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yebai authored Sep 2, 2023
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127 changes: 70 additions & 57 deletions tutorials/00-introduction/Manifest.toml
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
# This file is machine-generated - editing it directly is not advised

julia_version = "1.9.2"
julia_version = "1.9.3"
manifest_format = "2.0"
project_hash = "b45878f3df6dffef908d7ec87e98124988d559f6"

[[deps.ADTypes]]
git-tree-sha1 = "f5c25e8a5b29b5e941b7408bc8cc79fea4d9ef9a"
git-tree-sha1 = "a4c8e0f8c09d4aa708289c1a5fc23e2d1970017a"
uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
version = "0.1.6"
version = "0.2.1"

[[deps.AbstractFFTs]]
deps = ["LinearAlgebra"]
Expand All @@ -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"
Expand All @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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 = "fab5c22262fe24cbb09e8ddd34b7a1fe6d5bba23"
uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
version = "0.23.0"
version = "0.23.15"
weakdeps = ["MCMCChains"]

[deps.DynamicPPL.extensions]
DynamicPPLMCMCChainsExt = ["MCMCChains"]

[[deps.EllipticalSliceSampling]]
deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"]
Expand Down Expand Up @@ -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"]
Expand Down Expand Up @@ -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"]
Expand Down Expand Up @@ -894,10 +903,10 @@ uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8"
version = "1.42.0+0"

[[deps.Libiconv_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71"
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175"
uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
version = "1.16.1+2"
version = "1.17.0+0"

[[deps.Libmount_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
Expand Down Expand Up @@ -935,12 +944,11 @@ version = "2.1.1"

[[deps.LogDensityProblemsAD]]
deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"]
git-tree-sha1 = "7841ebecc60703fa978cbe9623e1a37dcaf96b75"
git-tree-sha1 = "a0512ad65f849536b5a52e59b05c59c25cdad943"
uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1"
version = "1.6.1"
version = "1.5.0"

[deps.LogDensityProblemsAD.extensions]
LogDensityProblemsADADTypesExt = "ADTypes"
LogDensityProblemsADEnzymeExt = "Enzyme"
LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences"
LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"]
Expand All @@ -950,7 +958,6 @@ version = "1.6.1"
LogDensityProblemsADZygoteExt = "Zygote"

[deps.LogDensityProblemsAD.weakdeps]
ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000"
Expand All @@ -961,9 +968,9 @@ version = "1.6.1"

[[deps.LogExpFunctions]]
deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
git-tree-sha1 = "c3ce8e7420b3a6e071e0fe4745f5d4300e37b13f"
git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa"
uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
version = "0.3.24"
version = "0.3.26"
weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"]

[deps.LogExpFunctions.extensions]
Expand All @@ -976,9 +983,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"

[[deps.LoggingExtras]]
deps = ["Dates", "Logging"]
git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e"
git-tree-sha1 = "0d097476b6c381ab7906460ef1ef1638fbce1d91"
uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36"
version = "1.0.0"
version = "1.0.2"

[[deps.MCMCChains]]
deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"]
Expand All @@ -1000,15 +1007,15 @@ version = "2023.2.0+0"

[[deps.MLJModelInterface]]
deps = ["Random", "ScientificTypesBase", "StatisticalTraits"]
git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128"
git-tree-sha1 = "03ae109be87f460fe3c96b8a0dbbf9c7bf840bd5"
uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea"
version = "1.8.0"
version = "1.9.2"

[[deps.MacroTools]]
deps = ["Markdown", "Random"]
git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2"
git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48"
uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
version = "0.5.10"
version = "0.5.11"

[[deps.MappedArrays]]
git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e"
Expand Down Expand Up @@ -1084,9 +1091,9 @@ version = "1.0.2"

[[deps.NamedArrays]]
deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"]
git-tree-sha1 = "b84e17976a40cb2bfe3ae7edb3673a8c630d4f95"
git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb"
uuid = "86f7a689-2022-50b4-a561-43c23ac3c673"
version = "0.9.8"
version = "0.10.0"

