diff --git a/tutorials/00-introduction/Manifest.toml b/tutorials/00-introduction/Manifest.toml index 97f7916bc..1c5b12602 100644 --- a/tutorials/00-introduction/Manifest.toml +++ b/tutorials/00-introduction/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/01-gaussian-mixture-model/Manifest.toml b/tutorials/01-gaussian-mixture-model/Manifest.toml index acfe5b335..49e368672 100644 --- a/tutorials/01-gaussian-mixture-model/Manifest.toml +++ b/tutorials/01-gaussian-mixture-model/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/02-logistic-regression/Manifest.toml b/tutorials/02-logistic-regression/Manifest.toml index 7740030b9..453b1b0eb 100644 --- a/tutorials/02-logistic-regression/Manifest.toml +++ b/tutorials/02-logistic-regression/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -1021,9 +1030,9 @@ 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 +1045,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1081,9 @@ 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 +1093,9 @@ 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" @@ -1168,9 +1177,9 @@ 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 +1243,9 @@ 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"] @@ -1322,9 +1331,9 @@ 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 +1359,9 @@ 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"] @@ -1478,9 +1487,9 @@ 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" @@ -1580,9 +1589,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1686,6 +1695,12 @@ 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 +1741,10 @@ 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", "RecipesBase", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "8dfeeb90ba3fda8c69873c961e397b6541bdc4e6" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.12.0" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1780,9 +1795,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1812,9 +1827,9 @@ 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] diff --git a/tutorials/03-bayesian-neural-network/Manifest.toml b/tutorials/03-bayesian-neural-network/Manifest.toml index b0316c702..a9b714ddd 100644 --- a/tutorials/03-bayesian-neural-network/Manifest.toml +++ b/tutorials/03-bayesian-neural-network/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -987,9 +996,9 @@ 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 +1011,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1035,9 @@ 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 +1052,9 @@ 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" @@ -1121,9 +1130,9 @@ 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 +1191,9 @@ 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"] @@ -1264,9 +1273,9 @@ 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 +1306,9 @@ 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"] @@ -1401,9 +1410,9 @@ 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 +1428,9 @@ 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" @@ -1521,9 +1530,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1697,9 +1706,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1729,9 +1738,9 @@ 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] diff --git a/tutorials/04-hidden-markov-model/Manifest.toml b/tutorials/04-hidden-markov-model/Manifest.toml index db6541d8b..d476c6a9f 100644 --- a/tutorials/04-hidden-markov-model/Manifest.toml +++ b/tutorials/04-hidden-markov-model/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/05-linear-regression/Manifest.toml b/tutorials/05-linear-regression/Manifest.toml index 154c6c14a..be34c6358 100644 --- a/tutorials/05-linear-regression/Manifest.toml +++ b/tutorials/05-linear-regression/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -1039,9 +1048,9 @@ 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 +1063,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1087,9 @@ 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 +1104,9 @@ 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" @@ -1185,9 +1194,9 @@ 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 +1260,9 @@ 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"] @@ -1339,9 +1348,9 @@ 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 +1381,9 @@ 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"] @@ -1500,9 +1509,9 @@ 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" @@ -1613,9 +1622,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1719,6 +1728,12 @@ 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 +1774,10 @@ 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", "RecipesBase", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "8dfeeb90ba3fda8c69873c961e397b6541bdc4e6" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.12.0" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1813,9 +1828,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1845,9 +1860,9 @@ 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] diff --git a/tutorials/06-infinite-mixture-model/Manifest.toml b/tutorials/06-infinite-mixture-model/Manifest.toml index cc9e97304..00e09af82 100644 --- a/tutorials/06-infinite-mixture-model/Manifest.toml +++ b/tutorials/06-infinite-mixture-model/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -933,9 +942,9 @@ 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 +957,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +981,15 @@ 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" @@ -1050,9 +1059,9 @@ 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 +1114,9 @@ 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"] @@ -1187,9 +1196,9 @@ 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 +1224,9 @@ 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 +1340,9 @@ 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" @@ -1422,9 +1431,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1598,9 +1607,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1630,9 +1639,9 @@ 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] diff --git a/tutorials/07-poisson-regression/Manifest.toml b/tutorials/07-poisson-regression/Manifest.toml index e97d16ded..b3fca5655 100644 --- a/tutorials/07-poisson-regression/Manifest.toml +++ b/tutorials/07-poisson-regression/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -1021,9 +1030,9 @@ 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 +1045,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1081,9 @@ 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 +1093,9 @@ 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" @@ -1168,9 +1177,9 @@ 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 +1243,9 @@ 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"] @@ -1322,9 +1331,9 @@ 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 +1359,9 @@ 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"] @@ -1478,9 +1487,9 @@ 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" @@ -1580,9 +1589,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1686,6 +1695,12 @@ 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 +1741,10 @@ 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", "RecipesBase", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "8dfeeb90ba3fda8c69873c961e397b6541bdc4e6" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.12.0" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1780,9 +1795,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1812,9 +1827,9 @@ 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] diff --git a/tutorials/08-multinomial-logistic-regression/Manifest.toml b/tutorials/08-multinomial-logistic-regression/Manifest.toml index c5d58dda8..110c2490a 100644 --- a/tutorials/08-multinomial-logistic-regression/Manifest.toml +++ b/tutorials/08-multinomial-logistic-regression/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -1015,9 +1024,9 @@ 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 +1039,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1075,9 @@ 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 +1087,9 @@ 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" @@ -1162,9 +1171,9 @@ 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 +1237,9 @@ 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"] @@ -1316,9 +1325,9 @@ 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 +1353,9 @@ 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"] @@ -1472,9 +1481,9 @@ 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" @@ -1569,9 +1578,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1669,6 +1678,12 @@ 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 +1724,10 @@ 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", "RecipesBase", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "8dfeeb90ba3fda8c69873c961e397b6541bdc4e6" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.12.0" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1763,9 +1778,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1795,9 +1810,9 @@ 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] diff --git a/tutorials/09-variational-inference/Manifest.toml b/tutorials/09-variational-inference/Manifest.toml index 3f682995f..38fbf2194 100644 --- a/tutorials/09-variational-inference/Manifest.toml +++ b/tutorials/09-variational-inference/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -533,9 +533,13 @@ 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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] @@ -617,10 +621,15 @@ 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"] @@ -865,10 +874,10 @@ 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"] @@ -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 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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" @@ -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"] @@ -1402,9 +1411,9 @@ 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 +1444,9 @@ 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"] @@ -1563,9 +1572,9 @@ 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" @@ -1682,9 +1691,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1805,6 +1814,12 @@ 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 +1860,10 @@ 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", "RecipesBase", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "8dfeeb90ba3fda8c69873c961e397b6541bdc4e6" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.12.0" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1899,9 +1914,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1936,9 +1951,9 @@ 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] diff --git a/tutorials/10-bayesian-differential-equations/Manifest.toml b/tutorials/10-bayesian-differential-equations/Manifest.toml index 6f8b936f7..f66b941d5 100644 --- a/tutorials/10-bayesian-differential-equations/Manifest.toml +++ b/tutorials/10-bayesian-differential-equations/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [deps.AdvancedHMC.extensions] AdvancedHMCCUDAExt = "CUDA" @@ -144,9 +144,9 @@ version = "0.1.29" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "6189f7819e6345bcc097331c7db571f2f211364f" +git-tree-sha1 = "609e6019f91369149556628d90345a1316f8dbd3" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.1.1" +version = "1.2.1" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -171,9 +171,9 @@ version = "0.4.7" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "6e9b384d5e21452bc81cae3552c74f430e320985" +git-tree-sha1 = "106122bad983acd8e21aef3f7a7f91a3ac739077" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "0.17.35" +version = "0.17.36" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] @@ -208,10 +208,10 @@ 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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -241,10 +241,10 @@ 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 = ["BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NonlinearSolve", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "TruncatedStacktraces"] +git-tree-sha1 = "039775034259dfc1f106b195f69af7741f90ef10" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "2.11.0" +version = "3.0.0" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -276,9 +276,9 @@ 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"] @@ -472,9 +472,9 @@ 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 +500,9 @@ 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 = "b93afdf0f82246e75a5d65750eca6b275df08e1c" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.27.0" +version = "2.29.0" weakdeps = ["OrdinaryDiffEq", "Sundials"] [[deps.DiffEqNoiseProcess]] @@ -529,9 +529,9 @@ 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 = "9b2fef0d520066196dbd6761bbc15da5e6282d9e" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.8.0" +version = "7.9.0" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] @@ -595,9 +595,13 @@ 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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +weakdeps = ["MCMCChains"] + + [deps.DynamicPPL.extensions] + DynamicPPLMCMCChainsExt = ["MCMCChains"] [[deps.EllipsisNotation]] deps = ["StaticArrayInterface"] @@ -617,10 +621,10 @@ 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 +634,9 @@ 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 +706,15 @@ 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"] @@ -965,10 +974,10 @@ 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"] @@ -1192,9 +1201,9 @@ 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 +1211,7 @@ version = "2.5.0" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKrylovKitExt = "KrylovKit" LinearSolveMKLExt = "MKL_jll" + LinearSolveMetalExt = "Metal" LinearSolvePardisoExt = "Pardiso" [deps.LinearSolve.weakdeps] @@ -1210,6 +1220,7 @@ 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]] @@ -1246,9 +1257,9 @@ 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 +1272,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[deps.LoopVectorization]] deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] @@ -1296,15 +1307,15 @@ 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" @@ -1402,9 +1413,9 @@ 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" @@ -1429,9 +1440,9 @@ version = "1.9.0" [[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 +1491,15 @@ 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 +1514,9 @@ 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 = "2758190d4b01182e2278b772339daa83e209d45a" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.53.4" +version = "6.54.