Turing v0.45

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.11.9"
 manifest_format = "2.0"
-project_hash = "75240642ac9209edc6934c6d8a26cefb5226af2f"
+project_hash = "b115e243a73218a9880a8c1e62286d045b25694d"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "bbc22a9a08a0ef6460041086d8a7b27940ed4ffd"
@@ -121,13 +121,18 @@ deps = ["AbstractMCMC", "Distributions", "DocStringExtensions", "FillArrays", "L
 git-tree-sha1 = "62ddbccf0ce5c26f8ef3cebe4bedef6b1599d616"
 uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"
 version = "0.8.10"
-weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"]
 
     [deps.AdvancedMH.extensions]
     AdvancedMHForwardDiffExt = ["DiffResults", "ForwardDiff"]
     AdvancedMHMCMCChainsExt = "MCMCChains"
     AdvancedMHStructArraysExt = "StructArrays"
 
+    [deps.AdvancedMH.weakdeps]
+    DiffResults = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"
+    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+    MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
+    StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
+
 [[deps.AdvancedPS]]
 deps = ["AbstractMCMC", "Distributions", "Random", "Random123", "Requires", "SSMProblems", "StatsFuns"]
 git-tree-sha1 = "d92dd3fb4cc2748860ae8d5dd1d324cf0715a53b"
@@ -248,12 +253,6 @@ git-tree-sha1 = "01b8ccb13d68535d73d2b0c23e39bd23155fb712"
 uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950"
 version = "1.1.0"
 
-[[deps.AxisArrays]]
-deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"]
-git-tree-sha1 = "4126b08903b777c88edf1754288144a0492c05ad"
-uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
-version = "0.4.8"
-
 [[deps.BangBang]]
 deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra"]
 git-tree-sha1 = "cceb62468025be98d42a5dc581b163c20896b040"
@@ -753,6 +752,42 @@ version = "0.7.17"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
     Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
+[[deps.DimensionalData]]
+deps = ["ConstructionBase", "DataAPI", "Dates", "Extents", "Interfaces", "IntervalSets", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "PrecompileTools", "Random", "Statistics", "TableTraits", "Tables"]
+git-tree-sha1 = "57bbee194533adaa755b5cae528eabdea5d05039"
+uuid = "0703355e-b756-11e9-17c0-8b28908087d0"
+version = "0.30.1"
+
+    [deps.DimensionalData.extensions]
+    DimensionalDataAbstractFFTsExt = "AbstractFFTs"
+    DimensionalDataAdaptExt = "Adapt"
+    DimensionalDataAlgebraOfGraphicsExt = "AlgebraOfGraphics"
+    DimensionalDataArrayInterfaceExt = "ArrayInterface"
+    DimensionalDataCategoricalArraysExt = "CategoricalArrays"
+    DimensionalDataChainRulesCoreExt = "ChainRulesCore"
+    DimensionalDataDiskArraysExt = "DiskArrays"
+    DimensionalDataMakieExt = "Makie"
+    DimensionalDataNearestNeighborsExt = "NearestNeighbors"
+    DimensionalDataPythonCallExt = "PythonCall"
+    DimensionalDataRecipesBaseExt = "RecipesBase"
+    DimensionalDataSparseArraysExt = "SparseArrays"
+    DimensionalDataStatsBaseExt = "StatsBase"
+
+    [deps.DimensionalData.weakdeps]
+    AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"
+    Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
+    AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
+    ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
+    CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
+    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    DiskArrays = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
+    Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+    NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
+    PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+    RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+    StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+
 [[deps.DispatchDoctor]]
 deps = ["MacroTools", "Preferences"]
 git-tree-sha1 = "42cd00edaac86f941815fe557c1d01e11913e07c"
@@ -810,11 +845,12 @@ version = "3.6.0"
 
 [[deps.DynamicPPL]]
 deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "FillArrays", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "PartitionedDistributions", "PrecompileTools", "Preferences", "Printf", "Random", "Statistics", "Test"]
-git-tree-sha1 = "23ad4cb791a4725698268684555d937c26da0d54"
+git-tree-sha1 = "c46e2b68a20a695df01ce316c08c977a1bb4c5b8"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.41.6"
+version = "0.41.7"
 
     [deps.DynamicPPL.extensions]
+    DynamicPPLComponentArraysExt = ["ComponentArrays"]
     DynamicPPLEnzymeCoreExt = ["EnzymeCore"]
     DynamicPPLForwardDiffExt = ["ForwardDiff"]
     DynamicPPLMCMCChainsExt = ["MCMCChains"]
@@ -823,6 +859,7 @@ version = "0.41.6"
     DynamicPPLReverseDiffExt = ["ReverseDiff"]
 
     [deps.DynamicPPL.weakdeps]
+    ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
     EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
     ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
     KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
@@ -924,6 +961,11 @@ git-tree-sha1 = "c13f0b150373771b0fdc1713c97860f8df12e6c2"
 uuid = "55351af7-c7e9-48d6-89ff-24e801d99491"
 version = "0.10.14"
 
