diff --git a/tutorials/00-introduction/Manifest.toml b/tutorials/00-introduction/Manifest.toml index 97f7916bc..56d0ab07e 100644 --- a/tutorials/00-introduction/Manifest.toml +++ b/tutorials/00-introduction/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "b45878f3df6dffef908d7ec87e98124988d559f6" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/01-gaussian-mixture-model/Manifest.toml b/tutorials/01-gaussian-mixture-model/Manifest.toml index acfe5b335..1026b1358 100644 --- a/tutorials/01-gaussian-mixture-model/Manifest.toml +++ b/tutorials/01-gaussian-mixture-model/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "a0a3ca6aa1eb54296a719c0190365d414d855bc0" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/02-logistic-regression/Manifest.toml b/tutorials/02-logistic-regression/Manifest.toml index 7740030b9..bb1c3aaec 100644 --- a/tutorials/02-logistic-regression/Manifest.toml +++ b/tutorials/02-logistic-regression/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "e25051313213ab9b94363dd6ade21d1145ab1ba1" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -254,10 +254,10 @@ version = "0.10.8" StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -369,9 +369,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -505,9 +505,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -577,10 +581,15 @@ version = "0.9.20" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -680,10 +689,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -790,10 +799,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -839,15 +848,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -954,10 +963,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -995,12 +1004,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -1010,7 +1018,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -1021,9 +1028,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1036,9 +1043,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1072,9 +1079,9 @@ version = "0.5.4" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MLLabelUtils]] deps = ["LearnBase", "MappedArrays", "StatsBase"] @@ -1084,9 +1091,9 @@ version = "0.5.7" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1146,9 +1153,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1168,9 +1175,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1234,9 +1241,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1296,9 +1303,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1322,9 +1329,9 @@ version = "1.4.2" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1350,9 +1357,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1433,9 +1440,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1478,9 +1485,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1503,10 +1510,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1578,11 +1591,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1596,9 +1615,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1622,9 +1641,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1656,15 +1675,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1686,6 +1706,12 @@ deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" version = "1.0.3" +[[deps.TZJData]] +deps = ["Artifacts"] +git-tree-sha1 = "d39314cdbaf5b90a047db33858626f8d1cc973e1" +uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" +version = "1.0.0+2023c" + [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] git-tree-sha1 = "e383c87cf2a1dc41fa30c093b2a19877c83e1bc1" @@ -1726,10 +1752,14 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimeZones]] -deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "Unicode"] -git-tree-sha1 = "5b347464bdac31eccfdbe1504d9484c31645cafc" +deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.13.0" +weakdeps = ["RecipesBase"] + + [deps.TimeZones.extensions] + TimeZonesRecipesBaseExt = "RecipesBase" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1779,10 +1809,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1812,9 +1842,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1879,10 +1909,10 @@ uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" version = "1.6.1" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/03-bayesian-neural-network/Manifest.toml b/tutorials/03-bayesian-neural-network/Manifest.toml index b0316c702..26dd7b8f5 100644 --- a/tutorials/03-bayesian-neural-network/Manifest.toml +++ b/tutorials/03-bayesian-neural-network/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "7168816b9d483eadc3c00203d16ab269e5dc5bfd" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -168,10 +168,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -218,10 +218,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -327,9 +327,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -453,9 +453,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -525,10 +529,15 @@ version = "0.1.1" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -538,9 +547,9 @@ version = "0.8.4" [[deps.Flux]] deps = ["Adapt", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] -git-tree-sha1 = "863218453b276cad81ab750579cf429bfe6a62c9" +git-tree-sha1 = "7ffd73e8ca363f80367123aab0c5d0edabab4e60" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.14.2" +version = "0.14.5" [deps.Flux.extensions] FluxAMDGPUExt = "AMDGPU" @@ -617,9 +626,9 @@ version = "3.3.8+0" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "2e57b4a4f9cc15e85a24d603256fe08e527f48d1" +git-tree-sha1 = "8ad8f375ae365aa1eb2f42e2565a40b55a4b69a8" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.8.1" +version = "9.0.0" [[deps.GPUArraysCore]] deps = ["Adapt"] @@ -646,10 +655,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -756,10 +765,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -811,15 +820,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -920,10 +929,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -961,12 +970,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -976,7 +984,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -987,9 +994,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1002,9 +1009,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1026,9 +1033,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1043,9 +1050,9 @@ version = "0.4.3" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1093,9 +1100,9 @@ version = "2022.10.11" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1121,9 +1128,9 @@ version = "0.1.5" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1182,9 +1189,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1244,9 +1251,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1264,9 +1271,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1297,9 +1304,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1368,9 +1375,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1401,9 +1408,9 @@ version = "1.3.0" [[deps.ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "18ed404e60753972ffd459c0db9725ff34d6e60d" +git-tree-sha1 = "d1235bdd57a93bd7504225b792b867e9a7df38d5" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.15.0" +version = "1.15.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -1419,9 +1426,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1444,10 +1451,14 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" +weakdeps = ["Zygote"] + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1519,11 +1530,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1537,9 +1554,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1563,9 +1580,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1585,15 +1602,16 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] StatsFunsInverseFunctionsExt = "InverseFunctions" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1696,10 +1714,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1729,9 +1747,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1779,10 +1797,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -1935,9 +1953,9 @@ version = "1.5.5+0" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "e2fe78907130b521619bc88408c859a472c4172b" +git-tree-sha1 = "b97c927497c1de55a78dc9030f6068be5d83ef80" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.63" +version = "0.6.64" [deps.Zygote.extensions] ZygoteColorsExt = "Colors" diff --git a/tutorials/04-hidden-markov-model/Manifest.toml b/tutorials/04-hidden-markov-model/Manifest.toml index db6541d8b..25bb69908 100644 --- a/tutorials/04-hidden-markov-model/Manifest.toml +++ b/tutorials/04-hidden-markov-model/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "22534c8a743be6cd79b588fb185e78dd8614a6d2" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/05-linear-regression/Manifest.toml b/tutorials/05-linear-regression/Manifest.toml index 154c6c14a..4bae9ed21 100644 --- a/tutorials/05-linear-regression/Manifest.toml +++ b/tutorials/05-linear-regression/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "9182614b755dc32fb5fc91ef98f1dbba04d8ffaf" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -254,10 +254,10 @@ version = "0.10.8" StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -369,9 +369,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -511,9 +511,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -595,10 +599,15 @@ version = "0.9.20" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -698,10 +707,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -808,10 +817,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -863,15 +872,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -972,10 +981,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1013,12 +1022,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -1028,7 +1036,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -1039,9 +1046,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1054,9 +1061,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1078,9 +1085,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1095,9 +1102,9 @@ version = "0.4.3" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1157,9 +1164,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1185,9 +1192,9 @@ version = "0.1.5" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1251,9 +1258,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1313,9 +1320,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1339,9 +1346,9 @@ version = "1.4.2" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1372,9 +1379,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1455,9 +1462,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1500,9 +1507,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1525,10 +1532,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1611,11 +1624,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1629,9 +1648,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1655,9 +1674,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1689,15 +1708,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1719,6 +1739,12 @@ deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" version = "1.0.3" +[[deps.TZJData]] +deps = ["Artifacts"] +git-tree-sha1 = "d39314cdbaf5b90a047db33858626f8d1cc973e1" +uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" +version = "1.0.0+2023c" + [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] git-tree-sha1 = "e383c87cf2a1dc41fa30c093b2a19877c83e1bc1" @@ -1759,10 +1785,14 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimeZones]] -deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "Unicode"] -git-tree-sha1 = "5b347464bdac31eccfdbe1504d9484c31645cafc" +deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.13.0" +weakdeps = ["RecipesBase"] + + [deps.TimeZones.extensions] + TimeZonesRecipesBaseExt = "RecipesBase" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1812,10 +1842,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1845,9 +1875,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1912,10 +1942,10 @@ uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" version = "1.6.1" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/06-infinite-mixture-model/Manifest.toml b/tutorials/06-infinite-mixture-model/Manifest.toml index cc9e97304..690d42e80 100644 --- a/tutorials/06-infinite-mixture-model/Manifest.toml +++ b/tutorials/06-infinite-mixture-model/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "22d77437d5f9cc37590eb650c66a832d7f8185cb" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -168,10 +168,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -218,10 +218,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -327,9 +327,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -447,9 +447,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -507,10 +511,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -604,10 +613,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -708,10 +717,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -757,15 +766,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -866,10 +875,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -907,12 +916,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -922,7 +930,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -933,9 +940,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -948,9 +955,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -972,15 +979,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1028,9 +1035,9 @@ version = "2022.10.11" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1050,9 +1057,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1105,9 +1112,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1167,9 +1174,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1187,9 +1194,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1215,9 +1222,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1286,9 +1293,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1331,9 +1338,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1356,10 +1363,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1420,11 +1433,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1438,9 +1457,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1464,9 +1483,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1486,15 +1505,16 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] StatsFunsInverseFunctionsExt = "InverseFunctions" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1597,10 +1617,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1630,9 +1650,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1680,10 +1700,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/07-poisson-regression/Manifest.toml b/tutorials/07-poisson-regression/Manifest.toml index e97d16ded..703126b50 100644 --- a/tutorials/07-poisson-regression/Manifest.toml +++ b/tutorials/07-poisson-regression/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "0517af877736a403423fea5e79af9a2622617f81" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -254,10 +254,10 @@ version = "0.10.8" StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -369,9 +369,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -505,9 +505,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -577,10 +581,15 @@ version = "0.9.20" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -680,10 +689,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -790,10 +799,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -839,15 +848,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -954,10 +963,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -995,12 +1004,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -1010,7 +1018,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -1021,9 +1028,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1036,9 +1043,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1072,9 +1079,9 @@ version = "0.5.4" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MLLabelUtils]] deps = ["LearnBase", "MappedArrays", "StatsBase"] @@ -1084,9 +1091,9 @@ version = "0.5.7" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1146,9 +1153,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1168,9 +1175,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1234,9 +1241,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1296,9 +1303,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1322,9 +1329,9 @@ version = "1.4.2" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1350,9 +1357,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1433,9 +1440,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1478,9 +1485,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1503,10 +1510,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1578,11 +1591,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1596,9 +1615,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1622,9 +1641,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1656,15 +1675,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1686,6 +1706,12 @@ deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" version = "1.0.3" +[[deps.TZJData]] +deps = ["Artifacts"] +git-tree-sha1 = "d39314cdbaf5b90a047db33858626f8d1cc973e1" +uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" +version = "1.0.0+2023c" + [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] git-tree-sha1 = "e383c87cf2a1dc41fa30c093b2a19877c83e1bc1" @@ -1726,10 +1752,14 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimeZones]] -deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "Unicode"] -git-tree-sha1 = "5b347464bdac31eccfdbe1504d9484c31645cafc" +deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.13.0" +weakdeps = ["RecipesBase"] + + [deps.TimeZones.extensions] + TimeZonesRecipesBaseExt = "RecipesBase" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1779,10 +1809,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1812,9 +1842,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1879,10 +1909,10 @@ uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" version = "1.6.1" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/08-multinomial-logistic-regression/Manifest.toml b/tutorials/08-multinomial-logistic-regression/Manifest.toml index c5d58dda8..4621e4771 100644 --- a/tutorials/08-multinomial-logistic-regression/Manifest.toml +++ b/tutorials/08-multinomial-logistic-regression/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "53f714f9c520703858bde7881fd306675a4a29d7" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -254,10 +254,10 @@ version = "0.10.8" StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -369,9 +369,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -505,9 +505,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -577,10 +581,15 @@ version = "0.9.20" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -674,10 +683,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -784,10 +793,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -833,15 +842,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -948,10 +957,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -989,12 +998,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -1004,7 +1012,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -1015,9 +1022,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1030,9 +1037,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1066,9 +1073,9 @@ version = "0.5.4" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MLLabelUtils]] deps = ["LearnBase", "MappedArrays", "StatsBase"] @@ -1078,9 +1085,9 @@ version = "0.5.7" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1140,9 +1147,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1162,9 +1169,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1228,9 +1235,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1290,9 +1297,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1316,9 +1323,9 @@ version = "1.4.2" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1344,9 +1351,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1427,9 +1434,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1472,9 +1479,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1497,10 +1504,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1567,11 +1580,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1585,9 +1604,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1611,9 +1630,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1639,15 +1658,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1669,6 +1689,12 @@ deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" version = "1.0.3" +[[deps.TZJData]] +deps = ["Artifacts"] +git-tree-sha1 = "d39314cdbaf5b90a047db33858626f8d1cc973e1" +uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" +version = "1.0.0+2023c" + [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] git-tree-sha1 = "e383c87cf2a1dc41fa30c093b2a19877c83e1bc1" @@ -1709,10 +1735,14 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimeZones]] -deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "Unicode"] -git-tree-sha1 = "5b347464bdac31eccfdbe1504d9484c31645cafc" +deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.13.0" +weakdeps = ["RecipesBase"] + + [deps.TimeZones.extensions] + TimeZonesRecipesBaseExt = "RecipesBase" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1762,10 +1792,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1795,9 +1825,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1862,10 +1892,10 @@ uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" version = "1.6.1" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/09-variational-inference/Manifest.toml b/tutorials/09-variational-inference/Manifest.toml index 3f682995f..d306ca28c 100644 --- a/tutorials/09-variational-inference/Manifest.toml +++ b/tutorials/09-variational-inference/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "a797d593ed4ed55905ba6ad67df963533cfbc8d6" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -254,10 +254,10 @@ version = "0.10.8" StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -347,12 +347,13 @@ uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" version = "1.0.5+0" [[deps.ComponentArrays]] -deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "Functors", "LinearAlgebra", "Requires", "StaticArrayInterface"] -git-tree-sha1 = "e1a6694a62f7a00cf2c4f65dccd118ac28a6c099" +deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "Functors", "LinearAlgebra", "PackageExtensionCompat", "StaticArrayInterface"] +git-tree-sha1 = "fb28e65c339c7fe2d6b4d1776c8c92dd5a828dce" uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -version = "0.14.0" +version = "0.14.1" [deps.ComponentArrays.extensions] + ComponentArraysAdaptExt = "Adapt" ComponentArraysConstructionBaseExt = "ConstructionBase" ComponentArraysGPUArraysExt = "GPUArrays" ComponentArraysRecursiveArrayToolsExt = "RecursiveArrayTools" @@ -361,6 +362,7 @@ version = "0.14.0" ComponentArraysStaticArraysExt = "StaticArrays" [deps.ComponentArrays.weakdeps] + Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" @@ -391,9 +393,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -533,9 +535,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -617,10 +623,15 @@ version = "0.9.20" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -630,9 +641,9 @@ version = "0.8.4" [[deps.Flux]] deps = ["Adapt", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] -git-tree-sha1 = "863218453b276cad81ab750579cf429bfe6a62c9" +git-tree-sha1 = "7ffd73e8ca363f80367123aab0c5d0edabab4e60" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.14.2" +version = "0.14.5" [deps.Flux.extensions] FluxAMDGPUExt = "AMDGPU" @@ -715,9 +726,9 @@ version = "1.8.3" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "2e57b4a4f9cc15e85a24d603256fe08e527f48d1" +git-tree-sha1 = "8ad8f375ae365aa1eb2f42e2565a40b55a4b69a8" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.8.1" +version = "9.0.0" [[deps.GPUArraysCore]] deps = ["Adapt"] @@ -744,10 +755,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -865,10 +876,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -920,15 +931,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1029,10 +1040,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1070,12 +1081,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -1085,7 +1095,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -1096,9 +1105,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1111,9 +1120,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1135,9 +1144,9 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1152,9 +1161,9 @@ version = "0.4.3" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1214,9 +1223,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1242,9 +1251,9 @@ version = "0.1.5" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1314,9 +1323,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1340,6 +1349,12 @@ git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" version = "0.11.17" +[[deps.PackageExtensionCompat]] +git-tree-sha1 = "f9b1e033c2b1205cf30fd119f4e50881316c1923" +uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" +version = "1.0.1" +weakdeps = ["Requires", "TOML"] + [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851" @@ -1376,9 +1391,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1402,9 +1417,9 @@ version = "1.4.2" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1435,9 +1450,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1518,9 +1533,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1563,9 +1578,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1588,10 +1603,14 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" +weakdeps = ["Zygote"] + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1661,12 +1680,6 @@ git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" uuid = "ce78b400-467f-4804-87d8-8f486da07d0a" version = "1.1.0" -[[deps.SnoopPrecompile]] -deps = ["Preferences"] -git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" -uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" -version = "1.0.3" - [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1680,11 +1693,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1703,10 +1722,10 @@ uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" version = "0.8.8" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "33040351d2403b84afce74dae2e22d3f5b18edcb" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] +git-tree-sha1 = "03fec6800a986d191f64f5c0996b59ed526eda25" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.4.0" +version = "1.4.1" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -1715,9 +1734,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1741,9 +1760,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1775,15 +1794,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1805,6 +1825,12 @@ deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" version = "1.0.3" +[[deps.TZJData]] +deps = ["Artifacts"] +git-tree-sha1 = "d39314cdbaf5b90a047db33858626f8d1cc973e1" +uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" +version = "1.0.0+2023c" + [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] git-tree-sha1 = "e383c87cf2a1dc41fa30c093b2a19877c83e1bc1" @@ -1845,10 +1871,14 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimeZones]] -deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "Unicode"] -git-tree-sha1 = "5b347464bdac31eccfdbe1504d9484c31645cafc" +deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.13.0" +weakdeps = ["RecipesBase"] + + [deps.TimeZones.extensions] + TimeZonesRecipesBaseExt = "RecipesBase" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1898,10 +1928,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1936,9 +1966,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -2003,10 +2033,10 @@ uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" version = "1.6.1" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -2159,9 +2189,9 @@ version = "1.5.5+0" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "e2fe78907130b521619bc88408c859a472c4172b" +git-tree-sha1 = "b97c927497c1de55a78dc9030f6068be5d83ef80" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.63" +version = "0.6.64" weakdeps = ["Colors", "Distances", "Tracker"] [deps.Zygote.extensions] diff --git a/tutorials/10-bayesian-differential-equations/Manifest.toml b/tutorials/10-bayesian-differential-equations/Manifest.toml index 6f8b936f7..40b09fd66 100644 --- a/tutorials/10-bayesian-differential-equations/Manifest.toml +++ b/tutorials/10-bayesian-differential-equations/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "1cf8b95959ac0235940751347a1e8ff1481cfa25" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -143,10 +143,14 @@ uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" version = "0.1.29" [[deps.ArrayLayouts]] -deps = ["FillArrays", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "6189f7819e6345bcc097331c7db571f2f211364f" +deps = ["FillArrays", "LinearAlgebra"] +git-tree-sha1 = "dcda7e0ac618210eabf43751d5cafde100dd539b" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.1.1" +version = "1.3.0" +weakdeps = ["SparseArrays"] + + [deps.ArrayLayouts.extensions] + ArrayLayoutsSparseArraysExt = "SparseArrays" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -171,9 +175,9 @@ version = "0.4.7" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "6e9b384d5e21452bc81cae3552c74f430e320985" +git-tree-sha1 = "0b816941273b5b162be122a6c94d706e3b3125ca" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "0.17.35" +version = "0.17.38" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] @@ -208,10 +212,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -241,10 +245,10 @@ uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.5" [[deps.BoundaryValueDiffEq]] -deps = ["BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase", "SparseArrays"] -git-tree-sha1 = "ed8e837bfb3d1e3157022c9636ec1c722b637318" +deps = ["ArrayInterface", "BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NonlinearSolve", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "TruncatedStacktraces", "UnPack"] +git-tree-sha1 = "f7392ce20e6dafa8fee406142b1764de7d7cd911" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "2.11.0" +version = "4.0.1" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -276,15 +280,15 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.Cassette]] -git-tree-sha1 = "a70f220ea09ec61401745ff338f8fb340420165c" +git-tree-sha1 = "415a5e8101d37582c0d912de8f7665b37e05ea5c" uuid = "7057c7e9-c182-5462-911a-8362d720325c" -version = "0.3.11" +version = "0.3.12" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -402,9 +406,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -472,9 +476,9 @@ version = "0.4.0" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] -git-tree-sha1 = "ed586656058844e48660c6d6fdb384e83afc50db" +git-tree-sha1 = "df8638dbfa03d1b336c410e23a9dfbf89cb53937" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.128.0" +version = "6.128.2" [deps.DiffEqBase.extensions] DiffEqBaseDistributionsExt = "Distributions" @@ -500,9 +504,9 @@ version = "6.128.0" [[deps.DiffEqCallbacks]] deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "303ab70e4524843653e55e16a3dc7b75e677a3dd" +git-tree-sha1 = "9c7d3a84264d935f6981504388b202a770113faa" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.27.0" +version = "2.29.1" weakdeps = ["OrdinaryDiffEq", "Sundials"] [[deps.DiffEqNoiseProcess]] @@ -529,9 +533,9 @@ version = "1.15.1" [[deps.DifferentialEquations]] deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] -git-tree-sha1 = "1cfe0178410e1bb4b14058c537d0f347eb9d95dc" +git-tree-sha1 = "c3d11164d1b08c379bc3c6abae45fcd7250e8e35" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.8.0" +version = "7.9.1" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] @@ -595,9 +599,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipsisNotation]] deps = ["StaticArrayInterface"] @@ -617,10 +625,10 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.Enzyme]] -deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Printf", "Random"] -git-tree-sha1 = "5eb8de9b18c31683be5c7b5a5034aaf5e24dd068" +deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Preferences", "Printf", "Random"] +git-tree-sha1 = "1f85bc8a9da6118abb95d134efc68cf4a6957341" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.11.6" +version = "0.11.7" [[deps.EnzymeCore]] deps = ["Adapt"] @@ -630,9 +638,9 @@ version = "0.5.2" [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "dca536dc737737d14228b485bb46abeeecfa9695" +git-tree-sha1 = "ffa4926cc857bcc5c256825bd7273a6ac989eb34" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.78+0" +version = "0.0.80+0" [[deps.ExceptionUnwrapping]] deps = ["Test"] @@ -702,10 +710,15 @@ version = "2.0.0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] @@ -792,9 +805,9 @@ version = "3.3.8+0" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "2e57b4a4f9cc15e85a24d603256fe08e527f48d1" +git-tree-sha1 = "8ad8f375ae365aa1eb2f42e2565a40b55a4b69a8" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.8.1" +version = "9.0.0" [[deps.GPUArraysCore]] deps = ["Adapt"] @@ -833,10 +846,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -965,10 +978,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -984,9 +997,13 @@ version = "2.1.91+0" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "add0bfe9091a0148a358dc8c52d5ac60806da76c" +git-tree-sha1 = "61068b4df1e434c26ff8b876fbaf2be3e3e44d27" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.7.2" +version = "9.7.3" +weakdeps = ["FastBroadcast"] + + [deps.JumpProcesses.extensions] + JumpProcessFastBroadcastExt = "FastBroadcast" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] @@ -1012,9 +1029,9 @@ version = "0.6.7" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "fbda7c58464204d92f3b158578fb0b3d4224cea5" +git-tree-sha1 = "17e462054b42dcdda73e9a9ba0c67754170c88ae" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.3" +version = "0.9.4" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1030,15 +1047,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1151,10 +1168,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1192,9 +1209,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] deps = ["ArrayInterface", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] -git-tree-sha1 = "f746a5b9522815bf098049f9cbfbfcae53f29450" +git-tree-sha1 = "69cbd612e6e67ba2f8121bc8725bc9d04d803599" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.5.0" +version = "2.5.1" [deps.LinearSolve.extensions] LinearSolveCUDAExt = "CUDA" @@ -1202,6 +1219,7 @@ version = "2.5.0" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKrylovKitExt = "KrylovKit" LinearSolveMKLExt = "MKL_jll" + LinearSolveMetalExt = "Metal" LinearSolvePardisoExt = "Pardiso" [deps.LinearSolve.weakdeps] @@ -1210,6 +1228,7 @@ version = "2.5.0" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" MKL_jll = "856f044c-d86e-5d09-b602-aeab76dc8ba7" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" [[deps.LogDensityProblems]] @@ -1220,12 +1239,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -1235,7 +1253,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -1246,9 +1263,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1261,9 +1278,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.LoopVectorization]] deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] @@ -1296,15 +1313,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1380,9 +1397,9 @@ version = "4.5.1" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1402,9 +1419,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1423,15 +1440,15 @@ version = "1.2.0" [[deps.NonlinearSolve]] deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "23dabe80f8ebec9a68b0db4cd02f2d2cdbc4f653" +git-tree-sha1 = "ee53089df81a6bdf3c06c17cf674e90931b10a73" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "1.9.0" +version = "1.10.0" [[deps.ObjectFile]] deps = ["Reexport", "StructIO"] -git-tree-sha1 = "69607899b46e1f8ead70396bc51a4c361478d8f6" +git-tree-sha1 = "195e0a19842f678dd3473ceafbe9d82dfacc583c" uuid = "d8793406-e978-5875-9003-1fc021f44a92" -version = "0.4.0" +version = "0.4.1" [[deps.Observables]] git-tree-sha1 = "6862738f9796b3edc1c09d0890afce4eca9e7e93" @@ -1480,15 +1497,15 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "e3a6546c1577bfd701771b477b794a52949e7594" +git-tree-sha1 = "963b004d15216f8129f6c0f7d187efa136570be0" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.6" +version = "1.7.7" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1503,9 +1520,9 @@ version = "1.6.2" [[deps.OrdinaryDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "47c560dcb059570bdbd9f887a6b8958190e498a4" +git-tree-sha1 = "ba3ed480f991b846cf9a8118d3370d9752e7166d" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.53.4" +version = "6.55.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1566,9 +1583,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1620,9 +1637,9 @@ weakdeps = ["ReverseDiff"] [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1648,9 +1665,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1719,9 +1736,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1764,9 +1781,9 @@ version = "1.1.1" [[deps.ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "18ed404e60753972ffd459c0db9725ff34d6e60d" +git-tree-sha1 = "d1235bdd57a93bd7504225b792b867e9a7df38d5" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.15.0" +version = "1.15.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -1782,9 +1799,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1818,10 +1835,14 @@ uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" version = "0.6.39" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" +weakdeps = ["Zygote"] + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" [[deps.SciMLNLSolve]] deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] @@ -1836,10 +1857,10 @@ uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" version = "0.3.6" [[deps.SciMLSensitivity]] -deps = ["Adapt", "ArrayInterface", "Cassette", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEq", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SparseDiffTools", "StaticArraysCore", "Statistics", "StochasticDiffEq", "Tracker", "TruncatedStacktraces", "Zygote", "ZygoteRules"] -git-tree-sha1 = "8f90cc3583e4f6e341f558a0c7c4b1b3d581cbb3" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Cassette", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEq", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SparseDiffTools", "StaticArraysCore", "Statistics", "StochasticDiffEq", "Tracker", "TruncatedStacktraces", "Zygote", "ZygoteRules"] +git-tree-sha1 = "dd225a880a9bcd1a862fb9ea540731a70cccb338" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.36.0" +version = "7.38.0" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -1923,15 +1944,27 @@ deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "Reexport", "Requires", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "VertexSafeGraphs"] -git-tree-sha1 = "4c1a57bcbc0b795fbfdc2009e70f9c2fd2815bfe" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "b3eb6747277d9919f5527ad9053f6d2fb1166516" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.4.1" -weakdeps = ["Zygote"] +version = "2.5.1" [deps.SparseDiffTools.extensions] + SparseDiffToolsEnzymeExt = "Enzyme" + SparseDiffToolsSymbolicsExt = "Symbolics" SparseDiffToolsZygoteExt = "Zygote" + [deps.SparseDiffTools.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" @@ -1940,9 +1973,9 @@ version = "0.3.9" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1961,10 +1994,10 @@ uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" version = "0.8.8" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "33040351d2403b84afce74dae2e22d3f5b18edcb" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] +git-tree-sha1 = "03fec6800a986d191f64f5c0996b59ed526eda25" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.4.0" +version = "1.4.1" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -1973,9 +2006,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1999,9 +2032,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -2045,15 +2078,16 @@ uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" version = "0.4.17" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.StructIO]] deps = ["Test"] @@ -2204,10 +2238,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -2242,9 +2276,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -2310,10 +2344,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -2466,9 +2500,9 @@ version = "1.5.5+0" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "e2fe78907130b521619bc88408c859a472c4172b" +git-tree-sha1 = "b97c927497c1de55a78dc9030f6068be5d83ef80" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.63" +version = "0.6.64" weakdeps = ["Colors", "Distances", "Tracker"] [deps.Zygote.extensions] diff --git a/tutorials/11-probabilistic-pca/Manifest.toml b/tutorials/11-probabilistic-pca/Manifest.toml index d4a718fdc..c00d1a239 100644 --- a/tutorials/11-probabilistic-pca/Manifest.toml +++ b/tutorials/11-probabilistic-pca/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "ef462fc173a4ba83c350dd73690f805ff0c2abe7" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -481,9 +481,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -541,10 +545,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -638,10 +647,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -748,10 +757,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -797,15 +806,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -906,10 +915,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -947,12 +956,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -962,7 +970,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -973,9 +980,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -988,9 +995,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1012,15 +1019,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1074,9 +1081,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1096,9 +1103,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1162,9 +1169,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1224,9 +1231,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1250,9 +1257,9 @@ version = "1.4.2" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1278,9 +1285,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1349,9 +1356,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1382,9 +1389,9 @@ version = "1.3.0" [[deps.ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "18ed404e60753972ffd459c0db9725ff34d6e60d" +git-tree-sha1 = "d1235bdd57a93bd7504225b792b867e9a7df38d5" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.15.0" +version = "1.15.