From 48796d9172cff2cbc2b4ac5414c20abb3cf4e335 Mon Sep 17 00:00:00 2001 From: Shravan Goswami Date: Sun, 20 Sep 2026 01:24:52 +0530 Subject: [PATCH 1/3] Update to Turing v0.49 --- Manifest.toml | 147 +++++++++++++++++++++++++------------------------- Project.toml | 2 +- _quarto.yml | 2 +- 3 files changed, 77 insertions(+), 74 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 1cad3f940..1976e10d1 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.11.9" manifest_format = "2.0" -project_hash = "b4a761718945dc70cbfca75bb26db68fe2d9d3e7" +project_hash = "42e671566b992ddd52591546a8b7787641dde4d2" [[deps.ADTypes]] deps = ["PrecompileTools"] @@ -98,9 +98,9 @@ version = "0.1.45" [[deps.Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "daa72978cd7a624246e894a4f4f067706d4e17e2" +git-tree-sha1 = "7c2c19b5a26e601634bf718490b89d59685f122e" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.7.0" +version = "4.7.1" weakdeps = ["SparseArrays", "StaticArrays"] [deps.Adapt.extensions] @@ -186,9 +186,9 @@ version = "3.5.2+0" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "daf5b2aab5b1c1fdcb65b05883cdb4b18abac1b9" +git-tree-sha1 = "1aec1ff0dcaa83a484e7f72097562fa3102c6722" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.30.1" +version = "7.30.2" [deps.ArrayInterface.extensions] ArrayInterfaceAMDGPUExt = "AMDGPU" @@ -239,9 +239,9 @@ version = "1.11.0" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "b8651b2eb5796a386b0398a20b519a6a6150f75c" +git-tree-sha1 = "1bbcf97714051f302b3beafab65bcdeb6044c4df" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "1.1.3" +version = "1.2.1" [deps.Atomix.extensions] AtomixCUDAExt = "CUDA" @@ -263,9 +263,9 @@ version = "1.1.0" [[deps.BFloat16s]] deps = ["LinearAlgebra", "Printf", "Random"] -git-tree-sha1 = "e386db8b4753b42caac75ac81d0a4fe161a68a97" +git-tree-sha1 = "e9f53743fbe41a7e794d58f79d7a13699d9748fa" uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" -version = "0.6.1" +version = "0.6.2" [[deps.BangBang]] deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra"] @@ -295,9 +295,9 @@ version = "1.11.0" [[deps.Bijectors]] deps = ["ADTypes", "AbstractPPL", "ArgCheck", "ChangesOfVariables", "Distributions", "DocStringExtensions", "FillArrays", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics", "Test"] -git-tree-sha1 = "1eddcf2576939a8990350c1d23eb51a14752b7b9" +git-tree-sha1 = "a58fb73182f07a5a561bfadbe40efb9c6c892853" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.16.2" +version = "0.16.3" [deps.Bijectors.extensions] BijectorsChainRulesCoreExt = "ChainRulesCore" @@ -492,9 +492,9 @@ version = "0.3.1" [[deps.CommonWorldInvalidations]] deps = ["PrecompileTools"] -git-tree-sha1 = "6600cd2b039cd07dd8043fd05b0ff2899d9da73b" +git-tree-sha1 = "7c4ea0adfb7238bf4678aa36325863fab6163f6f" uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" -version = "1.2.1" +version = "1.2.2" [[deps.Compat]] deps = ["TOML", "UUIDs"] @@ -785,9 +785,9 @@ version = "0.30.2" [[deps.DispatchDoctor]] deps = ["MacroTools", "Preferences"] -git-tree-sha1 = "42cd00edaac86f941815fe557c1d01e11913e07c" +git-tree-sha1 = "278d0120d7c22ef36bd8d22f349868d6a782a949" uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" -version = "0.4.28" +version = "0.4.29" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.DispatchDoctor.extensions] @@ -840,16 +840,17 @@ uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb" version = "3.6.1" [[deps.DynamicPPL]] -deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "FillArrays", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "LogExpFunctions", "MacroTools", "OrderedCollections", "PartitionedDistributions", "PrecompileTools", "Preferences", "Printf", "Random", "SpecialFunctions", "Statistics", "Test"] -git-tree-sha1 = "e9ba7870f264dd456a4fc9d9d9b59670eff0698a" +deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "FillArrays", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "LogExpFunctions", "MacroTools", "OrderedCollections", "PartitionedDistributions", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "Test"] +git-tree-sha1 = "8f9dc691ddef45d534e9ca1ddea33101a02283c7" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.42.11" +version = "0.42.13" [deps.DynamicPPL.extensions] DynamicPPLBridgeStanExt = ["BridgeStan"] DynamicPPLComponentArraysExt = ["ComponentArrays"] DynamicPPLEnzymeCoreExt = ["EnzymeCore"] DynamicPPLForwardDiffExt = ["ForwardDiff"] + DynamicPPLInputProvenanceExt = ["ForwardDiff"] DynamicPPLMCMCChainsExt = ["MCMCChains"] DynamicPPLMarginalLogDensitiesExt = ["MarginalLogDensities"] DynamicPPLMooncakeExt = ["Mooncake"] @@ -878,10 +879,10 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.7" [[deps.Enzyme]] -deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "0b11d39c3659bce5f83a3fc47020cc994e785392" +deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "ScopedValues", "SparseArrays"] +git-tree-sha1 = "d242d84323f15c1b4788e9eaaca3f8d5ca08dca3" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.200" +version = "0.13.204" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -916,9 +917,9 @@ weakdeps = ["Adapt", "ChainRulesCore"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "d2c552cb05ab0455fdb53ab40a905a1d8e4db2cd" +git-tree-sha1 = "d405b496023e00071fcf874377e7d3e455badd66" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.291+1" +version = "0.0.293+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -928,9 +929,9 @@ version = "0.0.20230411+1" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f4d39eee89f1e58c26bf447f1d4156c0125d6838" +git-tree-sha1 = "2bfb1e047e2ad0a5ca94365340bde8005d637568" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.8.3+0" +version = "2.8.4+0" [[deps.ExponentialUtilities]] deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] @@ -1092,9 +1093,9 @@ version = "0.8.6" [[deps.FlexiChains]] deps = ["AbstractMCMC", "AbstractPPL", "DelimitedFiles", "DimensionalData", "DocStringExtensions", "LinearAlgebra", "MCMCDiagnosticTools", "OrderedCollections", "PrecompileTools", "Printf", "Random", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "844fa0c4d78d1f8d09ac3933a239b4a05b31cb64" +git-tree-sha1 = "d1eedcfb6d10fa29ba8e262dd6b07312b7a36a90" uuid = "4a37a8b9-6e57-4b92-8664-298d46e639f7" -version = "0.6.38" +version = "0.6.40" [deps.FlexiChains.extensions] FlexiChainsAdvancedHMCExt = ["AdvancedHMC", "DimensionalData"] @@ -1146,9 +1147,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "1b86cca764a61dcac4fef4c5e16e378e5ed6953c" +git-tree-sha1 = "3b0f72e2ffef1a139ac450725c9ecd01c0a3c050" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "1.4.5" +version = "1.4.6" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -1282,9 +1283,9 @@ version = "1.3.16+0" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] -git-tree-sha1 = "c3f99f8e7c98031b8845ece9db86dca713ab9bf8" +git-tree-sha1 = "9d9531a9cb63a9edc33836414e82a07e81710de2" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "100.14003.0+0" +version = "100.14004.0+0" [[deps.HashArrayMappedTries]] git-tree-sha1 = "2eaa69a7cab70a52b9687c8bf950a5a93ec895ae" @@ -1421,9 +1422,9 @@ version = "1.8.0" [[deps.JSON]] deps = ["Dates", "Logging", "Parsers", "PrecompileTools", "StructUtils", "UUIDs", "Unicode"] -git-tree-sha1 = "c7345ab1a7ca4dc8a02c9f6510da0d9857bbe513" +git-tree-sha1 = "cb5b63c11dd08229716a8b41a2325ab941a7b797" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "1.7.1" +version = "1.8.1" [deps.JSON.extensions] JSONArrowExt = ["ArrowTypes"] @@ -1469,9 +1470,9 @@ version = "0.10.67" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "71e740d00d71cdb15145d7fe0d6000ec70534598" +git-tree-sha1 = "909890a0d1486c392128cf4bd6e038ee0c6a7af4" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.10.9" +version = "0.10.10" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1481,9 +1482,9 @@ version = "3.100.3+0" [[deps.LERC_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "17b94ecafcfa45e8360a4fc9ca6b583b049e4e37" +git-tree-sha1 = "39bca05343661c347aae0bca57a5994a0bf4f08d" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "4.1.0+0" +version = "4.2.0+0" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "PrecompileTools", "Preferences", "Printf", "Unicode"] @@ -1503,9 +1504,9 @@ version = "0.0.47+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "b7970cef8ae1c990ba0c09cd8bdc1145e006632f" +git-tree-sha1 = "e5b100780d4d30d63b4618d7930d48af409c1772" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "22.1.7+0" +version = "23.1.1+0" [[deps.LaTeXStrings]] git-tree-sha1 = "f88f3ccef05a6a72a0cf0ed417c8fd68530f4ab2" @@ -1642,9 +1643,9 @@ weakdeps = ["LineSearches"] [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Printf"] -git-tree-sha1 = "b4f9762e3ad693626ffd51ae4be359c0a7b08469" +git-tree-sha1 = "a09a85e94e681def2446752cddaf9401a4d82b6d" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.8.1" +version = "7.8.2" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -2062,9 +2063,9 @@ version = "0.8.1" [[deps.Mooncake]] deps = ["ADTypes", "ChainRulesCore", "DispatchDoctor", "ExprTools", "LinearAlgebra", "MistyClosures", "PrecompileTools", "Random", "Test"] -git-tree-sha1 = "c639c9891bc1687dee5f91b92b8b2cfec882f7fc" +git-tree-sha1 = "b5353bf33ecb401a5d6a0d9ba38247f53eb3d6bb" uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" -version = "0.5.51" +version = "0.5.59" [deps.Mooncake.extensions] MooncakeAllocCheckExt = "AllocCheck" @@ -2339,9 +2340,9 @@ version = "0.5.6+0" [[deps.Optim]] deps = ["ADTypes", "EnumX", "FillArrays", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "PositiveFactorizations", "Printf", "SparseArrays", "Statistics"] -git-tree-sha1 = "ece78ffe4fcee487b858ecaf184b8d7c2a79e015" +git-tree-sha1 = "81f338ad984b25bc82471db4d235e7b8bf21b8d6" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "2.3.1" +version = "2.3.2" [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" @@ -2650,9 +2651,9 @@ version = "2.8.8" [[deps.PartitionedDistributions]] deps = ["Distributions", "FillArrays", "InvertedIndices", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "PDMats", "SpecialFunctions", "StatsBase"] -git-tree-sha1 = "621944b594bec8df388aeecd2d694824cbe71ecd" +git-tree-sha1 = "f4fdc1c69051e2610337545416d3777868a98021" uuid = "569bd051-8d7b-4221-bcb8-d78512b5866a" -version = "0.1.0" +version = "0.1.2" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] @@ -2676,10 +2677,10 @@ uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" version = "3.3.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] -git-tree-sha1 = "26ca162858917496748aad52bb5d3be4d26a228a" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Reexport", "Statistics"] +git-tree-sha1 = "f20e945b895d2009c6c28d8bbf40a5cd846f7c2f" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.4" +version = "1.5.0" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "Unzip"] @@ -2751,9 +2752,9 @@ version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "8b770b60760d4451834fe79dd483e318eee709c4" +git-tree-sha1 = "5005266de4bfe50e53ff44a5cb5c540b6e47a254" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.5.2" +version = "1.6.0" [[deps.PrettyTables]] deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "REPL", "Reexport", "StringManipulation", "Tables"] @@ -2799,9 +2800,9 @@ version = "1.4.0" [[deps.PureKLU]] deps = ["LinearAlgebra", "PrecompileTools", "SparseArrays"] -git-tree-sha1 = "ef341b8e734ffa12c0464a58ca1c8a214d7a4235" +git-tree-sha1 = "6719681d517f9b02fc3e3c3a0befbde5e4a2320e" uuid = "0c0d3e7f-3a8b-4f7e-b6f1-9a4d2e7c1f01" -version = "1.4.1" +version = "1.5.0" weakdeps = ["ForwardDiff"] [deps.PureKLU.extensions] @@ -2893,9 +2894,9 @@ weakdeps = ["FixedPointNumbers"] [[deps.ReactantCore]] deps = ["ExpressionExplorer", "MacroTools"] -git-tree-sha1 = "9ae01d91c9326873cea17b97ad198befdf231661" +git-tree-sha1 = "7ff99a4f1d30a9bca5ad786aab68458a9c46ca86" uuid = "a3311ec8-5e00-46d5-b541-4f83e724a433" -version = "0.1.21" +version = "0.1.22" [[deps.RealDot]] deps = ["LinearAlgebra"] @@ -2976,9 +2977,9 @@ version = "1.4.0" [[deps.ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "f5f3c09103951beae390666a18e084655996370b" +git-tree-sha1 = "4e99749f3e5617a2dd6edfd62832e27f18720fb6" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.17.0" +version = "1.17.3" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -3016,9 +3017,9 @@ version = "3.0.8" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "PrecompileTools", "SHA", "Serialization"] -git-tree-sha1 = "6cb9b83354089fcb33c643773acfd3235f2f1bf5" +git-tree-sha1 = "1719b26eee2c5e40d4b41c647b91dbaac1dcbf05" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.25" +version = "0.5.26" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -3092,9 +3093,9 @@ weakdeps = ["Tracy"] [[deps.SciMLOperators]] deps = ["Accessors", "Adapt", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "PrecompileTools", "SciMLPublic"] -git-tree-sha1 = "0b5b895913f1269a8c80b59435c61d5a7d79970c" +git-tree-sha1 = "9eba48f738160e04268c0770e01dae2451199bc2" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "1.30.0" +version = "1.30.1" [deps.SciMLOperators.extensions] SciMLOperatorsLoopVectorizationExt = "LoopVectorization" @@ -3305,9 +3306,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "e206cf4850fd7ac4255ffd2b98922f563e18ac53" +git-tree-sha1 = "39e70e0ab5d7f89833a62ab7c79df15d4fc417c1" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.20" +version = "1.9.22" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -3440,16 +3441,18 @@ version = "0.3.1" [[deps.StructUtils]] deps = ["Dates", "UUIDs"] -git-tree-sha1 = "2d0fc55c61321ba245c47be599570d11bac50303" +git-tree-sha1 = "b814d5005d6a529d740ffe06f8a86396f6501138" uuid = "ec057cc2-7a8d-4b58-b3b3-92acb9f63b42" -version = "2.8.5" +version = "2.9.2" [deps.StructUtils.extensions] + StructUtilsLazilyInitializedFieldsExt = ["LazilyInitializedFields"] StructUtilsMeasurementsExt = ["Measurements"] StructUtilsStaticArraysCoreExt = ["StaticArraysCore"] StructUtilsTablesExt = ["Tables"] [deps.StructUtils.weakdeps] + LazilyInitializedFields = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" @@ -3484,9 +3487,9 @@ version = "1.0.3" [[deps.TZJData]] deps = ["Artifacts"] -git-tree-sha1 = "d3b30a9f29a898e21fb4bdf280101b7a12e1f39c" +git-tree-sha1 = "1ce1f307e71046701e278bad521986cb22c0d1a7" uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" -version = "1.5.1+2025b" +version = "1.7.0+2026a" [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] @@ -3608,9 +3611,9 @@ version = "1.6.0" [[deps.Turing]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "FlexiChains", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Random123", "Reexport", "SciMLBase", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "6ae6ea2c2c83718587ba504f78235e460cce9551" +git-tree-sha1 = "92b456a228ba157b0d8ee4309f82769e6f672671" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.48.0" +version = "0.49.0" [deps.Turing.extensions] TuringDistributionsExt = "Distributions" @@ -3707,9 +3710,9 @@ version = "1.6.1" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "b29c22e245d092b8b4e8d3c09ad7baa586d9f573" +git-tree-sha1 = "e52eca002a11c30a858185efdfb15311e1c7a6bf" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.8.3+0" +version = "5.8.4+0" [[deps.Xorg_libICE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] diff --git a/Project.toml b/Project.toml index c8d69fb8f..a46ed7c66 100644 --- a/Project.toml +++ b/Project.toml @@ -53,4 +53,4 @@ StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] -Turing = "0.48" +Turing = "0.49" diff --git a/_quarto.yml b/_quarto.yml index dc245f4d8..80c9ec45d 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -43,7 +43,7 @@ website: href: https://turinglang.org/team/ right: # Current version - - text: "v0.48" + - text: "v0.49" menu: - text: Changelog href: https://turinglang.org/docs/changelog.html From 3db59a00a79c9259bfbe62f05915ef35428e9e97 Mon Sep 17 00:00:00 2001 From: Shravan Goswami Date: Sun, 20 Sep 2026 01:24:52 +0530 Subject: [PATCH 2/3] Document the check_model overwrite warning --- usage/debugging/index.qmd | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/usage/debugging/index.qmd b/usage/debugging/index.qmd index a9fe0fb03..52e8fb162 100644 --- a/usage/debugging/index.qmd +++ b/usage/debugging/index.qmd @@ -26,11 +26,13 @@ Specifically, it checks for: - the same variable, or overlapping variables (such as `x` and `x[1]`), appearing on the left-hand side of more than one tilde statement; - `NaN` values on the left-hand side of observe statements; +- a latent variable whose value was computed from a model input before its tilde statement, since that value is about to be overwritten and the variable was probably meant to be an observation; - with the keyword argument `fail_if_discrete=true`, the presence of discrete random variables, which gradient-based samplers such as HMC and NUTS cannot handle. It is equally important to know what it does not catch. The model is evaluated a single time, with values drawn from the prior, so problems that only occur for some parameter values (for example, in a branch that this particular evaluation does not take) can be missed. It also checks only the structure of the model, not its statistical soundness: it cannot tell you that a prior is unreasonable or that parameters are not identifiable. +The overwrite check needs ForwardDiff to be loaded, and is best effort even then, so it can miss a dependency that runs through an untaken branch, a condition, or code it cannot differentiate. Type instability and incorrect gradients are separate concerns, covered by the checks in the following sections. For example, this model observes a `NaN` value, which usually indicates a bug in the data preparation: @@ -52,6 +54,21 @@ whereas the same model with valid data passes: check_model(gaussian(1.5)) ``` +The overwrite check catches a different kind of mistake, where a value derived from the data is given a prior instead of being observed: + +```{julia} +@model function overwritten(y) + z = 2y + z ~ Normal() + return y ~ Normal(z) +end + +check_model(overwritten(1.5)) +``` + +Here `z` is computed from `y` and then immediately discarded, because `z ~ Normal()` samples a fresh value for it. +Note that the check warns but still returns `true`, since this is legal Julia and legal DynamicPPL, just rarely what was meant. + Turing runs this check automatically at the start of `sample` (and the mode estimation functions). For gradient-based samplers, this includes the discrete-variable check. If the check reports a false positive for your model, you can disable it by passing `check_model=false` to `sample`. From 6deb12a21b887eab13ed7ce2e1e75acb6afe22ad Mon Sep 17 00:00:00 2001 From: Shravan Goswami Date: Sun, 20 Sep 2026 01:24:52 +0530 Subject: [PATCH 3/3] Say DynamicPPL.Model rather than Turing.Model --- tutorials/variational-inference/index.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd index efe16cdb6..7151a2600 100755 --- a/tutorials/variational-inference/index.qmd +++ b/tutorials/variational-inference/index.qmd @@ -17,7 +17,7 @@ This post will focus on the usage of VI in Turing rather than the principles and If you are interested in understanding the mathematics you can checkout [our write-up]({{}}) or any other resource online (there are a lot of great ones). Let's start with a minimal example. -Consider a `Turing.Model`, which we denote as `model`. +Consider a `DynamicPPL.Model`, which we denote as `model`. Approximating the posterior associated with `model` via VI is as simple as ```julia