From 5443a9537b83a5d85e381b9fc6a88628cf4987aa Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Wed, 13 Aug 2025 17:08:18 +0100 Subject: [PATCH 01/13] Update to Turing 0.40 --- Manifest.toml | 359 ++++++++++++++++++++++++++------------------------ Project.toml | 2 +- 2 files changed, 191 insertions(+), 170 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index c94baf232..2f8687805 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,12 +2,12 @@ julia_version = "1.11.6" manifest_format = "2.0" -project_hash = "3c5b0696513a84be8573e377b59e1ab532411868" +project_hash = "0250fe85007baf77c93e2189ee544ed354b8099e" [[deps.ADTypes]] -git-tree-sha1 = "7927b9af540ee964cc5d1b73293f1eb0b761a3a1" +git-tree-sha1 = "60665b326b75db6517939d0e1875850bc4a54368" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.16.0" +version = "1.17.0" weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] [deps.ADTypes.extensions] @@ -40,9 +40,13 @@ version = "5.7.2" [[deps.AbstractPPL]] deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random", "StatsBase"] -git-tree-sha1 = "478b0b6176125cf0a5e6e9fd69fdd0923754531c" +git-tree-sha1 = "b7a856399119394a573141c553aeb5b674a500b5" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.12.0" +version = "0.13.0" +weakdeps = ["Distributions", "LinearAlgebra"] + + [deps.AbstractPPL.extensions] + AbstractPPLDistributionsExt = ["Distributions", "LinearAlgebra"] [[deps.AbstractTrees]] git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" @@ -86,9 +90,9 @@ weakdeps = ["SparseArrays", "StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Setfield", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "9f75990a04e3ee45d80b19778ba9d2bb7ad4d5ee" +git-tree-sha1 = "22496647c061d00217759e95a18d601c959df0c9" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.8.0" +version = "0.8.1" [deps.AdvancedHMC.extensions] AdvancedHMCADTypesExt = "ADTypes" @@ -223,9 +227,9 @@ version = "1.11.0" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "b5bb4dc6248fde467be2a863eb8452993e74d402" +git-tree-sha1 = "29bb0eb6f578a587a49da16564705968667f5fa8" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "1.1.1" +version = "1.1.2" [deps.Atomix.extensions] AtomixCUDAExt = "CUDA" @@ -298,9 +302,9 @@ version = "0.1.1" [[deps.Bijectors]] deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "5eb5a58ed34e012d7f8d665cb5198252e128e907" +git-tree-sha1 = "35ba30573d4f83242f1e788c87ca792c83553c9e" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.15.8" +version = "0.15.9" weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker"] [deps.Bijectors.extensions] @@ -395,10 +399,10 @@ uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.5.0" [[deps.CPUSummary]] -deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] -git-tree-sha1 = "5a97e67919535d6841172016c9530fd69494e5ec" +deps = ["CpuId", "IfElse", "PrecompileTools", "Preferences", "Static"] +git-tree-sha1 = "f3a21d7fc84ba618a779d1ed2fcca2e682865bab" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.2.6" +version = "0.2.7" [[deps.CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] @@ -443,9 +447,9 @@ version = "1.72.5" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "06ee8d1aa558d2833aa799f6f0b31b30cada405f" +git-tree-sha1 = "e4c6a16e77171a5f5e25e9646617ab1c276c5607" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.25.2" +version = "1.26.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -685,9 +689,9 @@ version = "0.1.2" [[deps.DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "FastBroadcast", "ForwardDiff", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack", "SymbolicIndexingInterface"] -git-tree-sha1 = "484cceb16c5ed95f4a2a405f3579f480ec0dff9a" +git-tree-sha1 = "d9b1e66070ce15bc2b9c3d5af6b94f693fc03ba4" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.55.0" +version = "5.58.0" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -703,9 +707,9 @@ version = "0.4.0" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "6f8f25122389ba34e491bdfe143ae16fda37cad3" +git-tree-sha1 = "6fecfae8b2d9983e939378c8eacff6562e8a2567" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.180.0" +version = "6.183.0" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -743,9 +747,9 @@ version = "6.180.0" [[deps.DiffEqCallbacks]] deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "80a782f3e65d4900dcf5f2cb71f5e19d9459c04a" +git-tree-sha1 = "397ef6fffcf418ba55264ba785b032b8a136903b" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "4.8.0" +version = "4.9.0" [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] @@ -777,9 +781,9 @@ version = "7.16.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "f620da805b82bec64ab4d5f881c7592c82dbc08a" +git-tree-sha1 = "54d7b8c74408048aea9c055ac8573b2b5c5ec11f" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.7.3" +version = "0.7.4" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -894,10 +898,10 @@ uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb" version = "3.5.1" [[deps.DynamicPPL]] -deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Requires", "Statistics", "Test"] -git-tree-sha1 = "07218fc45d4f1abc9de4498e8cf966b6672c84f0" +deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Printf", "Random", "Requires", "Statistics", "Test"] +git-tree-sha1 = "e36add2952240379bd53b83e76cfd3a8c56748d6" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.36.15" +version = "0.37.0" [deps.DynamicPPL.extensions] DynamicPPLChainRulesCoreExt = ["ChainRulesCore"] @@ -929,9 +933,9 @@ version = "1.0.5" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "e36968f0a43d9a3b627ac94d5346b458ce14066d" +git-tree-sha1 = "1a9c9e3401f5d024612a70d24a19517b2dbc1824" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.65" +version = "0.13.67" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -1123,9 +1127,9 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] -git-tree-sha1 = "f089ab1f834470c525562030c8cfde4025d5e915" +git-tree-sha1 = "d84e026183bb3fc764110ae98792c2e004f8c240" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.27.0" +version = "2.28.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" @@ -1466,10 +1470,13 @@ version = "0.2.4" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] -git-tree-sha1 = "f8da88993c914357031daf0023f18748ff473924" +git-tree-sha1 = "f5b57507a36f05509e72120aa84d5c3747dbd70e" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.16.1" -weakdeps = ["FastBroadcast"] +version = "9.17.0" +weakdeps = ["Adapt", "FastBroadcast", "KernelAbstractions"] + + [deps.JumpProcesses.extensions] + JumpProcessesKernelAbstractionsExt = ["Adapt", "KernelAbstractions"] [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] @@ -1562,9 +1569,9 @@ version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "4f34eaabe49ecb3fb0d58d6015e32fd31a733199" +git-tree-sha1 = "52e1296ebbde0db845b356abbbe67fb82a0a116c" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.8" +version = "0.16.9" [deps.Latexify.extensions] DataFramesExt = "DataFrames" @@ -1731,15 +1738,18 @@ version = "1.11.0" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "d768ff40cc3fe42581708696b24ee65dccc9c6ba" +git-tree-sha1 = "1c597eceb5ead73dae17ffa4dcc1160e3e4da1f3" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "3.24.0" +version = "3.28.0" [deps.LinearSolve.extensions] + LinearSolveAMDGPUExt = "AMDGPU" + LinearSolveBLISExt = ["blis_jll", "LAPACK_jll"] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" LinearSolveCUDSSExt = "CUDSS" + LinearSolveCUSOLVERRFExt = ["CUSOLVERRF", "SparseArrays"] LinearSolveEnzymeExt = "EnzymeCore" LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveFastLapackInterfaceExt = "FastLapackInterface" @@ -1755,10 +1765,12 @@ version = "3.24.0" LinearSolveSparspakExt = ["SparseArrays", "Sparspak"] [deps.LinearSolve.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + CUSOLVERRF = "a8cc9031-bad2-4722-94f5-40deabb4245c" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641" @@ -1767,11 +1779,13 @@ version = "3.24.0" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" + LAPACK_jll = "51474c39-65e3-53ba-86ba-03b1b862ec14" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Sparspak = "e56a9233-b9d6-4f03-8d0f-1825330902ac" + blis_jll = "6136c539-28a5-5bf0-87cc-b183200dce32" [[deps.LogDensityProblems]] deps = ["ArgCheck", "DocStringExtensions", "Random"] @@ -1870,9 +1884,9 @@ version = "1.16.0" [[deps.LuxCore]] deps = ["Compat", "DispatchDoctor", "Random"] -git-tree-sha1 = "48d45736aae190b1b41c1db5242fad955f0eff1d" +git-tree-sha1 = "a72b6b530f39a87d1327b90f5def4bce48eb1a52" uuid = "bb33d45b-7691-41d6-9220-0943567d0623" -version = "1.2.6" +version = "1.3.0" [deps.LuxCore.extensions] LuxCoreArrayInterfaceReverseDiffExt = ["ArrayInterface", "ReverseDiff"] @@ -1942,9 +1956,9 @@ version = "7.1.0" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "a586f05dd16a50c490ed95415b2a829b8cf5d57f" +git-tree-sha1 = "526c98cd41028da22c01cb8a203246799ad853a8" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.3.14" +version = "0.3.15" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] @@ -2114,9 +2128,9 @@ uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" version = "1.2.0" [[deps.MistyClosures]] -git-tree-sha1 = "1142aefd845c608f3c70e4c202c4aae725cab67b" +git-tree-sha1 = "d1a692e293c2a0dc8fda79c04cad60582f3d4de3" uuid = "dbe65cb8-6be2-42dd-bbc5-4196aaced4f4" -version = "2.0.0" +version = "2.