AbstractMCMC", "Adapt", "Distributions", "ForwardDiff", "HDF5", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "MCMCDiagnosticTools", "Markdown", "ProgressMeter", "Random", "Statistics"] -git-tree-sha1 = "99fd367f8b8fc9d479420d33e8f16f3dab3162f4" -uuid = "234d2aa0-2291-45f7-9047-6fa6f316b0a8" -version = "0.1.6" - [[deps.MicroCollections]] deps = ["Accessors", "BangBang", "InitialValues"] git-tree-sha1 = "44d32db644e84c75dab479f1bc15ee76a1a3618f" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" version = "0.2.0" -[[deps.MicrosoftMPI_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bc95bf4149bf535c09602e3acdf950d9b4376227" -uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" -version = "10.1.4+3" - [[deps.Missings]] deps = ["DataAPI"] git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" @@ -2193,9 +2130,9 @@ 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 +2185,9 @@ 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 +2209,9 @@ 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 +2266,9 @@ 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 +2298,9 @@ 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 = "ee395563ae6ffaecbdf86d430440fddc779253a4" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "1.12.0" +version = "1.13.0" weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"] [deps.NonlinearSolveBase.extensions] @@ -2377,15 +2314,15 @@ 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 = "65101a20b135616a13625ae6f84b052ef5780363" uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" -version = "1.5.0" +version = "1.6.0" [[deps.NonlinearSolveQuasiNewton]] deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] -git-tree-sha1 = "e3888bdbab6e0bfadbc3164ef4595e40e7b7e954" +git-tree-sha1 = "3e04c917d4e3cd48b2a5091b6f76c720bb3f7362" uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" -version = "1.6.0" +version = "1.7.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveQuasiNewton.extensions] @@ -2443,12 +2380,6 @@ deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" version = "0.8.5+0" -[[deps.OpenMPI_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"] -git-tree-sha1 = "ec764453819f802fc1e144bfe750c454181bd66d" -uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" -version = "5.0.8+0" - [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] git-tree-sha1 = "f1a7e086c677df53e064e0fdd2c9d0b0833e3f6e" @@ -2497,15 +2428,15 @@ 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" @@ -2554,9 +2485,9 @@ 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"] @@ -2566,9 +2497,9 @@ 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 = "9124a686af119063bb4d3a8f87044a8f312fcad9" +git-tree-sha1 = "b0bbc6541ea4a27974bd67e0a10b26211cb95e58" uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" -version = "1.6.0" +version = "1.7.0" [[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"] @@ -2589,9 +2520,9 @@ version = "1.5.0" [[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 = "382a4bf7795eee0298221c37099db770be524bab" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.10.0" +version = "1.10.1" [[deps.OrdinaryDiffEqExplicitRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"] @@ -2600,10 +2531,10 @@ uuid = "9286f039-9fbf-40e8-bf65-aa933bdc4db0" version = "1.1.0" [[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 = "585f73f10a1b444654d739853a9328d1bb7fce6b" uuid = "e0540318-69ee-4070-8777-9e2de6de23de" -version = "1.4.0" +version = "1.5.0" [[deps.OrdinaryDiffEqExtrapolation]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] @@ -2613,9 +2544,9 @@ 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 = "0da8ec3491821262a3d2828e6370e76b51a770a3" +git-tree-sha1 = "d7cbd84ba96a91e765fc20d2c3b3b1702c15eeed" uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125" -version = "1.12.0" +version = "1.13.0" [[deps.OrdinaryDiffEqFeagin]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2625,21 +2556,21 @@ version = "1.1.0" [[deps.OrdinaryDiffEqFunctionMap]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] -git-tree-sha1 = "925a91583d1ab84f1f0fea121be1abf1179c5926" +git-tree-sha1 = "a4cb67794464352b69331c903cfa91a40e9a79ac" uuid = "d3585ca7-f5d3-4ba6-8057-292ed1abd90f" -version = "1.1.1" +version = "1.2.0" [[deps.OrdinaryDiffEqHighOrderRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "103e017ff186ac39d731904045781c9bacfca2b0" +git-tree-sha1 = "3466ac9ba5121c700a17e1d5ba42757405d636d4" uuid = "d28bc4f8-55e1-4f49-af69-84c1a99f0f58" -version = "1.1.0" +version = "1.2.0" [[deps.OrdinaryDiffEqIMEXMultistep]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Reexport"] -git-tree-sha1 = "095bab73a3ff185e9ef971fc42ecc93c7824e589" +git-tree-sha1 = "f2e7decd8b8b92a13e9d48f87780fdfecbc85708" uuid = "9f002381-b378-40b7-97a6-27a27c83f129" -version = "1.3.0" +version = "1.4.0" [[deps.OrdinaryDiffEqLinear]] deps = ["DiffEqBase", "ExponentialUtilities", "LinearAlgebra", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators"] @@ -2649,9 +2580,9 @@ version = "1.3.0" [[deps.OrdinaryDiffEqLowOrderRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] -git-tree-sha1 = "d4bb32e09d6b68ce2eb45fb81001eab46f60717a" +git-tree-sha1 = "2b7a3ef765c5e3e9d8eee6031da143a0b1c0805c" uuid = "1344f307-1e59-4825-a18e-ace9aa3fa4c6" -version = "1.2.0" +version = "1.3.0" [[deps.OrdinaryDiffEqLowStorageRK]] deps = ["Adapt", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "StaticArrays"] @@ -2661,9 +2592,9 @@ 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 = "ffdb0f5207b0e30f8b1edf99b3b9546d9c48ccaf" +git-tree-sha1 = "e98aa2f8da8386bc26daeb7c9b161bc351ea6a77" uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8" -version = "1.10.0" +version = "1.11.0" [[deps.OrdinaryDiffEqNordsieck]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2691,21 +2622,21 @@ version = "1.1.0" [[deps.OrdinaryDiffEqRKN]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "41c09d9c20877546490f907d8dffdd52690dd65f" +git-tree-sha1 = "6548bff67665b13a60abfb33e95fcf7ae08d186d" uuid = "af6ede74-add8-4cfd-b1df-9a4dbb109d7a" -version = "1.1.0" +version = "1.2.0" [[deps.OrdinaryDiffEqRosenbrock]] deps = ["ADTypes", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "1ce0096d920e95773220e818f29bf4b37ea2bb78" +git-tree-sha1 = "a2f83c9b6e977c8dc5f37e0b448ad64f17c3a9c1" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.11.0" +version = "1.12.0" [[deps.OrdinaryDiffEqSDIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] -git-tree-sha1 = "b3a7e3a2f355d837c823b435630f035aef446b45" +git-tree-sha1 = "62327171ae40737b7874d4bdf70e0a213d60086a" uuid = "2d112036-d095-4a1e-ab9a-08536f3ecdbf" -version = "1.3.0" +version = "1.4.0" [[deps.OrdinaryDiffEqSSPRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "StaticArrays"] @@ -2721,27 +2652,27 @@ version = "1.3.0" [[deps.OrdinaryDiffEqStabilizedRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "StaticArrays"] -git-tree-sha1 = "1b0d894c880e25f7d0b022d7257638cf8ce5b311" +git-tree-sha1 = "8b54bcaf8634548bd13c0bd9a0522f15e5438b67" uuid = "358294b1-0aab-51c3-aafe-ad5ab194a2ad" -version = "1.1.0" +version = "1.2.0" [[deps.OrdinaryDiffEqSymplecticRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "a13d59a2d6cfb6a3332a7782638ca6e1cb6ca688" +git-tree-sha1 = "0d3e0527149d7ece68850c51de67e99bc4477b1b" uuid = "fa646aed-7ef9-47eb-84c4-9443fc8cbfa8" -version = "1.3.0" +version = "1.4.0" [[deps.OrdinaryDiffEqTsit5]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "96552f7d4619fabab4038a29ed37dd55e9eb513a" +git-tree-sha1 = "d0b069075f4a5e54b29e412419e5a733a83e6240" uuid = "b1df2697-797e-41e3-8120-5422d3b24e4a" -version = "1.1.0" +version = "1.2.0" [[deps.OrdinaryDiffEqVerner]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "08f2d3be30874b6e2e937a06b501fb9811f7d8bd" +git-tree-sha1 = "91f0a004785791c8c538d34a67c19cf3f7776e85" uuid = "79d7bb75-1356-48c1-b8c0-6832512096c2" -version = "1.2.0" +version = "1.3.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -2807,9 +2738,9 @@ 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 = "3db9167c618b290a05d4345ca70de6d95304a32a" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.16" +version = "1.40.17" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -2857,9 +2788,9 @@ version = "0.2.4" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "7a5e02659e293b25a4bfaeeb6cd268acd0742eba" +git-tree-sha1 = "2cc315bb7f6e4d59081bad744cdb911d6374fc7f" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.28" +version = "0.4.29" weakdeps = ["ReverseDiff", "SparseConnectivityTracer"] [deps.PreallocationTools.extensions] @@ -3014,9 +2945,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "efc718978d97745c58e69c5115a35c51a080e45e" +git-tree-sha1 = "f8726bd5a8b7f5f5d3f6c0ce4793454a599b5243" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.34.1" +version = "3.36.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -3126,9 +3057,9 @@ version = "0.5.0" [[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 = "1c7fd50df465f0684f04f3a63736eac01999c659" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.103.0" +version = "2.107.