Update to v0.39 (#612)

* Bump to v0.39

* Update addlogprob exports

* Fix more imports

* Update Manifest

* enable error:true for VI tutorial just so that it builds

* Update deps

* Disable error=true

* add required dependencies, update tutorial

* update tutorial

* update VI tutorial

* fix error

* fix typo add references

* minor text fixes

---------

Co-authored-by: Kyurae Kim <[email protected]>

Author: penelopeysm

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.11.5"
 manifest_format = "2.0"
-project_hash = "93e3f90921e5771e56e7b8d21131b1107faa4765"
+project_hash = "5ea45087374f193fc9b541533d3ffc8025f44bcd"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "e2478490447631aedba0823d4d7a80b2cc8cdb32"
@@ -127,17 +127,14 @@ weakdeps = ["Libtask"]
     AdvancedPSLibtaskExt = "Libtask"
 
 [[deps.AdvancedVI]]
-deps = ["ADTypes", "Bijectors", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"]
-git-tree-sha1 = "e913c2794cf9d2db9d36d28f67abd27595101f49"
+deps = ["ADTypes", "Accessors", "DiffResults", "DifferentiationInterface", "Distributions", "DocStringExtensions", "FillArrays", "Functors", "LinearAlgebra", "LogDensityProblems", "Optimisers", "ProgressMeter", "Random", "StatsBase"]
+git-tree-sha1 = "59c9723a71ed815eafec430d4cafa592b5889b96"
 uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c"
-version = "0.2.12"
-weakdeps = ["Enzyme", "Flux", "ReverseDiff", "Zygote"]
+version = "0.4.1"
+weakdeps = ["Bijectors"]
 
     [deps.AdvancedVI.extensions]
-    AdvancedVIEnzymeExt = ["Enzyme"]
-    AdvancedVIFluxExt = ["Flux"]
-    AdvancedVIReverseDiffExt = ["ReverseDiff"]
-    AdvancedVIZygoteExt = ["Zygote"]
+    AdvancedVIBijectorsExt = "Bijectors"
 
 [[deps.AliasTables]]
 deps = ["PtrArrays", "Random"]
@@ -747,9 +744,9 @@ version = "6.176.0"
 
 [[deps.DiffEqCallbacks]]
 deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"]
-git-tree-sha1 = "b1f970a2873a2cf76ce35fb0ed2b755a11b31052"
+git-tree-sha1 = "76292e889472e810d40a844b714743c0ffb1c53b"
 uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def"
-version = "4.1.0"
+version = "4.6.0"
 
 [[deps.DiffEqNoiseProcess]]
 deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"]
@@ -773,12 +770,6 @@ git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272"
 uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
 version = "1.15.1"
 
-[[deps.DiffTests]]
-deps = ["LinearAlgebra", "SparseArrays", "Statistics"]
-git-tree-sha1 = "b92beb1933df01bf4915d3a05e54c2a0aad312c7"
-uuid = "de460e47-3fe3-5279-bb4a-814414816d5d"
-version = "0.1.2"
-
 [[deps.DifferentialEquations]]
 deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"]
 git-tree-sha1 = "afdc7dfee475828b4f0286d63ffe66b97d7a3fa7"
@@ -1154,10 +1145,10 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 version = "0.8.5"
 
 [[deps.Flux]]
-deps = ["Adapt", "ChainRulesCore", "Compat", "Functors", "LinearAlgebra", "MLDataDevices", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"]
-git-tree-sha1 = "df520a0727f843576801a0294f5be1a94be28e23"
+deps = ["Adapt", "ChainRulesCore", "Compat", "EnzymeCore", "Functors", "LinearAlgebra", "MLCore", "MLDataDevices", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"]
+git-tree-sha1 = "2c35003ec8dafabdc48549102208b1b15552cb33"
 uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c"
-version = "0.14.25"
+version = "0.16.4"
 
     [deps.Flux.extensions]
     FluxAMDGPUExt = "AMDGPU"
@@ -1226,10 +1217,10 @@ uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf"
 version = "0.1.3"
 
 [[deps.Functors]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "64d8e93700c7a3f28f717d265382d52fac9fa1c1"
+deps = ["Compat", "ConstructionBase", "LinearAlgebra", "Random"]
+git-tree-sha1 = "60a0339f28a233601cb74468032b5c302d5067de"
 uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
-version = "0.4.12"
+version = "0.5.2"
 