+[[deps.Extents]]
+git-tree-sha1 = "b309b36a9e02fe7be71270dd8c0fd873625332b4"
+uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910"
+version = "0.1.6"
+
 [[deps.FFMPEG]]
 deps = ["FFMPEG_jll"]
 git-tree-sha1 = "95ecf07c2eea562b5adbd0696af6db62c0f52560"
@@ -1061,6 +1103,40 @@ git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172"
 uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 version = "0.8.5"
 
+[[deps.FlexiChains]]
+deps = ["AbstractMCMC", "AbstractPPL", "DelimitedFiles", "DimensionalData", "DocStringExtensions", "MCMCDiagnosticTools", "OrderedCollections", "PrecompileTools", "Printf", "Random", "Statistics", "StatsBase", "Tables"]
+git-tree-sha1 = "d959cdc91cc71191f7097b02d21c3520c7993fd8"
+uuid = "4a37a8b9-6e57-4b92-8664-298d46e639f7"
+version = "0.6.2"
+
+    [deps.FlexiChains.extensions]
+    FlexiChainsAdvancedHMCExt = ["AdvancedHMC", "DimensionalData"]
+    FlexiChainsComponentArraysExt = ["ComponentArrays"]
+    FlexiChainsDynamicPPLExt = ["DynamicPPL", "Random", "DimensionalData", "OrderedCollections", "Distributions"]
+    FlexiChainsMCMCChainsExt = ["MCMCChains", "OrderedCollections"]
+    FlexiChainsMakieExt = ["Makie"]
+    FlexiChainsPairPlotsExt = ["PairPlots", "Makie"]
+    FlexiChainsPosteriorDBExt = ["PosteriorDB", "OrderedCollections"]
+    FlexiChainsPosteriorStatsDynamicPPLExt = ["PosteriorStats", "DynamicPPL"]
+    FlexiChainsPosteriorStatsExt = ["PosteriorStats", "DimensionalData"]
+    FlexiChainsRecipesBaseExt = ["RecipesBase", "StatsBase"]
+    FlexiChainsStanSampleExt = ["StanSample"]
+    FlexiChainsStatsPlotsExt = ["StatsPlots", "DimensionalData"]
+
+    [deps.FlexiChains.weakdeps]
+    AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
+    ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
+    Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+    DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
+    MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
+    Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+    PairPlots = "43a3c2be-4208-490b-832a-a21dcd55d7da"
+    PosteriorDB = "1c4bc282-d2f5-44f9-b6d1-8c4424a23ad4"
+    PosteriorStats = "7f36be82-ad55-44ba-a5c0-b8b5480d7aa5"
+    RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+    StanSample = "c1514b29-d3a0-5178-b312-660c88baa699"
+    StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
+
 [[deps.Fontconfig_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"]
 git-tree-sha1 = "f85dac9a96a01087df6e3a749840015a0ca3817d"
@@ -1297,6 +1373,11 @@ deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 version = "1.11.0"
 
+[[deps.Interfaces]]
+git-tree-sha1 = "331ff37738aea1a3cf841ddf085442f31b84324f"
+uuid = "85a1e053-f937-4924-92a5-1367d23b7b87"
+version = "0.3.2"
+
 [[deps.Interpolations]]
 deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"]
 git-tree-sha1 = "65d505fa4c0d7072990d659ef3fc086eb6da8208"
@@ -1342,11 +1423,6 @@ git-tree-sha1 = "b2d91fe939cae05960e760110b328288867b5758"
 uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
 version = "0.2.6"
 
-[[deps.IterTools]]
-git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023"
-uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
-version = "1.10.0"
-
 [[deps.IteratorInterfaceExtensions]]
 git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
 uuid = "82899510-4779-5014-852e-03e436cf321d"
@@ -1585,9 +1661,9 @@ version = "2.42.0+0"
 
 [[deps.LineSearch]]
 deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"]
-git-tree-sha1 = "25454bc65c3eec4656cbe201c3d9336af49178c7"
+git-tree-sha1 = "fd58a77c92e7c8f1db25c9839127d52943a49349"
 uuid = "87fe0de2-c867-4266-b59a-2f0a94fc965b"
-version = "0.1.8"
+version = "0.1.9"
 weakdeps = ["LineSearches"]
 
     [deps.LineSearch.extensions]
@@ -1844,12 +1920,6 @@ version = "1.15.9"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
     cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd"
 
-[[deps.MCMCChains]]
-deps = ["AbstractMCMC", "AxisArrays", "DataAPI", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"]
-git-tree-sha1 = "060d6bc7cf60e621dfd056ed2c1a2db1e68db0fe"
-uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
-version = "7.7.0"
-
 [[deps.MCMCDiagnosticTools]]
 deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"]
 git-tree-sha1 = "2f464b68e84673727b4e4216a6254fba7da5cf4e"
@@ -1870,9 +1940,9 @@ version = "1.0.0"
 