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3153,15 +3084,15 @@ 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 = "7d3a1519dc4d433a6b20035eaff20bde8be77c66" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "1.3.1" +version = "1.4.0" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -3170,9 +3101,9 @@ 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 = "a5d3e3ccedbce9c0c07b4ffa60787b58bdc6d360" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.87.0" +version = "7.88.0" weakdeps = ["Mooncake"] [deps.SciMLSensitivity.extensions] @@ -3191,9 +3122,9 @@ 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 +3176,9 @@ 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] @@ -3284,24 +3215,17 @@ 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 +3289,9 @@ 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] @@ -3438,9 +3362,9 @@ 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 +3444,9 @@ 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 +3513,9 @@ 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 +3601,9 @@ 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 = "3fd5118fd33c708bec35d892f86a5455e9402d66" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.39.4" +version = "0.39.9" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] @@ -3713,9 +3637,9 @@ 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 +3688,9 @@ 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"] @@ -3994,23 +3918,17 @@ git-tree-sha1 = "b6a34e0e0960190ac2a4363a1bd003504772d631" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" version = "0.61.1+0" -[[deps.libaec_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f5733a5a9047722470b95a81e1b172383971105c" -uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" -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 +3994,16 @@ 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/Project.toml b/Project.toml index 6489bd760..af37a3fd6 100644 --- a/Project.toml +++ b/Project.toml @@ -35,7 +35,6 @@ MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54" MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" Measures = "442fdcdd-2543-5da2-b0f3-8c86c306513e" Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" -MicroCanonicalHMC = "234d2aa0-2291-45f7-9047-6fa6f316b0a8" Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2" diff --git a/usage/external-samplers/index.qmd b/usage/external-samplers/index.qmd index 016a719e0..3e278b40e 100755 --- a/usage/external-samplers/index.qmd +++ b/usage/external-samplers/index.qmd @@ -83,79 +83,67 @@ You can see an example of how to use `Pathfinder` with Turing in [`Pathfinder`'s ## Using new inference methods So far we have used Turing's support for external samplers to go beyond the capabilities of the wrappers. -We want to use this support to employ a sampler not supported within Turing's ecosystem yet. -We will use the recently developed Micro-Cannoncial Hamiltonian Monte Carlo (MCHMC) sampler to showcase this. -MCHMC[[^3],[^4]] ((MCHMC's GitHub)[https://github.com/JaimeRZP/MicroCanonicalHMC.jl]) is HMC sampler that uses one single Hamiltonian energy level to explore the whole parameter space. -This is achieved by simulating the dynamics of a microcanonical Hamiltonian with an additional noise term to ensure ergodicity. +This is made possible by an interface for external samplers, which is [described in the Turing.jl documentation here](https://turinglang.org/Turing.jl/stable/api/Inference/#Turing.Inference.ExternalSampler): if you are implementing your own sampler and would like it to work with Turing.jl models, that link describes the methods that you need to overload. -Using this as well as other inference methods outside the Turing ecosystem is as simple as executing the code shown below: +For an example of an 'external sampler' that works in this way with Turing, we recommend the [SliceSampling.jl library](https://github.com/TuringLang/SliceSampling.jl). +Note that although this library is hosted under the TuringLang GitHub organisation, it is not a Turing.jl dependency, and thus from Turing's perspective it is truly an 'external' sampler. -```{julia} -using MicroCanonicalHMC -# Create MCHMC sampler -n_adapts = 1_000 # adaptation steps -tev = 0.01 # target energy variance -mchmc = MCHMC(n_adapts, tev; adaptive=true) - -# Sample -chain = sample(model, externalsampler(mchmc), 10_000) -``` - -The only requirement to work with `externalsampler` is that the provided `sampler` must implement the AbstractMCMC.jl-interface [INSERT LINK] for a `model` of type `AbstractMCMC.LogDensityModel` [INSERT LINK]. - -As previously stated, in order to use external sampling libraries within `Turing` they must follow the `AbstractMCMC` API. -In this section, we will briefly dwell on what this entails. -First and foremost, the sampler should be a subtype of `AbstractMCMC.AbstractSampler`. -Second, the stepping function of the MCMC algorithm must be made defined using `AbstractMCMC.step` and follow the structure below: +In this section, we will briefly go through the interface requirements for external