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -2298,9 +2312,9 @@ version = "4.10.0" [[deps.NonlinearSolveBase]] deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "ee395563ae6ffaecbdf86d430440fddc779253a4" +git-tree-sha1 = "1d42a315ba627ca0027d49d0efb44e3d88db24aa" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "1.13.0" +version = "1.14.0" weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"] [deps.NonlinearSolveBase.extensions] @@ -2314,15 +2328,15 @@ weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "Linear [[deps.NonlinearSolveFirstOrder]] deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "65101a20b135616a13625ae6f84b052ef5780363" +git-tree-sha1 = "3f1198ae5cbf21e84b8251a9e62fa1f888f3e4cb" uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" -version = "1.6.0" +version = "1.7.0" [[deps.NonlinearSolveQuasiNewton]] deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] -git-tree-sha1 = "3e04c917d4e3cd48b2a5091b6f76c720bb3f7362" +git-tree-sha1 = "40dfaf1bf74f1f700f81d0002d4dd90999598eb2" uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" -version = "1.7.0" +version = "1.8.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveQuasiNewton.extensions] @@ -2330,9 +2344,9 @@ weakdeps = ["ForwardDiff"] [[deps.NonlinearSolveSpectralMethods]] deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "3398222199e4b9ca0b5840907fb509f28f1a2fdc" +git-tree-sha1 = "84de5a469e119eb2c22ae07c543dc4e7f7001ee7" uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" -version = "1.2.0" +version = "1.3.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveSpectralMethods.extensions] @@ -2340,9 +2354,9 @@ weakdeps = ["ForwardDiff"] [[deps.ObjectFile]] deps = ["Reexport", "StructIO"] -git-tree-sha1 = "09b1fe6ff16e6587fa240c165347474322e77cf1" +git-tree-sha1 = "22faba70c22d2f03e60fbc61da99c4ebfc3eb9ba" uuid = "d8793406-e978-5875-9003-1fc021f44a92" -version = "0.4.4" +version = "0.5.0" [[deps.Observables]] git-tree-sha1 = "7438a59546cf62428fc9d1bc94729146d37a7225" @@ -2388,9 +2402,9 @@ version = "1.5.0" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "87510f7292a2b21aeff97912b0898f9553cc5c2c" +git-tree-sha1 = "2ae7d4ddec2e13ad3bddf5c0796f7547cf682391" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.5.1+0" +version = "3.5.2+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -2490,22 +2504,22 @@ uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" version = "6.101.0" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] -deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "82f78099ecf4e0fa53545811318520d87e7fe0b8" +deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] +git-tree-sha1 = "09aae1486c767caa6bce9de892455cbdf5a6fbc8" uuid = "89bda076-bce5-4f1c-845f-551c83cdda9a" -version = "1.2.0" +version = "1.5.0" [[deps.OrdinaryDiffEqBDF]] -deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "b0bbc6541ea4a27974bd67e0a10b26211cb95e58" +deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "ce8db53fd1e4e41c020fd53961e7314f75e4c21c" uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" -version = "1.7.0" +version = "1.10.1" 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"FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "d0b069075f4a5e54b29e412419e5a733a83e6240" +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "778c7d379265f17f40dbe9aaa6f6a2a08bc7fa3e" uuid = "b1df2697-797e-41e3-8120-5422d3b24e4a" -version = "1.2.0" +version = "1.5.0" [[deps.OrdinaryDiffEqVerner]] -deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static", "TruncatedStacktraces"] -git-tree-sha1 = "91f0a004785791c8c538d34a67c19cf3f7776e85" +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "TruncatedStacktraces"] +git-tree-sha1 = "185578fa7c38119d4318326f9375f1cba0f0ce53" uuid = "79d7bb75-1356-48c1-b8c0-6832512096c2" -version = "1.3.0" +version = "1.6.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -2738,9 +2752,9 @@ version = "1.4.3" [[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", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "3db9167c618b290a05d4345ca70de6d95304a32a" +git-tree-sha1 = "9a9216c0cf706cb2cc58fd194878180e3e51e8c0" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.17" +version = "1.40.18" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -2758,9 +2772,9 @@ version = "1.40.17" [[deps.PoissonRandom]] deps = ["LogExpFunctions", "Random"] -git-tree-sha1 = "bb178012780b34046c6d1600a315d8dbee89d83d" +git-tree-sha1 = "c1ea45aa9f209fe97192afa233907bc4e551c8aa" uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" -version = "0.4.5" +version = "0.4.6" [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] @@ -2787,13 +2801,14 @@ uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" [[deps.PreallocationTools]] -deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "2cc315bb7f6e4d59081bad744cdb911d6374fc7f" +deps = ["Adapt", "ArrayInterface", "PrecompileTools"] +git-tree-sha1 = "a0d5f963cfee70bee26dfa137a732e759e24436a" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.29" -weakdeps = ["ReverseDiff", "SparseConnectivityTracer"] +version = "0.4.31" +weakdeps = ["ForwardDiff", "ReverseDiff", "SparseConnectivityTracer"] [deps.PreallocationTools.extensions] + PreallocationToolsForwardDiffExt = "ForwardDiff" PreallocationToolsReverseDiffExt = "ReverseDiff" PreallocationToolsSparseConnectivityTracerExt = "SparseConnectivityTracer" @@ -2805,9 +2820,9 @@ version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" +git-tree-sha1 = "0f27480397253da18fe2c12a4ba4eb9eb208bf3d" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.3" +version = "1.5.0" [[deps.PrettyPrint]] git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" @@ -2944,10 +2959,10 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "f8726bd5a8b7f5f5d3f6c0ce4793454a599b5243" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] +git-tree-sha1 = "7c7ac305885b1e0292585d087ecd60331a705965" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.36.0" +version = "3.37.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -2958,6 +2973,7 @@ version = "3.36.0" RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] RecursiveArrayToolsStructArraysExt = "StructArrays" + RecursiveArrayToolsTablesExt = ["Tables"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" @@ -2970,6 +2986,7 @@ version = "3.36.0" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -3051,15 +3068,15 @@ version = "0.1.0" [[deps.SSMProblems]] deps = ["AbstractMCMC", "Distributions", "Random"] -git-tree-sha1 = "4fedd69d5a5392cfed4edc647972de5b5b25a90a" +git-tree-sha1 = "b00814e67e8aacda2073865a3832e6cc378ea504" uuid = "26aad666-b158-4e64-9d35-0e672562fa48" -version = "0.5.0" +version = "0.5.1" [[deps.SciMLBase]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] -git-tree-sha1 = "1c7fd50df465f0684f04f3a63736eac01999c659" +git-tree-sha1 = "95ce48fe76b9530799429244392853b5405469c1" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.107.0" +version = "2.109.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3090,9 +3107,9 @@ version = "0.1.8" [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "7d3a1519dc4d433a6b20035eaff20bde8be77c66" +git-tree-sha1 = "aea915a39b547c48a18ee041120db1ae8df5a691" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "1.4.0" +version = "1.5.0" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -3101,9 +3118,9 @@ weakdeps = ["SparseArrays", "StaticArraysCore"] [[deps.SciMLSensitivity]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "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", "SciMLStructures", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"] -git-tree-sha1 = "a5d3e3ccedbce9c0c07b4ffa60787b58bdc6d360" +git-tree-sha1 = "e1b5f9b3be1452591c40a88de9efb265ebe76030" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.88.0" +version = "7.89.0" weakdeps = ["Mooncake"] [deps.SciMLSensitivity.extensions] @@ -3189,9 +3206,9 @@ weakdeps = ["ChainRulesCore", "DiffEqBase", "ReverseDiff", "Tracker"] [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] -git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" +git-tree-sha1 = "be8eeac05ec97d379347584fa9fe2f5f76795bcb" uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" -version = "0.9.4" +version = "0.9.5" [[deps.SimpleUnPack]] git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" @@ -3204,9 +3221,9 @@ version = "1.11.