From 639430348b883efcafee0f69d96e113f0d6ba9d4 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Wed, 22 Apr 2026 14:39:03 +0100 Subject: [PATCH 1/4] Update --- Manifest.toml | 440 ++++++++++++++++++++++++++------------------------ Project.toml | 2 +- _quarto.yml | 2 +- 3 files changed, 228 insertions(+), 216 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 66789937c..315352296 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.11.9" manifest_format = "2.0" -project_hash = "e1514f1c2f1d0ee5cb42fcae104797660088ebbe" +project_hash = "febad8c4a969e1e9d534d8cb92e36f104e7c03a6" [[deps.ADTypes]] git-tree-sha1 = "f7304359109c768cf32dc5fa2d371565bb63b68a" @@ -33,10 +33,10 @@ uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" version = "0.5.24" [[deps.AbstractMCMC]] -deps = ["BangBang", "ConsoleProgressMonitor", "Dates", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers", "UUIDs"] -git-tree-sha1 = "511d0d8cbf38045be05188ae26880afb57342a88" +deps = ["BangBang", "ConsoleProgressMonitor", "Dates", "Distributed", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "UUIDs"] +git-tree-sha1 = "8ac6182431567907e0d5170bcac6dd48fa541f78" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "5.14.0" +version = "5.15.1" [deps.AbstractMCMC.extensions] AbstractMCMCOnlineStatsExt = "OnlineStats" @@ -48,9 +48,9 @@ version = "5.14.0" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "Accessors", "BangBang", "DensityInterface", "JSON", "LinearAlgebra", "MacroTools", "OrderedCollections", "Random", "StatsBase"] -git-tree-sha1 = "cc74854881ab9531bde1ecc624ef3f9821497717" +git-tree-sha1 = "e7be2de9646c1f61332de9f1e32c7dedf1e00831" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.14.1" +version = "0.14.2" weakdeps = ["Distributions"] [deps.AbstractPPL.extensions] @@ -87,9 +87,9 @@ version = "0.1.44" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "35ea197a51ce46fcd01c4a44befce0578a1aaeca" +git-tree-sha1 = "0761717147821d696c9470a7a86364b2fbd22fd8" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.5.0" +version = "4.5.2" weakdeps = ["SparseArrays", "StaticArrays"] [deps.Adapt.extensions] @@ -186,9 +186,9 @@ version = "3.5.2+0" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "78b3a7a536b4b0a747a0f296ea77091ca0a9f9a3" +git-tree-sha1 = "54f895554d05c83e3dd59f6a396671dae8999573" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.23.0" +version = "7.24.0" [deps.ArrayInterface.extensions] ArrayInterfaceAMDGPUExt = "AMDGPU" @@ -286,10 +286,10 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.Bijectors]] -deps = ["AbstractPPL", "ArgCheck", "ChainRulesCore", "ChangesOfVariables", "DifferentiationInterface", "Distributions", "DocStringExtensions", "EnzymeCore", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics", "Test"] -git-tree-sha1 = "e876fd33fef2708270d8f72b4491af71fed12ec6" +deps = ["AbstractPPL", "ArgCheck", "ChainRulesCore", "ChangesOfVariables", "DifferentiationInterface", "Distributions", "DocStringExtensions", "EnzymeCore", "FillArrays", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics", "Test"] +git-tree-sha1 = "d6ee8f89dd20f933fbdad578a798e32babb617ee" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.15.18" +version = "0.15.20" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -320,9 +320,9 @@ version = "0.1.6" [[deps.BracketingNonlinearSolve]] deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "d9b66401c1fa982c7ca984d0566af5a9b3551420" +git-tree-sha1 = "7ad7171d693ae5552ac43862e7f6b61df4471c2b" uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e" -version = "1.12.0" +version = "1.12.1" weakdeps = ["ChainRulesCore", "ForwardDiff"] [deps.BracketingNonlinearSolve.extensions] @@ -353,10 +353,10 @@ uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" version = "0.10.16" [[deps.Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a21c5464519504e41e0cbc91f0188e8ca23d7440" +deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "d0efe2c6fdcdaa1c161d206aa8b933788397ec71" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.5+1" +version = "1.18.6+0" [[deps.Cassette]] git-tree-sha1 = "f8764df8d9d2aec2812f009a1ac39e46c33354b8" @@ -393,9 +393,9 @@ version = "1.73.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "e4c6a16e77171a5f5e25e9646617ab1c276c5607" +git-tree-sha1 = "12177ad6b3cad7fd50c8b3825ce24a99ad61c18f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.26.0" +version = "1.26.1" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -569,9 +569,9 @@ version = "1.16.0" [[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 = "d8928e9169ff76c6281f39a659f9bca3a573f24c" +git-tree-sha1 = "5fab31e2e01e70ad66e3e24c968c264d1cf166d6" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.8.1" +version = "1.8.2" [[deps.DataStructures]] deps = ["OrderedCollections"] @@ -602,9 +602,9 @@ version = "0.1.2" [[deps.DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "FastBroadcast", "ForwardDiff", "LinearAlgebra", "Logging", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLLogging", "SimpleNonlinearSolve", "SymbolicIndexingInterface"] -git-tree-sha1 = "398214a0318a2a02128603a26ad4ecd1ffa65115" +git-tree-sha1 = "50ee49f1cd42985431636ee99a938e4b186b376b" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.70.0" +version = "5.74.1" [deps.DelayDiffEq.extensions] DelayDiffEqStochasticDiffEqCoreExt = ["StochasticDiffEqCore", "DiffEqNoiseProcess", "Random"] @@ -627,10 +627,10 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "BracketingNonlinearSolve", "ConcreteStructs", "DocStringExtensions", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "c5fe5125fcba8f98cdc5c7221b6c324883899c07" +deps = ["ArrayInterface", "BracketingNonlinearSolve", "ConcreteStructs", "DocStringExtensions", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLLogging", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"] +git-tree-sha1 = "9d333db14895e8c7d4857ed228eb1e72d3b302ec" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.213.0" +version = "6.218.0" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -671,9 +671,9 @@ version = "6.213.0" [[deps.DiffEqCallbacks]] deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "LinearAlgebra", "Markdown", "PrecompileTools", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "f17b863c2d5d496363fe36c8d8535cc6a33c9952" +git-tree-sha1 = "522a0fae4cadc98f20cfcc8001c1d4a906c5a3cd" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "4.12.0" +version = "4.16.0" weakdeps = ["Functors"] [deps.DiffEqCallbacks.extensions] @@ -681,9 +681,9 @@ weakdeps = ["Functors"] [[deps.DiffEqNoiseProcess]] deps = ["CommonSolve", "DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "PoissonRandom", "QuadGK", "Random", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "b879ca516034469f28becdf01f85f56b45f518b9" +git-tree-sha1 = "3b5ead2d14aad3807e427255d078057c4c70ca6d" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.27.0" +version = "5.30.0" weakdeps = ["Optim", "ReverseDiff"] [deps.DiffEqNoiseProcess.extensions] @@ -781,9 +781,9 @@ version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "fbcc7610f6d8348428f722ecbe0e6cfe22e672c6" +git-tree-sha1 = "e421c1938fafab0165b04dc1a9dbe2a26272952c" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.123" +version = "0.25.125" weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [deps.Distributions.extensions] @@ -809,9 +809,9 @@ 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", "PrecompileTools", "Preferences", "Printf", "Random", "Statistics", "Test"] -git-tree-sha1 = "7255f9493bb497ddb13b1bf48564289688869755" +git-tree-sha1 = "5d9daef4703e9bbd98dc4ba7bba5d137d1541c8a" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.40.18" +version = "0.41.3" [deps.DynamicPPL.extensions] DynamicPPLEnzymeCoreExt = ["EnzymeCore"] @@ -843,9 +843,9 @@ 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 = "7383238b1524e0df25a98924c9070d0d231f5b8c" +git-tree-sha1 = "d6dd65421104fa9f7d5cc37283a998937f359a39" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.136" +version = "0.13.138" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -954,10 +954,15 @@ uuid = "b9860ae5-e623-471e-878b-f6a53c775ea6" version = "0.1.1" [[deps.FastBroadcast]] -deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "ab1b34570bcdf272899062e1a56285a53ecaae08" +deps = ["ArrayInterface", "LinearAlgebra"] +git-tree-sha1 = "e3e64918b1604ba8b1734c4a27febdfe5d09e235" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.3.5" +version = "1.3.1" +weakdeps = ["Polyester", "Static"] + + [deps.FastBroadcast.extensions] + FastBroadcastPolyesterExt = "Polyester" + FastBroadcastStaticExt = "Static" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -1033,9 +1038,9 @@ weakdeps = ["PDMats", "SparseArrays", "StaticArrays", "Statistics"] [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] -git-tree-sha1 = "9340ca07ca27093ff68418b7558ca37b05f8aeb1" +git-tree-sha1 = "73e879af0e767bd6dfade7c5b09d7b05657a8284" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.29.0" +version = "2.30.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" @@ -1100,10 +1105,15 @@ uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" version = "1.1.3" [[deps.FunctionWrappersWrappers]] -deps = ["FunctionWrappers"] -git-tree-sha1 = "b104d487b34566608f8b4e1c39fb0b10aa279ff8" +deps = ["FunctionWrappers", "PrecompileTools", "TruncatedStacktraces"] +git-tree-sha1 = "a100fa86d86ff062e6ea24d4a7427247a4eebf9b" uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf" -version = "0.1.3" +version = "1.7.0" +weakdeps = ["Enzyme", "EnzymeCore", "Mooncake"] + + [deps.FunctionWrappersWrappers.extensions] + FunctionWrappersWrappersEnzymeExt = ["Enzyme", "EnzymeCore"] + FunctionWrappersWrappersMooncakeExt = "Mooncake" [[deps.Functors]] deps = ["Compat", "ConstructionBase", "LinearAlgebra", "Random"] @@ -1118,15 +1128,15 @@ version = "1.11.0" [[deps.GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] -git-tree-sha1 = "b7bfd56fa66616138dfe5237da4dc13bbd83c67f" +git-tree-sha1 = "9e0fb9e54594c47f278d75063980e43066e26e20" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.4.1+0" +version = "3.4.1+1" [[deps.GLM]] deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "StatsModels"] -git-tree-sha1 = "3bcb30438ee1655e3b9c42d97544de7addc9c589" +git-tree-sha1 = "b715b0156c01f27c94595290ec6abdab98ae7427" uuid = "38e38edf-8417-5370-95a0-9cbb8c7f171a" -version = "1.9.3" +version = "1.9.4" [[deps.GPUArraysCore]] deps = ["Adapt"] @@ -1301,9 +1311,9 @@ version = "0.16.2" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.IntervalSets]] -git-tree-sha1 = "d966f85b3b7a8e49d034d27a189e9a4874b4391a" +git-tree-sha1 = "79d6bd28c8d9bccc2229784f1bd637689b256377" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.13" +version = "0.7.14" weakdeps = ["Random", "RecipesBase", "Statistics"] [deps.IntervalSets.extensions] @@ -1355,9 +1365,9 @@ version = "1.7.1" [[deps.JSON]] deps = ["Dates", "Logging", "Parsers", "PrecompileTools", "StructUtils", "UUIDs", "Unicode"] -git-tree-sha1 = "b3ad4a0255688dcb895a52fafbaae3023b588a90" +git-tree-sha1 = "67c6f1f085cb2671c93fe34244c9cccde30f7a26" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "1.4.0" +version = "1.5.0" [deps.JSON.extensions] JSONArrowExt = ["ArrowTypes"] @@ -1373,9 +1383,9 @@ version = "0.2.1" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "b6893345fd6658c8e475d40155789f4860ac3b21" +git-tree-sha1 = "c0c9b76f3520863909825cbecdef58cd63de705a" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.1.4+0" +version = "3.1.5+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1421,9 +1431,9 @@ version = "3.100.3+0" [[deps.LERC_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "aaafe88dccbd957a8d82f7d05be9b69172e0cee3" +git-tree-sha1 = "17b94ecafcfa45e8360a4fc9ca6b583b049e4e37" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "4.0.1+0" +version = "4.1.0+0" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] @@ -1449,12 +1459,6 @@ git-tree-sha1 = "eb62a3deb62fc6d8822c0c4bef73e4412419c5d8" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" version = "18.1.8+0" -[[deps.LZO_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1c602b1127f4751facb671441ca72715cc95938a" -uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.3+0" - [[deps.LaTeXStrings]] git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" @@ -1556,9 +1560,9 @@ version = "1.18.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "97bbca976196f2a1eb9607131cb108c69ec3f8a6" +git-tree-sha1 = "cc3ad4faf30015a3e8094c9b5b7f19e85bdf2386" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.41.3+0" +version = "2.42.0+0" [[deps.Libtask]] deps = ["MistyClosures", "Test"] @@ -1574,15 +1578,15 @@ version = "4.7.2+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "d0205286d9eceadc518742860bf23f703779a3d6" +git-tree-sha1 = "d620582b1f0cbe2c72dd1d5bd195a9ce73370ab1" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.41.3+0" +version = "2.42.0+0" [[deps.LineSearch]] deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] -git-tree-sha1 = "9f7253c0574b4b585c8909232adb890930da980a" +git-tree-sha1 = "25454bc65c3eec4656cbe201c3d9336af49178c7" uuid = "87fe0de2-c867-4266-b59a-2f0a94fc965b" -version = "0.1.6" +version = "0.1.8" weakdeps = ["LineSearches"] [deps.LineSearch.extensions] @@ -1590,9 +1594,9 @@ weakdeps = ["LineSearches"] [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Printf"] -git-tree-sha1 = "738bdcacfef25b3a9e4a39c28613717a6b23751e" +git-tree-sha1 = "a666999510c794fe1d9dfa629ef33366f11103aa" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.6.0" +version = "7.6.1" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -1601,9 +1605,9 @@ version = "1.11.0" [[deps.LinearSolve]] deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "OpenBLAS_jll", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLLogging", "SciMLOperators", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "1ddad5f2b0717f71f1588b3519e2f7d80fc2ce65" +git-tree-sha1 = "42b5cb44317e89ef75dd841c9c8eba9045bf9ff0" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "3.69.0" +version = "3.75.0" [deps.LinearSolve.extensions] LinearSolveAMDGPUExt = "AMDGPU" @@ -1616,6 +1620,7 @@ version = "3.69.0" LinearSolveCUSOLVERRFExt = ["CUSOLVERRF", "SparseArrays"] LinearSolveChainRulesCoreExt = "ChainRulesCore" LinearSolveCliqueTreesExt = ["CliqueTrees", "SparseArrays"] + LinearSolveElementalExt = "Elemental" LinearSolveEnzymeExt = ["EnzymeCore", "SparseArrays"] LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveFastLapackInterfaceExt = "FastLapackInterface" @@ -1627,7 +1632,9 @@ version = "3.69.0" LinearSolveKrylovKitExt = "KrylovKit" LinearSolveMetalExt = "Metal" LinearSolveMooncakeExt = "Mooncake" + LinearSolvePETScCSRExt = ["PETSc", "SparseArrays", "SparseMatricesCSR"] LinearSolvePETScExt = ["PETSc", "SparseArrays"] + LinearSolvePETScMPIExt = ["PETSc", "PartitionedArrays", "SparseArrays", "SparseMatricesCSR"] LinearSolveParUExt = ["ParU_jll", "SparseArrays"] LinearSolvePardisoExt = ["Pardiso", "SparseArrays"] LinearSolveRecursiveFactorizationExt = "RecursiveFactorization" @@ -1644,6 +1651,7 @@ version = "3.69.0" CUSOLVERRF = "a8cc9031-bad2-4722-94f5-40deabb4245c" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8" + Elemental = "902c3f28-d1ec-5e7e-8399-a24c3845ee38" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641" @@ -1659,8 +1667,10 @@ version = "3.69.0" PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0" ParU_jll = "9e0b026c-e8ce-559c-a2c4-6a3d5c955bc9" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" + PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9" RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1" Sparspak = "e56a9233-b9d6-4f03-8d0f-1825330902ac" blis_jll = "6136c539-28a5-5bf0-87cc-b183200dce32" @@ -1722,9 +1732,9 @@ version = "1.2.0" [[deps.Lux]] deps = ["ADTypes", "Adapt", "ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DiffResults", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "PrecompileTools", "Preferences", "Random", "ReactantCore", "Reexport", "SciMLPublic", "Setfield", "Static", "StaticArraysCore", "Statistics", "UUIDs", "WeightInitializers"] -git-tree-sha1 = "334de475ff414c8eb67f88f57f7b02d40cd8f320" +git-tree-sha1 = "b7654d9b1144792d7fa165add2e07434329e3193" uuid = "b2108857-7c20-44ae-9111-449ecde12c47" -version = "1.31.3" +version = "1.31.4" [deps.Lux.extensions] ComponentArraysExt = "ComponentArrays" @@ -1792,9 +1802,9 @@ version = "1.5.3" [[deps.LuxLib]] deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "DispatchDoctor", "EnzymeCore", "FastClosures", "Functors", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Preferences", "Random", "Reexport", "SciMLPublic", "Static", "StaticArraysCore", "Statistics", "UUIDs"] -git-tree-sha1 = "77f3257b18e9fedd39b7b7990f0d3a0800a834ae" +git-tree-sha1 = "6a6453d556f7bc3870d797657636b1ad5f45fd27" uuid = "82251201-b29d-42c6-8e01-566dec8acb11" -version = "1.15.6" +version = "1.15.9" [deps.LuxLib.extensions] AppleAccelerateExt = "AppleAccelerate" @@ -1859,9 +1869,9 @@ version = "1.0.0" [[deps.MLDataDevices]] deps = ["Adapt", "Functors", "Preferences", "Random", "SciMLPublic"] -git-tree-sha1 = "39a69ca451c3e78b9a6a2e42ef894fdf7505e629" +git-tree-sha1 = "2dfe3b4b96c6ecbea7c798dfbe96d493fd7a1848" uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" -version = "1.17.5" +version = "1.17.8" [deps.MLDataDevices.extensions] AMDGPUExt = "AMDGPU" @@ -2084,9 +2094,9 @@ version = "2.10.0+0" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "ScopedValues", "Statistics"] -git-tree-sha1 = "6dc9ffc3a9931e6b988f913b49630d0fb986d0a8" +git-tree-sha1 = "78cd28dbd5f03f99ccaba45c987107adcb61c115" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.33" +version = "0.9.34" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -2136,10 +2146,10 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SciMLLogging", "SimpleNonlinearSolve", "StaticArraysCore", "SymbolicIndexingInterface"] -git-tree-sha1 = "d27bcf0cebf8786edcc2eaa4455c959e680334e7" +deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SciMLLogging", "Setfield", "SimpleNonlinearSolve", "StaticArraysCore", "SymbolicIndexingInterface"] +git-tree-sha1 = "a2db21951cd1cd46a3ef8ba4bbfc84ddc9a5b3fb" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "4.16.0" +version = "4.18.0" [deps.NonlinearSolve.extensions] NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" @@ -2169,10 +2179,10 @@ version = "4.16.0" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" [[deps.NonlinearSolveBase]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "LogExpFunctions", "Markdown", "MaybeInplace", "PreallocationTools", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLLogging", "SciMLOperators", "SciMLStructures", "Setfield", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "a89529d343dbb09670a24df090787dc3475fba5d" +deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "LogExpFunctions", "Markdown", "MaybeInplace", "PreallocationTools", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLLogging", "SciMLOperators", "SciMLStructures", "Setfield", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "a19a5df29ef2b197499fc631fa1a59385ae15262" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "2.19.0" +version = "2.25.0" [deps.NonlinearSolveBase.extensions] NonlinearSolveBaseBandedMatricesExt = "BandedMatrices" @@ -2202,15 +2212,15 @@ version = "2.19.0" [[deps.NonlinearSolveFirstOrder]] deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "eea7cbe389b168c77df7ff779fb7277019c685c8" +git-tree-sha1 = "ce68820a4f421fb5bee7ec4dcf875aff33886bfb" uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" -version = "2.0.0" +version = "2.1.1" [[deps.NonlinearSolveQuasiNewton]] deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] -git-tree-sha1 = "ade27e8e9566b6cec63ee62f6a6650a11cf9a2eb" +git-tree-sha1 = "538432ca1aea8bf63db02929bf870501f8a7c64c" uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" -version = "1.12.0" +version = "1.13.1" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveQuasiNewton.extensions] @@ -2218,9 +2228,9 @@ weakdeps = ["ForwardDiff"] [[deps.NonlinearSolveSpectralMethods]] deps = ["CommonSolve", "ConcreteStructs", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "eafd027b5cd768f19bb5de76c0e908a9065ddd36" +git-tree-sha1 = "a3781e12becdf0ce5520bd97ec617e879bf4e9f2" uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" -version = "1.6.0" +version = "1.7.1" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveSpectralMethods.extensions] @@ -2270,9 +2280,9 @@ version = "1.6.1" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c9cbeda6aceffc52d8a0017e71db27c7a7c0beaf" +git-tree-sha1 = "2ac022577e5eac7da040de17776d51bb770cd895" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.5.5+0" +version = "3.5.6+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -2369,27 +2379,27 @@ version = "1.8.1" [[deps.OrdinaryDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SparseArrays", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "621790374f3945db30f871313c131e5b9c956f63" +git-tree-sha1 = "47271adac597af08263b6ea2669e93040b45c4d0" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.109.0" +version = "6.111.0" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] -git-tree-sha1 = "79f756d4a593a99ab47c8a8ee72061e7d60cd9c0" +git-tree-sha1 = "2e44acb684dfcdc2e41851a988733e30b28a8478" uuid = "89bda076-bce5-4f1c-845f-551c83cdda9a" -version = "1.10.0" +version = "1.11.0" [[deps.OrdinaryDiffEqBDF]] -deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "4758206b7578c8f884915ad589e6bd18548e16f3" +deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] +git-tree-sha1 = "d7f69947e070a6a89aaf583e8aa2fada199fc292" uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" -version = "1.23.0" +version = "1.26.0" [[deps.OrdinaryDiffEqCore]] -deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ConcreteStructs", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLLogging", "SciMLOperators", "SciMLStructures", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "629c0e6984889759f4efd21e43c36307f5cff85a" +deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ConcreteStructs", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLLogging", "SciMLOperators", "SciMLStructures", "Static", "SymbolicIndexingInterface", "TruncatedStacktraces"] +git-tree-sha1 = "2b55a12e68d2e9eb9f06c00cde116356c2d3823d" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "3.24.0" +version = "3.33.0" weakdeps = ["Mooncake", "SparseArrays"] [deps.OrdinaryDiffEqCore.extensions] @@ -2403,10 +2413,10 @@ uuid = "50262376-6c5a-4cf5-baba-aaf4f84d72d7" version = "1.14.0" [[deps.OrdinaryDiffEqDifferentiation]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"] -git-tree-sha1 = "50c57c04c8058008bf4e4e8bb345925ec0ffef54" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseMatrixColorings", "StaticArraysCore"] +git-tree-sha1 = "f3976b6baeb64051f41ed461a1933b7501a4f38e" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "2.3.0" +version = "2.9.0" weakdeps = ["SparseArrays"] [deps.OrdinaryDiffEqDifferentiation.extensions] @@ -2414,153 +2424,153 @@ weakdeps = ["SparseArrays"] [[deps.OrdinaryDiffEqExplicitRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] -git-tree-sha1 = "0b70d2d78d21b3c9fb200c7921750ca863302204" +git-tree-sha1 = "54346c3d7a9932ab11743a99afed8a3ff0a65fea" uuid = "9286f039-9fbf-40e8-bf65-aa933bdc4db0" -version = "1.10.0" +version = "1.12.0" [[deps.OrdinaryDiffEqExponentialRK]] deps = ["ADTypes", "DiffEqBase", "ExponentialUtilities", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "RecursiveArrayTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "71acd5838f981f6a53b1db3fab73ed9de1234659" +git-tree-sha1 = "32fb54c8000c82fd32c55f7bf52f4651a3bd0e61" uuid = "e0540318-69ee-4070-8777-9e2de6de23de" -version = "1.14.0" +version = "1.15.0" [[deps.OrdinaryDiffEqExtrapolation]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "0784508fa880dde8ffead9aa3a927d97ff005c24" +git-tree-sha1 = "57bf89f5b144f6e5af1146fb7aee1544c6b76950" uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4" -version = "1.17.0" +version = "1.18.0" [[deps.OrdinaryDiffEqFIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastGaussQuadrature", "FastPower", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators"] -git-tree-sha1 = "004e41228d375cb549ae7835e1bb80e24acab13d" +git-tree-sha1 = "3339f3a26974a37666c74b95bdb54aefc63b9a56" uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125" -version = "1.24.0" +version = "1.26.0" [[deps.OrdinaryDiffEqFeagin]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", 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"SciMLBase", "StaticArrays"] -git-tree-sha1 = "0ad9fef7b61715f706d5a04e039273c4242bbadf" +deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqStabilizedRK", "RecursiveArrayTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "226226d334fe295885df6ecb2d110c22ead79983" uuid = "e3e12d00-db14-5390-b879-ac3dd2ef6296" -version = "1.12.0" +version = "1.14.0" [[deps.OrdinaryDiffEqStabilizedRK]] -deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays"] -git-tree-sha1 = "6382a6caa2cc4488f4b9654ca5f26ad0130bec7b" +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "764e11fb6a26ee8f2d2d10778d531fd708f35d28" uuid = "358294b1-0aab-51c3-aafe-ad5ab194a2ad" -version = "1.9.0" +version = "1.11.1" [[deps.OrdinaryDiffEqSymplecticRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "7276967b405c048adb52a090f1c5b1df88501631" +git-tree-sha1 = "b18a4e7973e73e84cfd79222e2389565b323b588" uuid = "fa646aed-7ef9-47eb-84c4-9443fc8cbfa8" -version = "1.12.0" +version = "1.13.0" [[deps.OrdinaryDiffEqTsit5]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "6e6173f4d0db8b8136d5fccdcdb7e8abe800a352" +git-tree-sha1 = "6bd89fce8a0b198ac9fe98dc80362a92a2a13ae5" uuid = "b1df2697-797e-41e3-8120-5422d3b24e4a" -version = "1.10.0" +version = "1.12.0" [[deps.OrdinaryDiffEqVerner]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "3bcd3987d1c54d22bcccc1dfdb60b7481746c122" +git-tree-sha1 = "58dc7756825ca46e5a601a5aeba7d26a071d373a" uuid = "79d7bb75-1356-48c1-b8c0-6832512096c2" -version = "1.12.0" +version = "1.14.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -2577,17 +2587,11 @@ weakdeps = ["StatsBase"] [deps.PDMats.extensions] StatsBaseExt = "StatsBase" -[[deps.PackageExtensionCompat]] -git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" -uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" -version = "1.0.2" -weakdeps = ["Requires", "TOML"] - [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "0662b083e11420952f2e62e17eddae7fc07d5997" +git-tree-sha1 = "58e5ed5e386e156bd93e86b305ebd21ac63d2d04" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.57.0+0" +version = "1.57.1+0" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] @@ -2773,9 +2777,9 @@ version = "6.10.2+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "9da16da70037ba9d701192e27befedefb91ec284" +git-tree-sha1 = "5e8e8b0ab68215d7a2b14b9921a946fee794749e" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.11.2" +version = "2.11.3" weakdeps = ["Enzyme"] [deps.QuadGK.extensions] @@ -2856,12 +2860,13 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "LinearAlgebra", "PrecompileTools", "RecipesBase", "StaticArraysCore", "SymbolicIndexingInterface"] -git-tree-sha1 = "76a9c4d3f7b256dd34074e714ffe0ced8d3d21de" +git-tree-sha1 = "d0282d612f22dcad7b81cf487b746e63aa2a6709" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.50.0" +version = "3.54.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" + RecursiveArrayToolsFastBroadcastPolyesterExt = ["FastBroadcast", "Polyester"] RecursiveArrayToolsForwardDiffExt = "ForwardDiff" RecursiveArrayToolsKernelAbstractionsExt = "KernelAbstractions" RecursiveArrayToolsMeasurementsExt = "Measurements" @@ -2880,6 +2885,7 @@ version = "3.50.0" KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" @@ -2931,9 +2937,9 @@ version = "0.5.1+0" [[deps.Roots]] deps = ["Accessors", "CommonSolve", "Printf"] -git-tree-sha1 = "b2f70f34eb9973572d55c332933c6a04c911f549" +git-tree-sha1 = "3eff988b9bd09543783e2e051b0a1eef11f65c2d" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.2.14" +version = "2.3.0" [deps.Roots.extensions] RootsChainRulesCoreExt = "ChainRulesCore" @@ -2953,9 +2959,9 @@ version = "2.2.14" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "7257165d5477fd1025f7cb656019dcb6b0512c38" +git-tree-sha1 = "cfcdc949c4660544ab0fdeed169561cb22f835f4" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.17" +version = "0.5.18" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -2974,9 +2980,9 @@ 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 = "bdbc7c751d36fdb104d437361950d884d489af85" +git-tree-sha1 = "4ab0641a10918b1a2d8f59c22ff641fc478332e3" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.153.1" +version = "2.155.