Merge branch 'master' into py/transforms

Author: penelopeysm

Manifest.toml

@@ -2,12 +2,12 @@
 
 julia_version = "1.11.3"
 manifest_format = "2.0"
-project_hash = "53e97ef537fe2e98eecbe367cd36c4bc6a201e3e"
+project_hash = "547d92b7c2cee83d66812c3662de0a43b46d819f"
 
 [[deps.ADTypes]]
-git-tree-sha1 = "ab3815fc06f9c171ee81277f00ecee19b47e0b91"
+git-tree-sha1 = "e1ce448a0d7f88168ffe2eeac4549c32d45a42d1"
 uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
-version = "1.12.0"
+version = "1.12.1"
 weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"]
 
     [deps.ADTypes.extensions]
@@ -39,10 +39,10 @@ uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 version = "5.6.0"
 
 [[deps.AbstractPPL]]
-deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random"]
-git-tree-sha1 = "bdb19638644450ee1b0fd63740381835069d34b9"
+deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random", "StatsBase"]
+git-tree-sha1 = "b155685b5daa9d9d19dfe42684a53fa8cbbb83b8"
 uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
-version = "0.9.0"
+version = "0.10.1"
 
 [[deps.AbstractTrees]]
 git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
@@ -222,18 +222,20 @@ version = "1.11.0"
 
 [[deps.Atomix]]
 deps = ["UnsafeAtomics"]
-git-tree-sha1 = "c3b238aa28c1bebd4b5ea4988bebf27e9a01b72b"
+git-tree-sha1 = "93da6c8228993b0052e358ad592ee7c1eccaa639"
 uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458"
-version = "1.0.1"
+version = "1.1.0"
 
     [deps.Atomix.extensions]
     AtomixCUDAExt = "CUDA"
     AtomixMetalExt = "Metal"
+    AtomixOpenCLExt = "OpenCL"
     AtomixoneAPIExt = "oneAPI"
 
     [deps.Atomix.weakdeps]
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
     Metal = "dde4c033-4e86-420c-a63e-0dd931031962"
+    OpenCL = "08131aa3-fb12-5dee-8b74-c09406e224a2"
     oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b"
 
 [[deps.AxisAlgorithms]]
@@ -638,12 +640,6 @@ git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
 version = "1.16.0"
 
-[[deps.DataDeps]]
-deps = ["HTTP", "Libdl", "Reexport", "SHA", "Scratch", "p7zip_jll"]
-git-tree-sha1 = "8ae085b71c462c2cb1cfedcb10c3c877ec6cf03f"
-uuid = "124859b0-ceae-595e-8997-d05f6a7a8dfe"
-version = "0.7.13"
-
 [[deps.DataFrames]]
 deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
 git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6"
@@ -771,9 +767,9 @@ version = "7.15.0"
 
 [[deps.DifferentiationInterface]]
 deps = ["ADTypes", "LinearAlgebra"]
-git-tree-sha1 = "d86f29074367f1bb92957e8d0b77badd187a97bc"
+git-tree-sha1 = "b44d8cedd863c1c7a9f3ec82555539ec9935d07f"
 uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
-version = "0.6.32"
+version = "0.6.33"
 
     [deps.DifferentiationInterface.extensions]
     DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore"
@@ -783,6 +779,7 @@ version = "0.6.32"
     DifferentiationInterfaceFiniteDiffExt = "FiniteDiff"
     DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences"
     DifferentiationInterfaceForwardDiffExt = ["ForwardDiff", "DiffResults"]
+    DifferentiationInterfaceGTPSAExt = "GTPSA"
     DifferentiationInterfaceMooncakeExt = "Mooncake"
     DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff"
     DifferentiationInterfaceReverseDiffExt = ["ReverseDiff", "DiffResults"]
@@ -803,6 +800,7 @@ version = "0.6.32"
     FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
     FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000"
     ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+    GTPSA = "b27dd330-f138-47c5-815b-40db9dd9b6e8"
     Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
     PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
@@ -883,10 +881,10 @@ uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb"
 version = "3.5.0"
 
 [[deps.DynamicPPL]]
-deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"]
-git-tree-sha1 = "5c2bc37cbc946902e1af5ae8486f24bb585d20cb"
+deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "InteractiveUtils", "KernelAbstractions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"]
+git-tree-sha1 = "18fcc77ba683967339473b731143fa269ea671f5"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.32.2"
+version = "0.34.2"
 