 [[deps.Future]]
 deps = ["Random"]
@@ -1358,16 +1349,6 @@ weakdeps = ["Distributions"]
     [deps.HiddenMarkovModels.extensions]
     HiddenMarkovModelsDistributionsExt = "Distributions"
 
-[[deps.Hwloc]]
-deps = ["CEnum", "Hwloc_jll", "Printf"]
-git-tree-sha1 = "6a3d80f31ff87bc94ab22a7b8ec2f263f9a6a583"
-uuid = "0e44f5e4-bd66-52a0-8798-143a42290a1d"
-version = "3.3.0"
-weakdeps = ["AbstractTrees"]
-
-    [deps.Hwloc.extensions]
-    HwlocTrees = "AbstractTrees"
-
 [[deps.Hwloc_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
 git-tree-sha1 = "92f65c4d78ce8cdbb6b68daf88889950b0a99d11"
@@ -1513,10 +1494,10 @@ uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec"
 version = "0.2.4"
 
 [[deps.JumpProcesses]]
-deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"]
-git-tree-sha1 = "f2bdec5b4580414aee3178c8caa6e46c344c0bbc"
+deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"]
+git-tree-sha1 = "fb7fd516de38db80f50fe15e57d44da2836365e7"
 uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
-version = "9.14.3"
+version = "9.16.0"
 weakdeps = ["FastBroadcast"]
 
 [[deps.KernelAbstractions]]
@@ -1885,10 +1866,10 @@ uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36"
 version = "1.1.0"
 
 [[deps.Lux]]
-deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "WeightInitializers"]
-git-tree-sha1 = "39cc335d2601d4b0d74b209f718e7e3641771448"
+deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DiffResults", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "WeightInitializers"]
+git-tree-sha1 = "4bf87816440bec8e64b610de8724c04a58e65928"
 uuid = "b2108857-7c20-44ae-9111-449ecde12c47"
-version = "1.2.3"
+version = "1.13.4"
 
     [deps.Lux.extensions]
     LuxComponentArraysExt = "ComponentArrays"
@@ -1898,7 +1879,7 @@ version = "1.2.3"
     LuxMLUtilsExt = "MLUtils"
     LuxMPIExt = "MPI"
     LuxMPINCCLExt = ["CUDA", "MPI", "NCCL"]
-    LuxReactantExt = ["Enzyme", "Reactant"]
+    LuxReactantExt = ["Enzyme", "Reactant", "ReactantCore"]
     LuxReverseDiffExt = ["FunctionWrappers", "ReverseDiff"]
     LuxSimpleChainsExt = "SimpleChains"
     LuxTrackerExt = "Tracker"
@@ -1915,28 +1896,30 @@ version = "1.2.3"
     MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
     NCCL = "3fe64909-d7a1-4096-9b7d-7a0f12cf0f6b"
     Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
+    ReactantCore = "a3311ec8-5e00-46d5-b541-4f83e724a433"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     SimpleChains = "de6bee2f-e2f4-4ec7-b6ed-219cc6f6e9e5"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
     Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [[deps.LuxCore]]
 deps = ["Compat", "DispatchDoctor", "Random"]
-git-tree-sha1 = "9f71aea19be890e429ee21adfeda1e63d01ec610"
+git-tree-sha1 = "48d45736aae190b1b41c1db5242fad955f0eff1d"
 uuid = "bb33d45b-7691-41d6-9220-0943567d0623"
-version = "1.1.0"
+version = "1.2.6"
 
     [deps.LuxCore.extensions]
     LuxCoreArrayInterfaceReverseDiffExt = ["ArrayInterface", "ReverseDiff"]
     LuxCoreArrayInterfaceTrackerExt = ["ArrayInterface", "Tracker"]
     LuxCoreChainRulesCoreExt = "ChainRulesCore"
     LuxCoreEnzymeCoreExt = "EnzymeCore"
     LuxCoreFunctorsExt = "Functors"
-    LuxCoreMLDataDevicesExt = "MLDataDevices"
+    LuxCoreMLDataDevicesExt = ["Adapt", "MLDataDevices"]
     LuxCoreReactantExt = "Reactant"
     LuxCoreSetfieldExt = "Setfield"
 