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" +git-tree-sha1 = "64d974c2e6fdf07f8155b5b2ca2ffa9069b608d9" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.2.1" +version = "1.2.2" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] @@ -3344,9 +3361,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] [[deps.StatsModels]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "9022bcaa2fc1d484f1326eaa4db8db543ca8c66d" +git-tree-sha1 = "728d276a5adc2f1cbb800eec4b63d0a8221024b4" uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" -version = "0.7.4" +version = "0.7.5" [[deps.StatsPlots]] deps = ["AbstractFFTs", "Clustering", "DataStructures", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] @@ -3443,10 +3460,14 @@ uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164" version = "5.2.3+0" [[deps.SymbolicIndexingInterface]] -deps = ["Accessors", "ArrayInterface", "PrettyTables", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "59ca6eddaaa9849e7de9fd1153b6faf0b1db7b80" +deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] +git-tree-sha1 = "93104ca226670c0cb92ba8bc6998852ad55a2d4c" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.42" +version = "0.3.43" +weakdeps = ["PrettyTables"] + + [deps.SymbolicIndexingInterface.extensions] + SymbolicIndexingInterfacePrettyTablesExt = "PrettyTables" [[deps.TOML]] deps = ["Dates"] @@ -3601,9 +3622,9 @@ version = "1.6.0" [[deps.Turing]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "3fd5118fd33c708bec35d892f86a5455e9402d66" +git-tree-sha1 = "ed944065575fd4a6d9d2b802bbd914b53f08bce8" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.39.9" +version = "0.40.1" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] diff --git a/Project.toml b/Project.toml index af37a3fd6..852391861 100644 --- a/Project.toml +++ b/Project.toml @@ -55,4 +55,4 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" [compat] -Turing = "0.39" +Turing = "0.40" From e7232b6cef04c3ba1eae8acb843bd0d3dbdf16d1 Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Wed, 13 Aug 2025 17:24:40 +0100 Subject: [PATCH 02/13] Update version in _quarto.yml --- _quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_quarto.yml b/_quarto.yml index 9bab2644c..4ecace484 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -41,7 +41,7 @@ website: href: https://turinglang.org/team/ right: # Current version - - text: "v0.39" + - text: "v0.40" menu: - text: Changelog href: https://turinglang.org/docs/changelog.html From 0ca80621ca75243809a021360f3971e0c004a49e Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Wed, 13 Aug 2025 17:45:44 +0100 Subject: [PATCH 03/13] Fix DPPL 0.37 run_ad change --- usage/automatic-differentiation/index.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/usage/automatic-differentiation/index.qmd b/usage/automatic-differentiation/index.qmd index 768845942..5ae168473 100755 --- a/usage/automatic-differentiation/index.qmd +++ b/usage/automatic-differentiation/index.qmd @@ -91,7 +91,7 @@ model = gdemo(1.5, 2) for adtype in [AutoForwardDiff(), AutoReverseDiff()] result = run_ad(model, adtype; benchmark=true) - @show result.time_vs_primal + @show result.grad_time / result.primal_time end ``` From 0e3828033f9f2db95912fef57b98724fffec662d Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Wed, 20 Aug 2025 10:08:46 +0100 Subject: [PATCH 04/13] Fix VI tutorial --- tutorials/variational-inference/index.qmd | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd index cd814b156..7d89ba904 100755 --- a/tutorials/variational-inference/index.qmd +++ b/tutorials/variational-inference/index.qmd @@ -182,8 +182,8 @@ Usually, `q_avg` will perform better than the last-iterate `q_last`. For instance, 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, Turing.Variational.make_logdensity(m)), - ELBO_q_last = estimate_objective(AdvancedVI.RepGradELBO(32), q_last, Turing.Variational.make_logdensity(m)) + ELBO_q_avg = estimate_objective(AdvancedVI.RepGradELBO(32), q_avg, LogDensityFunction(m)), + ELBO_q_last = estimate_objective(AdvancedVI.RepGradELBO(32), q_last, LogDensityFunction(m)) ) ``` We can see that `ELBO_q_avg` is slightly more optimal. @@ -205,9 +205,9 @@ For example, the following callback function estimates the ELBO on `q_avg` every ```{julia} function callback(; stat, averaged_params, restructure, kwargs...) if mod(stat.iteration, 10) == 1 - q_avg = restructure(averaged_params) - obj = AdvancedVI.RepGradELBO(128) - elbo_avg = estimate_objective(obj, q_avg, Turing.Variational.make_logdensity(m)) + q_avg = restructure(averaged_params) + obj = AdvancedVI.RepGradELBO(128) + elbo_avg = estimate_objective(obj, q_avg, LogDensityFunction(m)) (elbo_avg = elbo_avg,) else nothing @@ -223,7 +223,7 @@ q_mf, _, info_mf, _ = vi(m, q_init, n_iters; show_progress=false, callback=callb Let's plot the result: ```{julia} -iters = 1:10:length(info_mf) +iters = 1:10:length(info_mf) elbo_mf = [i.elbo_avg for i in info_mf[iters]] Plots.plot!(iters, elbo_mf, xlabel="Iterations", ylabel="ELBO", label="callback", ylims=(-200,Inf)) ``` @@ -247,7 +247,7 @@ _, _, info_adam, _ = vi(m, q_init, n_iters; show_progress=false, callback=callba ``` ```{julia} -iters = 1:10:length(info_mf) +iters = 1:10:length(info_mf) 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") From 1fa486ea09604c962b3f3c883e43228d304a456c Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Thu, 21 Aug 2025 16:25:34 +0100 Subject: [PATCH 05/13] Fix model-manual's use of contexts --- developers/compiler/model-manual/index.qmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/developers/compiler/model-manual/index.qmd b/developers/compiler/model-manual/index.qmd index 4571254c8..a3e404122 100755 --- a/developers/compiler/model-manual/index.qmd +++ b/developers/compiler/model-manual/index.qmd @@ -33,21 +33,21 @@ Taking the `gdemo` model above as an example, the macro-based definition can be using DynamicPPL # Create the model function. -function gdemo2(model, varinfo, context, x) +function gdemo2(model, varinfo, x) # Assume s² has an InverseGamma distribution. s², varinfo = DynamicPPL.tilde_assume!!( - context, InverseGamma(2, 3), @varname(s²), varinfo + model.context, InverseGamma(2, 3), @varname(s²), varinfo ) # Assume m has a Normal distribution. m, varinfo = DynamicPPL.tilde_assume!!( - context, Normal(0, sqrt(s²)), @varname(m), varinfo + model.context, Normal(0, sqrt(s²)), @varname(m), varinfo ) # Observe each value of x[i] according to a Normal distribution. for i in eachindex(x) _retval, varinfo = DynamicPPL.tilde_observe!!( - context, Normal(m, sqrt(s²)), x[i], @varname(x[i]), varinfo + model.context, Normal(m, sqrt(s²)), x[i], @varname(x[i]), varinfo ) end From f7abf9a42a55f596cae9568a14c64e1359664f47 Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Thu, 21 Aug 2025 16:42:10 +0100 Subject: [PATCH 06/13] Fix references to __context__ --- developers/contexts/submodel-condition/index.qmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/developers/contexts/submodel-condition/index.qmd b/developers/contexts/submodel-condition/index.qmd index 69fad0bd8..0294ce9e8 100755 --- a/developers/contexts/submodel-condition/index.qmd +++ b/developers/contexts/submodel-condition/index.qmd @@ -108,13 +108,13 @@ unwrap_sampling_context(ctx::DynamicPPL.SamplingContext) = ctx.context unwrap_sampling_context(ctx::DynamicPPL.AbstractContext) = ctx @model function inner() - println("inner context: $(unwrap_sampling_context(__context__))") + println("inner context: $(unwrap_sampling_context(model.context))") x ~ Normal() return y ~ Normal() end @model function outer() - println("outer context: $(unwrap_sampling_context(__context__))") + println("outer context: $(unwrap_sampling_context(model.context))") return a ~ to_submodel(inner()) end @@ -124,7 +124,7 @@ with_outer_cond = outer() | (@varname(a.x) => 1.0) # 'Inner conditioning' inner_cond = inner() | (@varname(x) => 1.0) @model function outer2() - println("outer context: $(unwrap_sampling_context(__context__))") + println("outer context: $(unwrap_sampling_context(model.context))") return a ~ to_submodel(inner_cond) end with_inner_cond = outer2() From 1df2b45febce969ff0cdef2dc98d5a2a3c2d380e Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Thu, 21 Aug 2025 16:45:30 +0100 Subject: [PATCH 07/13] Fix use of addlogprob for log prior --- usage/modifying-logprob/index.qmd | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/usage/modifying-logprob/index.qmd b/usage/modifying-logprob/index.qmd index b3de9e7ee..0eb6f8b30 100755 --- a/usage/modifying-logprob/index.qmd +++ b/usage/modifying-logprob/index.qmd @@ -47,13 +47,10 @@ using LinearAlgebra end ``` -Note that `@addlogprob!` always increases the accumulated log probability, regardless of the provided -sampling context. -For instance, if you do not want to apply `@addlogprob!` when evaluating the prior of your model but only when computing the log likelihood and the log joint probability, then you should [check the type of the internal variable `__context_`](https://github.com/TuringLang/DynamicPPL.jl/issues/154), as in the following example: +Note that `@addlogprob!` increases the accumulated log likelihood. +If instead you want to add to the log prior, you can use ```{julia} #| eval: false -if DynamicPPL.leafcontext(__context__) !== Turing.PriorContext() - @addlogprob! myloglikelihood(x, μ) -end +@addlogprob! (; logprior=value_goes_here) ``` From cb2e1f91e4dca14641e7ecec9f4cda41ef2d71dd Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Tue, 16 Sep 2025 16:31:02 +0100 Subject: [PATCH 08/13] Fix typo --- developers/contexts/submodel-condition/index.qmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/developers/contexts/submodel-condition/index.qmd b/developers/contexts/submodel-condition/index.qmd index 0294ce9e8..3519116bf 100755 --- a/developers/contexts/submodel-condition/index.qmd +++ b/developers/contexts/submodel-condition/index.qmd @@ -108,13 +108,13 @@ unwrap_sampling_context(ctx::DynamicPPL.SamplingContext) = ctx.context unwrap_sampling_context(ctx::DynamicPPL.AbstractContext) = ctx @model function inner() - println("inner context: $(unwrap_sampling_context(model.context))") + println("inner context: $(unwrap_sampling_context(__model__.context))") x ~ Normal() return y ~ Normal() end @model function outer() - println("outer context: $(unwrap_sampling_context(model.context))") + println("outer context: $(unwrap_sampling_context(__model__.context))") return a ~ to_submodel(inner()) end @@ -124,7 +124,7 @@ with_outer_cond = outer() | (@varname(a.x) => 1.0) # 'Inner conditioning' inner_cond = inner() | (@varname(x) => 1.0) @model function outer2() - println("outer context: $(unwrap_sampling_context(model.context))") + println("outer context: $(unwrap_sampling_context(__model__.context))") return a ~ to_submodel(inner_cond) end with_inner_cond = outer2() From 414bd49a0136a34b7df1e1991d6fbb7d64fd6f5c Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Tue, 16 Sep 2025 16:55:56 +0100 Subject: [PATCH 09/13] Regenerate manifest --- Manifest.toml | 381 ++++++++++++++++++++++++++------------------------ 1 file changed, 200 insertions(+), 181 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index b141022e5..0a95cce1c 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -5,9 +5,9 @@ manifest_format = "2.0" project_hash = "9f86f29e94eb0d08fa3f55118bf3765e18345c9e" [[deps.ADTypes]] -git-tree-sha1 = "60665b326b75db6517939d0e1875850bc4a54368" +git-tree-sha1 = "27cecae79e5cc9935255f90c53bb831cc3c870d7" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.17.0" +version = "1.18.0" weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] [deps.ADTypes.extensions] @@ -34,19 +34,19 @@ version = "0.5.24" [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers", "UUIDs"] -git-tree-sha1 = "e4b6a25ba2e033c74ea11720daacafbc2ab50a7e" +git-tree-sha1 = "2b33cfcb3f32819e02bf949e7546a1d59247884e" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "5.7.2" +version = "5.8.0" [[deps.AbstractPPL]] -deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random", "StatsBase"] -git-tree-sha1 = "b7a856399119394a573141c553aeb5b674a500b5" +deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "LinearAlgebra", "Random", "StatsBase"] +git-tree-sha1 = "3a9c1e6e7418494454260b0c8efd7b00fca251bc" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.13.0" -weakdeps = ["Distributions", "LinearAlgebra"] +version = "0.13.1" +weakdeps = ["Distributions"] [deps.AbstractPPL.extensions] - AbstractPPLDistributionsExt = ["Distributions", "LinearAlgebra"] + AbstractPPLDistributionsExt = ["Distributions"] [[deps.AbstractTrees]] git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" @@ -90,9 +90,9 @@ weakdeps = ["SparseArrays", "StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Setfield", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "22496647c061d00217759e95a18d601c959df0c9" +git-tree-sha1 = "e5625ace51e1f11f479b24017193bc7fdfef73a2" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.8.1" +version = "0.8.2" [deps.AdvancedHMC.extensions] AdvancedHMCADTypesExt = "ADTypes" @@ -181,9 +181,9 @@ version = "3.5.1+1" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "9606d7832795cbef89e06a550475be300364a8aa" +git-tree-sha1 = "dbd8c3bbbdbb5c2778f85f4422c39960eac65a42" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.19.0" +version = "7.20.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" @@ -193,6 +193,7 @@ version = "7.19.0" ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceMetalExt = "Metal" ArrayInterfaceReverseDiffExt = "ReverseDiff" ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" @@ -206,6 +207,7 @@ version = "7.19.0" ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" @@ -251,9 +253,9 @@ version = "1.1.0" [[deps.AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] -git-tree-sha1 = "16351be62963a67ac4083f748fdb3cca58bfd52f" +git-tree-sha1 = "4126b08903b777c88edf1754288144a0492c05ad" uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" -version = "0.4.7" +version = "0.4.8" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] @@ -302,10 +304,10 @@ version = "0.1.1" [[deps.Bijectors]] deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "35ba30573d4f83242f1e788c87ca792c83553c9e" +git-tree-sha1 = "1f8e2022a4f6dbbe3c7b60f728647973e7b514ef" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.15.9" -weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker"] +version = "0.15.10" +weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff"] [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" @@ -315,7 +317,6 @@ weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyA BijectorsMooncakeExt = "Mooncake" BijectorsReverseDiffChainRulesExt = ["ChainRules", "ReverseDiff"] BijectorsReverseDiffExt = "ReverseDiff" - BijectorsTrackerExt = "Tracker" [[deps.BitFlags]] git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" @@ -378,9 +379,9 @@ version = "1.9.0" [[deps.BracketingNonlinearSolve]] deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "a9014924595b7a2c1dd14aac516e38fa10ada656" +git-tree-sha1 = "90740f16aef91d898424bc11c1cabada475435e0" uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e" -version = "1.3.0" +version = "1.4.0" weakdeps = ["ChainRulesCore", "ForwardDiff"] [deps.BracketingNonlinearSolve.extensions] @@ -496,9 +497,9 @@ version = "0.7.8" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "a656525c8b46aa6a1c76891552ed5381bb32ae7b" +git-tree-sha1 = "b0fd3f56fa442f81e0a47815c92245acfaaa4e34" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.30.0" +version = "3.31.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -656,9 +657,9 @@ 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 = "fb61b4812c49343d7ef0b533ba982c46021938a6" +git-tree-sha1 = "c967271c27a95160e30432e011b58f42cd7501b5" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.7.0" +version = "1.8.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -706,15 +707,14 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "1b1e070e57681d1176d99a5ec455717e24686612" +deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"] +git-tree-sha1 = "6df3b15d504315ec306118aed14f9d7af9f83db1" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.183.2" +version = "6.189.1" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" DiffEqBaseChainRulesCoreExt = "ChainRulesCore" - DiffEqBaseDistributionsExt = "Distributions" DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] DiffEqBaseForwardDiffExt = ["ForwardDiff"] DiffEqBaseGTPSAExt = "GTPSA" @@ -781,9 +781,9 @@ version = "7.16.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "38989b1532a3c6e2341d52b77c5475c42c3318a8" +git-tree-sha1 = "16946a4d305607c3a4af54ff35d56f0e9444ed0e" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.7.6" +version = "0.7.7" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -899,9 +899,9 @@ version = "3.5.1" [[deps.DynamicPPL]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Printf", "Random", "Requires", "Statistics", "Test"] -git-tree-sha1 = "0cdb6cb40d00f38d3f2e4a73e16004402465dad7" +git-tree-sha1 = "65649377104973412c10fb00ebc2f8430dcf8b93" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.37.1" +version = "0.37.2" [deps.DynamicPPL.extensions] DynamicPPLChainRulesCoreExt = ["ChainRulesCore"] @@ -933,9 +933,9 @@ version = "1.0.5" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "3fef9076638b16d390d88c7c28f1fe6150b144f1" +git-tree-sha1 = "66ec698bd4791c8d2b2be2fe2a472d1dd76a5c7d" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.69" +version = "0.13.75" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -954,9 +954,9 @@ version = "0.13.69" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.EnzymeCore]] -git-tree-sha1 = "8272a687bca7b5c601c0c24fc0c71bff10aafdfd" +git-tree-sha1 = "787f5e2efb33af12cc3fde313c1b0195a3f08eba" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.8.12" +version = "0.8.13" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -964,9 +964,9 @@ weakdeps = ["Adapt"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "3f73e7e21c328bc3bda4a5e5842a0a143243690c" +git-tree-sha1 = "bf15bd2b3ddff92fc5bb5687ffe074ebd814c756" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.191+0" +version = "0.0.196+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1019,10 +1019,10 @@ uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" version = "7.1.1+0" [[deps.FFTW]] -deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "797762812ed063b9b94f6cc7742bc8883bb5e69e" +deps = ["AbstractFFTs", "FFTW_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] +git-tree-sha1 = "97f08406df914023af55ade2f843c39e99c5d969" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.9.0" +version = "1.10.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1115,9 +1115,9 @@ version = "1.11.0" [[deps.FillArrays]] deps = ["LinearAlgebra"] -git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a" +git-tree-sha1 = "173e4d8f14230a7523ae11b9a3fa9edb3e0efd78" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.13.0" +version = "1.14.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -1173,9 +1173,9 @@ version = "0.16.5" [[deps.Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] -git-tree-sha1 = "301b5d5d731a0654825f1f2e906990f7141a106b" +git-tree-sha1 = "f85dac9a96a01087df6e3a749840015a0ca3817d" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.16.0+0" +version = "2.17.1+0" [[deps.Format]] git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" @@ -1184,9 +1184,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "910febccb28d493032495b7009dce7d7f7aee554" +git-tree-sha1 = "dc41303865a16274ecb8450c220021ce1e0cf05f" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "1.0.1" +version = "1.2.1" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -1280,11 +1280,17 @@ git-tree-sha1 = "45288942190db7c5f760f59c04495064eedf9340" uuid = "b0724c58-0f36-5564-988d-3bb0596ebc4a" version = "0.22.4+0" +[[deps.Ghostscript_jll]] +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Zlib_jll"] +git-tree-sha1 = "38044a04637976140074d0b0621c1edf0eb531fd" +uuid = "61579ee1-b43e-5ca0-a5da-69d92c66a64b" +version = "9.55.1+0" + [[deps.Glib_jll]] deps = ["Artifacts", "GettextRuntime_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "35fbd0cefb04a516104b8e183ce0df11b70a3f1a" +git-tree-sha1 = "50c11ffab2a3d50192a228c313f05b5b5dc5acb2" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.84.3+0" +version = "2.86.0+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1358,9 +1364,9 @@ uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" version = "0.3.1" [[deps.InlineStrings]] -git-tree-sha1 = "8594fac023c5ce1ef78260f24d1ad18b4327b420" +git-tree-sha1 = "8f3d257792a522b4601c24a577954b0a8cd7334d" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.4.4" +version = "1.4.5" [deps.InlineStrings.extensions] ArrowTypesExt = "ArrowTypes" @@ -1458,9 +1464,9 @@ version = "0.2.1" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e95866623950267c1e4878846f848d94810de475" +git-tree-sha1 = "4255f0032eafd6451d707a51d5f0248b8a165e4d" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.1.2+0" +version = "3.1.3+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1469,10 +1475,10 @@ uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" [[deps.JumpProcesses]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] -git-tree-sha1 = "f5b57507a36f05509e72120aa84d5c3747dbd70e" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "PoissonRandom", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] +git-tree-sha1 = "905a2a28770e23f3ed750306ef48eb8c46c3a002" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.17.0" +version = "9.19.1" weakdeps = ["Adapt", "FastBroadcast", "KernelAbstractions"] [deps.JumpProcesses.extensions] @@ -1568,10 +1574,10 @@ uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" version = "1.4.0" [[deps.Latexify]] -deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "52e1296ebbde0db845b356abbbe67fb82a0a116c" +deps = ["Format", "Ghostscript_jll", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] +git-tree-sha1 = "44f93c47f9cd6c7e431f2f2091fcba8f01cd7e8f" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.9" +version = "0.16.10" [deps.Latexify.extensions] DataFramesExt = "DataFrames" @@ -1693,9 +1699,9 @@ version = "1.18.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a31572773ac1b745e0343fe5e2c8ddda7a37e997" +git-tree-sha1 = "706dfd3c0dd56ca090e86884db6eda70fa7dd4af" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.41.0+0" +version = "2.41.1+0" [[deps.Libtask]] deps = ["MistyClosures", "Test"] @@ -1711,9 +1717,9 @@ version = "4.7.1+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "321ccef73a96ba828cd51f2ab5b9f917fa73945a" +git-tree-sha1 = "d3c8af829abaeba27181db4acb485b18d15d89c6" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.41.0+0" +version = "2.41.1+0" [[deps.LineSearch]] deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] @@ -1737,10 +1743,10 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" version = "1.11.0" [[deps.LinearSolve]] -deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLLogging", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "eaef503c581f5325d7202ebfd13298975e1269d6" +deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "OpenBLAS_jll", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "69cee52e516c859e64adba702ac382c0498a4e29" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "3.33.0" +version = "3.40.0" [deps.LinearSolve.extensions] LinearSolveAMDGPUExt = "AMDGPU" @@ -1847,9 +1853,9 @@ version = "1.1.0" [[deps.Lux]] deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DiffResults", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "WeightInitializers"] -git-tree-sha1 = "c01b012bbf84e6d5aab7b75782a73f453d34be87" +git-tree-sha1 = "c300d2df439a343a840dd8ef6b0910ce4cafc8c6" uuid = "b2108857-7c20-44ae-9111-449ecde12c47" -version = "1.17.0" +version = "1.21.1" [deps.Lux.extensions] LuxComponentArraysExt = "ComponentArrays" @@ -1886,9 +1892,9 @@ version = "1.17.0" [[deps.LuxCore]] deps = ["Compat", "DispatchDoctor", "Random"] -git-tree-sha1 = "a72b6b530f39a87d1327b90f5def4bce48eb1a52" +git-tree-sha1 = "cf12c8eba464132e781d7e000bcc4090e2b6e115" uuid = "bb33d45b-7691-41d6-9220-0943567d0623" -version = "1.3.0" +version = "1.4.1" [deps.LuxCore.extensions] LuxCoreArrayInterfaceReverseDiffExt = ["ArrayInterface", "ReverseDiff"] @@ -1905,6 +1911,7 @@ version = "1.3.0" ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196" MLDataDevices = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" @@ -1914,9 +1921,9 @@ version = "1.3.0" [[deps.LuxLib]] deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "Compat", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "5d1d796c8b2878b5cad2849970c52897ff8c0271" +git-tree-sha1 = "109240d7ba4698e7eb60b11f190424b8ca018318" uuid = "82251201-b29d-42c6-8e01-566dec8acb11" -version = "1.10.2" +version = "1.11.2" [deps.LuxLib.extensions] LuxLibAppleAccelerateExt = "AppleAccelerate" @@ -1926,7 +1933,7 @@ version = "1.10.2" LuxLibLoopVectorizationExt = "LoopVectorization" LuxLibMKLExt = "MKL" LuxLibOctavianExt = ["Octavian", "LoopVectorization"] - LuxLibReactantExt = "Reactant" + LuxLibReactantExt = ["Reactant", "ReactantCore"] LuxLibReverseDiffExt = "ReverseDiff" LuxLibSLEEFPiratesExt = "SLEEFPirates" LuxLibTrackerAMDGPUExt = ["AMDGPU", "Tracker"] @@ -1943,6 +1950,7 @@ version = "1.10.2" MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2" Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4" Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" + ReactantCore = "a3311ec8-5e00-46d5-b541-4f83e724a433" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" @@ -1950,9 +1958,9 @@ version = "1.10.2" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "DataAPI", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] -git-tree-sha1 = "f3993c723865f670102011ef22811e2bbb0ef1a8" +git-tree-sha1 = "902175f1618baa58dc50dc2894d382bbd484adf4" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "7.2.0" +version = "7.3.0" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] @@ -1974,9 +1982,9 @@ version = "1.0.0" [[deps.MLDataDevices]] deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"] -git-tree-sha1 = "0ad0d8f83ddf28a7eba28ed94d0d68015ce645b7" +git-tree-sha1 = "39bac90ff3e88e086426f05a3e97646f91088a7f" uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" -version = "1.11.1" +version = "1.12.0" [deps.MLDataDevices.extensions] MLDataDevicesAMDGPUExt = "AMDGPU" @@ -2144,9 +2152,9 @@ version = "0.8.1" [[deps.Mooncake]] deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DispatchDoctor", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Test"] -git-tree-sha1 = "955bad945bc815c4b48fb4d17ce39cf3ba6abcf3" +git-tree-sha1 = "2aa902cb9f45dbeaaae5eaa98559d600b1f5deb7" uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" -version = "0.4.150" +version = "0.4.159" [deps.Mooncake.extensions] MooncakeAllocCheckExt = "AllocCheck" @@ -2313,42 +2321,46 @@ version = "4.10.0" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" [[deps.NonlinearSolveBase]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "1d42a315ba627ca0027d49d0efb44e3d88db24aa" +deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "Setfield", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] +git-tree-sha1 = "99a400f7ad42e56431c76f3eadee0755f2123fda" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "1.14.0" -weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"] +version = "1.15.0" +weakdeps = ["BandedMatrices", "ChainRulesCore", "Enzyme", "ForwardDiff", "LineSearch", "LinearSolve", "Mooncake", "ReverseDiff", "SparseArrays", "SparseMatrixColorings", "Tracker"] [deps.NonlinearSolveBase.extensions] NonlinearSolveBaseBandedMatricesExt = "BandedMatrices" - NonlinearSolveBaseDiffEqBaseExt = "DiffEqBase" + NonlinearSolveBaseChainRulesCoreExt = "ChainRulesCore" + NonlinearSolveBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] NonlinearSolveBaseForwardDiffExt = "ForwardDiff" NonlinearSolveBaseLineSearchExt = "LineSearch" NonlinearSolveBaseLinearSolveExt = "LinearSolve" + NonlinearSolveBaseMooncakeExt = "Mooncake" + NonlinearSolveBaseReverseDiffExt = "ReverseDiff" NonlinearSolveBaseSparseArraysExt = "SparseArrays" NonlinearSolveBaseSparseMatrixColoringsExt = "SparseMatrixColorings" + NonlinearSolveBaseTrackerExt = "Tracker" [[deps.NonlinearSolveFirstOrder]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "3f1198ae5cbf21e84b8251a9e62fa1f888f3e4cb" +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "b9702235120d1161f8041b326eccebd334340de2" uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" -version = "1.7.0" +version = "1.8.0" [[deps.NonlinearSolveQuasiNewton]] -deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] -git-tree-sha1 = "40dfaf1bf74f1f700f81d0002d4dd90999598eb2" +deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] +git-tree-sha1 = "4e0e34601c6c9890aa9443003180967f75c6929d" uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" -version = "1.8.0" +version = "1.9.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveQuasiNewton.extensions] NonlinearSolveQuasiNewtonForwardDiffExt = "ForwardDiff" [[deps.NonlinearSolveSpectralMethods]] -deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "84de5a469e119eb2c22ae07c543dc4e7f7001ee7" +deps = ["CommonSolve", "ConcreteStructs", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "6c613302febe2bb408a888105d07073cf6824911" uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" -version = "1.3.0" +version = "1.4.