Update all Manifest files for docs and tutorials. (#410)

* Update all Manifest files for docs and tutorials. * Update DynamicNUTS interface. (#411)
TuringLang · Jul 30, 2023 · 58cf276 · 58cf276
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diff --git a/tutorials/00-introduction/Manifest.toml b/tutorials/00-introduction/Manifest.toml
@@ -11,13 +11,14 @@ version = "0.1.6"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "cad4c758c0038eea30394b1b671526921ca85b21"
+git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef"
 uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
-version = "1.4.0"
-weakdeps = ["ChainRulesCore"]
+version = "1.5.0"
+weakdeps = ["ChainRulesCore", "Test"]
 
     [deps.AbstractFFTs.extensions]
     AbstractFFTsChainRulesCoreExt = "ChainRulesCore"
+    AbstractFFTsTestExt = "Test"
 
 [[deps.AbstractMCMC]]
 deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"]
@@ -48,9 +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 = "3bf24030e85b1d6d298e4f483f6aeff6f38462db"
+git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.4.6"
+version = "0.5.3"
 
     [deps.AdvancedHMC.extensions]
     AdvancedHMCCUDAExt = "CUDA"
@@ -694,9 +695,9 @@ version = "0.14.7"
 
 [[deps.IntervalSets]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "19ef25c6befb8076aefbc6f89d9011b415fb25da"
+git-tree-sha1 = "8e59ea773deee525c99a8018409f64f19fb719e6"
 uuid = "8197267c-284f-5f27-9208-e0e47529a953"
-version = "0.7.5"
+version = "0.7.7"
 weakdeps = ["Statistics"]
 
     [deps.IntervalSets.extensions]
@@ -1177,9 +1178,9 @@ version = "0.11.17"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29"
+git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.7.1"
+version = "2.7.2"
 
 [[deps.Pipe]]
 git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d"
@@ -1660,14 +1661,16 @@ 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 = "8e62d26f99ad2cc6f496e2132a6172eabb5d27de"
+git-tree-sha1 = "89fa5db8e86044c15bfe6d86a1231b46aebe2e70"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.27.0"
+version = "0.28.0"
 
     [deps.Turing.extensions]
+    TuringDynamicHMCExt = "DynamicHMC"
     TuringOptimExt = "Optim"
 
     [deps.Turing.weakdeps]
+    DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
     Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 
 [[deps.URIs]]

diff --git a/tutorials/01-gaussian-mixture-model/Manifest.toml b/tutorials/01-gaussian-mixture-model/Manifest.toml
@@ -11,13 +11,14 @@ version = "0.1.6"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "cad4c758c0038eea30394b1b671526921ca85b21"
+git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef"
 uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
-version = "1.4.0"
-weakdeps = ["ChainRulesCore"]
+version = "1.5.0"
+weakdeps = ["ChainRulesCore", "Test"]
 
     [deps.AbstractFFTs.extensions]
     AbstractFFTsChainRulesCoreExt = "ChainRulesCore"
+    AbstractFFTsTestExt = "Test"
 
 [[deps.AbstractMCMC]]
 deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"]
@@ -48,9 +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 = "3bf24030e85b1d6d298e4f483f6aeff6f38462db"
+git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.4.6"
+version = "0.5.3"
 
     [deps.AdvancedHMC.extensions]
     AdvancedHMCCUDAExt = "CUDA"
@@ -694,9 +695,9 @@ version = "0.14.7"
 
 [[deps.IntervalSets]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "19ef25c6befb8076aefbc6f89d9011b415fb25da"
+git-tree-sha1 = "8e59ea773deee525c99a8018409f64f19fb719e6"
 uuid = "8197267c-284f-5f27-9208-e0e47529a953"
-version = "0.7.5"
+version = "0.7.7"
 weakdeps = ["Statistics"]
 
     [deps.IntervalSets.extensions]
@@ -1177,9 +1178,9 @@ version = "0.11.17"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29"
+git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.7.1"
+version = "2.7.2"
 
 [[deps.Pipe]]
 git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d"
@@ -1660,14 +1661,16 @@ 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 = "8e62d26f99ad2cc6f496e2132a6172eabb5d27de"
+git-tree-sha1 = "89fa5db8e86044c15bfe6d86a1231b46aebe2e70"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.27.0"
+version = "0.28.0"
 
     [deps.Turing.extensions]
+    TuringDynamicHMCExt = "DynamicHMC"
     TuringOptimExt = "Optim"
 
     [deps.Turing.weakdeps]
+    DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
     Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 
 [[deps.URIs]]

diff --git a/tutorials/02-logistic-regression/Manifest.toml b/tutorials/02-logistic-regression/Manifest.toml
@@ -11,13 +11,14 @@ version = "0.1.6"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "cad4c758c0038eea30394b1b671526921ca85b21"
+git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef"
 uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
-version = "1.4.0"
-weakdeps = ["ChainRulesCore"]
+version = "1.5.0"
+weakdeps = ["ChainRulesCore", "Test"]
 
     [deps.AbstractFFTs.extensions]
     AbstractFFTsChainRulesCoreExt = "ChainRulesCore"
+    AbstractFFTsTestExt = "Test"
 
 [[deps.AbstractMCMC]]
 deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"]
@@ -48,9 +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 = "3bf24030e85b1d6d298e4f483f6aeff6f38462db"
+git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.4.6"
+version = "0.5.3"
 
     [deps.AdvancedHMC.extensions]
     AdvancedHMCCUDAExt = "CUDA"
@@ -748,9 +749,9 @@ version = "0.14.7"
 