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3019,9 +3025,9 @@ version = "2.153.1" [[deps.SciMLJacobianOperators]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] -git-tree-sha1 = "e96d5e96debf7f80a50d0b976a13dea556ccfd3a" +git-tree-sha1 = "7156a5b51cba1bea33a82a036939ead4131f92bc" uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" -version = "0.1.12" +version = "0.1.13" [[deps.SciMLLogging]] deps = ["Logging", "LoggingExtras", "Preferences"] @@ -3035,9 +3041,9 @@ weakdeps = ["Tracy"] [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra"] -git-tree-sha1 = "794c760e6aafe9f40dcd7dd30526ea33f0adc8b7" +git-tree-sha1 = "0e34162268883db01c04f988895a80d0659071bb" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "1.15.1" +version = "1.17.0" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -3051,9 +3057,9 @@ version = "1.0.1" [[deps.SciMLSensitivity]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "ConstructionBase", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "Enzyme", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEqCore", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLJacobianOperators", "SciMLLogging", "SciMLStructures", "SparseArrays", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"] -git-tree-sha1 = "d94f224a2e7d5a7a5cc6a0abb64323fcf8076fb1" +git-tree-sha1 = "ebf21e8d9dee914bffee3ae846187be197dcec15" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.100.0" +version = "7.103.0" [deps.SciMLSensitivity.extensions] SciMLSensitivityMooncakeExt = "Mooncake" @@ -3131,9 +3137,9 @@ version = "1.2.0" [[deps.SimpleNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "744c3f0fb186ad28376199c1e72ca39d0c614b5d" +git-tree-sha1 = "d688de789b7e643326caf9a1051376dadbcd8873" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "2.11.0" +version = "2.11.1" weakdeps = ["ChainRulesCore", "ReverseDiff", "Tracker"] [deps.SimpleNonlinearSolve.extensions] @@ -3184,22 +3190,25 @@ version = "0.1.2" [[deps.SparseMatrixColorings]] deps = ["ADTypes", "DocStringExtensions", "LinearAlgebra", "PrecompileTools", "Random", "SparseArrays"] -git-tree-sha1 = "1c1be8c6fdfaf9b6c9e156c509e672953b8e6af7" +git-tree-sha1 = "f63d76c7b7c329cf11badd564fd8ba877b09c3fe" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.4.26" +version = "0.4.27" [deps.SparseMatrixColorings.extensions] - SparseMatrixColoringsCUDAExt = "CUDA" + SparseMatrixColoringsCUDAExt = ["CUDA", "cuSPARSE"] SparseMatrixColoringsCliqueTreesExt = "CliqueTrees" SparseMatrixColoringsColorsExt = "Colors" + SparseMatrixColoringsGPUArraysExt = "GPUArrays" SparseMatrixColoringsJuMPExt = ["JuMP", "MathOptInterface"] [deps.SparseMatrixColorings.weakdeps] CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8" Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" + GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" JuMP = "4076af6c-e467-56ae-b986-b466b2749572" MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" + cuSPARSE = "b26da814-b3bc-49ef-b0ee-c816305aa060" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] @@ -3315,38 +3324,41 @@ version = "0.5.8" [[deps.Strided]] deps = ["LinearAlgebra", "StridedViews", "TupleTools"] -git-tree-sha1 = "0fa01489ecc57749f2f7dcbc2918e46a164af8b2" +git-tree-sha1 = "b68ca48c87685dba1e121d846416309158da116b" uuid = "5e0ebb24-38b0-5f93-81fe-25c709ecae67" -version = "2.3.4" +version = "2.4.0" [deps.Strided.extensions] StridedAMDGPUExt = "AMDGPU" - StridedCUDAExt = "CUDA" + StridedCUDACoreExt = "CUDACore" StridedGPUArraysExt = "GPUArrays" StridedJLArraysExt = "JLArrays" [deps.Strided.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" - CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDACore = "bd0ed864-bdfe-4181-a5ed-ce625a5fdea2" GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" JLArrays = "27aeb0d3-9eb9-45fb-866b-73c2ecf80fcb" [[deps.StridedViews]] -deps = ["LinearAlgebra", "PackageExtensionCompat"] -git-tree-sha1 = "b1b42ff0249fbb02df163633adc612b943c6ac74" +deps = ["LinearAlgebra"] +git-tree-sha1 = "0481af1fe93b9141cb5341dfc9e524ae95421a41" uuid = "4db3bf67-4bd7-4b4e-b153-31dc3fb37143" -version = "0.4.6" +version = "0.5.1" [deps.StridedViews.extensions] StridedViewsAMDGPUExt = "AMDGPU" - StridedViewsCUDAExt = "CUDA" + StridedViewsAdaptExt = "Adapt" + StridedViewsCUDACoreExt = "CUDACore" StridedViewsJLArraysExt = "JLArrays" StridedViewsPtrArraysExt = "PtrArrays" [deps.StridedViews.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" - CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" + CUDACore = "bd0ed864-bdfe-4181-a5ed-ce625a5fdea2" JLArrays = "27aeb0d3-9eb9-45fb-866b-73c2ecf80fcb" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" PtrArrays = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" [[deps.StringManipulation]] @@ -3376,9 +3388,9 @@ version = "0.3.1" [[deps.StructUtils]] deps = ["Dates", "UUIDs"] -git-tree-sha1 = "fa95b3b097bcef5845c142ea2e085f1b2591e92c" +git-tree-sha1 = "aab80fbf866600f3299dd7f6656d80e7be177cfe" uuid = "ec057cc2-7a8d-4b58-b3b3-92acb9f63b42" -version = "2.7.1" +version = "2.7.2" [deps.StructUtils.extensions] StructUtilsMeasurementsExt = ["Measurements"] @@ -3566,9 +3578,9 @@ 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 = "d2acfbc45409aca79f673ade98ecfbae2a7d3c79" +git-tree-sha1 = "c0edb00eb840eb24b13e639796d1d7045a842efa" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.43.3" +version = "0.44.0" weakdeps = ["DynamicHMC"] [deps.Turing.extensions] @@ -3628,9 +3640,9 @@ version = "1.4.2" [[deps.WeightInitializers]] deps = ["ConcreteStructs", "GPUArraysCore", "LinearAlgebra", "Random", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "d79b71da9e7be904db615bdb99187d30753822a4" +git-tree-sha1 = "2af44c69f5c37b7b1d14e262347a24ba349052d6" uuid = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d" -version = "1.3.1" +version = "1.3.3" [deps.WeightInitializers.extensions] AMDGPUExt = "AMDGPU" @@ -3665,9 +3677,9 @@ version = "1.6.1" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "9cce64c0fdd1960b597ba7ecda2950b5ed957438" +git-tree-sha1 = "b29c22e245d092b8b4e8d3c09ad7baa586d9f573" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.8.2+0" +version = "5.8.3+0" [[deps.Xorg_libICE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -3862,9 +3874,9 @@ version = "0.61.1+0" [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "371cc681c00a3ccc3fbc5c0fb91f58ba9bec1ecf" +git-tree-sha1 = "850b06095ee71f0135d644ffd8a52850699581ed" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.13.1+0" +version = "3.13.3+0" [[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] @@ -3909,9 +3921,9 @@ version = "1.28.1+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "e2a7072fc0cdd7949528c1455a3e5da4122e1153" +git-tree-sha1 = "e51150d5ab85cee6fc36726850f0e627ad2e4aba" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.56+0" +version = "1.6.58+0" [[deps.libva_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll", "Xorg_libXfixes_jll", "libdrm_jll"] diff --git a/Project.toml b/Project.toml index 790aa498a..1e52833bd 100644 --- a/Project.toml +++ b/Project.toml @@ -50,4 +50,4 @@ StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] -Turing = "0.43" +Turing = "0.44" diff --git a/_quarto.yml b/_quarto.yml index 998a63c57..9056a93ea 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -43,7 +43,7 @@ website: href: https://turinglang.org/team/ right: # Current version - - text: "v0.43" + - text: "v0.44" menu: - text: Changelog href: https://turinglang.org/docs/changelog.html From 68ba24b8971bdbdf6e2cf75b48b3f1fa6e06e697 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Wed, 22 Apr 2026 23:59:53 +0100 Subject: [PATCH 2/4] More bumps --- Manifest.toml | 18 +++---- tutorials/variational-inference/index.qmd | 60 +++++++++++++---------- 2 files changed, 42 insertions(+), 36 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 315352296..479ea9c71 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1436,10 +1436,10 @@ uuid = "88015f11-f218-50d7-93a8-a6af411a945d" version = "4.1.0+0" [[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] -git-tree-sha1 = "69e4739502b7ab5176117e97e1664ed181c35036" +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "PrecompileTools", "Preferences", "Printf", "Unicode"] +git-tree-sha1 = "bb3492cc442118d4b12242e7efd8618336caec47" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "9.4.6" +version = "9.5.0" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1449,9 +1449,9 @@ version = "9.4.6" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "8e76807afb59ebb833e9b131ebf1a8c006510f33" +git-tree-sha1 = "4a50a4ab3f83a75a451ffa5ba5ad3093b85e7943" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.38+0" +version = "0.0.40+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -3388,9 +3388,9 @@ version = "0.3.1" [[deps.StructUtils]] deps = ["Dates", "UUIDs"] -git-tree-sha1 = "aab80fbf866600f3299dd7f6656d80e7be177cfe" +git-tree-sha1 = "86f5831495301b2a1387476cb30f86af7ab99194" uuid = "ec057cc2-7a8d-4b58-b3b3-92acb9f63b42" -version = "2.7.2" +version = "2.8.0" [deps.StructUtils.extensions] StructUtilsMeasurementsExt = ["Measurements"] @@ -3578,9 +3578,9 @@ 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 = "c0edb00eb840eb24b13e639796d1d7045a842efa" +path = "/Users/pyong/ppl/lib" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.44.0" +version = "0.44.2" weakdeps = ["DynamicHMC"] [deps.Turing.extensions] diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd index 56f0b0951..c9a8b869b 100755 --- a/tutorials/variational-inference/index.qmd +++ b/tutorials/variational-inference/index.qmd @@ -22,8 +22,8 @@ Approximating the posterior associated with `model` via VI is as simple as ```julia m = model(data...) # instantiate model on the data -q_init = q_fullrank_gaussian(m) # initial variational approximation -vi(m, q_init, 1000) # perform VI with the default algorithm on `m` for 1000 iterations +q_init = q_fullrank_gaussian # how to generate initial variational approximation +result = vi(m, q_init, 1000) # perform VI with the default algorithm on `m` for 1000 iterations ``` Thus, it's no more work than standard MCMC sampling in Turing. @@ -145,14 +145,8 @@ m = linear_regression(train, train_label, n_obs, n_vars) ## Basic Usage To run VI, we must first set a *variational family*. For instance, the most commonly used family is the mean-field Gaussian family. -For this, Turing provides functions that automatically construct the initialisation corresponding to the model `m`: - -```{julia} -q_init = q_meanfield_gaussian(m) -``` - -`vi` will automatically recognise the variational family through the type of `q_init`. -Here is a detailed documentation for the constructor: +For this, Turing provides functions that automatically construct the initialisation corresponding to the model `m`. +For example, for the mean-field Gaussian family, we can use: ```{julia} @doc(Variational.q_meanfield_gaussian) @@ -164,7 +158,7 @@ Let's run VI with the default setting: ```{julia} n_iters = 1000 -q_avg, info, state = vi(m, q_init, n_iters; show_progress=false); +result_avg = vi(m, q_meanfield_gaussian, n_iters; show_progress=false) ``` The default setting uses the `AdvancedVI.RepGradELBO` objective, which corresponds to a variant of what is known as *automatic differentiation VI*[^KTRGB2017] or *stochastic gradient VI*[^TL2014] or *black-box VI*[^RGB2014] with the reparameterization gradient[^KW2014][^RMW2014][^TL2014]. @@ -178,14 +172,26 @@ First, here is the full documentation for `vi`: ``` ## Values Returned by `vi` -The main output of the algorithm is `q_avg`, the average of the parameters generated by the optimisation algorithm. -For computing `q_avg`, the default setting uses what is known as polynomial averaging[^SZ2013]. -Usually, `q_avg` will perform better than the last-iterate `q_last`, which cana be obtained by disabling averaging: + +`vi` returns a single object, which is a `VIResult`. + +The main output of the algorithm is the `q` field, which is the variational approximation itself. +This represents the average of the parameters generated by the optimisation algorithm, and is computed using what is known as polynomial averaging[^SZ2013]. + +```{julia} +result_avg.q +``` + +:::{.callout-note} +## Averaging + +Usually, averaging will lead to better performance than simply using the last iterate. +If you want the last iterate, you can disable averaging in the algorithm: ```{julia} -q_last, _, _ = vi( +result_last = vi( m, - q_init, + q_meanfield_gaussian, n_iters; show_progress=false, algorithm=KLMinRepGradDescent( @@ -194,23 +200,26 @@ q_last, _, _ = vi( averager=AdvancedVI.NoAveraging() ), ); +result_last.q ``` -For instance, we can compare the ELBO of the two: +To see the difference, we can compare the ELBO of the two: ```{julia} @info("Objective of q_avg and q_last", - ELBO_q_avg = estimate_objective(AdvancedVI.RepGradELBO(32), q_avg, LogDensityFunction(m)), - ELBO_q_last = estimate_objective(AdvancedVI.RepGradELBO(32), q_last, LogDensityFunction(m)) + ELBO_q_avg = estimate_objective(AdvancedVI.RepGradELBO(32), result_avg.q, result_avg.ldf), + ELBO_q_last = estimate_objective(AdvancedVI.RepGradELBO(32), result_last.q, result_last.ldf) ) ``` We can see that `ELBO_q_avg` is slightly more optimal. +::: + -Now, `info` contains information generated during optimisation that could be useful for diagnostics. +`result.info` also contains information generated during optimisation that could be useful for diagnostics. For the default setting, which is `RepGradELBO`, it contains the ELBO estimated at each step, which can be plotted as follows: ```{julia} -Plots.plot([i.elbo for i in info], xlabel="Iterations", ylabel="ELBO", label="info") +Plots.plot([i.elbo for i in result_avg.info], xlabel="Iterations", ylabel="ELBO", label="info") ``` Since the ELBO is estimated by a small number of samples, it appears noisy. @@ -222,14 +231,11 @@ To inspect the progress of optimisation in more detail, one can define a custom For example, the following callback function estimates the ELBO on `q_avg` every 10 steps with a larger number of samples: ```{julia} -using DynamicPPL: DynamicPPL -linked_vi = DynamicPPL.link!!