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveSpectralMethods.extensions] @@ -2443,16 +2455,16 @@ version = "0.4.6" Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" [[deps.Optimization]] -deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "41902230755effe29a8599ea4b61dc3ffc2c952d" +deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Random", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] +git-tree-sha1 = "1e02b79bf6175d723a40745f622e9513253bab55" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "4.5.0" +version = "4.7.0" [[deps.OptimizationBase]] -deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] -git-tree-sha1 = "474b2fa6de9288d34b8ad42c9c500088132621a7" +deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] +git-tree-sha1 = "4f6098addb09203f35de1b21d5e668315544ff26" uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb" -version = "2.10.0" +version = "2.11.0" [deps.OptimizationBase.extensions] OptimizationEnzymeExt = "Enzyme" @@ -2478,15 +2490,15 @@ version = "2.10.0" [[deps.OptimizationNLopt]] deps = ["NLopt", "Optimization", "Random", "Reexport"] -git-tree-sha1 = "da55bae039168c0ef977bd5926cd5208c6cd13cf" +git-tree-sha1 = "83e469a5b058250e95121afeea71da14034b24a4" uuid = "4e6fcdb7-1186-4e1f-a706-475e75c168bb" -version = "0.3.2" +version = "0.3.3" [[deps.OptimizationOptimJL]] deps = ["Optim", "Optimization", "PrecompileTools", "Reexport", "SparseArrays"] -git-tree-sha1 = "6f228118b81ce4e849091ee0d00805f2ecb18f54" +git-tree-sha1 = "a6194340cb4f7d61cec9d6f605848d6a187c64b6" uuid = "36348300-93cb-4f02-beb5-3c3902f8871e" -version = "0.4.3" +version = "0.4.4" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2500,10 +2512,10 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.8.1" [[deps.OrdinaryDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "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", "SimpleUnPack", "SparseArrays", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "55c21fdb4626037cdbcb04fec3afa192345a24de" +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", "SimpleUnPack", "SparseArrays", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "89cd4e81d7a668f8858fba6779212f41a0360260" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.101.0" +version = "6.102.1" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"] @@ -2519,9 +2531,9 @@ version = "1.10.1" [[deps.OrdinaryDiffEqCore]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "e579c9a4f9102e82da3d97c349a74d6bc11cf8dc" +git-tree-sha1 = "688c717e8eee84dcfef02ddf71c8028215b329ca" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.30.0" +version = "1.34.0" weakdeps = ["EnzymeCore", "Mooncake"] [deps.OrdinaryDiffEqCore.extensions] @@ -2535,10 +2547,14 @@ uuid = "50262376-6c5a-4cf5-baba-aaf4f84d72d7" version = "1.8.0" [[deps.OrdinaryDiffEqDifferentiation]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"] -git-tree-sha1 = "4c270747152db513dd80bfd5f2f9df48befff28a" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"] +git-tree-sha1 = "1fff7356ccb79ca1b1ff3276135fda68d4d661be" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.14.0" +version = "1.16.0" +weakdeps = ["SparseArrays"] + + [deps.OrdinaryDiffEqDifferentiation.extensions] + OrdinaryDiffEqDifferentiationSparseArraysExt = "SparseArrays" [[deps.OrdinaryDiffEqExplicitRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] @@ -2554,9 +2570,9 @@ version = "1.8.0" [[deps.OrdinaryDiffEqExtrapolation]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "ee2cba2533e9faf71b09a319a910d4886931e7a6" +git-tree-sha1 = "9e1b11cf448a2c1bca640103c1c848a20aa2f967" uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4" -version = "1.8.0" +version = "1.9.0" [[deps.OrdinaryDiffEqFIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FastGaussQuadrature", "FastPower", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators"] @@ -2602,9 +2618,9 @@ version = "1.6.0" [[deps.OrdinaryDiffEqLowStorageRK]] deps = ["Adapt", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "StaticArrays"] -git-tree-sha1 = "9291cdfd2e8c91e900c48d71d76618de47daeede" +git-tree-sha1 = "e6bd0a7fb6643a57b06a90415608a81aaf7bd772" uuid = "b0944070-b475-4768-8dec-fb6eb410534d" -version = "1.6.0" +version = "1.7.0" [[deps.OrdinaryDiffEqNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "PreallocationTools", "RecursiveArrayTools", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "StaticArrays"] @@ -2644,9 +2660,9 @@ version = "1.5.0" [[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 = "a06c1263d71ea42a1881b4d49c8a087035d4a3ff" +git-tree-sha1 = "f60d7201a2ceaa7e9a406942f0a2fa3e920715fa" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.16.1" +version = "1.18.0" [[deps.OrdinaryDiffEqSDIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] @@ -2656,9 +2672,9 @@ version = "1.7.0" [[deps.OrdinaryDiffEqSSPRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static", "StaticArrays"] -git-tree-sha1 = "af955c61407631d281dd4c2e8331cdfea1af49be" +git-tree-sha1 = "3bce87977264916bd92455754ab336faec68bf8a" uuid = "669c94d9-1f4b-4b64-b377-1aa079aa2388" -version = "1.6.0" +version = "1.7.0" [[deps.OrdinaryDiffEqStabilizedIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqStabilizedRK", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays"] @@ -2709,9 +2725,9 @@ 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 = "275a9a6d85dc86c24d03d1837a0010226a96f540" +git-tree-sha1 = "1f7f9bbd5f7a2e5a9f7d96e51c9754454ea7f60b" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.56.3+0" +version = "1.56.4+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -2754,9 +2770,9 @@ version = "1.4.3" [[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", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "9a9216c0cf706cb2cc58fd194878180e3e51e8c0" +git-tree-sha1 = "bfe839e9668f0c58367fb62d8757315c0eac8777" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.18" +version = "1.40.20" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -2804,9 +2820,9 @@ version = "0.2.4" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "PrecompileTools"] -git-tree-sha1 = "520070df581845686c8c488b6dadce6b2c316856" +git-tree-sha1 = "c05b4c6325262152483a1ecb6c69846d2e01727b" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.32" +version = "0.4.34" weakdeps = ["ForwardDiff", "ReverseDiff", "SparseConnectivityTracer"] [deps.PreallocationTools.extensions] @@ -2850,9 +2866,9 @@ version = "0.1.5" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "13c5103482a8ed1536a54c08d0e742ae3dca2d42" +git-tree-sha1 = "fbb92c6c56b34e1a2c4c36058f68f332bec840e7" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.10.4" +version = "1.11.0" [[deps.PtrArrays]] git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d" @@ -3035,9 +3051,9 @@ version = "0.5.1+0" [[deps.Roots]] deps = ["Accessors", "CommonSolve", "Printf"] -git-tree-sha1 = "668e411c0616a70860249b4c96e5d35296631a1d" +git-tree-sha1 = "8a433b1ede5e9be9a7ba5b1cc6698daa8d718f1d" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.2.8" +version = "2.2.10" [deps.Roots.extensions] RootsChainRulesCoreExt = "ChainRulesCore" @@ -3045,6 +3061,7 @@ version = "2.2.8" RootsIntervalRootFindingExt = "IntervalRootFinding" RootsSymPyExt = "SymPy" RootsSymPyPythonCallExt = "SymPyPythonCall" + RootsUnitfulExt = "Unitful" [deps.Roots.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" @@ -3052,6 +3069,7 @@ version = "2.2.8" IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" SymPyPythonCall = "bc8888f7-b21e-4b7c-a06a-5d9c9496438c" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] @@ -3070,59 +3088,64 @@ version = "0.1.0" [[deps.SSMProblems]] deps = ["AbstractMCMC", "Distributions", "Random"] -git-tree-sha1 = "b00814e67e8aacda2073865a3832e6cc378ea504" +git-tree-sha1 = "5dd0431563784b468db06335ce8777653092d621" uuid = "26aad666-b158-4e64-9d35-0e672562fa48" -version = "0.5.1" - -[[deps.SafeTestsets]] -git-tree-sha1 = "81ec49d645af090901120a1542e67ecbbe044db3" -uuid = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f" -version = "0.1.0" +version = "0.5.2" [[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", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] -git-tree-sha1 = "4398bda451c3c7aaca91a8077bcba227fe236d72" +git-tree-sha1 = "dfec1fce27c829814348266486b4cb8fdcb263fb" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.111.1" +version = "2.119.