 [[deps.IntervalSets]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "19ef25c6befb8076aefbc6f89d9011b415fb25da"
+git-tree-sha1 = "8e59ea773deee525c99a8018409f64f19fb719e6"
 uuid = "8197267c-284f-5f27-9208-e0e47529a953"
-version = "0.7.5"
+version = "0.7.7"
 weakdeps = ["Statistics"]
 
     [deps.IntervalSets.extensions]
@@ -1261,9 +1262,9 @@ version = "0.11.17"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29"
+git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.7.1"
+version = "2.7.2"
 
 [[deps.Pipe]]
 git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d"
@@ -1779,14 +1780,16 @@ 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 = "8e62d26f99ad2cc6f496e2132a6172eabb5d27de"
+git-tree-sha1 = "89fa5db8e86044c15bfe6d86a1231b46aebe2e70"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.27.0"
+version = "0.28.0"
 
     [deps.Turing.extensions]
+    TuringDynamicHMCExt = "DynamicHMC"
     TuringOptimExt = "Optim"
 
     [deps.Turing.weakdeps]
+    DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
     Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 
 [[deps.URIs]]

diff --git a/tutorials/03-bayesian-neural-network/Manifest.toml b/tutorials/03-bayesian-neural-network/Manifest.toml
@@ -11,13 +11,14 @@ version = "0.1.6"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "cad4c758c0038eea30394b1b671526921ca85b21"
+git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef"
 uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
-version = "1.4.0"
-weakdeps = ["ChainRulesCore"]
+version = "1.5.0"
+weakdeps = ["ChainRulesCore", "Test"]
 
     [deps.AbstractFFTs.extensions]
     AbstractFFTsChainRulesCoreExt = "ChainRulesCore"
+    AbstractFFTsTestExt = "Test"
 
 [[deps.AbstractMCMC]]
 deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"]
@@ -48,9 +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 = "3bf24030e85b1d6d298e4f483f6aeff6f38462db"
+git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.4.6"
+version = "0.5.3"
 
     [deps.AdvancedHMC.extensions]
     AdvancedHMCCUDAExt = "CUDA"
@@ -714,9 +715,9 @@ version = "0.14.7"
 
 [[deps.IntervalSets]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "19ef25c6befb8076aefbc6f89d9011b415fb25da"
+git-tree-sha1 = "8e59ea773deee525c99a8018409f64f19fb719e6"
 uuid = "8197267c-284f-5f27-9208-e0e47529a953"
-version = "0.7.5"
+version = "0.7.7"
 weakdeps = ["Statistics"]
 
     [deps.IntervalSets.extensions]
@@ -1209,9 +1210,9 @@ version = "0.11.17"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29"
+git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.7.1"
+version = "2.7.2"
 
 [[deps.Pipe]]
 git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d"
@@ -1696,14 +1697,16 @@ 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 = "8e62d26f99ad2cc6f496e2132a6172eabb5d27de"
+git-tree-sha1 = "89fa5db8e86044c15bfe6d86a1231b46aebe2e70"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.27.0"
+version = "0.28.0"
 
     [deps.Turing.extensions]
+    TuringDynamicHMCExt = "DynamicHMC"
     TuringOptimExt = "Optim"
 
     [deps.Turing.weakdeps]
+    DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
     Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 
 [[deps.URIs]]

diff --git a/tutorials/04-hidden-markov-model/Manifest.toml b/tutorials/04-hidden-markov-model/Manifest.toml
@@ -11,13 +11,14 @@ version = "0.1.6"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "cad4c758c0038eea30394b1b671526921ca85b21"
+git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef"
 uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
-version = "1.4.0"
-weakdeps = ["ChainRulesCore"]
+version = "1.5.0"
+weakdeps = ["ChainRulesCore", "Test"]
 
     [deps.AbstractFFTs.extensions]
     AbstractFFTsChainRulesCoreExt = "ChainRulesCore"
+    AbstractFFTsTestExt = "Test"
 
 [[deps.AbstractMCMC]]
 deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"]
@@ -48,9 +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 = "3bf24030e85b1d6d298e4f483f6aeff6f38462db"
+git-tree-sha1 = "d4986b2575ad5710b322a1bbc4939e0208f9f498"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.4.6"
+version = "0.5.3"
 
     [deps.AdvancedHMC.extensions]
     AdvancedHMCCUDAExt = "CUDA"
@@ -694,9 +695,9 @@ version = "0.14.7"
 
 [[deps.IntervalSets]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "19ef25c6befb8076aefbc6f89d9011b415fb25da"
+git-tree-sha1 = "8e59ea773deee525c99a8018409f64f19fb719e6"
 uuid = "8197267c-284f-5f27-9208-e0e47529a953"
-version = "0.7.5"
+version = "0.7.7"
 weakdeps = ["Statistics"]
 
     [deps.IntervalSets.extensions]
@@ -1177,9 +1178,9 @@ version = "0.11.17"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29"
+git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.7.1"
+version = "2.7.2"
 
 [[deps.Pipe]]
 git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d"
@@ -1660,14 +1661,16 @@ 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 = "8e62d26f99ad2cc6f496e2132a6172eabb5d27de"
+git-tree-sha1 = "89fa5db8e86044c15bfe6d86a1231b46aebe2e70"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.27.0"
+version = "0.28.0"
 
     [deps.Turing.extensions]
+    TuringDynamicHMCExt = "DynamicHMC"
     TuringOptimExt = "Optim"
 
     [deps.Turing.weakdeps]
+    DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
     Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 
 [[deps.URIs]]