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1620,9 +1631,9 @@ 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 +1659,9 @@ 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"] @@ -1764,9 +1775,9 @@ 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 +1793,9 @@ 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" @@ -1836,10 +1847,10 @@ 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 = "2887c7e4483009e8d87b27c144cd19b2e1ba2325" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.36.0" +version = "7.37.1" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -1940,9 +1951,9 @@ 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] @@ -2205,9 +2216,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -2242,9 +2253,9 @@ 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] diff --git a/tutorials/11-probabilistic-pca/Manifest.toml b/tutorials/11-probabilistic-pca/Manifest.toml index d4a718fdc..63ff30f16 100644 --- a/tutorials/11-probabilistic-pca/Manifest.toml +++ b/tutorials/11-probabilistic-pca/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -973,9 +982,9 @@ 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 +997,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1021,15 @@ 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" @@ -1096,9 +1105,9 @@ 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 +1171,9 @@ 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"] @@ -1250,9 +1259,9 @@ 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 +1287,9 @@ 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"] @@ -1382,9 +1391,9 @@ 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 +1409,9 @@ 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" @@ -1497,9 +1506,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1685,9 +1694,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1717,9 +1726,9 @@ 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] diff --git a/tutorials/12-gaussian-process/Manifest.toml b/tutorials/12-gaussian-process/Manifest.toml index 3f154c4c1..4569b0818 100644 --- a/tutorials/12-gaussian-process/Manifest.toml +++ b/tutorials/12-gaussian-process/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -1003,9 +1012,9 @@ 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 +1027,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1051,15 @@ 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" @@ -1126,9 +1135,9 @@ 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 +1190,9 @@ 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"] @@ -1269,9 +1278,9 @@ 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 +1306,9 @@ 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"] @@ -1413,9 +1422,9 @@ 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 +1440,9 @@ 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" @@ -1528,9 +1537,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1622,6 +1631,12 @@ 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 +1671,10 @@ 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", "RecipesBase", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "8dfeeb90ba3fda8c69873c961e397b6541bdc4e6" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.11.0" +version = "1.12.0" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -1710,9 +1725,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1742,9 +1757,9 @@ 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] diff --git a/tutorials/13-seasonal-time-series/Manifest.toml b/tutorials/13-seasonal-time-series/Manifest.toml index 6d5f5263e..ce056bba1 100644 --- a/tutorials/13-seasonal-time-series/Manifest.toml +++ b/tutorials/13-seasonal-time-series/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/14-minituring/Manifest.toml b/tutorials/14-minituring/Manifest.toml index eaa6adf5c..89bb11151 100644 --- a/tutorials/14-minituring/Manifest.toml +++ b/tutorials/14-minituring/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -666,9 +675,9 @@ 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 +690,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +714,15 @@ 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" @@ -772,9 +781,9 @@ 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 +818,9 @@ 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 +840,9 @@ 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 +868,9 @@ 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"] @@ -959,9 +968,9 @@ 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" @@ -1033,9 +1042,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1197,9 +1206,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [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..e9c3f2d6d 100644 --- a/tutorials/docs-00-getting-started/Manifest.toml +++ b/tutorials/docs-00-getting-started/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-01-contributing-guide/Manifest.toml b/tutorials/docs-01-contributing-guide/Manifest.toml index 9f4ff6272..e9c3f2d6d 100644 --- a/tutorials/docs-01-contributing-guide/Manifest.toml +++ b/tutorials/docs-01-contributing-guide/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-02-contributing-style-guide/Manifest.toml b/tutorials/docs-02-contributing-style-guide/Manifest.toml index 9f4ff6272..e9c3f2d6d 100644 --- a/tutorials/docs-02-contributing-style-guide/Manifest.toml +++ b/tutorials/docs-02-contributing-style-guide/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml b/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml index 800beb573..03513be8c 100644 --- a/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml +++ b/tutorials/docs-03-using-turing-sampler-viz/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml b/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml index 9f4ff6272..e9c3f2d6d 100644 --- a/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml +++ b/tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-05-for-developers-compiler/Manifest.toml b/tutorials/docs-05-for-developers-compiler/Manifest.toml index 9f4ff6272..e9c3f2d6d 100644 --- a/tutorials/docs-05-for-developers-compiler/Manifest.toml +++ b/tutorials/docs-05-for-developers-compiler/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-06-for-developers-interface/Manifest.toml b/tutorials/docs-06-for-developers-interface/Manifest.toml