samplers. +First and foremost, the sampler `MySampler` should be a subtype of `AbstractMCMC.AbstractSampler`. +Second, the stepping function of the MCMC algorithm must be defined as new methods of `AbstractMCMC.step` following the structure below: -```{julia} -#| eval: false +```julia # First step -function AbstractMCMC.step{T<:AbstractMCMC.AbstractSampler}( +function AbstractMCMC.step( rng::Random.AbstractRNG, model::AbstractMCMC.LogDensityModel, - spl::T; + spl::MySampler; kwargs..., ) [...] - return transition, sample + return transition, state end # N+1 step -function AbstractMCMC.step{T<:AbstractMCMC.AbstractSampler}( +function AbstractMCMC.step( rng::Random.AbstractRNG, model::AbstractMCMC.LogDensityModel, - sampler::T, + sampler::MySampler, state; kwargs..., ) [...] - return transition, sample + return transition, state end ``` -There are several characteristics to note in these functions: +Note that the `model` argument here must be [an `AbstractMCMC.LogDensityModel`](https://turinglang.org/AbstractMCMC.jl/stable/api/#AbstractMCMC.LogDensityModel). +This is a thin wrapper around an object which satisfies the `LogDensityProblems.jl` interface. +Thus, in your external sampler, you can access the inner object with `model.logdensity` and call `LogDensityProblems.logdensity(model.logdensity, params)` to calculate the (unnormalised) log density of the model at `params`. - - There must be two `step` functions: +As shown above, there must be two `step` methods: - + A function that performs the first step and initializes the sampler. - + A function that performs the following steps and takes an extra input, `state`, which carries the initialization information. + - A method that performs the first step, performing any initialisation it needs to; and + - A method that performs the following steps and takes an extra input, `state`, which carries the initialization information. - - The functions must follow the displayed signatures. - - The output of the functions must be a transition, the current state of the sampler, and a sample, what is saved to the MCMC chain. +The output of both of these methods must be a tuple containing: + - a 'transition', which is essentially the 'visible output' of the sampler: this object is later used to construct an `MCMCChains.Chains`; + - a 'state', representing the current state of the sampler, which is passed to the next step of the MCMC algorithm. -The last requirement is that the transition must be structured with a field `θ`, which contains the values of the parameters of the model for said transition. -This allows `Turing` to seamlessly extract the parameter values at each step of the chain when bundling the chains. -Note that if the external sampler produces transitions that Turing cannot parse, the bundling of the samples will be different or fail. +Apart from this, your sampler state should also implement `Turing.Inference.getparams(model, transition)` to return the parameters of the model as a vector. +Here, `transition` represents the first output of the `step` function. -For practical examples of how to adapt a sampling library to the `AbstractMCMC` interface, the readers can consult the following libraries: +```julia +function Turing.Inference.getparams(model::DynamicPPL.Model, state::MyTransition) + # Return a vector containing the parameters of the model. +end +``` - - [AdvancedMH](https://github.com/TuringLang/AdvancedMH.jl/blob/458a602ac32a8514a117d4c671396a9ba8acbdab/src/mh-core.jl#L73-L115) - - [AdvancedHMC](https://github.com/TuringLang/AdvancedHMC.jl/blob/762e55f894d142495a41a6eba0eed9201da0a600/src/abstractmcmc.jl#L102-L170) - - [MicroCanonicalHMC](https://github.com/JaimeRZP/MicroCanonicalHMC.jl/blob/master/src/abstractmcmc.jl) +These functions are the bare minimum that your external sampler must implement to work with Turing models. +There are other methods which can be overloaded to improve the performance or other features of the sampler; please refer to the documentation linked above for more details. +In general, we recommend that the `AbstractMCMC` interface is implemented directly in your library. +However, any DynamicPPL- or Turing-specific functionality is best implemented in a `MySamplerTuringExt` extension. [^1]: Xu et al., [AdvancedHMC.jl: A robust, modular and efficient implementation of advanced HMC algorithms](http://proceedings.mlr.press/v118/xu20a/xu20a.pdf), 2019 [^2]: Zhang et al., [Pathfinder: Parallel quasi-Newton variational inference](https://arxiv.org/abs/2108.03782), 2021 -[^3]: Robnik et al, [Microcanonical Hamiltonian Monte Carlo](https://arxiv.org/abs/2212.08549), 2022 -[^4]: Robnik and Seljak, [Langevine Hamiltonian Monte Carlo](https://arxiv.org/abs/2303.18221), 2023