     [deps.DynamicPPL.extensions]
     DynamicPPLChainRulesCoreExt = ["ChainRulesCore"]
@@ -993,11 +991,6 @@ git-tree-sha1 = "fc3951d4d398b5515f91d7fe5d45fc31dccb3c9b"
 uuid = "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636"
 version = "0.8.5"
 
-[[deps.ExternalDocstrings]]
-git-tree-sha1 = "1224740fc4d07c989949e1c1b508ebd49a65a5f6"
-uuid = "e189563c-0753-4f5e-ad5c-be4293c83fb4"
-version = "0.1.1"
-
 [[deps.FFMPEG]]
 deps = ["FFMPEG_jll"]
 git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00"
@@ -1167,18 +1160,6 @@ version = "0.14.25"
     NCCL = "3fe64909-d7a1-4096-9b7d-7a0f12cf0f6b"
     cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd"
 
-[[deps.Folds]]
-deps = ["Accessors", "BangBang", "Baselet", "DefineSingletons", "Distributed", "ExternalDocstrings", "InitialValues", "MicroCollections", "Referenceables", "Requires", "Test", "ThreadedScans", "Transducers"]
-git-tree-sha1 = "7eb4bc88d8295e387a667fd43d67c157ddee76cf"
-uuid = "41a02a25-b8f0-4f67-bc48-60067656b558"
-version = "0.2.10"
-
-    [deps.Folds.extensions]
-    FoldsOnlineStatsBaseExt = "OnlineStatsBase"
-
-    [deps.Folds.weakdeps]
-    OnlineStatsBase = "925886fa-5bf2-5e8e-b522-a9147a512338"
-
 [[deps.Fontconfig_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"]
 git-tree-sha1 = "21fac3c77d7b5a9fc03b0ec503aa1a6392c34d2b"
@@ -1522,9 +1503,9 @@ version = "0.6.0"
 
 [[deps.KernelAbstractions]]
 deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"]
-git-tree-sha1 = "d5bc0b079382e89bfa91433639bc74b9f9e17ae7"
+git-tree-sha1 = "b9a838cd3028785ac23822cded5126b3da394d1a"
 uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
-version = "0.9.33"
+version = "0.9.31"
 weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"]
 
     [deps.KernelAbstractions.extensions]
@@ -1642,9 +1623,9 @@ version = "0.1.17"
 
 [[deps.LazyArrays]]
 deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"]
-git-tree-sha1 = "bf3957638b78521f286f3b2ebaa46a475dc74817"
+git-tree-sha1 = "795ae125c98c58ceb1de562633703e0b120a1b17"
 uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02"
-version = "2.3.2"
+version = "2.4.0"
 
     [deps.LazyArrays.extensions]
     LazyArraysBandedMatricesExt = "BandedMatrices"
@@ -2566,9 +2547,9 @@ version = "1.2.0"
 
 [[deps.OrdinaryDiffEqCore]]
 deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"]
-git-tree-sha1 = "f5f5af4cd0776eb17bb0a90cf82c6d2be17b59b2"
+git-tree-sha1 = "6a58da59c5f7640fd09636231bd73dfb4744ce53"
 uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
-version = "1.15.0"
+version = "1.15.1"
 weakdeps = ["EnzymeCore"]
 
     [deps.OrdinaryDiffEqCore.extensions]
@@ -2747,12 +2728,6 @@ git-tree-sha1 = "966b85253e959ea89c53a9abebbf2e964fbf593b"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
 version = "0.11.32"
 
-[[deps.PSIS]]
-deps = ["LinearAlgebra", "LogExpFunctions", "Printf", "RecipesBase", "Statistics"]
-git-tree-sha1 = "e5433b4c59636f5e8fcb275edcd8e8017dee3fe2"
-uuid = "ce719bf2-d5d0-4fb9-925d-10a81b42ad04"
-version = "0.9.7"
-
 [[deps.PackageExtensionCompat]]
 git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518"
 uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930"
@@ -2777,17 +2752,6 @@ git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 version = "2.8.1"
 