     [deps.LuxCore.weakdeps]
+    Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
     ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
     EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
@@ -1948,10 +1931,10 @@ version = "1.1.0"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
 
 [[deps.LuxLib]]
-deps = ["ArrayInterface", "ChainRulesCore", "Compat", "CpuId", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Hwloc", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"]
-git-tree-sha1 = "a9e0f1477ac91623079f7a230f4de46170dc8817"
+deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "Compat", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"]
+git-tree-sha1 = "b06b83e48cfbfc2ea25ec673537e7eb7e69879e9"
 uuid = "82251201-b29d-42c6-8e01-566dec8acb11"
-version = "1.3.7"
+version = "1.8.0"
 
     [deps.LuxLib.extensions]
     LuxLibAppleAccelerateExt = "AppleAccelerate"
@@ -1961,6 +1944,7 @@ version = "1.3.7"
     LuxLibLoopVectorizationExt = "LoopVectorization"
     LuxLibMKLExt = "MKL"
     LuxLibOctavianExt = ["Octavian", "LoopVectorization"]
+    LuxLibReactantExt = "Reactant"
     LuxLibReverseDiffExt = "ReverseDiff"
     LuxLibSLEEFPiratesExt = "SLEEFPirates"
     LuxLibTrackerAMDGPUExt = ["AMDGPU", "Tracker"]
@@ -1976,6 +1960,7 @@ version = "1.3.7"
     LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890"
     MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
     Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4"
+    Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
@@ -2007,15 +1992,16 @@ version = "1.0.0"
 
 [[deps.MLDataDevices]]
 deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"]
-git-tree-sha1 = "85b47bc5a8bf0c886286638585df3bec7c9f8269"
+git-tree-sha1 = "a47f08b67298dee5778cf279a9a735ca2d11a890"
 uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40"
-version = "1.5.3"
+version = "1.10.0"
 
     [deps.MLDataDevices.extensions]
     MLDataDevicesAMDGPUExt = "AMDGPU"
     MLDataDevicesCUDAExt = "CUDA"
     MLDataDevicesChainRulesCoreExt = "ChainRulesCore"
     MLDataDevicesChainRulesExt = "ChainRules"
+    MLDataDevicesComponentArraysExt = "ComponentArrays"
     MLDataDevicesFillArraysExt = "FillArrays"
     MLDataDevicesGPUArraysExt = "GPUArrays"
     MLDataDevicesMLUtilsExt = "MLUtils"
@@ -2035,6 +2021,7 @@ version = "1.5.3"
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
     ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2"
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
     FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
     GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
     MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54"
@@ -2204,14 +2191,15 @@ uuid = "78c3b35d-d492-501b-9361-3d52fe80e533"
 version = "0.8.1"
 
 [[deps.Mooncake]]
-deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DiffTests", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Setfield", "Test"]
-git-tree-sha1 = "68c31b62f4957a76aaf379092d13475a62f7658b"
+deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Test"]
+git-tree-sha1 = "e4811fc54aa752d4a9a5cc9bed5cd85b8ab75db0"
 uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
-version = "0.4.104"
+version = "0.4.122"
 
     [deps.Mooncake.extensions]
     MooncakeAllocCheckExt = "AllocCheck"
     MooncakeCUDAExt = "CUDA"
+    MooncakeFluxExt = "Flux"
     MooncakeJETExt = "JET"
     MooncakeLuxLibExt = "LuxLib"
     MooncakeLuxLibSLEEFPiratesExtension = ["LuxLib", "SLEEFPirates"]
@@ -2221,6 +2209,7 @@ version = "0.4.104"
     [deps.Mooncake.weakdeps]
     AllocCheck = "9b6a8646-10ed-4001-bbdc-1d2f46dfbb1a"
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+    Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
     JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
     LuxLib = "82251201-b29d-42c6-8e01-566dec8acb11"
     NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
@@ -2488,10 +2477,20 @@ version = "1.13.1"
     MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
 