index 7e0175174..43555b0be 100644 --- a/tutorials/docs-06-for-developers-interface/Manifest.toml +++ b/tutorials/docs-06-for-developers-interface/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-07-for-developers-variational-inference/Manifest.toml b/tutorials/docs-07-for-developers-variational-inference/Manifest.toml index 9f4ff6272..e9c3f2d6d 100644 --- a/tutorials/docs-07-for-developers-variational-inference/Manifest.toml +++ b/tutorials/docs-07-for-developers-variational-inference/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-08-using-turing/Manifest.toml b/tutorials/docs-08-using-turing/Manifest.toml index 9f4ff6272..e9c3f2d6d 100644 --- a/tutorials/docs-08-using-turing/Manifest.toml +++ b/tutorials/docs-08-using-turing/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-09-using-turing-advanced/Manifest.toml b/tutorials/docs-09-using-turing-advanced/Manifest.toml index 065784c4b..75bd7a604 100644 --- a/tutorials/docs-09-using-turing-advanced/Manifest.toml +++ b/tutorials/docs-09-using-turing-advanced/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-10-using-turing-autodiff/Manifest.toml b/tutorials/docs-10-using-turing-autodiff/Manifest.toml index 9f4ff6272..e9c3f2d6d 100644 --- a/tutorials/docs-10-using-turing-autodiff/Manifest.toml +++ b/tutorials/docs-10-using-turing-autodiff/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml b/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml index b092f03b8..93d31152a 100644 --- a/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml +++ b/tutorials/docs-11-using-turing-dynamichmc/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -973,9 +982,9 @@ 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 +997,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1021,15 @@ 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" @@ -1096,9 +1105,9 @@ 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 +1171,9 @@ 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 +1253,9 @@ 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 +1281,9 @@ 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"] @@ -1388,9 +1397,9 @@ 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" @@ -1485,9 +1494,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1696,9 +1705,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1728,9 +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] diff --git a/tutorials/docs-12-using-turing-guide/Manifest.toml b/tutorials/docs-12-using-turing-guide/Manifest.toml index 4f426900d..920d3de38 100644 --- a/tutorials/docs-12-using-turing-guide/Manifest.toml +++ b/tutorials/docs-12-using-turing-guide/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -983,9 +992,9 @@ 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 +1007,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1031,15 @@ 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" @@ -1112,9 +1121,9 @@ 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 +1187,15 @@ 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"] @@ -1278,9 +1287,9 @@ 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 +1315,9 @@ 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"] @@ -1422,9 +1431,9 @@ 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" @@ -1519,9 +1528,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1707,9 +1716,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1744,9 +1753,9 @@ 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] diff --git a/tutorials/docs-13-using-turing-performance-tips/Manifest.toml b/tutorials/docs-13-using-turing-performance-tips/Manifest.toml index 7d7d28135..83fd452e8 100644 --- a/tutorials/docs-13-using-turing-performance-tips/Manifest.toml +++ b/tutorials/docs-13-using-turing-performance-tips/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -666,9 +675,9 @@ 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 +690,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +714,15 @@ 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" @@ -778,9 +787,9 @@ 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 +824,9 @@ 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 +846,9 @@ 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 +874,9 @@ 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"] @@ -965,9 +974,9 @@ 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" @@ -1039,9 +1048,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1203,9 +1212,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [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..e9c3f2d6d 100644 --- a/tutorials/docs-14-using-turing-quick-start/Manifest.toml +++ b/tutorials/docs-14-using-turing-quick-start/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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] diff --git a/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml b/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml index e2883d662..51bfa4ddd 100644 --- a/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml +++ b/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml @@ -1,6 +1,6 @@ # 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" @@ -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 = "d782efeacf92a1dcc65a77ea1507577d4dc843fe" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.5.3" +version = "0.5.4" [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 = "af192c7c235264bdc6f67321fd1c57be0dd7ffb5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.12.8" +version = "0.13.6" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -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 = "c85676be0049fd673c71d655b7a308c09eb83ed6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.23.0" +version = "0.23.13" +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"] @@ -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"] @@ -961,9 +970,9 @@ 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 +985,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[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 +1009,15 @@ 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" @@ -1084,9 +1093,9 @@ 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 +1159,9 @@ 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"] @@ -1232,9 +1241,9 @@ 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 +1269,9 @@ 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"] @@ -1376,9 +1385,9 @@ 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" @@ -1473,9 +1482,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[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] @@ -1661,9 +1670,9 @@ 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" +git-tree-sha1 = "172b7a658d7ea91dad3203e711d83d9c91d01fed" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.28.1" +version = "0.28.2" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -1693,9 +1702,9 @@ 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]