-[[deps.Pathfinder]]
-deps = ["ADTypes", "Distributions", "Folds", "IrrationalConstants", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "Optim", "Optimization", "OptimizationOptimJL", "PDMats", "PSIS", "ProgressLogging", "Random", "Requires", "SciMLBase", "Statistics", "StatsBase", "Transducers"]
-git-tree-sha1 = "3a28e8450b63d3657adf804984ed0dd081a74447"
-uuid = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454"
-version = "0.9.9"
-weakdeps = ["Accessors", "DynamicHMC", "DynamicPPL", "MCMCChains", "Turing"]
-
-    [deps.Pathfinder.extensions]
-    PathfinderDynamicHMCExt = "DynamicHMC"
-    PathfinderTuringExt = ["Accessors", "DynamicPPL", "MCMCChains", "Turing"]
-
 [[deps.Pipe]]
 git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d"
 uuid = "b98c9c47-44ae-5843-9183-064241ee97a0"
@@ -3032,9 +2996,9 @@ version = "0.6.12"
 
 [[deps.RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
-git-tree-sha1 = "32f824db4e5bab64e25a12b22483a30a6b813d08"
+git-tree-sha1 = "ea6ad53c168c7c1c2e8f870aefda269692a8a91f"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "3.27.4"
+version = "3.28.0"
 
     [deps.RecursiveArrayTools.extensions]
     RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
@@ -3069,12 +3033,6 @@ git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
 version = "1.2.2"
 
-[[deps.Referenceables]]
-deps = ["Adapt"]
-git-tree-sha1 = "02d31ad62838181c1a3a5fd23a1ce5914a643601"
-uuid = "42d2dcc6-99eb-4e98-b66c-637b7d73030e"
-version = "0.1.3"
-
 [[deps.RelocatableFolders]]
 deps = ["SHA", "Scratch"]
 git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864"
@@ -3160,9 +3118,9 @@ version = "0.1.1"
 
 [[deps.SciMLBase]]
 deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "80396dc3496a1718fc356797fa54034b6c533a18"
+git-tree-sha1 = "fcb73c66a5071d4d026aa84f9950a4d1f0dadf33"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.72.0"
+version = "2.72.1"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -3310,9 +3268,9 @@ version = "1.11.0"
 
 [[deps.SparseConnectivityTracer]]
 deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "010b3c44301805d1ede9159f449a351d61172aa6"
+git-tree-sha1 = "f6d636dcf886cf498b3bc484f48c37741d8aac6e"
 uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
-version = "0.6.9"
+version = "0.6.10"
 
     [deps.SparseConnectivityTracer.extensions]
     SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations"
@@ -3411,9 +3369,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"]
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
-git-tree-sha1 = "47091a0340a675c738b1304b58161f3b0839d454"
+git-tree-sha1 = "02c8bd479d26dbeff8a7eb1d77edfc10dacabc01"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.10"
+version = "1.9.11"
 weakdeps = ["ChainRulesCore", "Statistics"]
 
     [deps.StaticArrays.extensions]
@@ -3483,10 +3441,10 @@ uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 version = "2.4.1"
 
 [[deps.StochasticDiffEq]]
-deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
-git-tree-sha1 = "b0a5dce397b3bc5478ee1de3127878daa061db28"
+deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
+git-tree-sha1 = "1f1161aca132f7f776acfb3785abf449aa99a1e9"
 uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-version = "6.72.1"
+version = "6.73.0"
 
 [[deps.StrideArraysCore]]
 deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"]
@@ -3624,12 +3582,6 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 version = "1.11.0"
 
-[[deps.ThreadedScans]]
-deps = ["ArgCheck"]
-git-tree-sha1 = "ca1ba3000289eacba571aaa4efcefb642e7a1de6"
-uuid = "24d252fe-5d94-4a69-83ea-56a14333d47a"
-version = "0.1.0"
-
 [[deps.ThreadingUtilities]]
 deps = ["ManualMemory"]
 git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27"
@@ -3714,9 +3666,9 @@ version = "1.6.0"
 
 [[deps.Turing]]
 deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "d1b261f1a37d5daed651ef6f332d09b9cf22823d"
+git-tree-sha1 = "5218eb833eaaffa0021de7a550564ff6bd53b96c"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.35.5"
+version = "0.36.2"
 weakdeps = ["DynamicHMC", "Optim"]
 
     [deps.Turing.extensions]
@@ -3882,9 +3834,9 @@ version = "1.1.42+0"
 
 [[deps.XZ_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "beef98d5aad604d9e7d60b2ece5181f7888e2fd6"
+git-tree-sha1 = "56c6604ec8b2d82cc4cfe01aa03b00426aac7e1f"
 uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
-version = "5.6.4+0"
+version = "5.6.4+1"
 