 [[deps.Optimisers]]
-deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "c9ff5c686240c31eb8570b662dd1f66f4b183116"
+deps = ["ChainRulesCore", "ConstructionBase", "Functors", "LinearAlgebra", "Random", "Statistics"]
+git-tree-sha1 = "131dc319e7c58317e8c6d5170440f6bdaee0a959"
 uuid = "3bd65402-5787-11e9-1adc-39752487f4e2"
-version = "0.3.4"
+version = "0.4.6"
+
+    [deps.Optimisers.extensions]
+    OptimisersAdaptExt = ["Adapt"]
+    OptimisersEnzymeCoreExt = "EnzymeCore"
+    OptimisersReactantExt = "Reactant"
+
+    [deps.Optimisers.weakdeps]
+    Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
+    EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
+    Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
 
 [[deps.Optimization]]
 deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"]
@@ -3670,9 +3669,9 @@ 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", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "e306992e20e271c9834f65fc41972c7f3877c112"
+git-tree-sha1 = "282ca358181f585fbb271eb9301e16b6fe5c80e0"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.38.6"
+version = "0.39.1"
 weakdeps = ["DynamicHMC", "Optim"]
 
     [deps.Turing.extensions]

Project.toml

@@ -5,6 +5,7 @@ AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 AbstractPPL = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
 AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
 AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"
+AdvancedVI = "b5ca4192-6429-45e5-a2d9-87aec30a685c"
 Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
@@ -13,6 +14,7 @@ DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c"
 DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
@@ -36,6 +38,7 @@ Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73"
 MicroCanonicalHMC = "234d2aa0-2291-45f7-9047-6fa6f316b0a8"
 Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
 NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
+Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
@@ -54,4 +57,4 @@ UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
-Turing = "0.38"
+Turing = "0.39"

_quarto.yml

@@ -32,7 +32,7 @@ website:
         text: Team
     right:
       # Current version
-      - text: "v0.38"
+      - text: "v0.39"
         menu:
           - text: Changelog
             href: https://turinglang.org/docs/changelog.html

developers/compiler/minituring-contexts/index.qmd

@@ -294,7 +294,7 @@ Of course, using an MCMC algorithm to sample from the prior is unnecessary and s
 The use of contexts also goes far beyond just evaluating log probabilities and sampling. Some examples from Turing are
 
 * `FixedContext`, which fixes some variables to given values and removes them completely from the evaluation of any log probabilities. They power the `Turing.fix` and `Turing.unfix` functions.
-* `ConditionContext` conditions the model on fixed values for some parameters. They are used by `Turing.condition` and `Turing.uncondition`, i.e. the `model | (parameter=value,)` syntax. The difference between `fix` and `condition` is whether the log probability for the corresponding variable is included in the overall log density. 
+* `ConditionContext` conditions the model on fixed values for some parameters. They are used by `Turing.condition` and `Turing.decondition`, i.e. the `model | (parameter=value,)` syntax. The difference between `fix` and `condition` is whether the log probability for the corresponding variable is included in the overall log density. 
 
 * `PriorExtractorContext` collects information about what the prior distribution of each variable is.
 * `PrefixContext` adds prefixes to variable names, allowing models to be used within other models without variable name collisions.

developers/compiler/model-manual/index.qmd

@@ -36,26 +36,26 @@ using DynamicPPL
 function gdemo2(model, varinfo, context, x)
     # Assume s² has an InverseGamma distribution.
     s², varinfo = DynamicPPL.tilde_assume!!(
-        context, InverseGamma(2, 3), Turing.@varname(s²), varinfo
+        context, InverseGamma(2, 3), @varname(s²), varinfo
     )
 
     # Assume m has a Normal distribution.
     m, varinfo = DynamicPPL.tilde_assume!!(
-        context, Normal(0, sqrt(s²)), Turing.@varname(m), varinfo
+        context, Normal(0, sqrt(s²)), @varname(m), varinfo
     )
 
     # Observe each value of x[i] according to a Normal distribution.
     for i in eachindex(x)
         _retval, varinfo = DynamicPPL.tilde_observe!!(
-            context, Normal(m, sqrt(s²)), x[i], Turing.@varname(x[i]), varinfo
+            context, Normal(m, sqrt(s²)), x[i], @varname(x[i]), varinfo
         )
     end
 
     # The final return statement should comprise both the original return
     # value and the updated varinfo.
     return nothing, varinfo
 end
-gdemo2(x) = Turing.Model(gdemo2, (; x))
+gdemo2(x) = DynamicPPL.Model(gdemo2, (; x))
 
 # Instantiate a Model object with our data variables.
 model2 = gdemo2([1.5, 2.0])