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -1400,9 +1407,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1425,10 +1432,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1495,11 +1508,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1513,9 +1532,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1539,9 +1558,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1567,15 +1586,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1684,10 +1704,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1717,9 +1737,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1773,10 +1793,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/12-gaussian-process/Manifest.toml b/tutorials/12-gaussian-process/Manifest.toml index 3f154c4c1..265945b2a 100644 --- a/tutorials/12-gaussian-process/Manifest.toml +++ b/tutorials/12-gaussian-process/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "390f0ff830d7e11242f044c4b0d23eedcbb7a091" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -34,9 +34,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -55,9 +55,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -174,10 +174,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -248,10 +248,10 @@ version = "0.10.8" StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -357,9 +357,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -493,9 +493,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -565,10 +569,15 @@ version = "0.9.20" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -662,10 +671,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -772,10 +781,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -827,15 +836,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -936,10 +945,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -977,12 +986,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -992,7 +1000,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -1003,9 +1010,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1018,9 +1025,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1042,15 +1049,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1104,9 +1111,9 @@ version = "2022.10.11" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1126,9 +1133,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1181,9 +1188,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1243,9 +1250,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1269,9 +1276,9 @@ version = "1.4.2" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1297,9 +1304,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1380,9 +1387,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1413,9 +1420,9 @@ version = "1.3.0" [[deps.ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "18ed404e60753972ffd459c0db9725ff34d6e60d" +git-tree-sha1 = "d1235bdd57a93bd7504225b792b867e9a7df38d5" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.15.0" +version = "1.15.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -1431,9 +1438,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1456,10 +1463,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1526,11 +1539,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1544,9 +1563,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1570,9 +1589,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1592,15 +1611,16 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] StatsFunsInverseFunctionsExt = "InverseFunctions" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1622,6 +1642,12 @@ deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" version = "1.0.3" +[[deps.TZJData]] +deps = ["Artifacts"] +git-tree-sha1 = "d39314cdbaf5b90a047db33858626f8d1cc973e1" +uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" +version = "1.0.0+2023c" + [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" @@ -1656,10 +1682,14 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimeZones]] -deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "Unicode"] -git-tree-sha1 = "5b347464bdac31eccfdbe1504d9484c31645cafc" +deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "89e64d61ef3cd9e80f7fc12b7d13db2d75a23c03" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.13.0" +weakdeps = ["RecipesBase"] + + [deps.TimeZones.extensions] + TimeZonesRecipesBaseExt = "RecipesBase" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1709,10 +1739,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1742,9 +1772,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1803,10 +1833,10 @@ uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" version = "1.6.1" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/13-seasonal-time-series/Manifest.toml b/tutorials/13-seasonal-time-series/Manifest.toml index 6d5f5263e..7dd2bcb91 100644 --- a/tutorials/13-seasonal-time-series/Manifest.toml +++ b/tutorials/13-seasonal-time-series/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "8465c369abb7f6ef05a55c9b93c53a6097762489" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/14-minituring/Manifest.toml b/tutorials/14-minituring/Manifest.toml index eaa6adf5c..e3bfb2940 100644 --- a/tutorials/14-minituring/Manifest.toml +++ b/tutorials/14-minituring/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "31266805170f7b1d6aa8609e6114be070df1b249" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -168,10 +168,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -201,10 +201,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -270,9 +270,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -385,9 +385,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -421,10 +425,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.Formatting]] deps = ["Printf"] @@ -539,10 +548,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] @@ -564,15 +573,15 @@ version = "0.6.7" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LRUCache]] git-tree-sha1 = "48c10e3cc27e30de82463c27bef0b8bdbd1dc634" @@ -640,12 +649,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -655,7 +663,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -666,9 +673,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -681,9 +688,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -705,15 +712,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -750,9 +757,9 @@ version = "2022.10.11" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -772,9 +779,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -809,9 +816,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.OrderedCollections]] git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3" @@ -831,9 +838,9 @@ version = "1.9.2" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -859,9 +866,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] @@ -920,9 +927,9 @@ version = "1.3.4" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -959,9 +966,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -984,10 +991,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1031,11 +1044,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1049,9 +1068,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1075,9 +1094,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1097,15 +1116,16 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] StatsFunsInverseFunctionsExt = "InverseFunctions" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1196,10 +1216,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" diff --git a/tutorials/docs-00-getting-started/Manifest.toml b/tutorials/docs-00-getting-started/Manifest.toml index 9f4ff6272..e3c5ee20f 100644 --- a/tutorials/docs-00-getting-started/Manifest.toml +++ b/tutorials/docs-00-getting-started/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "102d486b18af7951cac72d56aec7c8e37b50a316" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-01-contributing-guide/Manifest.toml b/tutorials/docs-01-contributing-guide/Manifest.toml index 9f4ff6272..e3c5ee20f 100644 --- a/tutorials/docs-01-contributing-guide/Manifest.toml +++ b/tutorials/docs-01-contributing-guide/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "102d486b18af7951cac72d56aec7c8e37b50a316" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-02-contributing-style-guide/Manifest.toml b/tutorials/docs-02-contributing-style-guide/Manifest.toml index 9f4ff6272..e3c5ee20f 100644 --- a/tutorials/docs-02-contributing-style-guide/Manifest.toml +++ b/tutorials/docs-02-contributing-style-guide/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "102d486b18af7951cac72d56aec7c8e37b50a316" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml b/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml index 800beb573..f099be58d 100644 --- a/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml +++ b/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "5d3b8b9eb7683443ea8ae96e6fef297715042a31" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml b/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml index 9f4ff6272..e3c5ee20f 100644 --- a/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml +++ b/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "102d486b18af7951cac72d56aec7c8e37b50a316" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-05-for-developers-compiler/Manifest.toml b/tutorials/docs-05-for-developers-compiler/Manifest.toml index 9f4ff6272..e3c5ee20f 100644 --- a/tutorials/docs-05-for-developers-compiler/Manifest.toml +++ b/tutorials/docs-05-for-developers-compiler/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "102d486b18af7951cac72d56aec7c8e37b50a316" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-06-for-developers-interface/Manifest.toml b/tutorials/docs-06-for-developers-interface/Manifest.toml index 7e0175174..f1da18783 100644 --- a/tutorials/docs-06-for-developers-interface/Manifest.toml +++ b/tutorials/docs-06-for-developers-interface/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "c2c40f5436f7cfb3d611046e88c24da658e5bf55" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-07-for-developers-variational-inference/Manifest.toml b/tutorials/docs-07-for-developers-variational-inference/Manifest.toml index 