(DynamicPPL.VarInfo(m), m); - -function callback(; iteration, averaged_params, restructure, kwargs...) +function callback(; iteration, averaged_params, restructure, state, kwargs...) if mod(iteration, 10) == 1 q_avg = restructure(averaged_params) obj = AdvancedVI.RepGradELBO(128) # 128 samples for ELBO estimation - elbo_avg = -estimate_objective(obj, q_avg, LogDensityFunction(m, DynamicPPL.getlogjoint_internal, linked_vi)) + elbo_avg = -estimate_objective(obj, q_avg, state.prob) (elbo_avg = elbo_avg,) else nothing @@ -242,7 +248,7 @@ The `NamedTuple` returned by `callback` will be appended to the corresponding en The custom callback can be supplied to `vi` as a keyword argument: ```{julia} -q_mf, info_mf, _ = vi(m, q_init, n_iters; show_progress=false, callback=callback); +result_with_callback = vi(m, q_meanfield_gaussian, n_iters; show_progress=false, callback=callback); ``` Let's plot the result: From 1efba240af9c445c5a98377abf40d8eeb1d9cd7b Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Thu, 23 Apr 2026 00:12:42 +0100 Subject: [PATCH 3/4] Fix VI doc --- Manifest.toml | 2 +- tutorials/variational-inference/index.qmd | 65 ++++++++++------------- 2 files changed, 28 insertions(+), 39 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 479ea9c71..d14bd1562 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -3578,7 +3578,7 @@ 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"] -path = "/Users/pyong/ppl/lib" +git-tree-sha1 = "5954cbf6eff301ef172899b78da1ed2beb994976" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" version = "0.44.2" weakdeps = ["DynamicHMC"] diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd index c9a8b869b..d56e60e68 100755 --- a/tutorials/variational-inference/index.qmd +++ b/tutorials/variational-inference/index.qmd @@ -248,15 +248,16 @@ The `NamedTuple` returned by `callback` will be appended to the corresponding en The custom callback can be supplied to `vi` as a keyword argument: ```{julia} -result_with_callback = vi(m, q_meanfield_gaussian, n_iters; show_progress=false, callback=callback); +result_mf = vi(m, q_meanfield_gaussian, n_iters; show_progress=false, callback=callback); ``` Let's plot the result: ```{julia} +info_mf = result_mf.info iters = 1:10:length(info_mf) elbo_mf = [i.elbo_avg for i in info_mf[iters]] -Plots.plot([i.elbo for i in info], xlabel="Iterations", ylabel="ELBO", label="info", linewidth=0.4) +Plots.plot([i.elbo for i in info_mf], xlabel="Iterations", ylabel="ELBO", label="info", linewidth=0.4) Plots.plot!(iters, elbo_mf, xlabel="Iterations", ylabel="ELBO", label="callback", ylims=(-200,Inf), linewidth=2) ``` @@ -278,8 +279,8 @@ Since `AdvancedVI` does not implement a proximal operator for `Optimisers.Adam`, ```{julia} using Optimisers -_, info_adam, _ = vi( - m, q_init, n_iters; +result = vi( + m, q_meanfield_gaussian, n_iters; show_progress=false, callback=callback, algorithm=KLMinRepGradDescent(AutoForwardDiff(); optimizer=Optimisers.Adam(3e-3), operator=ClipScale()) @@ -287,7 +288,8 @@ _, info_adam, _ = vi( ``` ```{julia} -iters = 1:10:length(info_mf) +info_adam = result.info +iters = 1:10:length(info_adam) elbo_adam = [i.elbo_avg for i in info_adam[iters]] Plots.plot(iters, elbo_mf, xlabel="Iterations", ylabel="ELBO", label="DoWG") Plots.plot!(iters, elbo_adam, xlabel="Iterations", ylabel="ELBO", label="Adam") @@ -304,10 +306,6 @@ So far, we have only used the mean-field Gaussian family. This, however, approximates the posterior covariance with a diagonal matrix. To model the full covariance matrix, we can use the *full-rank* Gaussian family[^TL2014][^KTRGB2017]: -```{julia} -q_init_fr = q_fullrank_gaussian(m); -``` - ```{julia} @doc(Variational.q_fullrank_gaussian) ``` @@ -318,11 +316,11 @@ This term, however, traditionally comes from the fact that full-rank families us In contrast to the mean-field family, the full-rank family will often result in more computation per optimisation step and slower convergence, especially in high dimensions: ```{julia} -q_fr, info_fr, state_fr = vi(m, q_init_fr, n_iters; show_progress=false, callback) +result_fr = vi(m, q_fullrank_gaussian, n_iters; show_progress=false, callback) Plots.plot(elbo_mf, xlabel="Iterations", ylabel="ELBO", label="Mean-Field", ylims=(-200, Inf)) -elbo_fr = [i.elbo_avg for i in info_fr[iters]] +elbo_fr = [i.elbo_avg for i in result_fr.info[iters]] Plots.plot!(elbo_fr, xlabel="Iterations", ylabel="ELBO", label="Full-Rank", ylims=(-200, Inf)) ``` @@ -331,45 +329,39 @@ Due to the relationship between the ELBO and the Kullback–Leibler divergence, This trade-off between statistical accuracy and optimisation speed is often referred to as the *statistical-computational trade-off*. The fact that we can control this trade-off through the choice of variational family is a strength, rather than a limitation, of variational inference. -We can also visualise the covariance matrix. - -```{julia} -heatmap(cov(rand(q_fr, 100_000), dims=2)) -``` - ## Obtaining Summary Statistics Let's inspect the resulting variational approximation in more detail and compare it against MCMC. -To obtain summary statistics from VI, we can draw samples from the resulting variational approximation: +To obtain summary statistics from VI, we can draw samples from the resulting variational approximation by calling `rand` on the `VIResult`. +Note that even though VI is often performed in transformed space, `rand(result)` will return samples in the original space of the parameters. ```{julia} -z = rand(q_fr, 100_000); +rand(result_fr) ``` -Now, we can, for example, look at expectations: +:::{.callout-note} +## Samples in transformed space -```{julia} -avg = vec(mean(z; dims=2)) -``` +If you want to obtain samples in transformed space, you can access `result_fr.ldf` to obtain the `LogDensityFunction` used for inference. +Calling `rand(result_fr.ldf)` will return a vector of samples in the transformed space. +However, note that these vectors are harder to interpret and work with. +::: -The vector has the same ordering as the parameters in the model: for example, in this case `σ²` will have index `1`, `intercept` has index `2` and `coefficients` has indices `3:12`. +Each sample is a [`DynamicPPL.VarNamedTuple`]({{< meta usage-varnamedtuple >}}), and a matrix of these can be converted into a `Chains` object. -:::{.callout-warning} -Note that the ordering of the parameters in the vector is an internal detail and is not guaranteed to be consistent across different versions of Turing, nor is it guaranteed to obey semantic versioning. -::: +```{julia} +z = rand(result_fr, 100_000, 1) +using AbstractMCMC: AbstractMCMC +vi_chain = AbstractMCMC.from_samples(MCMCChains.Chains, z) +``` -For further convenience, we can wrap the samples into a `Chains` object to summarise the results. +Now, we can, for example, look at expectations: ```{julia} -vnt = rand(m) -vns_and_values = Turing.DynamicPPL.varname_and_value_leaves(OrderedDict(pairs(vnt))) -varnames = map(first, vns_and_values) -vi_chain = Chains(reshape(z', (size(z,2), size(z,1), 1)), varnames) describe(vi_chain) ``` (Since we're drawing independent samples, we can simply ignore the ESS and Rhat metrics.) -Unfortunately, extracting `varnames` is a bit verbose at the moment, but hopefully will become simpler in the near future. Let's compare this against samples from `NUTS`: @@ -426,11 +418,8 @@ first(test_cut, 6) ```{julia} # Construct the Chains from the Variational Approximations -z_mf = rand(q_mf, 10_000); -z_fr = rand(q_fr, 10_000); - -vi_mf_chain = Chains(reshape(z_mf', (size(z_mf,2), size(z_mf,1), 1)), varnames); -vi_fr_chain = Chains(reshape(z_fr', (size(z_fr,2), size(z_fr,1), 1)), varnames); +vi_mf_chain = AbstractMCMC.from_samples(MCMCChains.Chains, rand(result_mf, 10_000, 1)) +vi_fr_chain = AbstractMCMC.from_samples(MCMCChains.Chains, rand(result_fr, 10_000, 1)) ``` ```{julia} From af4a430ff4beb215a533883c1a995be3baf81da8 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Thu, 23 Apr 2026 20:29:10 +0100 Subject: [PATCH 4/4] Pin SciMLBase to 2.154 --- Manifest.toml | 64 +++++++++++++++++++++++---------------------------- Project.toml | 3 +++ 2 files changed, 32 insertions(+), 35 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index d14bd1562..5a43e6837 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.11.9" manifest_format = "2.0" -project_hash = "febad8c4a969e1e9d534d8cb92e36f104e7c03a6" +project_hash = "75240642ac9209edc6934c6d8a26cefb5226af2f" [[deps.ADTypes]] git-tree-sha1 = "f7304359109c768cf32dc5fa2d371565bb63b68a" @@ -894,9 +894,9 @@ version = "0.1.11" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "27af30de8b5445644e8ffe3bcb0d72049c089cf1" +git-tree-sha1 = "9cb7fe11da6adb8683cbacf8aa9b5237941e3a75" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.7.3+0" +version = "2.7.5+0" [[deps.ExponentialUtilities]] deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] @@ -931,9 +931,9 @@ version = "0.4.5" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libva_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "66381d7059b5f3f6162f28831854008040a4e905" +git-tree-sha1 = "cac41ca6b2d399adfc95e51240566f8a60a80806" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "8.0.1+1" +version = "8.1.0+0" [[deps.FFTA]] deps = ["AbstractFFTs", "DocStringExtensions", "LinearAlgebra", "MuladdMacro", "Primes", "Random", "Reexport"] @@ -1106,9 +1106,9 @@ version = "1.1.3" [[deps.FunctionWrappersWrappers]] deps = ["FunctionWrappers", "PrecompileTools", "TruncatedStacktraces"] -git-tree-sha1 = "a100fa86d86ff062e6ea24d4a7427247a4eebf9b" +git-tree-sha1 = "c1b0c3a166a2a393257aa888787ca817532e14ce" uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf" -version = "1.7.0" +version = "1.8.0" weakdeps = ["Enzyme", "EnzymeCore", "Mooncake"] [deps.FunctionWrappersWrappers.extensions] @@ -1437,9 +1437,9 @@ version = "4.1.0+0" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "PrecompileTools", "Preferences", "Printf", "Unicode"] -git-tree-sha1 = "bb3492cc442118d4b12242e7efd8618336caec47" +git-tree-sha1 = "c0cec0c63687dda0115a51fe04d8f75902e181b3" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "9.5.0" +version = "9.6.0" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1449,9 +1449,9 @@ version = "9.5.0" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "4a50a4ab3f83a75a451ffa5ba5ad3093b85e7943" +git-tree-sha1 = "721fcd02aa06f8b2ed58d8db9914beab7a274b69" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.40+0" +version = "0.0.41+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2320,15 +2320,15 @@ version = "0.4.7" [[deps.Optimization]] deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "2c409c814c2d745620fdd55391a66ee514561146" +git-tree-sha1 = "5366b739224064a03399be1a21a18e4553631181" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "5.5.0" +version = "5.5.1" [[deps.OptimizationBase]] deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "PrecompileTools", "Reexport", "SciMLBase", "SciMLLogging", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings", "SymbolicIndexingInterface"] -git-tree-sha1 = "a3d7837832e515111c95a02df7dc55edbdf17d8a" +git-tree-sha1 = "642ea067d729f1f18795a434550b40de0a4fbbc8" uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb" -version = "5.1.0" +version = "5.1.1" [deps.OptimizationBase.extensions] OptimizationChainRulesCoreExt = "ChainRulesCore" @@ -2356,15 +2356,15 @@ version = "5.1.0" [[deps.OptimizationNLopt]] deps = ["NLopt", "OptimizationBase", "Random", "Reexport", "SciMLBase"] -git-tree-sha1 = "c266ab38c83b58dc5bb74f718f4b33d24d2dc0b6" +git-tree-sha1 = "2b4c6e38fa66bc17ffaea1ef8c5de3c13238c182" uuid = "4e6fcdb7-1186-4e1f-a706-475e75c168bb" -version = "0.3.10" +version = "0.3.11" [[deps.OptimizationOptimJL]] deps = ["Optim", "OptimizationBase", "Reexport", "SciMLBase", "SparseArrays"] -git-tree-sha1 = "eb89577770d4a956010745f182ebea9d8ea714f8" +git-tree-sha1 = "7ab4b611444e17652943e7f22b755bb7ed8ed1be" uuid = "36348300-93cb-4f02-beb5-3c3902f8871e" -version = "0.4.11" +version = "0.4.12" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2397,9 +2397,9 @@ version = "1.26.0" [[deps.OrdinaryDiffEqCore]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ConcreteStructs", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLLogging", "SciMLOperators", "SciMLStructures", "Static", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "2b55a12e68d2e9eb9f06c00cde116356c2d3823d" +git-tree-sha1 = "c0a22f012d3e98fd78afafe8e5152ace7a2276bc" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "3.33.0" +version = "3.33.1" weakdeps = ["Mooncake", "SparseArrays"] [deps.OrdinaryDiffEqCore.extensions] @@ -2526,9 +2526,9 @@ version = "1.12.0" [[deps.OrdinaryDiffEqRosenbrock]] deps = ["ADTypes", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] -git-tree-sha1 = "dc4c25c30e63b9ac50e332b030c6fa99f04034ab" +git-tree-sha1 = "3579d9272c286ffcceee794c5752e8cc7c3ae514" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.31.0" +version = "1.31.1" [[deps.OrdinaryDiffEqSDIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] @@ -2980,9 +2980,9 @@ 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 = "4ab0641a10918b1a2d8f59c22ff641fc478332e3" +git-tree-sha1 = "908c0bf271604d09393a21c142116ab26f66f67c" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.155.0" +version = "2.154.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3324,21 +3324,15 @@ version = "0.5.8" [[deps.Strided]] deps = ["LinearAlgebra", "StridedViews", "TupleTools"] -git-tree-sha1 = "b68ca48c87685dba1e121d846416309158da116b" +git-tree-sha1 = "b7476eb9926fd385063fdd8f880f8e831aac9490" uuid = "5e0ebb24-38b0-5f93-81fe-25c709ecae67" -version = "2.4.0" +version = "2.5.0" [deps.Strided.extensions] - StridedAMDGPUExt = "AMDGPU" - StridedCUDACoreExt = "CUDACore" StridedGPUArraysExt = "GPUArrays" - StridedJLArraysExt = "JLArrays" [deps.Strided.weakdeps] - AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" - CUDACore = "bd0ed864-bdfe-4181-a5ed-ce625a5fdea2" GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" - JLArrays = "27aeb0d3-9eb9-45fb-866b-73c2ecf80fcb" [[deps.StridedViews]] deps = ["LinearAlgebra"] @@ -3634,9 +3628,9 @@ version = "1.24.0+0" [[deps.WeakRefStrings]] deps = ["DataAPI", "InlineStrings", "Parsers"] -git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" +git-tree-sha1 = "0716e01c3b40413de5dedbc9c5c69f27cddfddfc" uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" -version = "1.4.2" +version = "1.4.3" [[deps.WeightInitializers]] deps = ["ConcreteStructs", "GPUArraysCore", "LinearAlgebra", "Random", "SpecialFunctions", "Statistics"] diff --git a/Project.toml b/Project.toml index 1e52833bd..02fe26958 100644 --- a/Project.toml +++ b/Project.toml @@ -41,6 +41,7 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" +SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1" StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" @@ -51,3 +52,5 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] Turing = "0.44" +# https://github.com/SciML/SciMLBase.jl/issues/1325 +SciMLBase = "=2.154.0"