 [[deps.Xorg_libICE_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]

Project.toml

@@ -7,7 +7,6 @@ AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"
 Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
-DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
@@ -39,7 +38,6 @@ Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150"
-Pathfinder = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -55,4 +53,4 @@ UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
-Turing = "0.35"
+Turing = "0.36.2"

_quarto.yml

@@ -32,7 +32,7 @@ website:
         text: Team
     right:
       # Current version
-      - text: "v0.35"
+      - text: "v0.36"
         menu:
           - text: Changelog
             href: https://turinglang.org/docs/changelog.html

core-functionality/index.qmd

@@ -63,7 +63,7 @@ We can perform inference by using the `sample` function, the first argument of w
 c1 = sample(gdemo(1.5, 2), SMC(), 1000)
 c2 = sample(gdemo(1.5, 2), PG(10), 1000)
 c3 = sample(gdemo(1.5, 2), HMC(0.1, 5), 1000)
-c4 = sample(gdemo(1.5, 2), Gibbs(PG(10, :m), HMC(0.1, 5, :s²)), 1000)
+c4 = sample(gdemo(1.5, 2), Gibbs(:m => PG(10), :s² => HMC(0.1, 5)), 1000)
 c5 = sample(gdemo(1.5, 2), HMCDA(0.15, 0.65), 1000)
 c6 = sample(gdemo(1.5, 2), NUTS(0.65), 1000)
 ```
@@ -452,7 +452,7 @@ end
 
 simple_choice_f = simple_choice([1.5, 2.0, 0.3])
 
-chn = sample(simple_choice_f, Gibbs(HMC(0.2, 3, :p), PG(20, :z)), 1000)
+chn = sample(simple_choice_f, Gibbs(:p => HMC(0.2, 3), :z => PG(20)), 1000)
 ```
 
 The `Gibbs` sampler can be used to specify unique automatic differentiation backends for different variable spaces. Please see the [Automatic Differentiation]({{<meta using-turing-autodiff>}}) article for more.

developers/compiler/design-overview/index.qmd

@@ -291,8 +291,7 @@ not. Let `md` be an instance of `Metadata`:
     `md.vns`, `md.ranges`, `md.dists`, `md.orders` and `md.flags`.
   - `md.vns[md.idcs[vn]] == vn`.
   - `md.dists[md.idcs[vn]]` is the distribution of `vn`.
-  - `md.gids[md.idcs[vn]]` is the set of algorithms used to sample `vn`. This is used in
-    the Gibbs sampling process.
+  - `md.gids[md.idcs[vn]]` is the set of algorithms used to sample `vn`. This was used by the Gibbs sampler. Since Turing v0.36 it is unused and will eventually be deleted.
   - `md.orders[md.idcs[vn]]` is the number of `observe` statements before `vn` is sampled.
   - `md.ranges[md.idcs[vn]]` is the index range of `vn` in `md.vals`.
   - `md.vals[md.ranges[md.idcs[vn]]]` is the linearized vector of values of corresponding to `vn`.

tutorials/gaussian-mixture-models/index.qmd

@@ -112,7 +112,7 @@ model = gaussian_mixture_model(x);
 ```
 
 We run a MCMC simulation to obtain an approximation of the posterior distribution of the parameters $\mu$ and $w$ and assignments $k$.
-We use a `Gibbs` sampler that combines a [particle Gibbs](https://www.stats.ox.ac.uk/%7Edoucet/andrieu_doucet_holenstein_PMCMC.pdf) sampler for the discrete parameters (assignments $k$) and a Hamiltonion Monte Carlo sampler for the continuous parameters ($\mu$ and $w$).
+We use a `Gibbs` sampler that combines a [particle Gibbs](https://www.stats.ox.ac.uk/%7Edoucet/andrieu_doucet_holenstein_PMCMC.pdf) sampler for the discrete parameters (assignments $k$) and a Hamiltonian Monte Carlo sampler for the continuous parameters ($\mu$ and $w$).
 We generate multiple chains in parallel using multi-threading.
 
 ```{julia}
@@ -123,8 +123,7 @@ setprogress!(false)
 
 ```{julia}
 #| output: false
-Random.seed!(42)
-sampler = Gibbs(PG(100, :k), HMC(0.05, 10, :μ, :w))
+sampler = Gibbs(:k => PG(100), (:μ, :w) => HMC(0.05, 10))
 nsamples = 150
 nchains = 4
 burn = 10