9f4ff6272..e3c5ee20f 100644 --- a/tutorials/docs-07-for-developers-variational-inference/Manifest.toml +++ b/tutorials/docs-07-for-developers-variational-inference/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "102d486b18af7951cac72d56aec7c8e37b50a316" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-08-using-turing/Manifest.toml b/tutorials/docs-08-using-turing/Manifest.toml index 9f4ff6272..e3c5ee20f 100644 --- a/tutorials/docs-08-using-turing/Manifest.toml +++ b/tutorials/docs-08-using-turing/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "102d486b18af7951cac72d56aec7c8e37b50a316" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-09-using-turing-advanced/Manifest.toml b/tutorials/docs-09-using-turing-advanced/Manifest.toml index 065784c4b..bb8605e02 100644 --- a/tutorials/docs-09-using-turing-advanced/Manifest.toml +++ b/tutorials/docs-09-using-turing-advanced/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "4c0c886318004c9a56b597cb6e8faf8fe1ac07ac" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-10-using-turing-autodiff/Manifest.toml b/tutorials/docs-10-using-turing-autodiff/Manifest.toml index 9f4ff6272..e3c5ee20f 100644 --- a/tutorials/docs-10-using-turing-autodiff/Manifest.toml +++ b/tutorials/docs-10-using-turing-autodiff/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "102d486b18af7951cac72d56aec7c8e37b50a316" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml b/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml index b092f03b8..27cc3ba99 100644 --- a/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml +++ b/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "f6bac772a1c0780a37a1f9e868095eea94af1f8e" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -481,9 +481,13 @@ version = "3.4.6" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -541,10 +545,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -638,10 +647,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -742,10 +751,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -791,15 +800,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -906,10 +915,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -947,12 +956,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -962,7 +970,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -973,9 +980,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -988,9 +995,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1012,15 +1019,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1074,9 +1081,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1096,9 +1103,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1162,9 +1169,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1224,9 +1231,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1244,9 +1251,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1272,9 +1279,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1343,9 +1350,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1388,9 +1395,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1413,10 +1420,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1483,11 +1496,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1501,9 +1520,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1527,9 +1546,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1561,15 +1580,16 @@ uuid = "5e0ebb24-38b0-5f93-81fe-25c709ecae67" version = "1.2.3" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1695,10 +1715,10 @@ uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6" version = "1.3.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1728,9 +1748,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1784,10 +1804,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-12-using-turing-guide/Manifest.toml b/tutorials/docs-12-using-turing-guide/Manifest.toml index 4f426900d..d88b8ce11 100644 --- a/tutorials/docs-12-using-turing-guide/Manifest.toml +++ b/tutorials/docs-12-using-turing-guide/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "b7d5f57d9eda90053bb4603ac4234cf8d9b7d1b7" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] @@ -648,10 +657,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -752,10 +761,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -801,15 +810,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -910,10 +919,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -957,12 +966,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -972,7 +980,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -983,9 +990,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -998,9 +1005,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1022,15 +1029,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1090,9 +1097,9 @@ version = "7.8.3" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1112,9 +1119,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1178,15 +1185,15 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "e3a6546c1577bfd701771b477b794a52949e7594" +git-tree-sha1 = "963b004d15216f8129f6c0f7d187efa136570be0" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.6" +version = "1.7.7" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1252,9 +1259,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1278,9 +1285,9 @@ version = "0.2.4" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1306,9 +1313,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1377,9 +1384,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1422,9 +1429,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1447,10 +1454,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1517,11 +1530,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1535,9 +1554,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1561,9 +1580,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1589,15 +1608,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1706,10 +1726,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1744,9 +1764,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1800,10 +1820,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-13-using-turing-performance-tips/Manifest.toml b/tutorials/docs-13-using-turing-performance-tips/Manifest.toml index 7d7d28135..09cfbf316 100644 --- a/tutorials/docs-13-using-turing-performance-tips/Manifest.toml +++ b/tutorials/docs-13-using-turing-performance-tips/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "f00de2f83fe88b91151dd081220b759ce23173e6" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -168,10 +168,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -201,10 +201,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -270,9 +270,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -385,9 +385,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -421,10 +425,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.Formatting]] deps = ["Printf"] @@ -539,10 +548,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] @@ -564,15 +573,15 @@ version = "0.6.7" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LRUCache]] git-tree-sha1 = "48c10e3cc27e30de82463c27bef0b8bdbd1dc634" @@ -640,12 +649,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -655,7 +663,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -666,9 +673,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -681,9 +688,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -705,15 +712,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -756,9 +763,9 @@ version = "2022.10.11" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -778,9 +785,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -815,9 +822,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.OrderedCollections]] git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3" @@ -837,9 +844,9 @@ version = "1.9.2" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -865,9 +872,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] @@ -926,9 +933,9 @@ version = "1.3.4" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -965,9 +972,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -990,10 +997,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1037,11 +1050,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1055,9 +1074,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1081,9 +1100,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1103,15 +1122,16 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] StatsFunsInverseFunctionsExt = "InverseFunctions" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1202,10 +1222,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" diff --git a/tutorials/docs-14-using-turing-quick-start/Manifest.toml b/tutorials/docs-14-using-turing-quick-start/Manifest.toml index 9f4ff6272..e3c5ee20f 100644 --- a/tutorials/docs-14-using-turing-quick-start/Manifest.toml +++ b/tutorials/docs-14-using-turing-quick-start/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "102d486b18af7951cac72d56aec7c8e37b50a316" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] diff --git a/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml b/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml index e2883d662..ace55750a 100644 --- a/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml +++ b/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.2" +julia_version = "1.9.3" manifest_format = "2.0" project_hash = "d42320247f27a85a88c7c5de8259eefe9da423db" [[deps.ADTypes]] -git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a" +git-tree-sha1 = "d68758475ff90600488eb975b5ac222709a7dd6f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.1.6" +version = "0.2.2" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -28,9 +28,9 @@ version = "4.4.