[[deps.NaturalSort]]
git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21"
Expand Down Expand Up @@ -1150,9 +1157,9 @@ version = "0.5.5+0"

[[deps.Optimisers]]
deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"]
git-tree-sha1 = "16776280310aa5553c370b9c7b17f34aadaf3c8e"
git-tree-sha1 = "c1fc26bab5df929a5172f296f25d7d08688fd25b"
uuid = "3bd65402-5787-11e9-1adc-39752487f4e2"
version = "0.2.19"
version = "0.2.20"

[[deps.Opus_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
Expand Down Expand Up @@ -1212,9 +1219,9 @@ version = "1.3.5"

[[deps.Plots]]
deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"]
git-tree-sha1 = "9f8675a55b37a70aa23177ec110f6e3f4dd68466"
git-tree-sha1 = "ccee59c6e48e6f2edf8a5b64dc817b6729f99eb5"
uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
version = "1.38.17"
version = "1.39.0"

[deps.Plots.extensions]
FileIOExt = "FileIO"
Expand All @@ -1232,9 +1239,9 @@ version = "1.38.17"

[[deps.PrecompileTools]]
deps = ["Preferences"]
git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81"
git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f"
uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
version = "1.1.2"
version = "1.2.0"

[[deps.Preferences]]
deps = ["TOML"]
Expand All @@ -1260,9 +1267,9 @@ version = "0.1.4"

[[deps.ProgressMeter]]
deps = ["Distributed", "Printf"]
git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9"
git-tree-sha1 = "ae36206463b2395804f2787ffe172f44452b538d"
uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
version = "1.7.2"
version = "1.8.0"

[[deps.Qt6Base_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"]
Expand Down Expand Up @@ -1376,9 +1383,9 @@ version = "0.4.0+0"

[[deps.Roots]]
deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"]
git-tree-sha1 = "de432823e8aab4dd1a985be4be768f95acf152d4"
git-tree-sha1 = "ff42754a57bb0d6dcfe302fd0d4272853190421f"
uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
version = "2.0.17"
version = "2.0.19"

[deps.Roots.extensions]
RootsForwardDiffExt = "ForwardDiff"
Expand All @@ -1401,10 +1408,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
version = "0.7.0"

[[deps.SciMLBase]]
deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"]
git-tree-sha1 = "04370090604cd399db5bebddb636d80ab9d338e9"
deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"]
git-tree-sha1 = "a1e295a85fd6fae9a7b2072dd4577001210f512d"
uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
version = "1.94.0"
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[deps.SciMLBase.extensions]
ZygoteExt = "Zygote"

[deps.SciMLBase.weakdeps]
Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"

[[deps.SciMLOperators]]
deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"]
Expand Down Expand Up @@ -1473,9 +1486,9 @@ 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]
Expand Down Expand Up @@ -1661,9 +1674,9 @@ 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 = "5e9b655060490d1a16cbe569acb276578ace48aa"
uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
version = "0.28.1"
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[deps.Turing.extensions]
TuringDynamicHMCExt = "DynamicHMC"
Expand Down Expand Up @@ -1693,9 +1706,9 @@ version = "0.4.1"

[[deps.Unitful]]
deps = ["Dates", "LinearAlgebra", "Random"]
git-tree-sha1 = "64eb17acef1d9734cf09967539818f38093d9b35"
git-tree-sha1 = "a72d22c7e13fe2de562feda8645aa134712a87ee"
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version = "1.16.2"
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weakdeps = ["ConstructionBase", "InverseFunctions"]

[deps.Unitful.extensions]
Expand Down Expand Up @@ -1749,10 +1762,10 @@ uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6"
version = "0.5.5"

[[deps.XML2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73"
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4"
uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
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version = "2.10.4+0"

[[deps.XSLT_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"]
Expand Down
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