 [[deps.MLDataDevices]]
 deps = ["Adapt", "Functors", "Preferences", "Random", "SciMLPublic"]
-git-tree-sha1 = "2dfe3b4b96c6ecbea7c798dfbe96d493fd7a1848"
+git-tree-sha1 = "29b00f22be6fd821a214760f0224329f21998a05"
 uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40"
-version = "1.17.8"
+version = "1.17.10"
 
     [deps.MLDataDevices.extensions]
     AMDGPUExt = "AMDGPU"
@@ -2133,11 +2203,6 @@ git-tree-sha1 = "1a0fa0e9613f46c9b8c11eee38ebb4f590013c5e"
 uuid = "71a1bf82-56d0-4bbc-8a3c-48b961074391"
 version = "0.1.5"
 
-[[deps.NaturalSort]]
-git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21"
-uuid = "c020b1a1-e9b0-503a-9c33-f039bfc54a85"
-version = "1.0.0"
-
 [[deps.NearestNeighbors]]
 deps = ["AbstractTrees", "Distances", "StaticArrays"]
 git-tree-sha1 = "e2c3bba08dd6dedfe17a17889131b885b8c082f0"
@@ -2828,11 +2893,6 @@ git-tree-sha1 = "c6ec94d2aaba1ab2ff983052cf6a606ca5985902"
 uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143"
 version = "1.6.0"
 
-[[deps.RangeArrays]]
-git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5"
-uuid = "b3c3ace0-ae52-54e7-9d0b-2c1406fd6b9d"
-version = "0.3.2"
-
 [[deps.Ratios]]
 deps = ["Requires"]
 git-tree-sha1 = "1342a47bf3260ee108163042310d26f2be5ec90b"
@@ -2989,9 +3049,9 @@ version = "0.6.1"
 
 [[deps.SciMLBase]]
 deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PreallocationTools", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLLogging", "SciMLOperators", "SciMLPublic", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "908c0bf271604d09393a21c142116ab26f66f67c"
+git-tree-sha1 = "a017ed325ac5e11438c888864fe83b124bb171b7"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.154.0"
+version = "2.155.1"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -3580,15 +3640,18 @@ uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6"
 version = "1.6.0"
 
 [[deps.Turing]]
-deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "DifferentiationInterface", "Distributions", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "666a4c4a3758e5b25eb100bce144f378addd8697"
+deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "DifferentiationInterface", "Distributions", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "FlexiChains", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
+git-tree-sha1 = "96cfabe16a96096d4864df1760187ee8814c17bf"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.44.5"
-weakdeps = ["DynamicHMC"]
+version = "0.45.0"
 
     [deps.Turing.extensions]
     TuringDynamicHMCExt = "DynamicHMC"
 
+    [deps.Turing.weakdeps]
+    DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
+    MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
+
 [[deps.URIs]]
 git-tree-sha1 = "bef26fb046d031353ef97a82e3fdb6afe7f21b1a"
 uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"

Project.toml

@@ -10,11 +10,13 @@ CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 Chairmarks = "0ca39b1e-fe0b-4e98-acfc-b1656634c4de"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DelayDiffEq = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
+DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
+FlexiChains = "4a37a8b9-6e57-4b92-8664-298d46e639f7"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
@@ -26,7 +28,7 @@ LogDensityProblemsAD = "996a588d-648d-4e1f-a8f0-a84b347e47b1"
 LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 Lux = "b2108857-7c20-44ae-9111-449ecde12c47"
-MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
+MCMCDiagnosticTools = "be115224-59cd-429b-ad48-344e309966f0"
 MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Measures = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
@@ -51,6 +53,4 @@ StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 
 [compat]
-Turing = "0.44"
-# https://github.com/SciML/SciMLBase.jl/issues/1325
-SciMLBase = "=2.154.0"
+Turing = "0.45"

_quarto.yml

@@ -43,7 +43,7 @@ website:
         href: https://turinglang.org/team/
     right:
       # Current version
-      - text: "v0.44"
+      - text: "v0.45"
         menu:
           - text: Changelog
             href: https://turinglang.org/docs/changelog.html
@@ -121,12 +121,6 @@ website:
 
         - section: "Developers"
           contents:
-          - section: "DynamicPPL's Compiler"
-            collapse-level: 1
-            contents:
-              - developers/compiler/minituring-compiler/index.qmd
-              - developers/compiler/minituring-contexts/index.qmd
-
           - section: "DynamicPPL Contexts"
             collapse-level: 1
             contents:
@@ -232,8 +226,6 @@ contributing-pull-requests: contributing/pull-requests
 contributing-code-formatting: contributing/code-formatting
 contributing-core-developers: contributing/core-developers
 dev-model-manual: developers/compiler/model-manual
-contexts: developers/compiler/minituring-contexts
-minituring: developers/compiler/minituring-compiler
 dev-variational-inference: developers/inference/variational-inference
 using-turing-implementing-samplers: developers/inference/implementing-samplers
 dev-transforms-distributions: developers/transforms/distributions