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] -git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +git-tree-sha1 = "caa9b62583577b0d6b222f11f54aa29fabbdb5ca" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.4" +version = "0.6.2" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -49,9 +49,9 @@ weakdeps = ["StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498" +git-tree-sha1 = "acbe805c3078ba0057bb56985248bd66bce016b1" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.5" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -180,10 +180,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "ff192d037dee3c05fe842a207f8c6b840b04cca2" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "8eacff457e5b8c13a97848484ad650dabbffa0fc" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.7" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -230,10 +230,10 @@ uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "f98ae934cd677d51d2941088849f0bf2f59e6f6e" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "dbeca245b0680f5393b4e6c40dcead7230ab0b3b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.53.0" +version = "1.54.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] @@ -345,9 +345,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" +git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.3" +version = "1.5.4" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -475,9 +475,13 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "e3518c62a998defe74c5cc64b2bf2a33b7a788b8" +git-tree-sha1 = "c65a403dbacd4e9f08141f030259fafc848a4f21" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.16" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -535,10 +539,15 @@ version = "3.3.10+0" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "f372472e8672b1d993e93dada09e23139b509f9e" +deps = ["LinearAlgebra", "Random"] +git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.5.0" +version = "1.6.1" +weakdeps = ["SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -632,10 +641,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.76.5+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -736,10 +745,10 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -785,15 +794,15 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "8695a49bfe05a2dc0feeefd06b4ca6361a018729" +git-tree-sha1 = "a9d2ce1d5007b1e8f6c5b89c5a31ff8bd146db5c" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.1.0" +version = "6.2.1" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c35203c1e1002747da220ffc3c0762ce7754b08c" +git-tree-sha1 = "7ca6850ae880cc99b59b88517545f91a52020afa" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.23+0" +version = "0.0.25+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" version = "1.42.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -935,12 +944,11 @@ version = "2.1.1" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] -git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75" +git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.6.1" +version = "1.5.0" [deps.LogDensityProblemsAD.extensions] - LogDensityProblemsADADTypesExt = "ADTypes" LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -950,7 +958,6 @@ version = "1.6.1" LogDensityProblemsADZygoteExt = "Zygote" [deps.LogDensityProblemsAD.weakdeps] - ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -961,9 +968,9 @@ version = "1.6.1" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f" +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.24" +version = "0.3.26" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] @@ -1000,15 +1007,15 @@ version = "2023.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" +git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.8.0" +version = "1.9.2" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" @@ -1062,9 +1069,9 @@ version = "0.10.2" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d42748c725c3f088bcda47fa2aca89e74d59d22" +git-tree-sha1 = "3b29fafcdfa66d6673306cf116a2dc243933e2c5" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.4" +version = "0.9.5" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1084,9 +1091,9 @@ version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95" +git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.8" +version = "0.10.0" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1150,9 +1157,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e" +git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.19" +version = "0.2.20" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1212,9 +1219,9 @@ version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466" +git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.38.17" +version = "1.39.0" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1232,9 +1239,9 @@ version = "1.38.17" [[deps.PrecompileTools]] deps = ["Preferences"] -git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81" +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.1.2" +version = "1.2.0" [[deps.Preferences]] deps = ["TOML"] @@ -1260,9 +1267,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" +git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" +version = "1.8.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] @@ -1331,9 +1338,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "7ed35fb5f831aaf09c2d7c8736d44667a1afdcb0" +git-tree-sha1 = "5f834446731ba29d1d68d91fddf8f9593b68b7a2" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.7" +version = "2.38.8" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -1376,9 +1383,9 @@ version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4" +git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.17" +version = "2.0.19" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "c0781c7ebb65776e9770d333b5e191d20dd45fcf" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.94.0" +version = "1.97.0" + + [deps.SciMLBase.extensions] + ZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] @@ -1471,11 +1484,17 @@ version = "1.1.1" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "91402087fd5d13b2d97e3ef29bbdf9d7859e678a" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.1" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3" +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.0" +version = "2.3.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1489,9 +1508,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" +git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.2" +version = "1.6.3" weakdeps = ["Statistics"] [deps.StaticArrays.extensions] @@ -1515,9 +1534,9 @@ version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" +git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.6.0" +version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1543,15 +1562,16 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.6" [[deps.StringManipulation]] -git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +deps = ["PrecompileTools"] +git-tree-sha1 = "25ad9b0ccbc6cc63dfff1eb3f4bbb4d3e0d8a491" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.0" +version = "0.3.2" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "521a0e828e98bb69042fec1809c1b5a680eb7389" +deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.15" +version = "0.6.16" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1660,10 +1680,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "6882a8be16767080b3edf2f6f2884ab71aa40e0a" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "83bcdf908c241f1ab54abc95af182f7b6550d591" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.29.0" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1713,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35" +git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.16.2" +version = "1.17.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -1749,10 +1769,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.10.4+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"]