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" + SciMLBaseDistributionsExt = "Distributions" + SciMLBaseEnzymeExt = "Enzyme" + SciMLBaseForwardDiffExt = "ForwardDiff" SciMLBaseMLStyleExt = "MLStyle" SciMLBaseMakieExt = "Makie" + SciMLBaseMeasurementsExt = "Measurements" + SciMLBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" + SciMLBaseMooncakeExt = "Mooncake" SciMLBasePartialFunctionsExt = "PartialFunctions" SciMLBasePyCallExt = "PyCall" SciMLBasePythonCallExt = "PythonCall" SciMLBaseRCallExt = "RCall" + SciMLBaseReverseDiffExt = "ReverseDiff" + SciMLBaseTrackerExt = "Tracker" SciMLBaseZygoteExt = ["Zygote", "ChainRulesCore"] [deps.SciMLBase.weakdeps] ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078" Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" RCall = "6f49c342-dc21-5d91-9882-a32aef131414" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLJacobianOperators]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] -git-tree-sha1 = "3414071e3458f3065de7fa5aed55283b236b4907" +git-tree-sha1 = "a273b291c90909ba6fe08402dd68e09aae423008" uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" -version = "0.1.8" - -[[deps.SciMLLogging]] -deps = ["DocStringExtensions", "Logging", "LoggingExtras", "Moshi", "SafeTestsets"] -git-tree-sha1 = "e8a13b37734bc601500cd29336f114f67c7fb353" -uuid = "a6db7da4-7206-11f0-1eab-35f2a5dbe1d1" -version = "1.0.0" +version = "0.1.11" [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "aea915a39b547c48a18ee041120db1ae8df5a691" +git-tree-sha1 = "024d829102878141aaee5cf8f8288bcabd2f57a0" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "1.5.0" +version = "1.7.2" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -3152,9 +3175,9 @@ version = "3.0.0" [[deps.ScopedValues]] deps = ["HashArrayMappedTries", "Logging"] -git-tree-sha1 = "7f44eef6b1d284465fafc66baf4d9bdcc239a15b" +git-tree-sha1 = "c3b2323466378a2ba15bea4b2f73b081e022f473" uuid = "7e506255-f358-4e82-b7e4-beb19740aa63" -version = "1.4.0" +version = "1.5.0" [[deps.Scratch]] deps = ["Dates"] @@ -3206,14 +3229,13 @@ 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 = "09d986e27a606f172c5b6cffbd8b8b2f10bf1c75" +git-tree-sha1 = "782c67176b473abf62a6786399c4b7ddcc1a2d77" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "2.7.0" -weakdeps = ["ChainRulesCore", "DiffEqBase", "ReverseDiff", "Tracker"] +version = "2.8.0" +weakdeps = ["ChainRulesCore", "ReverseDiff", "Tracker"] [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" - SimpleNonlinearSolveDiffEqBaseExt = "DiffEqBase" SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" SimpleNonlinearSolveTrackerExt = "Tracker" @@ -3245,9 +3267,9 @@ version = "1.11.0" [[deps.SparseConnectivityTracer]] deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "7bd2b8981cc57adcf5cf1add282aba2713a7058f" +git-tree-sha1 = "e49c106eb7c78f55cdfa39e8bddeda24e1e09fce" uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" -version = "1.0.0" +version = "1.0.2" weakdeps = ["LogExpFunctions", "NNlib", "NaNMath", "SpecialFunctions"] [deps.SparseConnectivityTracer.extensions] @@ -3319,9 +3341,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "cbea8a6bd7bed51b1619658dec70035e07b8502f" +git-tree-sha1 = "b8693004b385c842357406e3af647701fe783f98" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.14" +version = "1.9.15" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -3374,9 +3396,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] [[deps.StatsModels]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "728d276a5adc2f1cbb800eec4b63d0a8221024b4" +git-tree-sha1 = "85a43f6fc30dd80c61342519ca2fc36dac912eae" uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" -version = "0.7.5" +version = "0.7.6" [[deps.StatsPlots]] deps = ["AbstractFFTs", "Clustering", "DataStructures", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] @@ -3392,9 +3414,9 @@ version = "2.5.0" [[deps.StochasticDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "StaticArrays", "UnPack"] -git-tree-sha1 = "c3a55a2a1e180e249a0550d30a58c700487aa7ef" +git-tree-sha1 = "d9540e35a902512f6c86a6817120eddc8912f651" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.81.0" +version = "6.82.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] @@ -3579,9 +3601,9 @@ weakdeps = ["PDMats"] [[deps.Tracy]] deps = ["ExprTools", "LibTracyClient_jll", "Libdl"] -git-tree-sha1 = "91dbaee0f50faa4357f7e9fc69442c7b6364dfe5" +git-tree-sha1 = "73e3ff50fd3990874c59fef0f35d10644a1487bc" uuid = "e689c965-62c8-4b79-b2c5-8359227902fd" -version = "0.1.5" +version = "0.1.6" [deps.Tracy.extensions] TracyProfilerExt = "TracyProfiler_jll" @@ -3595,10 +3617,10 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.11.3" [[deps.Transducers]] -deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] -git-tree-sha1 = "7deeab4ff96b85c5f72c824cae53a1398da3d1cb" +deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "SplittablesBase", "Tables"] +git-tree-sha1 = "4aa1fdf6c1da74661f6f5d3edfd96648321dade9" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.84" +version = "0.4.85" [deps.Transducers.extensions] TransducersAdaptExt = "Adapt" @@ -3635,9 +3657,9 @@ version = "1.6.0" [[deps.Turing]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "33f6f6b0844b01bce45eba0311620ab2ddb7d37a" +git-tree-sha1 = "8e1e790cfdffd15524575b84c4709033d1ea9550" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.40.2" +version = "0.40.3" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] @@ -3671,15 +3693,16 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "6258d453843c466d84c17a58732dda5deeb8d3af" +git-tree-sha1 = "cec2df8cf14e0844a8c4d770d12347fda5931d72" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.24.0" -weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "Printf"] +version = "1.25.0" +weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "LaTeXStrings", "Latexify", "Printf"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" ForwardDiffExt = "ForwardDiff" InverseFunctionsUnitfulExt = "InverseFunctions" + LatexifyExt = ["Latexify", "LaTeXStrings"] PrintfExt = "Printf" [[deps.UnitfulLatexify]] @@ -3722,27 +3745,23 @@ version = "1.4.2" [[deps.WeightInitializers]] deps = ["ArgCheck", "ConcreteStructs", "GPUArraysCore", "LinearAlgebra", "Random", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "dd2e8eb0120c12eed3446cedee395ca7ac42a5db" +git-tree-sha1 = "2fe6d8bd39dc8d1f575963eef137f77bd47200c9" uuid = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d" -version = "1.1.4" +version = "1.2.0" [deps.WeightInitializers.extensions] - WeightInitializersAMDGPUExt = ["AMDGPU", "GPUArrays"] - WeightInitializersCUDAExt = ["CUDA", "GPUArrays"] + WeightInitializersAMDGPUExt = "AMDGPU" + WeightInitializersCUDAExt = "CUDA" WeightInitializersChainRulesCoreExt = "ChainRulesCore" WeightInitializersGPUArraysExt = "GPUArrays" - WeightInitializersMetalExt = ["Metal", "GPUArrays"] WeightInitializersReactantExt = "Reactant" - WeightInitializersoneAPIExt = ["oneAPI", "GPUArrays"] [deps.WeightInitializers.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" - Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" - oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" [[deps.Widgets]] deps = ["Colors", "Dates", "Observables", "OrderedCollections"] From 4a1d439725ede75990619735eabcea6f8e442525 Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Thu, 18 Sep 2025 12:03:30 +0100 Subject: [PATCH 10/13] Remove version pin of DelayDiffEq and update Manifest --- Manifest.toml | 71 +++++++++++++++++++++++++-------------------------- Project.toml | 1 - 2 files changed, 35 insertions(+), 37 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 0a95cce1c..c0c40d833 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,8 +1,8 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.6" +julia_version = "1.11.7" manifest_format = "2.0" -project_hash = "9f86f29e94eb0d08fa3f55118bf3765e18345c9e" +project_hash = "6ed163b5c6c108dfaae31b757b21ff71e297872f" [[deps.ADTypes]] git-tree-sha1 = "27cecae79e5cc9935255f90c53bb831cc3c870d7" @@ -690,9 +690,9 @@ version = "0.1.2" [[deps.DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "FastBroadcast", "ForwardDiff", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqRosenbrock", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack", "SymbolicIndexingInterface"] -git-tree-sha1 = "c50981fb5b6441a1213debb1423385a462e88032" +git-tree-sha1 = "bb84c7ab3de56ada66430b5671db3b3cdaadcd61" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.56.0" +version = "5.61.0" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -708,9 +708,9 @@ version = "0.4.0" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "6df3b15d504315ec306118aed14f9d7af9f83db1" +git-tree-sha1 = "087632db966c90079a5534e4147afea9136ca39a" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.189.1" +version = "6.190.2" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -933,9 +933,9 @@ version = "1.0.5" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "66ec698bd4791c8d2b2be2fe2a472d1dd76a5c7d" +git-tree-sha1 = "8bd38788cad934e433f944678885d8525cccc009" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.75" +version = "0.13.76" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -964,9 +964,9 @@ weakdeps = ["Adapt"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "bf15bd2b3ddff92fc5bb5687ffe074ebd814c756" +git-tree-sha1 = "440abfda8e1329662bed574250dde0dcd91f3181" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.196+0" +version = "0.0.197+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1599,9 +1599,9 @@ version = "0.1.17" [[deps.LazyArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "76627adb8c542c6b73f68d4bfd0aa71c9893a079" +git-tree-sha1 = "21057b6f4f5db1475e653735fda7d1de1c267b46" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "2.6.2" +version = "2.6.3" [deps.LazyArrays.extensions] LazyArraysBandedMatricesExt = "BandedMatrices" @@ -1743,10 +1743,10 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" version = "1.11.0" [[deps.LinearSolve]] -deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "OpenBLAS_jll", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "69cee52e516c859e64adba702ac382c0498a4e29" +deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "1c597eceb5ead73dae17ffa4dcc1160e3e4da1f3" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "3.40.0" +version = "3.28.0" [deps.LinearSolve.extensions] LinearSolveAMDGPUExt = "AMDGPU" @@ -1756,7 +1756,6 @@ version = "3.40.0" LinearSolveCUDAExt = "CUDA" LinearSolveCUDSSExt = "CUDSS" LinearSolveCUSOLVERRFExt = ["CUSOLVERRF", "SparseArrays"] - LinearSolveCliqueTreesExt = ["CliqueTrees", "SparseArrays"] LinearSolveEnzymeExt = "EnzymeCore" LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveFastLapackInterfaceExt = "FastLapackInterface" @@ -1778,7 +1777,6 @@ version = "3.40.0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" CUSOLVERRF = "a8cc9031-bad2-4722-94f5-40deabb4245c" - CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641" @@ -2152,9 +2150,9 @@ version = "0.8.1" [[deps.Mooncake]] deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DispatchDoctor", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Test"] -git-tree-sha1 = "2aa902cb9f45dbeaaae5eaa98559d600b1f5deb7" +git-tree-sha1 = "bc28c3170e7c78d671ff512ca80487ce7e375bb5" uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" -version = "0.4.159" +version = "0.4.160" [deps.Mooncake.extensions] MooncakeAllocCheckExt = "AllocCheck" @@ -2289,10 +2287,10 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"] -git-tree-sha1 = "d2ec18c1e4eccbb70b64be2435fc3b06fbcdc0a1" +deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "StaticArraysCore", "SymbolicIndexingInterface"] +git-tree-sha1 = "627967f6e36aac9f5afb2fb285e33b676a6892f9" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "4.10.0" +version = "4.11.0" [deps.NonlinearSolve.extensions] NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" @@ -2301,7 +2299,7 @@ version = "4.10.0" NonlinearSolveMINPACKExt = "MINPACK" NonlinearSolveNLSolversExt = "NLSolvers" NonlinearSolveNLsolveExt = ["NLsolve", "LineSearches"] - NonlinearSolvePETScExt = ["PETSc", "MPI"] + NonlinearSolvePETScExt = ["PETSc", "MPI", "SparseArrays"] NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" NonlinearSolveSpeedMappingExt = "SpeedMapping" NonlinearSolveSundialsExt = "Sundials" @@ -2317,14 +2315,15 @@ version = "4.10.0" NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0" SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" [[deps.NonlinearSolveBase]] deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "Setfield", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "99a400f7ad42e56431c76f3eadee0755f2123fda" +git-tree-sha1 = "bc0c764f8d4cbd75dc8e4968e62194495c2c6637" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "1.15.0" +version = "1.16.0" weakdeps = ["BandedMatrices", "ChainRulesCore", "Enzyme", "ForwardDiff", "LineSearch", "LinearSolve", "Mooncake", "ReverseDiff", "SparseArrays", "SparseMatrixColorings", "Tracker"] [deps.NonlinearSolveBase.extensions] @@ -3094,9 +3093,9 @@ version = "0.5.2" [[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", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] -git-tree-sha1 = "dfec1fce27c829814348266486b4cb8fdcb263fb" +git-tree-sha1 = "16fa030fb4bd4df373a677eca0460c3eee791ab2" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.119.0" +version = "2.120.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3267,12 +3266,13 @@ version = "1.11.0" [[deps.SparseConnectivityTracer]] deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "e49c106eb7c78f55cdfa39e8bddeda24e1e09fce" +git-tree-sha1 = "3c3a42a29f696f16273741ffe589b4003f539088" uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" -version = "1.0.2" -weakdeps = ["LogExpFunctions", "NNlib", "NaNMath", "SpecialFunctions"] +version = "1.1.0" +weakdeps = ["ChainRulesCore", "LogExpFunctions", "NNlib", "NaNMath", "SpecialFunctions"] [deps.SparseConnectivityTracer.extensions] + SparseConnectivityTracerChainRulesCoreExt = "ChainRulesCore" SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions" SparseConnectivityTracerNNlibExt = "NNlib" SparseConnectivityTracerNaNMathExt = "NaNMath" @@ -3496,9 +3496,9 @@ version = "5.2.3+0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "93104ca226670c0cb92ba8bc6998852ad55a2d4c" +git-tree-sha1 = "b19cf024a2b11d72bef7c74ac3d1cbe86ec9e4ed" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.43" +version = "0.3.44" weakdeps = ["PrettyTables"] [deps.SymbolicIndexingInterface.extensions] @@ -3693,16 +3693,15 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "cec2df8cf14e0844a8c4d770d12347fda5931d72" +git-tree-sha1 = "6258d453843c466d84c17a58732dda5deeb8d3af" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.25.0" -weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "LaTeXStrings", "Latexify", "Printf"] +version = "1.24.0" +weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "Printf"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" ForwardDiffExt = "ForwardDiff" InverseFunctionsUnitfulExt = "InverseFunctions" - LatexifyExt = ["Latexify", "LaTeXStrings"] PrintfExt = "Printf" [[deps.UnitfulLatexify]] diff --git a/Project.toml b/Project.toml index 5b9b96656..3498eed33 100644 --- a/Project.toml +++ b/Project.toml @@ -57,4 +57,3 @@ UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" [compat] Turing = "0.40" -DelayDiffEq = "~5.56" From 6a181f58fd59c4a4a6eb461da633eb696c296bc6 Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Thu, 18 Sep 2025 17:49:11 +0100 Subject: [PATCH 11/13] Fix call to evaluate --- developers/transforms/dynamicppl/index.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/developers/transforms/dynamicppl/index.qmd b/developers/transforms/dynamicppl/index.qmd index ae7722d48..a02dde7af 100644 --- a/developers/transforms/dynamicppl/index.qmd +++ b/developers/transforms/dynamicppl/index.qmd @@ -351,7 +351,7 @@ Hence, one might expect that if we try to evaluate the model using this `VarInfo Here, `evaluate!!` returns two things: the model's return value itself (which we defined above to be a `NamedTuple`), and the resulting `VarInfo` post-evaluation. ```{julia} -retval, ret_varinfo = DynamicPPL.evaluate!!(model, vi_linked, DefaultContext()) +retval, ret_varinfo = DynamicPPL.evaluate!!(model, vi_linked) getlogp(ret_varinfo) ``` From 2d2d86536b81208bdc0ad60488b93429879ccc25 Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Fri, 19 Sep 2025 17:08:32 +0100 Subject: [PATCH 12/13] Add note about contexts tutorial being out of date --- developers/compiler/minituring-contexts/index.qmd | 2 ++ 1 file changed, 2 insertions(+) diff --git a/developers/compiler/minituring-contexts/index.qmd b/developers/compiler/minituring-contexts/index.qmd index 4fcdda02b..b178e9708 100755 --- a/developers/compiler/minituring-contexts/index.qmd +++ b/developers/compiler/minituring-contexts/index.qmd @@ -14,6 +14,8 @@ Pkg.instantiate(); In the [Mini Turing]({{< meta minituring >}}) tutorial we developed a miniature version of the Turing language, to illustrate its core design. A passing mention was made of contexts. In this tutorial we develop that aspect of our mini Turing language further to demonstrate how and why contexts are an important part of Turing's design. +Note: The way Turing actually uses contexts changed somewhat in releases 0.39 and 0.40. The content of this page remains relevant, the principles of how contexts operate remain the same, and concepts like leaf and parent contexts still exist. However, we've moved away from using contexts for quite as many things as we used to. Most importantly, whether to accumulate the log joint, log prior, or log likelihood is no longer done using different contexts. Please keep this in mind as you read this page: The principles remain, but the details have changed. We will update this page once the refactoring of internals that is happening around releases like 0.39 and 0.40 is done. + # Mini Turing expanded, now with more contexts If you haven't read [Mini Turing]({{< meta minituring >}}) yet, you should do that first. We start by repeating verbatim much of the code from there. Define the type for holding values for variables: From 9c40e86da926fad17fac12379e4a6db60cd3e56d Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Mon, 22 Sep 2025 12:48:38 +0100 Subject: [PATCH 13/13] Apply suggestions from code review Co-authored-by: Penelope Yong --- developers/compiler/minituring-contexts/index.qmd | 2 ++ usage/modifying-logprob/index.qmd | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/developers/compiler/minituring-contexts/index.qmd b/developers/compiler/minituring-contexts/index.qmd index b178e9708..aa125b703 100755 --- a/developers/compiler/minituring-contexts/index.qmd +++ b/developers/compiler/minituring-contexts/index.qmd @@ -14,7 +14,9 @@ Pkg.instantiate(); In the [Mini Turing]({{< meta minituring >}}) tutorial we developed a miniature version of the Turing language, to illustrate its core design. A passing mention was made of contexts. In this tutorial we develop that aspect of our mini Turing language further to demonstrate how and why contexts are an important part of Turing's design. +::: {.callout-important} Note: The way Turing actually uses contexts changed somewhat in releases 0.39 and 0.40. The content of this page remains relevant, the principles of how contexts operate remain the same, and concepts like leaf and parent contexts still exist. However, we've moved away from using contexts for quite as many things as we used to. Most importantly, whether to accumulate the log joint, log prior, or log likelihood is no longer done using different contexts. Please keep this in mind as you read this page: The principles remain, but the details have changed. We will update this page once the refactoring of internals that is happening around releases like 0.39 and 0.40 is done. +::: # Mini Turing expanded, now with more contexts diff --git a/usage/modifying-logprob/index.qmd b/usage/modifying-logprob/index.qmd index 0eb6f8b30..892ac7ba8 100755 --- a/usage/modifying-logprob/index.qmd +++ b/usage/modifying-logprob/index.qmd @@ -47,7 +47,7 @@ using LinearAlgebra end ``` -Note that `@addlogprob!` increases the accumulated log likelihood. +Note that `@addlogprob! (p::Float64)` adds `p` to the log likelihood. If instead you want to add to the log prior, you can use ```{julia}